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Too few, too late: U.S. Endangered Species Act undermined by inaction and inadequate funding

Roles Conceptualization, Data curation, Formal analysis, Investigation, Methodology, Visualization, Writing – original draft, Writing – review & editing

* E-mail: [email protected]

Affiliation Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, New York, United States of America

Roles Conceptualization, Supervision, Writing – original draft, Writing – review & editing

Affiliations Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America, Princeton School of Public and International Affairs, Princeton University, Princeton, New Jersey, United States of America

Affiliations Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America, Santa Fe Institute, Santa Fe, New Mexico, United States of America

• Erich K. Eberhard, 
• David S. Wilcove, 
• Andrew P. Dobson

• Published: October 12, 2022
• https://doi.org/10.1371/journal.pone.0275322
• Reader Comments

This year, the Conference of Parties to the Convention on Biological Diversity will meet to finalize a post 2020-framework for biodiversity conservation, necessitating critical analysis of current barriers to conservation success. Here, we tackle one of the enduring puzzles about the U.S. Endangered Species Act, often considered a model for endangered species protection globally: Why have so few species been successfully recovered? For the period of 1992–2020, we analyzed trends in the population sizes of species of concern, trends in the time between when species are first petitioned for listing and when they actually receive protection, and trends in funding for the listing and recovery of imperiled species. We find that small population sizes at time of listing, coupled with delayed protection and insufficient funding, continue to undermine one of the world’s strongest laws for protecting biodiversity.

Citation: Eberhard EK, Wilcove DS, Dobson AP (2022) Too few, too late: U.S. Endangered Species Act undermined by inaction and inadequate funding. PLoS ONE 17(10): e0275322. https://doi.org/10.1371/journal.pone.0275322

Editor: Laurentiu Rozylowicz, University of Bucharest, ROMANIA

Received: June 10, 2022; Accepted: September 14, 2022; Published: October 12, 2022

Copyright: © 2022 Eberhard et al. This is an open access article distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Data Availability: All data are within the paper and Supporting Information files. The species data and appropriations data underlying the results presented in this study were collected from notices published by the U.S. Fish & Wildlife Service and annual budget legislation, all of which are publicly available through the Federal Registrar ( www.federalregistrar.gov ). The author's accessed FWS Notices through the Service's Environmental Conservation Online System (ECOS), which organizes documents by species name. This data base is also publicly accessible ( https://ecos.fws.gov/ecp/ ).

Funding: The author(s) received no specific funding for this work.

Competing interests: The authors have declared that no competing interests exist.

Introduction

Accelerating rates of species extinction are a matter of global concern [ 1 ] as exemplified in the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES) report that predicted the loss of over 1 million species in the foreseeable future, which will also have significant impacts on the delivery of ecosystem services [ 2 ]. The prevention of species extinction is a primary goal of the Convention on Biological Diversity and the UN Sustainable Development Goals. In the United States, the strongest law to prevent species extinctions is the Endangered Species Act (ESA) [ 3 ], which has served as a model for other nations since its passage by the Nixon Administration in 1973. A longstanding concern of both supporters and opponents of the law has been the relatively low number of listed species that have successfully recovered to the point where they no longer need protection. In the 48 years since enactment of the ESA, only 54 US species have been declared fully recovered and delisted [ 4 ].

Multiple explanations have been given for this low rate of recovery including: (a) a pattern of not protecting species until their populations have reached very low levels, which increases both the time to recovery and the likelihood that species will vanish entirely due to environmental, genetic, and demographic stochasticity [ 5 ]; (b) a lack of incentives to landowners to participate actively in efforts to increase populations of endangered species [ 6 ]; and (c) inadequate funding for recovery actions [ 7 ]. Here, we have used data from the Federal Register to examine trends in the population sizes of species at time of listing and the levels of funding available to list and recover them.

Evidence that species are not being protected under the ESA until their populations have reached dangerously low levels was initially provided in a 1993 paper by Wilcove et al. [ 8 ]. The authors found that the median population size at time of listing during the second decade of ‘legal protection’ by the ESA (1985–1991) was just 1075 for vertebrates and 999 individuals for invertebrates. The median population size at listing for plant species was less than 120 individuals. We repeated their methodology to determine whether the US Fish & Wildlife Service (FWS) has become more proactive as we approach the 50 th anniversary of the ESA and roughly 30 years since attention was first drawn to this problem.

We also examined trends in the length of time between when a species is identified as potentially deserving of protection and when it actually receives that protection under the ESA (hereafter, “wait times”). It should be noted that, in recent years, most of the species added to the ESA have been the result of petitions from non-governmental entities to FWS requesting protection of a given species. Frequently, listing follows litigation brought by environmental organizations when petition decisions are overdue or petitions are denied [ 9 ].

Finally, we examined trends in funding for the listing and recovery of imperiled species (we use “imperiled” to include both Endangered and Threatened species protected under the ESA, and, unless indicated otherwise, we use the word “species” to refer to any entity protected under the ESA, including subspecies and vertebrate populations). We give particular attention to trends in funding per species , in order to account for changes in the number of species listed each year.

Materials and methods

The list of plants and animals granted protection under the ESA was collated from annual listing records available through the U.S. Fish & Wildlife Service’s Environmental Conservation Online System (ECOS). Population data were obtained from Final and Proposed Listing Notices issued by the U.S. Fish & Wildlife Service. Our analysis was restricted to wild populations of plants and animals known to occur in the United States and its territories and did not include captive populations.

When presented with a range of values, or an upper limit, for the total number of individuals or populations at time of listing, we favored interpretations that maximized population size. For example, if a population was said to be “between 500 and 1000” individuals, we recorded the population as being 1000 individuals at time of listing. Similarly, a population said to be “<1000” was recorded as being 999 individuals at time of listing. This was done in order to obtain the largest possible estimate of each plant and animal population at time of listing, making our subsequent analyses an optimistic “best case scenario”. Six species were listed with no known individuals or populations surviving in the wild. In these instances, the total number of individuals or total number of populations was recorded as being zero. Population data for plants and animals listed between 1985–1991 were obtained from Wilcove et al. in order to facilitate comparison with their results. We performed a non-parametric Wilcoxon Rank-sum Test to compare the medians of continuous variable x , the number of individuals at time of listing for species listed between 1985–1992, and continuous variable y , the number of individuals at time of listing for species listed between 1993–2020. The same approach was used to compare the median number of populations at time of listing for each time period. We adopted a significance threshold of p = 0.05.

Data for Resource Management Appropriations (discretionary funding that supports the management and recovery of imperiled species by FWS) and Section 4 Appropriations (funding allocated specifically to ESA listing activities) were obtained from the text of annual federal budget legislation and corrected for inflation to 2019 USD. These documents are publicly accessible through the Federal Registrar . Funding per species was defined as the average funding available for the management of each species in a given year. We calculated this value by dividing annual Resource Management Appropriations by the total number of species protected under the ESA as of the first day of that calendar year.

From 1992–2020, the FWS listed a total of 970 species for protection under the ESA; 68% of these listings were plants, 18% were invertebrates, and 14% were vertebrates. Full species accounted for the majority of listings during this period (80%). Of the species listed, 602 had data on their total population size (total number of individuals) at time of listing, and 843 had data on the number of populations at time of listing. For each taxonomic group analyzed, the total population size at time of listing ( Fig 1A ) did not differ significantly between the 1985–1991 and 1992–2020 time periods (Wilcox Test values of p = 0.08, p = 0.41, and p = 0.66, for plants, vertebrates and invertebrates respectively). For plants and invertebrates, the total number of populations at time of listing ( Fig 1B ) also did not differ significantly between the 1985–1991 and 1992–2020 time periods (p = 0.91 and p = 0.06, respectively). However, the median number of vertebrate populations at time of listing was slightly greater in the 1992–2020 time period, increasing from 2 to 4 populations (p = 0.04).

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• TIFF original image

(A) Comparison of population size at time of listing for plants and animals. There are no significant differences between the two periods (Wilcox Test values of p = 0.08, p = 0.41, and p = 0.66, for plants, vertebrates and invertebrates respectively). (B) Comparison of number of populations at time of listing. There are no significant differences between the two periods for plants and invertebrates. Values of zero indicate species for which there were either no known individuals or no known populations at time of listing. Median values shown above each plot.

https://doi.org/10.1371/journal.pone.0275322.g001

Our analysis revealed longer wait times for species petitioned for listing during the 2000–2009 period (median = 9.1 years), compared to those petitioned for listing during the 1992–1999 period (median = 5.9 years), followed by shorter wait times for species petitioned for listing during the 2010–2020 period (median 3.0 years). The number of petitions received during each period also varied greatly ( n = 49, 203 and 26 for 1992–1999, 2000–2009 and 2010–2020, respectively). While wait times seem to decrease when fewer species are listed, there are insufficient data to test whether this effect is significant.

Resource Management Appropriations climbed modestly from 1996–2010 before beginning a decade-long decline that was halted only in 2020 ( Fig 2A ). The same trend is observed in Section 4 Appropriations, which peaked in 2010 at $25.9 million USD before dropping to $20.1 million USD by 2020. Concurrently, the number of species listed for protection under the ESA increased by over 300% between 1985–2020. As such, Resource Management Appropriations, when measured on a per species basis, have dropped by nearly 50% since 1985.

(A) Change in cumulative number of ESA listings compared to change in Resource Management Appropriations. The lower timeline illustrates political control of the Presidency and, by a majority, each house of Congress. (B) Number of species delisted for various reasons.

https://doi.org/10.1371/journal.pone.0275322.g002

Our analysis of trends in the protection of imperiled species under the US Endangered Species Act warrants a limited amount of optimism and a larger amount of pessimism: Most species are not receiving protection until they have reached dangerously low population sizes. First reported in 1993, this pattern has persisted throughout the intervening quarter century. We suspect that most of the species listed since 1993 had fallen to low population levels well before the time span of our study, a reflection of past anthropogenic activities. Their protection under the ESA implies a painfully slow process of clearing a backlog of rare but unprotected species as opposed to a failure to respond to recent, rapid population declines in formerly more common species.

The wait-times between when a species is first petitioned for protection under the ESA and when it finally receives that protection have waxed and waned since 1992. The period with the longest median wait time (2000–2009, with a median wait-time of 9.1 years), was also the period when the greatest number of petitions were received by FWS ( n = 203). The period with the shortest median wait time (2010–2020 with a median wait-time of 3.0 years) was the period when the fewest number of petitions were received ( n = 26). This suggests that wait times may be exacerbated when limited resources for listing are strained by a large influx of petitions. Consistently, very few species have received protection in the two-year period that is prescribed in the ESA. For species with very small or rapidly declining populations, a multi-year delay in receiving protection increases the risk of extinction.

Our data suggest that inadequate funding has persisted for decades, with no clear relationship as to which political party is in power ( Fig 2A ). The unfortunate conclusion is that FWS is being asked to do more with less resources. The combination of delays in listing rare species, the typically mall population sizes of species at time of listing, and inadequate funding for recovery actions, are the key factors that can explain the relatively small number of listed species that have fully recovered ( Fig 2B ). Resource allocation frameworks and other decision-support tools can help FWS make the most efficient use of the funds it receives [ 10 ], but increased funding is essential for sustained, substantial progress in protecting imperiled species [ 11 , 12 ]. Studies have shown that government expenditures for imperiled species management do contribute to an improvement in recovery status and averted extinctions [ 13 ].

Although the US is one of only a handful of nations that have failed to ratify the Convention on Biological Diversity, its commitment to preventing the loss of its own “non-voting” species dates back nearly half a century to the passage of the ESA in 1973. In December 2022, when international leaders gather in Montréal, Canada for the 15 th meeting of the Conference of Parties to the Convention on Biological Diversity, the failure of the US to have solved the funding gaps that hamper the ESA will stand as a stark reminder of the difference between a visionary promise and its functional implementation.

Supporting information

https://doi.org/10.1371/journal.pone.0275322.s001

• View Article
• PubMed/NCBI
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• 2. Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services, (IPBES). Global assessment report on biodiversity and ecosystem services of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services. IPBES Secretariat. 2019. Available from: https://ipbes.net/global-assessment
• 3. United States. The Endangered Species Act, Public Law 93–205, Section 3. Washington D.C. 1973.

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How passion, luck and sweat saved some of north america’s rarest plants.

Plant enthusiasts go to extremes trying to save beloved species

More than 60 years after the supposed extinction in the wild of California’s Franciscan manzanita, a lone survivor showed up in the path of highway construction. The 2010 transplant of a multi-ton shrub wasn’t easy.

John Huseby/Caltrans Bay Area

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By Susan Milius

November 5, 2020 at 10:30 am

No plant should have to end this way.

North America’s various beach plums bear purple-blue, cherry-sized fruits that make for a beloved New England jelly. The small trees’ tolerance for salty, wind-blasted shores impresses biologists. But even a beach plum has limits.

One of the plum’s distinctive forms, named in 1897 for physician Charles B. Graves who called attention to the plant, may have gone extinct in the wild in large part because people like a little privacy when they need a bathroom break on the beach.

All of the known Graves’ beach plums grew in a cluster on a ridge overlooking the Connecticut shore in Groton. It “was the only shade on the beach,” says botanist Wesley Knapp, who studies extinctions with the North Carolina Natural Heritage Program in Raleigh. Beachgoers seeking discreet foliage gravitated to Prunus maritima var. gravesii , relentlessly delivering excess nitrogen. “I can’t think of a worse way … to go extinct,” Knapp says.

He has now determined that Graves’ beach plum and four other kinds of U.S. plants that have been wiped out in the wild still grow in at least one garden somewhere. Ongoing quests might reveal two more. Dozens of others, however, are gone.

Focusing on U.S. and Canadian green heritage, Knapp and colleagues declared August 28 in Conservation Biology that 58 plants are extinct in the wild , with no miracle rescues in gardens. That totals 65 known losses from the wild, about 1.4 per decade, since Europeans started settling in the mid-1500s.

 “We are positive it is a gross underestimate,” Knapp cautions. The team’s methods were conservative: going plant name by name and declaring a loss of a full species or a distinctive lineage within a species only if detailed information existed.

Knapp, however, doesn’t come across as a gloomy guy. He calls his motivational spiel about conserving native plants “Tales from the Crypt,” and he chats colorfully about plants and the people who love them. Many of his colleagues do too. The possibility of snatching a flower or fern from the jaws of extinction has fired up a community of enthusiasts trying to document and protect what’s left of the rarest of native vegetation. The challenge is immense, but sometimes there are wins. It’s good practice in the art of hope.

Wild losses

To Anne Frances, a coauthor with Knapp on the extinction tally, “the one that stands out” is the Franciscan manzanita ( Arctostaphylos franciscana ), a sprawling woody plant with seeds that become more likely to sprout when cued by a fire’s smoke.

Frances watches over native flora as the lead botanist at NatureServe, a nonprofit based in Arlington, Va., that keeps a giant database on the status of plants in the United States and Canada. She’s the person who switches a plant’s status to “extinct” in the database, and those keystrokes still get to her.

She was recently pandemic-teleworking and listening to a meeting when she remembered she needed to update the status on a plant that hadn’t been seen for decades. The meeting suddenly stopped. Someone inquired if she was OK. She hadn’t realized that as she finally clicked the entry to “extinct,” she had let out a deep sigh.

The manzanita extinction story, though, has had a happy twist.

Tough, resilient Franciscan manzanita, which belongs to the same family as blueberries and rhododendrons, spreads red-barked, low-growing greenery and dangles pale little urn-shaped flowers. It’s one of several manzanitas that once grew on San Francisco’s serpentine barrens, dry outcroppings laden with heavy metals from greenish, vaguely snakeskin-textured rocks.

The shrub got its species name in 1905 from Toronto-born botanist Alice Eastwood, a rarity herself in the staggeringly male sciences. At age 6, she lost her mother. Despite her hard-luck childhood trying to look out for two younger siblings and cope with her father’s faltering business ventures, she finished high school in Denver. That was the end of her formal education, but she showed great aptitude for botany. During summers she went collecting, preferring to travel solo, even in rugged terrain. She switched from riding side-saddle in voluminous skirts to riding astride in (gasp) denim garments of her own practical design.

Being a woman didn’t prevent Eastwood from getting a botanist’s job at the California Academy of Sciences in San Francisco. She was recruited by Katharine Brandegee, a town constable’s widow who consoled herself by earning an M.D. from the University of California in 1878 and then took charge of the academy’s herbarium, a kind of library of preserved plant samples.

Eastwood took over from her, and before retiring at the age of 90, named dozens of species, including the Franciscan manzanita.

On the morning of the 1906 earthquake, as fire neared the academy, Eastwood and a few colleagues struggled into the damaged building for last-minute salvaging. The marble staircase was “in ruins and we went up chiefly by holding on to the iron railing and putting our feet between the rungs,” she wrote in a letter published in the May 25, 1906 Science . She and a helper lowered down with cords more than 1,000 of the most valuable pressed plants from an upper floor, including the definitive specimen of Franciscan manzanita.

Yet, as the city recovered and grew, serpentine barrens and their specialized plants disappeared under roads and buildings. Nurseries sold garden versions of it, but the last wild Franciscan manzanita sighting was recorded in 1947.

Of all places

It wasn’t truly the last, we now know. At some unknown point, another manzanita sprouted, unrecognized and in a most awkward spot. Overgrown by weedy Australian tea trees, English ivy and such, the last known wild Franciscan manzanita grew on a traffic island shaped like a teardrop.

On its east side sped six lanes of traffic to and from the Golden Gate Bridge and on the west lay a six-meter drop to a highway on-ramp. This section of Doyle Drive was deemed seismically unsafe, and California OK’d its demolition. Native plant activists didn’t protest to save the manzanita. They had no idea it was there.

By 2009, 100,000 vehicles whooshed by every day, oblivious. Even the impassioned protector of native plants and a coauthor on Knapp’s extinctions paper, Dan Gluesenkamp, “quite frequently” drove by, he says, on the way from his San Francisco home to 31 plant restoration sites he worked on to the north. “We all missed it,” he says.

As highway work progressed, a crew with a great roaring wood chipper arrived on the traffic island to grind up weeds. On this particular day, Gluesenkamp learned, a California highway patrol car had parked at the curb near the manzanita. The landscape crew positioned its machinery to spew chips away from, rather than toward, the law. While the rest of the island’s plants ended the day either as mulch or under it, the newly exposed manzanita lived to see another rush hour.

On October 16, Gluesenkamp was driving home from a conference where he had argued that the best strategy for conserving botanical heritage in a changing climate was to find all of California’s rare native plants and protect them individually.

“It’s really crazy that after making that pitch … I spotted an extinct plant,” he says. Drive-by resurrecting an impossible plant is rare even for him. “I was roaring by at (a little over) freeway speeds, but something just clicked,” he says.

Or almost clicked. He recognized an unusual manzanita, but suspected it was a different rarity: A. montana ssp. ravenii , which still hangs on, barely, elsewhere in the wild. But a new patch of any rare plant is good news. With such pathetically tiny shreds left of any rare plant’s original genetic diversity, even a single new wildling could improve a species’s chances of coping with our fast-changing world.

Gluesenkamp drove by the traffic island twice more. He made a phone call, and two botanists rushed over, dodging on foot lane after lane of traffic to see the plant up close. Not until a fourth expert weighed in, though, did realization dawn that this could be a species that had supposedly vanished from the wild more than 60 years earlier.

Electrifying as the rediscovery was, it didn’t stop highway construction. Conservationists eventually opted to try transplanting the priceless last wild manzanita to San Francisco’s Presidio park.

Moving day began on a Saturday in January 2010 at around 3 a.m. in rain with occasional hail. The storm so worried one of the operation’s contractors that an employee spent the night on the traffic island to make sure a canopy covering the plant did not blow away. A 75-ton crane nudged into place to pick up the plant with its own minor continent of surrounding soil.

To prepare for transporting this one plant to the park, San Francisco took the extraordinary step of shutting down the MacArthur Tunnel, one of its busiest arteries. While the city slept, Gluesenkamp says, “we had a crazy, slow-moving parade.”

He and colleagues described the rediscovery and replanting in a 2009/2010 issue of Fremontia in what must be one of the most suspenseful accounts ever published of transplanting shrubbery. Ten years later, Gluesenkamp, now director of the California Native Plant Society, still remembers those hours as “incredibly nerve-racking.”

The mother plant has survived so far, he reports. Carefully tended cuttings and shoots are doing well. All this coddling from specialists means the plant no longer really counts as a manzanita living on its own. So it has now gone extinct in the wild — for the second time.

Search parties

The tale of another plant on NatureServe’s extinction list follows a different arc. A tiny parasitic flower in a group called fairy lanterns was vanishingly rare to begin with. It’s the only one of more than 70 known species to have turned up — briefly — in North America. More people have walked on the moon than are on record as viewing Thismia americana growing on Earth. Yet for decades, crowds have shown up to keep searching.

The only places on the planet this Thismia has been reported were two marshy scraps of prairie in southeastern Chicago. The city had long drawn botanists of international standing. Classes at the University of Chicago even used one of the plant’s wetland homes for field trips. Yet that’s not how the discovery played out, according to letters written by the plant’s first chronicler, Norma Etta Pfeiffer.

In August 1912, Pfeiffer was a graduate student at the University of Chicago with bad luck in the job market. A college where she had accepted a job teaching botany had withdrawn the offer before she could arrive, according to family lore. The school had found a man willing to take the job after all.

Thus she was heading to the University of North Dakota as a botany instructor. The professor who hired her had been so evasive about exactly what her salary would be that she had agreed to work a second job as governess for his two daughters.

Pfeiffer was also unsure whether she would find plant materials there for her classes. So, before leaving Chicago, she and another female grad student went collecting in a swath of damp prairie called Solvay amid a riot of black-eyed Susan, multiple kinds of goldenrod, wild irises and other plants. It’s now concrete-covered cityscape near 119th Street and some railroad tracks.

Down on hands and knees looking for liver-worts, “suddenly I saw my first specimen of Thismia , a tiny flower half-imbedded in the soil,” she wrote.

About half as wide as a pinkie fingertip, Thismia ’s cup-shaped white flowers, with blue-green tints, sprout three petals that touch at the top, while flaps in between loll down like tongues. The rest of the plant lies underground as ghostly pale strings.

After baffling three of her professors, Pfeiffer tried a fourth. “With all his knowledge of world flora, he had never seen it,” she wrote. She had a new thesis topic.

She took specimens with her to her new job. “In North Dakota, I used all the time I was free from earning my living to make preparations and study them,” she wrote. In time she realized her odd plant belonged among the extreme parasites in the genus Thismia , described in 1844 and named as an anagram for English anatomist Thomas Smith. Smithia was already taken.

Her Thismia work earned her a Ph.D. from the University of Chicago in 1913. During a visit the next year, her first prairie site had a barn and no Thismia . A letter she wrote years later revealed a second prairie patch, where in 1916, she was the last person to document the plant’s presence. 

After a decade of teaching in North Dakota with various frustrations, she left and had a long career at the Boyce Thompson Institute in Yonkers, N.Y. (now in Ithaca). Her Thismia discovery got a one-sentence mention in her New York Times obituary in 1989. The headline read “Norma Pfeiffer, expert on lilies, dies at 100.”

By 1951, others were on the lookout for Thismia in Chicago. One search featured two lichen specialists, presumably experts in spotting tiny things. Later efforts attracted hot-shot botanists from out of state as well as local talent. The efforts succeeded in adding dozens of previously unnoticed plants to lists of riches in remaining prairies, but not in finding Thismia .

More recent searches have shifted to merry public events. “August is when Norma found the plant, so that is when we look for it,” says Linda Masters, a leader of multiple hunts and a restoration specialist at the regional conservation group Openlands in Chicago. “August in Chicago is notoriously hot, humid and buggy.” Yet usually a little more than 100 people show up. A couple of times, some promising little mystery nubbin that suggested Thismia turned up. “Hearts stopped, and people studied the discovery,” Masters says. “But nope.”

In 2017, a different long-lost Thismia , T. neptunis , resurfaced in Borneo . This species may not be astonishingly rare. It’s just really hard to spot. “Even if you know roughly what you are looking for, it takes weeks to find the first one,” says one of its rediscoverers, Michal Sochor of the Crop Research Institute in Olomouc, Czech Republic.

Variety show

The American Thismia ranks as a full species, but variations of species are important too; 14 kinds of plants on Knapp and company’s new list are distinct lineages within a species. Consider, for example, Cheatum’s Eastern wahoo.

In fall, the leaves and seedpods of Eastern wahoos ( Euonymus atropurpureus ), a kind of shrub native to the central and eastern United States, burst into various candy reds and purples. Botanists can find the species in the wild, and people plant them in their yards.

Conserving plants, however, is not like stamp collecting. Knapp and colleagues aren’t looking just for an exemplar or two of a plant. Instead, conservationists now seek genetic variation that gives the plants more options for what the future will throw at them. One taxonomist’s variety may be another’s “nothing special,” so the coauthors of the paper agreed to a voting system that would identify plant variations that the majority agreed were distinctive. Cheatum’s Eastern wahoo made the cut.

This wahoo grew in a small area around Dallas. Last reported in 1944, the shrub appears in the assessment as extinct in the wild (possibly done in by insects) but with a question mark about gardens. The last known place on Earth that a Cheatum’s Eastern wahoo from Texas might grow is the Jardin des Plantes in Paris. Knapp has his fingers crossed and is waiting to hear.

He’s also waiting to hear from the National Botanic Garden of Latvia, the last known hope for, of all things, the Delaware hawthorn, named after its American home state. That small white-flowered tree was named Crataegus delawarensis in 1903 by Charles Sprague Sargent, the first director of the Arnold Arboretum of Harvard University and an enthusiastic sharer of plants.

Knapp did hear back from a query that the Morton Arboretum in Lisle, Ill., had what could be another of Sargent’s hawthorns, C. fecunda . “I was really dubious, because these things can be easily misidentified,” Knapp says. Everyone had to wait until the next spring, because an important distinguishing trait shows up in flowers.

When the tree put out its clusters of white petals, Matt Lobdell, Morton’s curator of living collections, photographed the white flowers against a white sheet of paper. Scrutinizing the images, the author of a book on southeastern hawthorns decided that Morton’s single tree was the last of its species. “It was a real wow moment,” Knapp says.

He had three more occasions, while working on the extinction list, to startle caretakers with the news that they were managing catastrophically rare plants. Letting a species or variety dwindle to just a few individuals is a conservation nightmare.

The lone C. fecunda , growing at the Illinois arboretum since 1922, no longer shows much vigor, Lobdell says. That doesn’t bode well for next spring’s efforts to propagate the plant. “If we’d got on top of this … 70 years ago, we may have had more options,” he says.

Lobdell is trying to do just that for future conservation of three oak species, native to the southern United States. He’s gone plant collecting from South Carolina to Alabama to start banking oak genetic diversity in the arboretum. “Instead of having just three Georgia oaks, all from the same population, we can maybe have 50 or 200,” he says.

Exciting as it is to un-extinct species from a car window or keep hope alive for a miracle in next year’s prairie mud, what plants really need from humans is less drama and more smart planning.

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In Vitro Conservation of Endangered and Value-Added Plant Species

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A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section " Plant Development and Morphogenesis ".

Deadline for manuscript submissions: closed (31 January 2022) | Viewed by 34297

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Dear Colleagues,

Plant biodiversity is crucial for sustaining human life on our planet. There are approximately half a million plants on earth and of these around 50,000 species are used globally for food, feed, fiber, medicine and horticulture. It is estimated that at least 21% of all known vascular plants are either threatened, endangered or at the risk of extinction due to habitat loss, overexploitation, and the rapidly changing climate. In vitro technologies can play an important role in the species recovery projects and enhance plant populations in natural habitats. Micropropagation, an advanced plant tissue culture technique, is a tool that can be used to maintain living germplasm and produce large quantities of plants for replenishment, conservation and global distribution of endangered species and crops of economic importance. Cryopreservation allows the storage of genetic material at an ultra-low temperature (−196 °C), and the tissues can be maintained for decades with minimal loss of viability and genetic uniformity. Over 200 plant species including staple food crops, endangered species and plants of horticultural importance have been cryopreserved with varying degree of success. Thus, integrated plant systems utilizing micropropagation and cryopreservation technologies hold great potential in mitigating the impact of current ecological crisis while complementing global conservation strategies.

This Special Issue is dedicated to highlight the application of in vitro technologies for plant biodiversity conservation. Contributions are welcome on all aspects of in vitro technologies in relation to species recovery, conservation, cryopreservation, and industrial applications of cryo-biotechnologies for producing plant-derived bioactive compounds with potential application in pharmaceutical, cosmetic, and natural health product industries. The submission categories include original research papers, critical reviews (prior consultation with the editor recommended), and research reports or case studies describing a single noteworthy accomplishment.

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Extinction and the U.S. Endangered Species Act

Noah greenwald.

1 Center for Biological Diversity, Portland, OR, USA

Kieran F. Suckling

2 Center for Biological Diversity, Tucson, AZ, USA

Brett Hartl

3 Center for Biological Diversity, Washington, DC, USA

Loyal A. Mehrhoff

4 Center for Biological Diversity, Honolulu, HI, USA

Associated Data

The following information was supplied regarding data availability:

The raw data are available in a Supplementary File and include a complete list of the species we identified as extinct or possibly extinct along with all supporting information.

The U.S. Endangered Species Act is one of the strongest laws of any nation for preventing species extinction, but quantifying the Act’s effectiveness has proven difficult. To provide one measure of effectiveness, we identified listed species that have gone extinct and used previously developed methods to update an estimate of the number of species extinctions prevented by the Act. To date, only four species have been confirmed extinct with another 22 possibly extinct following protection. Another 71 listed species are extinct or possibly extinct, but were last seen before protections were enacted, meaning the Act’s protections never had the opportunity to save these species. In contrast, a total of 39 species have been fully recovered, including 23 in the last 10 years. We estimate the Endangered Species Act has prevented the extinction of roughly 291 species since passage in 1973, and has to date saved more than 99% of species under its protection.

Introduction

Passed in 1973, the U.S. Endangered Species Act (ESA) includes strong protections for listed threatened and endangered species and has helped stabilize and recover hundreds of listed species, such as the bald eagle and gray whale ( Taylor, Suckling & Rachlinski, 2005 ; Schwartz, 2008 ; Suckling et al., 2016 ). In part because of its strong protections, the ESA has engendered substantial opposition from industry lobby groups, who perceive the law as threatening their profits and have been effective in generating opposition to species protections among members of the U.S. Congress. One common refrain from opponents of the ESA in Congress and elsewhere is that the law is a failure because only 2% of listed species have been fully recovered and delisted ( Bishop, 2013 ).

The number of delistings, however, is a poor measure of the success of the ESA because most species have not been protected for sufficient time such that they would be expected to have recovered. Suckling et al. (2016) , for example, found that on average listed birds had been protected just 36 years, but their federal recovery plans estimated an average of 63 years for recovery. Short of recovery, a number of studies have found the ESA is effectively stabilizing or improving the status of species, using both biennial status assessments produced by the U.S. Fish and Wildlife Service for Congress and abundance trends ( Male & Bean, 2005 ; Taylor, Suckling & Rachlinski, 2005 ; Gibbs & Currie, 2012 ; Suckling et al., 2016 ).

In addition to recovering species, one of the primary purposes of the ESA is to prevent species extinction. Previous studies indicate the ESA has been successful in this regard ( McMillan & Wilcove, 1994 ; Scott et al., 2006 ). As of 2008, the ESA was estimated to have prevented the extinction of at least 227 species and the number of species delisted due to recovery outnumbered the number of species delisted for extinction by 14–7 ( Scott et al., 2006 ). In this study, we identified all ESA listed species that are extinct or possibly extinct to quantify the number of species for which ESA protections have failed and use these figures to update the estimated number of species extinctions prevented. This is the first study in over 20 years to compile data on extinction of ESA listed species, providing an important measure of one of the world’s strongest conservation laws ( McMillan & Wilcove, 1994 ).

To identify extinct or possibly extinct ESA listed species, we examined the status of all 1,747 (species, subspecies and distinct population segments) U.S. listed or formerly listed species, excluding species delisted based on a change in taxonomy or new information showing the original listing to have been erroneous. We determined species to be extinct or possibly extinct based on not being observed for at least 10 years, the occurrence of adequate surveys of their habitat, and presence of threats, such as destruction of habitat of the last known location or presence of invasive species known to eliminate the species.

To differentiate extinct and possibly extinct species we relied on determinations by the U.S. Fish and Wildlife Service, IUCN, species experts and other sources. In most cases, these determinations were qualitative rather quantitative. Species were considered extinct if surveys since the last observation were considered sufficient to conclude the species is highly likely to no longer exist, and possibly extinct if surveys were conducted after the last observation, but were not considered sufficient to conclude that extinction is highly likely ( Butchart, Stattersfield & Brooks, 2006 ; Scott et al., 2008 ).

Source information included 5-year reviews, listing rules and critical habitat designations by the U.S. Fish and Wildlife Service (for aquatic and terrestrial species) or NOAA Fisheries (for marine species), published and gray literature, personal communication with species experts and classifications and accounts by NatureServe, IUCN and the Hawaiian Plant Extinction Prevention program. For each species, we identified year of listing, year last seen, NatureServe and IUCN ranking, taxonomic group, and U.S. Fish and Wildlife Service region. For species last seen after listing, we also searched for abundance estimates at time of listing in order to give a sense of likelihood of survival regardless of ESA protection.

Following previously developed methods, we estimated the number of species extinctions prevented by the ESA by assuming that listed threatened and endangered species have a comparable extinction risk to IUCN endangered species, which was estimated as an average of 67% over 100 years ( Mace, 1995 ; Schwartz, 1999 ; Scott et al., 2006 ). We believe this estimate of extinction risk is conservative based on similarity of IUCN criteria to factors considered in ESA listings, observed low numbers for species at time of ESA listing and observed correspondence between ESA listed species and species classified as endangered or critically endangered by the IUCN ( Wilcove, McMillan & Winston, 1993 ; Wilcove & Master, 2005 ; Harris et al., 2012 ). Presumed extinction risk was then multiplied by the number of extant listed species and the proportion of a century in which species were protected by the ESA. Previous studies used the length of time the ESA has been in existence (1973-present) for the proportion of a century species have been protected ( Schwartz, 1999 ; Scott et al., 2006 ), but because many species have not been protected the entire 45 years the law has existed, we instead used the more conservative average length species were protected (25 years). This corresponds to the following formula:

We identified a total of 97 ESA listed species that are extinct (23) or possibly extinct (74). Of these, we found 71 extinct (19) or possibly extinct (52) species were last observed before they were listed under the ESA and thus are not relevant to determining the Act’s success in preventing extinction ( Table S1 ). These species were last seen an average of 24 years before protection was granted with a range of one to more than 80 years prior.

A total of 26 species were last seen after listing, of which four are confirmed extinct and 22 are possibly extinct ( Table S2 ). On average, these species were last seen 13 years after listing with a range of 2–23 years. We were able to find an abundance estimate at the time of listing for 19 of these species, ranging from one individual to more than 2,000 with an average of 272. In several cases, these estimates were based on extrapolations from very few sightings.

The distribution of extinct and possibly extinct species was non-random with 64 of the 97 species from Hawaii and other Pacific Islands, followed by 18 from the southeast ( Fig. 1 ). This was also the case for taxonomy. A total of 40 of the 97 species were mollusks dominated by Hawaiian tree snails and southeast mussels, followed by birds (18) and plants (17) ( Fig. 2 ).

Extinct or possibly extinct listed species by taxonomic group.

Extinct or possibly extinct listed species by U.S. Fish and Wildlife Service Region.

We identified several other species that have been missing for more than 10 years, but for which there has not been any effective surveys and thus classifying them as possibly extinct did not seem appropriate, including two Hawaiian yellow-faced bees ( Hylaeus facilis and Hylaeus hilaris ) (K. Magnacca, 2018, personal communication) and Fosberg’s love grass ( Eragrostis fosbergii ) ( U.S. Fish and Wildlife Service, 2011 ). If indeed extinct, all three were lost prior to protection under the ESA.

Including updated figures for number of listed species, time of protection and species extinctions, we estimate the ESA has prevented the extinction of roughly 291 species in its 45 year history. Based on the number of confirmed extinctions following listing, we further estimate that the ESA has to date prevented the extinction of more than 99% of species under its protection. To date, a total of 39 species have been delisted for recovery compared to four species that are extinct and 22 that are potentially extinct.

The few number of listed species that have gone extinct following protection combined with an estimated 291 species for which extinction was prevented demonstrate the ESA has achieved one of its core purposes—halting the loss of species. We will not attempt to catalog them here, but numerous individual examples provide further support for this conclusion. Well known species like the California condor ( Gymnogyps californianus ), black-footed ferret ( Mustela nigripes ) and Hawaiian monk seal ( Neomonachus schauinslandi ), as well as lesser known species like the yellowfin madtom ( Noturus flavipinnis ), are but a few of the species that likely would have been lost were it not for the ESA.

The madtom is a case in point. Wrongly presumed extinct when described in 1969, individual madtom were found in the Powell River in Tennessee and Copper Creek in Virginia and the species was protected under the ESA in 1977 ( U.S. Fish and Wildlife Service, 1977 ). Following protection, federal and state officials worked with a non-governmental organization, Conservation Fisheries Inc., to discover additional populations and repatriate the species to rivers and streams in its historic range and there are now populations of the yellowfin madtom in three different watersheds ( U.S. Fish and Wildlife Service, 2012a ). The history of the ESA is replete with similar such stories.

The distribution of extinct or possibly extinct listed species largely tracks those regions with the highest rates of species endangerment, including Hawaii and the Northern Mariana Islands with 64 of the 97 extinctions or possible extinctions, and the Southeast with 18 of the extinctions or possible extinctions, mostly freshwater species. The fragility of Hawaii’s endemic fauna to introduced species and habitat destruction and high degree of species imperilment is well recognized ( Duffy & Kraus, 2006 ). Similarly, the extinction and endangerment of freshwater fauna in the southeast is well documented ( Benz & Collins, 1997 ). To avoid further extinctions, these areas should be priorities for increased funding and effort.

Protection under the ESA came too late for the 71 species last seen prior to listing. It’s possible that some of these species survived undetected following listing, but we find this unlikely for most if not all of the species. It is very difficult to document extinction, but all of the species were the subject of survey both before and after listing, which is described in the listing rules and subsequent status surveys. In addition, the 71 species were last seen an average of 24 years prior to listing, providing a long window for detection prior to listing. If some of these species did survive after listing it was likely at very low numbers, such that recovery would have been difficult at best.

That these 71 species were lost before protections were applied clearly highlights the need to move quickly to protect species. Indeed, Suckling, Slack & Nowicki (2004) identified 42 species that went extinct while under consideration for protection. Since that analysis was completed, the U.S. Fish and Wildlife Service has determined five additional species did not qualify for protection because they were extinct, including the Tacoma pocket gopher ( Thomomys mazama tacomensis ), Tatum Cave beetle ( Pseudanophthalmus parvus ), Stephan’s riffle beetle ( Heterelmis stephani), beaverpond marstonia ( Marstonia castor ) and Ozark pyrg ( Marstonia ozarkensis ), meaning there are now 47 species that have gone extinct waiting for protection ( U.S. Fish and Wildlife Service, 2012b , 2016 , 2017 , 2018a ).

The U.S. Fish and Wildlife Service currently faces a backlog of more than 500 species that have been determined to potentially warrant protection, but which await a decision ( U.S. Fish and Wildlife Service, 2018b ). Under the ESA, decisions about protection for species are supposed to take 2 years, but on average it has taken the Fish and Wildlife Service 12 years ( Puckett, Kesler & Greenwald, 2016 ). Such lengthy wait times are certain to result in loss of further species and run counter to the purpose of the statute. This problem can be addressed by streamlining the Service’s process for listing species, which has become increasingly cumbersome, and by increasing funding for the listing program. For every species listed, the Service’s process includes review by upward of 20 people, including numerous individuals who have no specific knowledge of the species and in a number of cases are political appointees. We instead recommend that the Service adopt a process similar to scientific peer review, involving review by two to three qualified individuals.

The loss of 26 species after they were protected is indicative of conservation failure. This failure, however, in most cases cannot be wholly attributed to the ESA because most of these species were reduced to very low numbers by the time they were protected, making recovery difficult to impossible. Of the 19 species we could find an abundance estimate for at the time of listing, 13 had an estimated population fewer than 100 with eight having fewer than 10 individuals. Of the six other species, two Hawaiian birds, Oahu creeper ( Paroreomyza maculate ) and ‘O’u ( Psittirostra psittacea ) had estimated populations in the hundreds, but this was based on sightings of single individuals. Given the lack of further sightings and the presence of disease carrying mosquitoes throughout their habitat, these estimates were likely optimistic. The other four species, the dusky seaside sparrow ( Ammodramus maritimus nigrescens ), Morro Bay kangaroo rat ( Dipodomys heermanni morroensis ), pamakani ( Tetramolopium capillare ) and Curtis’ pearlymussel ( Epioblasma florentina curtisii ), had populations at the time of listing ranging from 100 to 3,000 individuals, but sufficient action was not taken to save them, making them true conservation failures.

At some level, all of the 97 ESA listed species that we identified as possibly extinct or extinct are conservation failures. For 42 of these species, the law itself was too late because they were last seen before the ESA was passed in 1973. But for others, there may have been time and we did not act quickly enough or dedicate sufficient resources to saving them. There are many examples of species both in the U.S. and internationally that have been successfully recovered even after dropping to very small numbers, but this can only occur with fast, effective action, resources and in many cases luck. The Mauritius kestrel ( Falco punctatus) , for example, was brought back from just two pairs ( Cade & Jones, 1993 ) and the Hawaiian plant extinction prevention program, which focuses on saving plants with fewer than 50 individuals, has rediscovered many species believed extinct, brought 177 species into cultivation, constructed fences to protect species from non-native predators and reintroduced many species into the wild ( Wood, 2012 , http://www.pepphi.org/ ).

The failure to provide sufficient resources for conservation of listed species, however, continues to the present. As many as 27 species of Oahu tree snail ( achatinella spp. ) are extinct or possibly extinct, yet expenditures for the species that still survive are inadequate to support minimal survey and captive propagation efforts. Likewise, the Hawaiian plant extinction prevention program, which has been so effective in saving species on the brink of extinction, is facing a budget cut of roughly 70% in 2019 ( http://www.pepphi.org/ ), which very likely could mean the extinction of dozens of plants that otherwise could be saved. Overall, Greenwald et al. (2016) estimate current recovery funding is roughly 3% of estimated recovery costs from federal recovery plans. We can save species from extinction, but it must be more of a priority for federal spending. Nevertheless, despite funding shortfalls and the tragedy of these species having gone extinct, the ESA has succeeded in preventing the extinction of the vast majority of listed species and in this regard is a success.

Management implications

Of the 97 species we identified as extinct or potentially extinct, only 11 have been delisted for extinction. Another 11 have been recommended for delisting due to extinction. The San Marcos gambusia ( Gambusia georgei ) could also be delisted since there is very little hope it survives. For the other 74 possibly extinct species, we recommend retaining protections in the hope that some will be rediscovered and because there is little cost in retaining listing.

Supplemental Information

Supplemental information 1.

Extinct or possibly extinct species broken out by whether last seen before or after protection was enacted, including relevant source data and literature cited.

Funding Statement

The authors received no funding for this work.

Additional Information and Declarations

All authors are employed by the Center for Biological Diversity which works to protect endangered species and their habitats.

Noah Greenwald conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Kieran F. Suckling conceived and designed the experiments, performed the experiments, analyzed the data, authored or reviewed drafts of the paper, approved the final draft.

Brett Hartl conceived and designed the experiments, performed the experiments, analyzed the data, authored or reviewed drafts of the paper, approved the final draft.

Loyal A. Mehrhoff conceived and designed the experiments, performed the experiments, analyzed the data, authored or reviewed drafts of the paper, approved the final draft.

• ENVIRONMENT

One million species at risk of extinction, UN report warns

A landmark global assessment warns that the window is closing to safeguard biodiversity and a healthy planet. Yet solutions are in sight.

The bonds that hold nature together may be at risk of unraveling from deforestation, overfishing, development, and other human activities, a landmark United Nations report warns. Thanks to human pressures, one million species may be pushed to extinction in the next few years, with serious consequences for human beings as well as the rest of life on Earth.

“The evidence is crystal clear: Nature is in trouble. Therefore we are in trouble,” said Sandra Díaz, one of the co-chairs of the Global Assessment Report on Biodiversity and Ecosystem Services. A 40-page “Summary for Policy Makers” of the forthcoming full report (expected to exceed 1,500 pages) was released May 6 in Paris.

Related: Iconic Endangered Species

Based on a review of about 15,000 scientific and government sources and compiled by 145 expert authors from 50 countries, the global report is the first comprehensive look in 15 years at the state of the planet’s biodiversity. This report includes, for the first time, indigenous and local knowledge as well as scientific studies. The authors say they found overwhelming evidence that human activities are behind nature’s decline. They ranked the major drivers of species decline as land conversion, including deforestation ; overfishing ; bush meat hunting and poaching; climate change; pollution; and invasive alien species.

The tremendous variety of living species—at least 8.7 million , but possibly many more —that make up our “life-supporting safety net” provide our food, clean water, air, energy, and more, said Díaz, an ecologist at the National University of Cordoba in Argentina, in an interview. “Not only is our safety net shrinking, it’s becoming more threadbare and holes are appearing.”

A world of green slime?

In parts of the ocean, little life remains but green slime. Some remote tropical forests are nearly silent as insects have vanished , and grasslands are increasingly becoming deserts. Human activity has resulted in the severe alteration of more than 75 percent of Earth’s land areas, the Global Assessment found. And 66 percent of the oceans, which cover most of our blue planet, have suffered significant human impacts. This includes more than 400 dead zones —where scant life can survive—that collectively would cover the state of Oregon or Wyoming.

The new report paints “an ominous picture” of the health of ecosystems rapidly deteriorating, said Sir Robert Watson, Chair of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES), which conducted the global assessment. IPBES is often described as the equivalent of the Intergovernmental Panel for Climate Change for biodiversity and does scientific assessments on the status of the non-human life that makes up the Earth’s life-support system.

“We are eroding the very foundations of our economies, livelihoods, food security, health, and quality of life worldwide,” Watson said in a statement.

“My biggest personal concern is the state of the oceans,” Watson told National Geographic. “ Plastics , dead zones, overfishing, acidification... We’re really screwing up the oceans in a big way.”

Saving more species

Protecting nature and saving species is all about securing the land and water plants and animals need to survive, said Jonathan Baillie , executive vice president and chief scientist of the National Geographic Society. Protecting half of the planet by 2050, with an interim target of 30 percent by 2030 , is the only way to meet the Paris climate targets or achieve the UN’s Sustainable Development Goals for the world, Baillie said.

Forests, oceans, and other parts of nature soak up 60 percent of global fossil fuel emissions every year, the report found. “We need to secure the biosphere to protect the climate and help buffer us from extreme weather events,” Baillie said.

Coral reefs and mangroves protect coastal areas from storms such as hurricanes. Wetlands reduce flooding by absorbing heavy rainfall. Yet each of these ecosystems has declined dramatically, with wetlands down to less than 15 percent of what they were 300 years ago and coral reefs facing a global bleaching crisis .

Nearly 100 groups around the world (including the National Geographic Society and the Wyss Campaign for Nature) have endorsed the goal of protecting half of the planet by 2050. Recently, 19 of the world’s leading scientists published a study to make a science-backed plan for an interim step that would protect 30 percent by 2030 under what’s called a Global Deal for Nature . The proposed protection does not mean “no go” areas, but rather areas protected from resource extraction and land conversion. Sustainable uses would be permitted in all but the most sensitive areas, the groups wrote.

“The international community has both the time and the tools to safeguard nature and slow the ongoing wildlife extinction crisis,” Brian O’Donnell, director of the Wyss Campaign for Nature, said in a statement.

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National Geographic Society and the Wyss Campaign for Nature are working together to inspire the protection of 30 percent of the planet by 2030 .

Such tools were under discussion during the week-long negotiations by IPBES country members who debated the key messages and policy options to be published in the “Summary for Policymakers.” The full Global Assessment report will be published later this year.

“The main message of our report is that transformative change is urgently needed. There are no other options” said David Obura, a marine biologist at the Coastal Oceans Research and Development – Indian Ocean in Mombasa, Kenya. “There’s so little time left to save corals. If we can save corals we could save everything.”

Value nature not stuff

In order to safeguard a healthy planet, society needs to shift from a sole focus on chasing economic growth, the summary report concludes. That won’t be easy, the report acknowledges. But it could get easier if countries begin to base their economies on an understanding that nature is the foundation for development. Shifting to nature-based planning can help provide a better quality of life with far less impact.

Putting that concept into practical terms, the report says countries need to reform hundreds of billions in dollars in subsidies and incentives that are currently given to the energy, fishing, agricultural, and forestry sectors. Instead of driving additional exploitation of the world’s natural resources, those monies should be shifted to incentivize protection and restoration of nature—such as underwriting new reserves or reforestation programs, the report said.

“We need to change what we value: nature, ecosystems, social equity, not growing the GDP,” Obura said.

The other evidence gathered by IPBES shows that nature managed by indigenous peoples and local communities is in generally better health than nature managed by national or corporate institutions, despite increasing pressures, said Joji Cariño, a senior policy advisor at the Forest Peoples Programme , a human rights organization.

At least a quarter of the global land area is traditionally owned, managed, used, or occupied by indigenous peoples. However, their land tenure and other rights are not always protected or recognized by all countries. Nor is their deep knowledge of the land and their values often considered in policies and decisions by governments. That needs to change, the Global Assessment noted.

“Indigenous peoples are key partners in the global transformation that’s needed,” said Cariño.

Yet countries still are slow to recognize this, she adds. As an example, she points to the Philippines. Forty years ago, indigenous people there stopped construction of dams on the Chico River because they were concerned about impacts on their land. Yet those dams are now being built by China under their trillion-dollar Belt and Road infrastructure initiative .

China has an important role to play in global discussions around biodiversity, because the country will host a major United Nations conference called the UN Convention on Biological Diversity in late 2020. Scientists hope a new, ambitious international agreement to protect the planet could happen there, akin to the Paris agreement around climate.

Assessment co-chair Díaz doesn’t yet know if a global agreement will arise as bold as protecting 30 percent by 2030. “If it were easy it would have already happened,” Diaz said.

“However, the evidence is clear: the future will be bad for us if we don’t act now. There is no future for us without nature.”

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Endangered Species Research (ESR) was founded in 2004 by leading ecologist Professor Otto Kinne as a major stage for publications on the ecology of endangered life, its requirements for survival, and its protection.

ESR has grown dynamically and is recognised as a central journal in this vital field. With its Editorial Board of acknowledged experts from around the world, it attracts papers on a wide range of subjects and species. It publishes Research Articles, Reviews, and Notes, as well as Comments/Reply Comments, Theme Sections and Opinion Pieces. (For more details see the Guidelines for Authors .)

Like all Inter-Research journals, ESR maintains the highest scientific standards in both manuscript review and production. All articles are published online with author-funded Open Access. Fees (Article Processing Charges - APCs) are very reasonable and special support can be applied for by authors from poorer countries (see ‘Open Access’ tab for details). The Impact Factor for 2023 (Journal Citation Reports 2024 Release) is 2.6 from 3111 total cites (5-year IF = 2.8), Immediacy Index = 0.5, Eigenfactor = 0.00221, JCI = 0.75, and Scimago ranks ESR in the first quartile in the categories 'Ecology' and 'Nature and Landscape Conservation'. ESR's strong presence in the Social Media is demonstrated by unusually high Altmetric scores — Altmetric reports that '…research outputs from this source typically receive a lot more attention than average'.

ESR aims at providing knowledge needed for practising human stewardship of the vast array of the earth’s species, many of which have become threatened, not least by human activities. Such stewardship has become vital for the future of the planet and is of primary importance for the long-term survival of Homo sapiens . While acknowledging that conservation has to occur at a landscape and ecosystem scale, there will always be a need to focus on certain species whose existence is in particular danger. ESR seeks to publish the best of such research that informs conservation or management.

ESR is international and interdisciplinary. It covers all endangered forms of life on Earth, the threats faced by species and their habitats and the necessary steps that must be undertaken to ensure their conservation. ESR publishes high quality contributions reporting research on all species (and habitats) of conservation concern, whether they be classified as Near Threatened or Threatened (Endangered or Vulnerable) by the International Union for the Conservation of Nature and Natural Resources (IUCN) or highlighted as part of national or regional conservation strategies. Submissions on all aspects of conservation science are welcome.

We especially invite contributions that synthesise key areas. Suggestions for Theme Sections on emerging topics of importance are invited. All submitted manuscripts will be subject to a thorough review process involving at least three reviewers. Current acceptance rates are about 50%.

Please submit manuscripts through the online management system or via e-mail to the Editor-in-Chief via the ESR Managing Editor (for details consult GUIDELINES FOR AUTHORS ).

Criticism and advice are invited (address to the Editor-in-Chief, Dr. Brendan J. Godley B.J.Godley(at)exeter.ac.uk ).

Production schedule

ESR volumes are built online, with articles appearing as soon as editorial modifications are approved by the authors. Production time (final acceptance to online publication) is 4-6 weeks. 

ESR encourages and facilitates the incorporation of essential supplementary material –– such as movies or oversize tables, figures or mathematics –– to assist authors in more effectively transmitting their research results.

High quality color illustrations are welcome and will be published without extra charge.

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ESR is published entirely Open Access (see the IR Open Access policy for details) under the Creative Commons by Attribution (CC-BY) Licence . Please refer to the ‘Open Access’ tab on the present page for pricing details as well as options for discounts and waivers for authors from certain countries. ESR does not charge authors for color figures or any additional page charges.

Authors, Reviewers and Editors must disclose relationships (e.g. financial, economic, institutional) that may affect the integrity of the scientific process. Please refer to our Conflict of Interest Policy for details.

Inter-Research journals are following the Committee of Publication Ethics advice on neutrality for editorial decisions. In brief, editorial decisions in Inter-Research journals shall not be affected by the origins of the manuscript, including the nationality, ethnicity, political beliefs, race or religion of the authors. Decisions to review, edit and publish shall not be determined by the policies of governments or other agencies, but just by the journals themselves, and are purely based on scientific merit of the submitted work and the work’s fit within each journal’s scope.

ESR is published entirely Open Access under the Creative Commons by Attribution (CC-BY) Licence .

The APC is based on article type and date of article submission, so the final APC price is already fixed for APC funding applications necessary prior to article submission.

The Article Processing Charges (APCs) are:

Articles submitted on or after 1 November 2022

• €2500 for Research or Review articles
• €1250 for Notes
• € 650 for Opinion Pieces or Comments

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• €1000 for Notes
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All ESR articles are available online and are freely accessible to all users. As from Volume 29 (2015/16), the print version has been discontinued. Thus subscriptions are no longer available.

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All You Need To Know About Endangered Plants Species

The extinction rate of plants is accelerating at an unprecedented speed: the 2020 State of the World’s Plants and Fungi Report found that 39.4% of the world’s plants are now threatened with extinction, a huge jump from the estimated one in five plants predicted in the 2016 report. There are many endangered plant species that are found all across the world but particularly in biodiversity ‘hotspots’ in the tropics and the Mediterranean. Countries such as Australia, India, and Hawaii have some of the highest amounts of endangered plants. The worrisome trend, experts argue, is desti ned to continue in the upcoming years. Indeed, as a 2018 study by botanist Alan Gray found: “ drivers of plant extinction may have an inertia that could last well into the future”. But what are these drivers, what are the main endangered species of plants, and what are the potential effects of plant loss?

Why Are Plants So Important?

Plants and fungi are the building blocks of life on planet Earth. They are used as medicines and treatments that save the lives of millions of people every year, they represent a source of food and energy, provide humanity with building materials and clean air, and they have the potential to solve urgent problems that threaten human life.

New data that emerged from the 2020 State of the World’s Plants and Fungi Report show that despite the existence of more than 7,000 edible and nutritious plants, 90% of humanity’s food energy intake derives from just 15 plants. Simultaneously, almost half of the world’s population relies on just three crops: rice, maize and wheat. As for their use in medicine, plants make up a huge portion of treatments, used to treat deadly illnesses such as cancer and heart diseases as well as several skin conditions. Approximately 4 billion people rely on herbal medicines as their primary source of healthcare. Out of the top 150 drugs prescribed in the United States, at least 118 are based on natural sources.

But plants are not only crucial for humans. Plant species such as seaweed, for example, are also vital for the conservation of shallow marine ecosystems . These algae break the flow of water and thus help to prevent coastal erosion. They also promote species diversity by providing habitat, nutrients, and energy for millions of animals. 

Another example of vital plants is trees: they represent a precious resource that can help tackle pollution, a threat to human health, climate and ecosystems around the world. According to the 2021 State of the World’s Trees Report , a third of the world’s trees are currently at risk of extinction. 

You might also like: 8 Stunning Endangered Species Facts to Know About

What Are the Drivers of Plant Extinction?

Deforestation, mass-agriculture, logging, and livestock farming are among the top threats to plant diversity. But climate change and extreme weather conditions are considered to be emerging dangers. 

Overharvesting of some plant species to satisfy human needs has placed many medical and food species at risk of extinction. The main drive of overexploitation stems from the unprecedented global demand for naturally-driven medicines and edible plants. Some examples of endangered species of plants that are highly valued for the medicines they provide are Black Cohosh – a root used to support women’s health ailments and to ease arthritis and inflammatory conditions, American and Asian Ginseng – famous for its healing properties, and Wild Yam, used to reduce inflammation and support metabolism.  

As mentioned before, around a dozen plants and just three crops are used to satisfy the food energy intake needs of more than 4 billion people. As experts argue, relying on a handful of crops to feed the global population accounts for the loss of 75% of global farmed plant diversity compared to pre-1900 . Endangered edible plant species include coffee plants -– two-thirds of which are at risk of extinction – cocoa plants, and staple crops such as maize and potatoes. While excessive demand and overexploitation of these plants put them at risk, climate change also plays a large role in their disappearance. As temperatures rise and rainfall drops, pests and diseases are more likely to spread, while insects or mould destroy outdoor crops. The loss of crops further leaves us vulnerable to climate change , contributing to malnutrition by reducing nutrient availability and affecting global food security.

The same discourse goes for the aforementioned seaweed, an overexploited plant used for direct human consumption as well as implemented for the preparation of feeds, fertilisers, biofuels, cosmetics, and medicines. As Juliet Brodie , Professor at the London Natural History Museum, said: “As we continue to exploit our coastal ecosystems, seaweeds face a race against time for us to understand and protect them before it’s too late.”

What Risks Do Endangered Plant Species Pose?

Losing plant species creates a dangerous domino effect as it drives a loss of animal diversity, makes ecosystems even more vulnerable to climate change, extreme weather, and puts human health and the entire food chain at risk. Indeed, ecosystems are a complex network made up of animals, plants, and other organisms coexisting and working together. Losing part of these species can have monumental effects across the entire ecosystem . As experts put it: ‘extinction breeds extinction’. Thus, protecting plant species is thus crucial not only to protect the environment but also to ensure food security and human health. 

What Can We Do to Protect Endangered Plants?

One of the most effective policies to date to protect plants and animal species threatened with extinction is the Endangered Species Act (ESA). The law, passed in the US in 1973, allows individuals and organisations to petition to have a species listed as endangered or threatened. After undergoing scientific review, classified endangered species are to be protected and to do so, long-term recovery plans for critical habitat areas are set up to prevent extinction. These plans cover a range of factors such as habitat, food availability, reproduction rate, and climate. 

The law is still the country’s best – and only – option to protect endangered species. And while it has proven to be more than 99% successful at preventing extinction, given that at least 227 endangered species have been saved since the law was passed five decades ago, there are other ways to help conserve plants and protect those at risk of extinction that everyone can do. First and foremost, we can educate ourselves and the people around us about threatened species, researching what plants are at risk in the areas we live in and the potential consequences we would face if they were to disappear. Another important way is to preserve the environment around us, leaving it untouched and undisturbed. Avoiding toxic pesticides and herbicides in our yard is also crucial, as the chemicals contained in these products are extremely detrimental. As for edible plants such as coffee and cocoa, opting for Fair Trade brands, whose production is ethical and involves the least amount of environmental destruction, is always a good choice. Finally, people must commit to reducing their environmental footprint as much as possible, avoiding activities that can pollute the habitat around us, and being conscious that our actions can have detrimental effects.

You might also like: 10 of the World’s Most Endangered Animals in 2022

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Endangered Species

An endangered species is a type of organism that is threatened by extinction. Species become endangered for two main reasons: loss of habitat and loss of genetic variation.

Biology, Ecology, Geography, Conservation

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An endangered species is a type of organism that is threatened by extinction . Species become endangered for two main reasons: loss of habitat and loss of genetic variation . Loss of Habitat A loss of habitat can happen naturally. Nonavian dinosaurs , for instance, lost their habitat about 65 million years ago. The hot, dry climate of the Cretaceous period changed very quickly, most likely because of an asteroid striking Earth. The impact of the asteroid forced debris into the atmosphere , reducing the amount of heat and light that reached Earth’s surface. The dinosaurs were unable to adapt to this new, cooler habitat. Nonavian dinosaurs became endangered, then extinct . Human activity can also contribute to a loss of habitat. Development for housing, industry , and agriculture reduces the habitat of native organisms. This can happen in a number of different ways. Development can eliminate habitat and native species directly. In the Amazon rainforest of South America, developers have cleared hundreds of thousands of acres. To “clear” a piece of land is to remove all trees and vegetation from it. The Amazon rainforest is cleared for cattle ranches , logging , and ur ban use. Development can also endanger species indirectly. Some species, such as fig trees of the rainforest, may provide habitat for other species. As trees are destroyed, species that depend on that tree habitat may also become endangered. Tree crowns provide habitat in the canopy , or top layer, of a rainforest . Plants such as vines, fungi such as mushrooms, and insects such as butterflies live in the rainforest canopy. So do hundreds of species of tropical birds and mammals such as monkeys. As trees are cut down, this habitat is lost. Species have less room to live and reproduce . Loss of habitat may happen as development takes place in a species range . Many animals have a range of hundreds of square kilometers. The mountain lion ( Puma concolor ) of North America, for instance, has a range of up to 1,000 square kilometers (386 square miles). To successfully live and reproduce, a single mountain lion patrols this much territory. Urban areas , such as Los Angeles, California, U.S.A., and Vancouver, British Columbia, Canada, grew rapidly during the 20th century. As these areas expanded into the wilderness, the mountain lion’s habitat became smaller. That means the habitat can support fewer mountain lions. Because enormous parts of the Sierra Nevada, Rocky, and Cascade mountain ranges remain undeveloped, however, mountain lions are not endangered. Loss of habitat can also lead to increased encounters between wild species and people. As development brings people deeper into a species range, they may have more exposure to wild species. Poisonous plants and fungi may grow closer to homes and schools. Wild animals are also spotted more frequently . These animals are simply patrolling their range, but interaction with people can be deadly. Polar bears ( Ursus maritimus ), mountain lions, and alligators are all predators brought into close contact with people as they lose their habitat to homes, farms , and businesses. As people kill these wild animals, through pesticides , accidents such as collisions with cars, or hunting, native species may become endangered.

Loss of Genetic Variation Genetic variation is the diversity found within a species. It’s why human beings may have blond, red, brown, or black hair. Genetic variation allows species to adapt to changes in the environment. Usually, the greater the population of a species, the greater its genetic variation. Inbreeding is reproduction with close family members. Groups of species that have a tendency to inbreed usually have little genetic variation, because no new genetic information is introduced to the group. Disease is much more common, and much more deadly, among inbred groups. Inbred species do not have the genetic variation to develop resistance to the disease. For this reason, fewer offspring of inbred groups survive to maturity. Loss of genetic variation can occur naturally. Cheetahs ( Acinonyx jubatus ) are a threatened species native to Africa and Asia. These big cats have very little genetic variation. Biologists say that during the last Ice Age , cheetahs went through a long period of inbreeding. As a result, there are very few genetic differences between cheetahs. They cannot adapt to changes in the environment as quickly as other animals, and fewer cheetahs survive to maturity. Cheetahs are also much more difficult to breed in captivity than other big cats, such as lions ( Panthera leo ). Human activity can also lead to a loss of genetic variation. Overhunting and overfishing have reduced the populations of many animals. Reduced population means there are fewer breeding pairs . A breeding pair is made up of two mature members of the species that are not closely related and can produce healthy offspring. With fewer breeding pairs, genetic variation shrinks. Monoculture , the agricultural method of growing a single crop , can also reduce genetic variation. Modern agribusiness relies on monocultures. Almost all potatoes cultivated , sold, and consumed, for instance, are from a single species, the Russet Burbank ( Solanum tuberosum ). Potatoes, native to the Andes Mountains of South America, have dozens of natural varieties. The genetic variation of wild potatoes allows them to adapt to climate change and disease. For Russet Burbanks, however, farmers must use fertilizers and pesticides to ensure healthy crops because the plant has almost no genetic variation. Plant breeders often go back to wild varieties to collect genes that will help cultivated plants resist pests and drought, and adapt to climate change. However, climate change is also threatening wild varieties. That means domesticated plants may lose an important source of traits that help them overcome new threats. The Red List The International Union for Conservation of Nature (IUCN) keeps a “Red List of Threatened Species.” The Red List de fines the severity and specific causes of a species’ threat of extinction. The Red List has seven levels of conservation: least concern , near threatened , vulnerable, endangered, critically endangered , extinct in the wild , and extinct. Each category represents a different threat level. Species that are not threatened by extinction are placed within the first two categories—least concern and near-threatened. Those that are most threatened are placed within the next three categories, known as the threatened categories —vulnerable, endangered, and critically endangered. Those species that are extinct in some form are placed within the last two categories—extinct in the wild and extinct. Classifying a species as endangered has to do with its range and habitat, as well as its actual population. For this reason, a species can be of least concern in one area and endangered in another. The gray whale ( Eschrichtius robustus ), for instance, has a healthy population in the eastern Pacific Ocean, along the coast of North and South America. The population in the western Pacific, however, is critically endangered.

Least Concern Least concern is the lowest level of conservation . A species of least concern is one that has a widespread and abundant population. Human beings are a species of least concern, along with most domestic animals , such as dogs ( Canis familiaris ) and cats ( Felis catus ). Many wild animals, such as pigeons and houseflies ( Musca domestica ), are also classified as least concern. Near Threatened A near threatened species is one that is likely to qualify for a threatened category in the near future. Many species of violets , native to tropical jungles in South America and Africa, are near threatened, for instance. They have healthy populations, but their rainforest habitat is disappearing at a fast pace. People are cutting down huge areas of rainforest for development and timber . Many violet species are likely to become threatened. Vulnerable Species The definitions of the three threatened categories (vulnerable, endangered, and critically endangered) are based on five criteria: population reduction rate , geographic range, population size, population restrictions , and probability of extinction . Threatened categories have different thresholds for these criteria. As the population and range of the species decreases, the species becomes more threatened. 1) Population reduction rate A species is classified as vulnerable if its population has declined between 30 and 50 percent. This decline is measured over 10 years or three generations of the species, whichever is longer. A generation is the period of time between the birth of an animal and the time it is able to reproduce. Mice are able to reproduce when they are about one month old. Mouse populations are mostly tracked over 10-year periods. An elephant's generation lasts about 15 years. So, elephant populations are measured over 45-year periods. A species is vulnerable if its population has declined at least 50 percent and the cause of the decline is known. Habitat loss is the leading known cause of population decline. A species is also classified as vulnerable if its population has declined at least 30 percent and the cause of the decline is not known. A new, unknown virus , for example, could kill hundreds or even thousands of individuals before being identified. 2) Geographic range A species is vulnerable if its “ extent of occurrence ” is estimated to be less than 20,000 square kilometers (7,722 square miles). An extent of occurrence is the smallest area that could contain all sites of a species’ population. If all members of a species could survive in a single area, the size of that area is the species’ extent of occurrence. A species is also classified as vulnerable if its “ area of occupancy ” is estimated to be less than 2,000 square kilometers (772 square miles). An area of occupancy is where a specific population of that species resides. This area is often a breeding or nesting site in a species range. 3) Population size Species with fewer than 10,000 mature individuals are vulnerable. The species is also vulnerable if that population declines by at least 10 percent within 10 years or three generations, whichever is longer. 4) Population restrictions Population restriction is a combination of population and area of occupancy. A species is vulnerable if it is restricted to less than 1,000 mature individuals or an area of occupancy of less than 20 square kilometers (8 square miles). 5) Probability of extinction in the wild is at least 10 percent within 100 years. Biologists, anthropologists, meteorologists , and other scientists have developed complex ways to determine a species’ probability of extinction. These formulas calculate the chances a species can survive, without human protection, in the wild. Vulnerable Species: Ethiopian Banana Frog The Ethiopian banana frog ( Afrixalus enseticola ) is a small frog native to high- altitude areas of southern Ethiopia. It is a vulnerable species because its area of occupancy is less than 2,000 square kilometers (772 square miles). The extent and quality of its forest habitat are in decline. Threats to this habitat include forest clearance, mostly for housing and agriculture. Vulnerable Species: Snaggletooth Shark The snaggletooth shark ( Hemipristis elongatus ) is found in the tropical, coastal waters of the Indian and Pacific Oceans. Its area of occupancy is enormous, from Southeast Africa to the Philippines, and from China to Australia. However, the snaggletooth shark is a vulnerable species because of a severe population reduction rate. Its population has fallen more than 10 percent over 10 years. The number of these sharks is declining due to fisheries, especially in the Java Sea and Gulf of Thailand. The snaggletooth shark’s flesh, fins, and liver are considered high-quality foods. They are sold in commercial fish markets, as well as restaurants. Vulnerable Species: Galapagos Kelp Galapagos kelp ( Eisenia galapagensis ) is a type of seaweed only found near the Galapagos Islands in the Pacific Ocean. Galapagos kelp is classified as vulnerable because its population has declined more than 10 percent over 10 years. Climate change is the leading cause of decline among Galapagos kelp. El Niño, the natural weather pattern that brings unusually warm water to the Galapagos, is the leading agent of climate change in this area. Galapagos kelp is a cold-water species and does not adapt quickly to changes in water temperature.

Endangered Species 1) Population reduction rate A species is classified as endangered when its population has declined between 50 and 70 percent. This decline is measured over 10 years or three generations of the species, whichever is longer. A species is classified as endangered when its population has declined at least 70 percent and the cause of the decline is known. A species is also classified as endangered when its population has declined at least 50 percent and the cause of the decline is not known. 2) Geographic range An endangered species’ extent of occurrence is less than 5,000 square kilometers (1,930 square miles). An endangered species’ area of occupancy is less than 500 square kilometers (193 square miles). 3) Population size A species is classified as endangered when there are fewer than 2,500 mature individuals. When a species population declines by at least 20 percent within five years or two generations, it is also classified as endangered. 4) Population restrictions A species is classified as endangered when its population is restricted to less than 250 mature individuals. When a species’ population is this low, its area of occupancy is not considered. 5) Probability of extinction in the wild is at least 20 percent within 20 years or five generations, whichever is longer.

Endangered Species: Scimitar -horned Oryx The scimitar-horned oryx ( Oryx dammah ) is a species of antelope with long horns. Its range extends across northern Africa. Previously, the scimitar-horned oryx was listed as extinct in the wild because the last confirmed sighting of one was in 1988. However, the first group of scimitar-horned oryx was released back into the wild in Chad, in August 2016, and the population is growing. Overhunting and habitat loss, including competition with domestic livestock , are the main reasons for the decline of the oryx’s wild population. Captive herds are now kept in protected areas of Tunisia, Senegal, and Morocco. Scimitar-horned oryxes are also found in many zoos . Critically Endangered Species 1) Population reduction rate A critically endangered species’ population has declined between 80 and 90 percent. This decline is measured over 10 years or three generations of the species, whichever is longer. A species is classified as critically endangered when its population has declined at least 90 percent and the cause of the decline is known. A species is also classified as endangered when its population has declined at least 80 percent and the cause of the decline is not known. 2) Geographic range A critically endangered species’ extent of occurrence is less than 100 square kilometers (39 square miles). A critically endangered species’ area of occupancy is estimated to be less than 10 square kilometers (4 square miles). 3) Population size A species is classified as critically endangered when there are fewer than 250 mature individuals. A species is also classified as critically endangered when the number of mature individuals declines by at least 25 percent within three years or one generation, whichever is longer. 4) Population restrictions A species is classified as critically endangered when its population is restricted to less than 50 mature individuals. When a species’ population is this low, its area of occupancy is not considered. 5) Probability of extinction in the wild is at least 50 percent within 10 years or three generations, whichever is longer. Critically Endangered Species: Bolivian Chinchilla Rat The Bolivian chinchilla rat ( Abrocoma boliviensis ) is a rodent found in a small section of the Santa Cruz region of Bolivia. It is critically endangered because its extent of occurrence is less than 100 square kilometers (39 square miles). The major threat to this species is loss of its cloud forest habitat. People are clearing forests to create cattle pastures .

Critically Endangered Species: Transcaucasian Racerunner The Transcaucasian racerunner ( Eremias pleskei ) is a lizard found on the Armenian Plateau , located in Armenia, Azerbaijan, Iran, and Turkey. The Transcaucasian racerunner is a critically endangered species because of a huge population decline, estimated at more than 80 percent during the past 10 years. Threats to this species include the salination , or increased saltiness, of soil . Fertilizers used for agricultural development seep into the soil, increasing its saltiness. Racerunners live in and among the rocks and soil, and cannot adapt to the increased salt in their food and shelter. The racerunner is also losing habitat as people create trash dumps on their area of occupancy. Critically Endangered Species: White Ferula Mushroom The white ferula mushroom ( Pleurotus nebrodensis ) is a critically endangered species of fungus. The mushroom is critically endangered because its extent of occurrence is less than 100 square kilometers (39 square miles). It is only found in the northern part of the Italian island of Sicily, in the Mediterranean Sea. The leading threats to white ferula mushrooms are loss of habitat and overharvesting. White ferula mushrooms are a gourmet food item. Farmers and amateur mushroom hunters harvest the fungus for food and profit. The mushrooms can be sold for up to $100 per kilogram (2.2 pounds). Extinct in the Wild A species is extinct in the wild when it only survives in cultivation (plants), in captivity (animals), or as a population well outside its established range. A species may be listed as extinct in the wild only after years of surveys have failed to record an individual in its native or expected habitat.

Extinct in the Wild: Monut Kaala Cyanea The Mount Kaala cyanea ( Cyanea superba ) is a large, flowering tree native to the island of Oahu, in the U.S. state of Hawai‘i. The Mount Kaala cyanea has large, broad leaves and fleshy fruit. The tree is extinct in the wild largely because of invasive species. Non-native plants crowded the cyanea out of its habitat, and non-native animals such as pigs, rats, and slugs ate its fruit more quickly than it could reproduce. Mount Kaala cyanea trees survive in tropical nurseries and botanical gardens . Many botanists and conservationists look forward to establishing a new population in the wild. Extinct A species is extinct when there is no reasonable doubt that the last remaining individual of that species has died. Extinct: Cuban Macaw The Cuban macaw ( Ara tricolor ) was a tropical parrot native to Cuba and a small Cuban island, Isla de la Juventud. Hunting and collecting the birds for pets led to the bird’s extinction. The last specimen of the Cuban macaw was collected in 1864. Extinct: Ridley’s Stick Insect Ridley’s stick insect ( Pseudobactricia ridleyi ) was native to the tropical jungle of the island of Singapore. This insect, whose long, segmented body resembled a tree limb, is only known through a single specimen, collected more than 100 years ago. During the 20th century, Singapore experienced rapid development. Almost the entire jungle was cleared, depriving the insect of its habitat.

Endangered Species and People When a species is classified as endangered, governments and international organizations can work to protect it. Laws may limit hunting and destruction of the species’ habitat. Individuals and organizations that break these laws may face huge fines. Because of such actions, many species have recovered from their endangered status. The brown pelican ( Pelecanus occidentalis ) was taken off the endangered species list in 2009, for instance. This seabird is native to the coasts of North America and South America, as well as the islands of the Caribbean Sea. It is the state bird of the U.S. state of Louisiana. In 1970, the number of brown pelicans in the wild was estimated at 10,000. The bird was classified as vulnerable. During the 1970s and 1980s, governments and conservation groups worked to help the brown pelican recover. Young chicks were reared in hatching sites, then released into the wild. Human access to nesting sites was severely restricted. The pesticide DDT , which damaged the eggs of the brown pelican, was banned. During the 1980s, the number of brown pelicans soared. In 1988, the IUCN “delisted” the brown pelican. The bird, whose population is now in the hundreds of thousands, is now in the category of least concern.

Convention on Biological Diversity The Convention on Biological Diversity is an international treaty to sustain and protect the diversity of life on Earth. This includes conservation, sustainability, and sharing the benefits of genetic research and resources. The Convention on Biological Diversity has adopted the IUCN Red List of endangered species in order to monitor and research species' population and habitats. Three nations have not ratified the Convention on Biological Diversity: Andorra, the Holy See (Vatican), and the United States.

Lonesome George Lonesome George was the only living member of the Pinta Island tortoise ( Chelonoidis abingdoni ) known to exist. The Pinta Island tortoise was only found on Pinta, one of the Galapagos Islands. The Charles Darwin Research Station, a scientific facility in the Galapagos, offered a $10,000 reward to any zoo or individual for locating a single Pinta Island tortoise female. On June 25, 2012, Lonesome George died, leaving one more extinct species in the world.

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Introduction, materials and methods, acknowledgements, author contributions, data availability, conflict of interest statement, supplementary data.

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The jacktree genome and population genomics provides insights for the mechanisms of the germination obstacle and the conservation of endangered ornamental plants

These authors contributed equally to this work.

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Sheng Zhu, Xue-Fen Wei, Yu-Xin Lu, Dao-Wu Zhang, Ze-Fu Wang, Jing Ge, Sheng-Lian Li, Yan-Feng Song, Yong Yang, Xian-Gui Yi, Min Zhang, Jia-Yu Xue, Yi-Fan Duan, The jacktree genome and population genomics provides insights for the mechanisms of the germination obstacle and the conservation of endangered ornamental plants, Horticulture Research , Volume 11, Issue 8, August 2024, uhae166, https://doi.org/10.1093/hr/uhae166

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Sinojackia Hu represents the first woody genus described by Chinese botanists, with all species classified as endangered ornamental plants endemic to China. Their characteristic spindle-shaped fruits confer high ornamental value to the plants, making them favored in gardens and parks. Nevertheless, the fruits likely pose a germination obstacle, contributing to the endangered status of this lineage. Here we report the chromosome-scale genome of S. xylocarpa , and explore the mechanisms underlying its endangered status, as well as its population dynamics throughout evolution. Population genomic analysis has indicated that S. xylocarpa experienced a bottleneck effect following the recent glacial period, leading to a continuous population reduction. Examination of the pericarp composition across six stages of fruit development revealed a consistent increase in the accumulation of lignin and fiber content, responsible for the sturdiness of mature fruits’ pericarps. At molecular level, enhanced gene expression in the biosynthesis of lignin, cellulose and hemicellulose was detected in pericarps. Therefore, we conclude that the highly lignified and fibrotic pericarps of S. xylocarpa , which inhibit its seed germination, should be its threatening mechanism, thus proposing corresponding strategies for improved conservation and restoration. This study serves as a seminal contribution to conservation biology, offering valuable insights for the study of other endangered ornamental plants.

Sinojackia Hu (Ericales: Styracaceae) represents the first woody genus discovered and described by Chinese plant taxonomists [ 1 ]. It is a rare Chinese endemic genus comprising merely seven species: S. henryi (Dummer) Merr., S. huangmeiensis J. W. Ge & X. H. Yao, S. microcarpa Tao Chen & G. Y. Li, S. oblongicarpa Tao Chen & T. R. Cao, S. rehderiana Hu, S. sarcocarpa L. Q. Luo and S. xylocarpa Hu [ 2 ]. All seven species are listed as a Grade II endangered protected plant in China, mainly due to their small population size and rare, scattered distributions ( http://www.iplant.cn/rep/protlist ).

S. xylocarpa Hu is the representative and first-discovered species in the genus, known as the ‘jacktree’ in honor of the botanist John George Jack [ 1 ]. It is a flowering deciduous shrub or dwarf tree, reaching heights of about 4.6~6.1 metres and a diameter of nearly 10 centimetres at breast height. S. xylocarpa has a highly aesthetic and ornamental value, primarily due to its egg-shaped woody fruits (drupes) that resemble a balanced weight set (‘Chengtuo’ in Chinese). In autumn, the abundant egg-shaped fruits hang in cascading clusters, adding to its distinctive ornamental value, which can enhance the beauty of courtyards or parks. Additionally, during the spring flowering period, the tree is covered with abundant pure white blossoms ( Fig. 1a ). However, the extant population size of S. xylocarpa is very limited in nature, and its distribution is also extremely fragmented in the subtropical zone of Eastern China (e.g., Jiangsu and Zhejiang Provinces). Its small population size and narrow distribution are mainly attributed to its low germination rate, probably caused by the recalcitrant seeds [ 3 ]. Therefore, S. xylocarpa is classified as vulnerable (VU) in the International Union for Conservation of Nature and Natural Resources (IUCN) Red List of Threatened Species ( https://www.iucnredlist.org/ ), attempting to raise public attention and promote protection. Botanical gardens, the primary protectors of endangered plants, have taken prioritizing action, introducing wild S. xylocarpa individuals into botanical gardens in Eastern China, such as Nanjing Botanical Garden Mem. Sun Yat-Sen and Shanghai Chenshan Botanical Garden, for decades.

Such strategies can certainly benefit the conservation of S. xylocarpa to a certain extent, potentially saving the species from extinction. In other words, by understanding the mechanism underlying the poor germination rate of S. xylocarpa seeds, we may be able to propose a highly targeted and efficient conservation plan to facilitate its sustainable recovery. Anatomically, S. xylocarpa seeds have extremely rigid external structure, consisting of indehiscent exocarp, corky mesocarp, lignified endocarp, and hard seed coat. The tough outer structure not only protects the seeds of S. xylocarpa but also renders them difficult to germinate within 2 to 3 years ( http://www.efloras.org/ ). Unfortunately, the molecular mechanism underlying the mechanical barriers of the fruit pericarp to germination remains largely unknown, mainly due to the absence of a high-quality nuclear genome assembly for S. xylocarpa .

Morphology and high-quality genome assembly of the Sinojackia xylocarpa . a Flowering and fruiting branches of S. xylocarpa . b Genome features across 12 chromosomes of S. xylocarpa . From the outermost to innermost circles are chromosome ideograms, gene density (from blue to red), GC content, TE (transposable elements) density (from blue to red), and collinear genomic blocks.

The reference genome is a fundamental resource for assessing, protecting, and restoring the biodiversity of endangered plants [ 4 ], including Ostrya rehderiana [ 5 ], Davidia involucrata [ 6 ], and Acer yangbiense [ 7 , 8 ]. Genomic comparative analysis of the endangered ironwood O. rehderiana and its non-endangered relative Ostrya chinensis revealed the genomic effects of population collapse in this species [ 5 ]. Genomic analysis of the endangered dove-tree D. involucrata demonstrated that its endangered status might be primarily influenced by genomic factors, genetic diversity and population structure [ 6 ]. Whole-genome resequencing of 105 individuals from ten extant A. yangbiense populations revealed that their small population size might be related to low genetic diversity, repeated bottleneck events, and deleterious mutation load [ 8 ]. Genetic diversity of endangered plant species is crucial for conserving their genetic resources [ 9 ]. At present, our knowledge of the phylogeny and genetic diversity of Sinojackia and Styracaceae is limited to chloroplast genomes [ 10–14 ] and microsatellite markers [ 15–17 ].

Many plants in the order Ericales possess high economic and ornamental values, for instance, Rhododendron simsii (azalea) [ 18 ], Actinidia eriantha (kiwifruit) [ 19 ], Diospyros oleifera (persimmon) [ 20 ] and Camellia sinensis (tea) [ 21 ]. As a result, the genomes of these valuable plants have already been sequenced; however, no genomes of Styracaceae species are available. Here, we reported a chromosome-level assembly of the S. xylocarpa genome, which is the first sequenced nuclear genome in Styracaceae. Based on the high-quality reference genome, we conducted comprehensive analyses combining bioinformatics and experiments. Our study provides evidence from anatomy, gene expression, and population genomics to explore the mechanisms for the germination barriers of S. xylocarpa seeds and its narrow distribution. This work establishes a genomic foundation for investigating the molecular biology and evolution of S. xylocarpa, as well as for its biodiversity maintenance and restoration.

Sequencing, assembly, and annotation of the S. xylocarpa genome

The genomic survey for the S. xylocarpa was conducted using Illumina data, and the estimated results by k-mer analysis ( k-mer  = 19) suggests a genome size of approximately 1.01 Gb, with a heterozygosity of around 0.91% ( Fig. S1 , see online supplementary material). To obtain a high-quality genome of S. xylocarpa , we employed a sequencing strategy combining high-fidelity (HiFi) long reads with a depth of nearly 17× (16.97 Gb) and Hi-C data of approximately 91× depth (98.6 Gb). The HiFi long reads were initially de novo assembled into 2138 contigs with a total length of 1072 Mb (N50 = 1.5 Mb). Subsequently, these contigs were ordered and oriented into 1168 scaffolds (N50 = 78.8 Mb) using Hi-C data. In total, 982 contigs (986 Mb) were anchored to 12 pseudochromosomes, representing for 91.98% of the entire S. xylocarpa genome ( Fig. S2 , see online supplementary material). Therefore, the resulting S. xylocarpa assembly is consistent with the estimated genome and should have achieved the chromosome-level in terms of continuity ( Fig. 1b and Table 1 ).

Statistics of the S. xylocarpa genome assembly and annotation

Gene annotation for the S. xylocarpa genome predicted a total of 40 924 protein-coding gene models using three gene prediction approaches: transcriptome-based, homology-based, and ab initio prediction. Among the predicted genes, 26 707 (65.26%) supported by transcriptome data, and 39 703 genes (97.02%) could be functionally annotated ( Table S1, see online supplementary material ). Our annotation identifies 1531 (94.86%) of the embryophyta benchmarking universal single-copy orthologs (BUSCOs) in the S. xylocarpa genome, with 1368 (84.76%) in single-copy and 163 (10.10%) in duplicate, indicating a high quality of gene prediction of S. xylocarpa genome.

Repeat sequences were also annotated, comprising 53.75% (576 Mb) of the assembly. Retroelements are the most abundant components (45.13%) among the repetitive sequences, with Gypsy and Copia comprising 21.39% and 8.46% of the genome ( Table S2 , see online supplementary material), respectively. Additionally, we identified 2111 transfer RNAs, 5315 ribosomal RNAs, 168 microRNAs, 152 small nuclear RNAs, and 129 small nucleolar RNAs in the S. xylocarpa genome.

Phylogenetic position of Ericales and relationships of lineages within Ericales

A total of 1291 low-copy orthologous genes were extracted from 27 angiosperm genomes and used to construct the sequence dataset for phylogenetic analyses. The concatenated amino acid dataset supported Ericales as the sister group of Cornales, another basal asterid lineage, with strong bootstrap support (100%, Fig. 2 ). The result based on the coalescent method was congruent ( Fig. S3 , see online supplementary material), suggesting a robust sister relationship for the two basal asterid orders.

Genome evolution analysis of Sinojackia xylocarpa . Expansion and contraction of gene families and phylogenetic relationships and divergence times between S. xylocarpa and other plant species. The light green numbers represent the numbers of expanded gene families, and the red numbers represent the numbers of contracted gene families.

S. xylocarpa was resolved as the sister to Galax urceolata , a species in the Diapensiaceae family, and the two corresponding taxa diverged approximately 61.18 million years ago (Mya). The two species were sisters to Symplocos tinctoria (Symplocaceae) ( Fig. 2 ). The monophyly of these three families has been robust and consistent across phylogenetic inferences based on organellar and nuclear data [ 22 , 23 ]. This monophyletic group was further recovered as the sister to another lineage comprising Roridulaceae, Actinidiaceae, and Ericaceae. However, the relationships between some other lineages in Ericales remain ambiguous due to an ancient rapid radiation [ 23 ], with multiple lineages collapsed into a polytomy [ 24 ], including Theaceae, Sapotaceae, Ebenaceae, and Primulaceae. Our concatenated super-matrix provided hypotheses for these unresolved lineages, with Theaceae being sister to Pentaphylacaceae, Sapotaceae being sister to Ebenaceae, and Primulaceae being sister to the Polemoniaceae-Fouquieriaceae lineage. However, these inferences were all weakly supported and sometimes conflicted with the results from the coalescent analyses ( Fig. S3 , see online supplementary material). Incongruence and/or weak support in phylogenetic reconstruction may be due to incomplete lineage sorting (ILS), a consequence of random distribution of ancestral allelic polymorphism in derived lineages through rapid radiation [ 25 ]. Therefore, we examined the single gene trees regarding the relationships of these unresolved lineages. As expected, none of the relationships were predominant among all single gene trees, with nearly equal support for alternative relationships ( Fig. 2; Fig. S3 , S4 , and Table S3 , see online supplementary material), suggesting substantial likely ILS during the evolution of Ericales.

Whole-genome duplication (WGD) events and karyotype evolution of S. xylocarpa

Previous genomic studies identified several independent whole-genome duplications (WGDs) in different Ericales taxa [ 18 , 26 , 27 ]. By comparing collinear genomic blocks ( Fig. S5 , see online supplementary material) and calculating the synonymous substitution rate ( K S ) of all paralogs in collinear regions (anchored paralogs) in the S. xylocarpa genome, we identified two Ks signature peaks approximately 1.3 and 0.4 ( Fig. 3a ), respectively, suggesting two rounds of WGD events.

Whole-genome duplication in the Sinojackia xylocarpa genome. a Distribution of overall synonymous substitution levels (Ks) for paralogs found in syntenic blocks of Actinidia eriantha , Rhododendron williamsianum , S. xylocarpa , and Solanum lycopersicum and for orthologs between R. williamsianum and S. xylocarpa and between A. eriantha and S. lycopersicum . The yellow dotted line indicates two WGD events in S. xylocarpa . The Ks distribution of S. xylocarpa showed two peaks, one at approximately 0.3 (WGD 2) and another at approximately 1.3 (WGD 1). The arrows in different colors indicate overestimations (to the right) of the divergence events and point to the Ks values after corrections of different substitution rates based on that in S. xylocarpa . The dotted curves also show the orthologous distributions after substitution rate corrections. b Genome duplication in Ericales and outgroup. A red star indicates the core-eudicot whole-genome triplication (γ-WGT) event that occurs in conjunction with other species. Two blue stars indicate a WGD event that is commonly experienced in Ericales and an Actinidiaceae-specific WGD, respectively. c The Venn diagram shows the relationships among WGD families and expanded families in the S. xylocarpa genome. d Chromosome karyotype evolution from AEK to S. xylocarpa . A red star indicates a WGT event. A blue star indicates a WGD event. Green rhombus indicates speciation event. Different color blocks represent different ancestral chromosomes.

To accurately date the two WGDs occurred in S. xylocarpa, we compared the orthologous Ks distributions of S. xylocarpa with that of tomato ( Solanum lycopersicum ), azaleas ( Rhododendron williamsianum ) and kiwifruit ( A. eriantha ) ( Fig. 3a ). The Ks peak value of 1.3 for S. xylocarpa should correspond to the whole-genome triplication (WGT, γ) shared by all eudicots [ 27 ]. Therefore, it is logical that the peak of γ-WGT is slightly larger than the peak representing the divergence between S. xylocarpa and tomato. The more recent polyploidy event identified in S. xylocarpa should be a WGD, as indicated by the 2:1 ratio of collinear blocks ( Fig. S5 and S6 , see online supplementary material). However, the differential Ks among S. xylocarpa , azaleas, and kiwifruit resulted in an overestimate for the divergences between S. xylocarpa and the other two Ericlaes taxa. We therefore conducted a relative rate test to adjust the synonymous substitution, thus recognizing the more recent WGD in S. xylocarpa to be likely shared by Styracaceae, Diapensiaceae, and Symplocaceae ( Fig. 3b ).

When examining the retained paralogous genes (15712) after the recent WGD in S. xylocarpa , we found that they are partially overlapping with the expanded gene families (2559 families, 7186 genes, Fig. 3c ) since the divergence with G. urceolata . GO analysis of these retained paralogs indicated that they are mainly enriched in ‘response to chemical and organic substance’, ‘developmental, catabolic and biological process’, and ‘organic substance catabolic and organonitrogen compound metabolic process’ with respect to ‘biological progress’, ‘ligase, transporter, acyltransferase, and kinase activity’, and ‘ATP binding’ with respect to ‘molecular function’ ( Fig. S7 , see online supplementary material).

WGDs are important evolutionary events that profoundly influence the genome evolution of organisms. Therefore, we reconstructed the process of karyotype variation of S. xylocarpa from the common ancestor of eudicots ( Fig. 3d ). The ancestral eudicot karyotype (AEK) was inferred to possess seven ancestral chromosomes before the γ-WGT [ 28 ]. Afterward, the triplicated AEK (21 chromosomes) underwent at least 10 chromosome fusions, 18 breaks, and six losses to form the karyotype in the common ancestor of S. xylocarpa , azaleas, and kiwifruit before their shared WGD (23 chromosomes). The recent WGD doubled the chromosome number, and 15 fusions, 0 breaks, and 0 losses reduced the chromosome number to 31 in the ancestor. Finally, extensive karyotype variations occurred (19 fusions, 0 breaks and 0 losses), leading to the current karyotype in S. xylocarpa .

Population genetic analyses of S. Xylocarpa

Natural populations of S. xylocarpa were found only in Nanjing, Jiangsu Province (118.39°N, 32.05°E) and Ningbo, Zhejiang Province (121.40°N, 30.08°E). We collected ten individuals from each of the two populations ( Fig. S8 , see online supplementary material) and conducted whole-genome resequencing on all 20 samples and obtained raw data with an average sequencing depth of 18.6×. Using a stringent GATK pipeline and strict filtering, we obtained a total of 43 817 152 single-nucleotide polymorphisms (SNPs), with approximately 65.79% of SNPs located in the intergenic regions and the remaining approximately 34.21% found in genic regions ( Table S4, see online supplementary material ). Phylogenetic analysis and principal component analysis (PCA) both revealed the clear divergence between the Ningbo population (Zhejiang Province) and the Nanjing population (Jiangsu Province) ( Figs. S9 and S10, see online supplementary material ). Based on the results of ADMIXTURE analysis, K  = 1 was the best-fitted model ( Table S5 , see online supplementary material), indicating the small effective population size ( N e ) usually possessed by the endangered species. However, the two populations (Nanjing and Ningbo) of S. xylocarpa were distinctly separated when K = 2 ( Fig. 4a ), consistent with the results from the PCA and the phylogenetic tree. We then estimated the historical changes of N e ; all sequenced S. xylocarpa individuals from the two populations showed a continuous decreasing trend over the recent one million years ( Fig. 4b; Fig. S10 and Table S6, see online supplementary material ), revealing the experienced bottleneck effect that was likely involved in the recent glacial periods. The gene flow analysis indicated the existence of bidirectional genetic communications between the two populations in NJ and NB, as well as a more predominant flow from NB to NJ ( Fig. S12 and Table S7 , see online supplementary material). This indicated that before the glacial period S. xylocarpa might have a continuous distribution area with frequent genetic exchange between different populations. During the glacial periods, its gene flow might be gradually restricted by habitat fragmentation and anthropogenic activities [ 29 ].

Genetic diversity and demographic history of Sinojackia xylocarpa . a Admixture analysis with the number of clusters (K) ranging from 1 to 2. b Demographic history of S. xylocarpa . The last glacial maximum (LGM), Riss glaciation, the Naynayxungla glaciation, and Pre-Pastonian glaciation are highlighted in light-blue vertical bars. c Linkage disequilibrium (LD) decay of the S. xylocarpa populations and the two non-endangered species, including Ostrya chinensis and Ziziphus jujuba . d The observed genetic diversity (π) of S. xylocarpa and the remaining 17 species. e The Venn diagram of genes having three detrimental mutations, including splice region variant, loss of start codon, or gain of stop codons.

S. xylocarpa had a relatively low genome-wide nucleotide diversity (π) value (5 × 10 −3 ), similar to other endangered plants, such as O. rehderiana (1.66 × 10 −3 ) [ 5 ], D. involucrata (5.85 × 10 −3 ) [ 6 ], and A. yangbiense (3.13 × 10 −3 ) [ 8 ] ( Fig. 4d ), suggesting common genomic characteristics among endangered plants. Theoretically, the low genomic diversity appears to be an inevitable consequence of being endangered species, due to their small population size. This was also illustrated by the slow linkage disequilibrium (LD) decay within S. xylocarpa , in which half of the maximum r 2 was not attained until ~500 kb. S. xylocarpa showed faster LD decay than two non-endangered species, including O. chinensis [ 5 ] and Ziziphus jujube [ 30 ] ( Fig. 4c ). We further estimated the inbreeding level via runs of homozygosity (ROH) ( Fig. S13 , see online supplementary material). The short ROHs occupied the majority (>99%) of the proportion, indicating the historical population bottleneck within S. xylocarpa .

Finally, we identified a total of 25 653 loss-of-function variations ( Fig. 4e ; Table S8, see online supplementary material ) in S. xylocarpa . Among them, the variations belonging to start lost, stop gained, and splice region variant were 1165, 12 205, and 22 542, respectively. We found that 26 genes in the lignin synthesis pathway produced deleterious variations, with the most abundant being the splice region variant ( Table S9 , see online supplementary material). For identification of environment-associated genetic variants, we used different climate and soil factors to explore the environmental adaptation of S. xylocarpa . The results revealed that six environmental factors were most correlated with its environmental adaptation, with three temperature-related factors, namely annual mean temperature, isothermality, and mean temperature of warmest quarter, and three others related to soil conditions, namely soil clay content, cation exchange capacity, and soil organic carbon content have a significant impact on the growth of S. xylocarpa ( Fig. S14 and Table S10 , see online supplementary material).

Highly lignified pericarps leading to the germination obstacle for S. xylocarpa

The stony pericarps can impose mechanical constraints on seed germination. A previous study proposed that the hard endocarp is likely the reason that inhibits the germination of S. xylocarpa seeds [ 3 ], which leads to the current small population size and extremely narrow distribution. To verify this hypothesis, we conducted an anatomical and staining experiment towards the longitudinal section of S. xylocarpa fruits. We observed that the seeds in the center were wrapped by hard and thick fruit pericarps composed of firm woody tissues and fibres, which is obviously the result of massive lignin and cellulose deposition ( Fig. 5a ). We subsequently measured the content of lignin, cellulose, and hemicellulose in pericarps at different developmental stages of fruits and found that the S. xylocarpa pericarps have continued to accumulate lignin, cellulose, and hemicellulose during the developmental process ( Fig. 5b ). This accumulation is likely the reason for the solid pericarps. Regarding the molecular mechanism, since the gene copy number of the LBP in S. xylocarpa does not significantly outnumber other species ( Table S19 , see online supplementary material), the underlying mechanism is likely related to gene expressions. When examining the lignin biosynthesis pathway (LBP), it is noticeable that some genes in the LBP showed a similar increasing expression pattern (gene IDs in red, Fig. 5c; Fig. S15 , see online supplementary material), which is consistent with the trend of lignin content accumulation during fruit development. These genes include two PALs (phenylalanine ammonia lyases), two C4Hs (cinnamate 4-hydroxylases), two HCTs (shikimate hydroxycinnamoyl transferases), one C3H (p-coumarate 3-hydroxylase), one 4CL (4-coumaric acid: coenzyme A ligase), one COMT (catechol-O-Methyltransferase), one F5H (ferulate-5-hydroxylase), one CCoAOMT (caffeoyl-CoA 3-O-methyltransferase), one CCR (cinnamoyl-coenzyme A reductase), and one CAD (carbamoyl-phosphate synthetase), covering every catalysing step. There are other copies of LBP genes that did not show an increasing pattern or were expressed at low levels during fruit development. For example, one SxCAD4/5 copy (Ssp12G005110.1) displayed an increased and high expression, but the other copy (Ssp05G014970.1) was lowly expressed ( Fig. 5c ). We infer that these copies may be responsible for lignin biosynthesis in other organs/tissues, but not in pericarps, with different organ/tissue expressing specificity, or they may simply represent functional redundancy. Additionally, all LBP genes have undergone strong purifying selection during evolution ( Table S11 , see online supplementary material).

The lignin biosynthesis pathways in Sinojackia xylocarpa fruit pericarp. ( a ) The cross-sections of S. xylocarpa pericarp. Lignin distributions of epicarp, mesocarp, and endocarp (from left to right) in S. xylocarpa pericarp were visualized via Safranin-O staining. ( b ) Mean values of cellulose, hemicellulose, and lignin contents of S. xylocarpa fruits during six different developmental stages. ( c ) Genes in the biosynthesis pathway of lignin and their expressions in pericarps. The genes marked in red are named as genes in the red module of the WGCNA analysis. ( d ) Gene regulatory networks associated with cellulose, hemicellulose, and lignin synthesis in the red module by WGCNA analysis, including the R2R3-MYB gene family involved in the regulation of lignin synthesis.

Naturally, in our constructed co-expression networks, the LBP genes showing a coincident increasing pattern were classified into the same module (red) by WGCNA ( Fig. 5d ; Table S12, see online supplementary material ), suggesting that they are all potentially associated with lignin biosynthesis in S. xylocarpa pericarps. The high expression of some LBP genes may be associated with their tandemly arranged physical arrays on chromosomes, e.g., one 4CL, one HCT, and one CCR on chromosome 9, one CCoAOMT and one CAD on chromosome 12 ( Fig. S16 , see online supplementary material), and such gene clusters are probably beneficial for transcriptional efficiency of genes in the same pathway. Interestingly, in the same module, we can also find CesA (cellulose synthase) and IRX (Irregular Xylem 7) genes responsible for cellulose and hemicellulose biosynthesis, which also displayed an increasing pattern during pericarp development and can explain the cellulose and hemicellulose accumulation in the process. Of all genes in the module, Ssp11G009220.1 (HCT) and Ssp01G009950.1 (IRX) were estimated as hub genes with extensive connections to other genes ( Table S12 , see online supplementary material), suggesting that lignin and hemicellulose biosynthesis are important physiological activities during pericarp development. These results indicate the accuracy and concordance between molecular evidence and phenotypes in this study. The genes in the red co-expression module were mainly enriched in ‘RNA modification’, ‘nucleic acid phosphodiester bond hydrolysis’, ‘xylan biosynthetic process’, and ‘xylan metabolic process’ with respect to ‘biological progress’, and ‘hydrolase activity, acting on ester bonds’, ‘nuclease activity’, ‘endonuclease activity’, and ‘RNA binding’ with respect to ‘molecular function’ ( Fig. S17 , see online supplementary material). In addition, the XP-CLR analysis suggested that two genes associated with lignin and hemicellulose biosynthesis are under selective sweeps, i.e., Ssp03G010310.1 (F5H) and Ssp01G009950.1 (IRX7) ( Fig. S18 and Table S13 , see online supplementary material), suggesting the preservation of their functional roles in the pathway during evolution.

Previous studies identified a number of transcription factors (TFs) regulating lignin biosynthesis in plants [ 31–34 ], and they all belong to the R2R3-MYB family. Therefore, we took a further look into the co-expression network, and tried to identify key regulators that may govern the LBP genes during pericarp development. Firstly, phylogenetic analysis incorporating S. xylocarpa and Arabidopsis thaliana MYB genes were performed to determine all R2R3-MYBs in S. xylocarpa ( Fig. S19 , see online supplementary material), then 33 TFs closely connected to the LBP genes in the co-expression module were identified ( Fig. S19 , see online supplementary material), and finally they were cross-compared with the R2R3-MYBs to screen out the most promising regulators, which in our analysis, included seven genes, namely SxMYB20 (Ssp07G007490.1), SxMYB42 (Ssp10G023140.1), SxMYB62 (Ssp08G018180.1), SxMYB83 (Ssp10G002340.1), SxMYB85 (Ssp09G003180.1), SxMYB86–1 (Ssp09G018570.1), and SxMYB86–2 (Ssp11G007090.1) ( Fig. 5d ). These TFs may be the reason that triggers the high expression of LBP genes.

To enhance plant conservation efforts for the threatened ornamental Sinojackia species, we assembled a high-quality genome of jacktree and conducted genomic resequencing of individuals in rare natural distribution habitats in Eastern China. To explore the phylogenetic positions of the jacktree and Ericales, we reconstructed a phylogenetic tree using the high-quality genome of the jacktree and another 26 angiosperms. However, our result is discordant with that of the Angiosperm Phylogeny Group IV (APG IV) [ 24 ], which recovers Cornales and Ericales as the successive sister groups to lamiids-campanulids. In fact, this discordance reflects the cyto-nuclear conflict, as plastid genome-based phylogenetic inferences mostly supported the same topology as APG IV [ 35–37 ], while recently growing nuclear evidences all favored the sister relationship between Cornales and Ericales [ 18 , 38–40 ]. These data will serve as the foundation to the reconstruction of the evolutionary history and exploring the endangered mechanisms of species.

The egg-shaped fruits exhibit the distinctive morphological characteristics of S. xylocarpa , which are primarily appreciated for their ornamental value. The pericarp serves to protect the seeds from environmental factors and predators, which is a common preservation strategy of plants. For example, pericarp thickness is a defensive traits of Camellia japonica against its seed predator ( Curculio camelliae ) [ 41 ]. Similarly, it is very possible that the thickened S. xylocarpa pericarps might have played a protective role for seeds during the glacial age. However, it might become a factor limiting seed germination after the glacial period, as the seed germination is thus limited by the mechanical constraints of its pericarps [ 3 ]. Deleterious variations were detected in the LBP genes, yet these genes have maintained their functionality and exhibit high expression levels. While deleterious mutations typically compromise gene function, these genes exhibit evidence of strong purifying selection, indicating the influence of contradicting selective forces that preserve their functional integrity. The thickened pericarps due to the highly expressed LBP genes may be adaptive during the recent glacial age, which began about two Mya and lasted till now, with multiple subglacial and interglacial periods. Thus, the evolution pressure requires the retained functions of the LBP genes, in case of the coming subglacial period.

Nonetheless, the hard and lignified fruit pericarps ( Fig. 5a ) likely contribute significantly to the small population and limited natural distribution of this species. Firstly, the heavy, indurate, and inedible fruits are challenging to disperse over long distances by winds or animals, and animals are unlikely to find them palatable. Secondly, during seed germination, the highly lignified fruit pericarps are difficult to break, requiring a significant biomechanical force, likely resulting in a low seed germination rate [ 3 ]. We investigated the genetic mechanism underlying the development of its hard and lignified fruit pericarps. Our biomass analytical assay reveals that S. xylocarpa fruits exhibit increasing levels of lignin, as well as cellulose and semi-cellulose during fruit development and ripening. These findings support our hypothesis that the woody and fibrous content of S. xylocarpa pericarps is negatively correlated with their germination ratio [ 42 ], and that fruits valued for their ornamental characteristics create a virtual barrier to successive seed germination in this species.

Lignin biosynthesis is a crucial biological process in woody plants, with pathway enzyme genes present in all seed plants [ 43 ], and the resulting products often accumulating in various organs (e.g., seed coats, petioles, stems, and roots) [ 44 , 45 ]. However, it appears that only S. xylocarpa fruit pericarps specifically accumulate high levels of lignin, likely related to the high expression of some, but not all LBP genes during fruit development ( Fig. 5c ). Because each LBP gene has multiple copies, largely due to tandem duplications ( Fig. S19 , see online supplementary material), it is possible that different copies have undergone functional divergence, leading to organ/tissue-specific catalytic activities. These highly expressed copies are likely the results of subfunctionalization and neofunctionalization, and are probably responsible for lignin biosynthesis specifically in fruit pericarps.

In addition to the functionally diverged enzyme genes themselves, their specific expression in fruit pericarps may also be influenced by regulatory elements. Previous studies have shown that TFs such as MYB, NAC (NAM/ATAF/CUC), and ARF (auxin response factor) play a regulatory role in lignin biosynthesis [ 46 , 47 ]. For instance, Ding et al. found that MYB9, MYB60, and MYB91 might participate in the regulation of PAL, C4H, 4CL, CCoAOMT, and COMT in the seed coat of Brassica napus L. [ 48 ]. Through co-expression network analysis, we identified seven R2R3-MYB genes that are closely connected to the highly expressed LBP genes in S. xylocarpa fruit pericarps, suggesting they may function as potential regulators for these genes. Another explanation for the high expression of LBP genes could be attributed to the physical arrangement of upstream and downstream genes in the same signalling pathway, as they often form gene clusters, which is proposed to be functionally beneficial to transcriptional efficiency. Coincidentally, we observed the two clustered loci, collectively comprising five LBP genes (one 4CL, one HCT and one CCR on chromosome 9, one CCoAOMT and one CAD on chromosome 12, Fig. S16 , see online supplementary material), and more importantly, these LBP genes are highly expressed in fruit pericarps ( Fig. 5c ), which strongly supports our hypothesis.

While the germination barriers of S. xylocarpa seeds can be explained based on the evidence from our experiments and multi-omics analyses, the ultimate question of how to efficiently conserve this endangered plant remains unanswered. Population genomic analysis not only reconstructed the evolutionary history but also provided insights into this ultimate question. Following the divergence of Nanjing and Ningbo populations, Nanjing continued to experience population size reduction, while Ningbo has maintained (or slightly recovered) its population size ( Fig. 4b ), resulting in Ningbo having a larger population size and a richer genetic diversity than Nanjing today. This discrepancy between the two populations may be attributed to different habitat conditions. Nanjing is an inland city, while Ningbo is located on the coast of the west Pacific and closer to the subtropics (Fig. S7, see online supplementary material), so the warm and moist air in Ningbo might soften S. xylocarpa fruit pericarps, thereby facilitating the germination process. Additionally, the two sharp declines in population size of S. xylocarpa correlate with the decline in atmospheric surface air temperature (Tsurf) and the escalation of the Chinese loess mass accumulation rate (MAR) ( Fig. 4b ), suggesting that its population evolutionary history was likely influenced by climatic changes and human activities. Based on these analytical results, we propose a strategy of providing additional artificial watering to the soil for in situ conservation. For ex situ conservation, priority can be given to botanical gardens in the coast areas of South and East China. Furthermore, the two populations (Nanjing and Ningbo) were genetically separated. Artificial cross-breeding is recommended as a means to increase its genetic diversity.

The interaction between plants and microbes can be considered as another conservation strategy. Certain microbes have the ability to degrade lignin in seed coat in an environmentally friendly and efficient way [ 49 ]. For instance, specific mycorrhizal fungi are required for the seed germination of threatened Paphiopedilum orchids [ 50 ]. S. xylocarpa seeds remain buried in soils for more than two years before germination. If there are specific microbes capable of degrading lignified S. xylocarpa fruit pericarps, we could isolate these microbes and apply them to the soils where S. xylocarpa fruits are buried for further propagation. This strategy aims to improve the germination rate of S. xylocarpa and can be adopted together with other strategies.

In summary, this work provides essential genomic data for the endangered ornamental plant jacktree, which serves as a valuable source for studying the evolutionary history and the endangerment mechanisms of this plant. Based on this data, a proper conservation and restoration plan has been proposed [ 4 ]. The molecular basis underlying high lignification in the S. xylocarpa pericarps suggests a direction for screening and developing new cultivars with low lignin content fruit pericarps, which may be better candidates for re-introduction into the wild fields to further enlarge the colony of S. xylocarpa . Owing to the similarity in biological features (e.g., lignified pericarps) among Sinojackia species, this study provides a starting point for exploring the causes of endangerment in other Sinojackia species. Additionally, this study provides a reference strategy in conservation biology, particularly for studies exploring the mechanisms of endangered ornamental woody plants.

Genome survey and assembly

An individual of S. xylocarpa was cultivated on campus at Nanjing Forestry University (118.81°N, 32.08°E), Nanjing, Jiangsu Province, China. The plant material was selected for genome survey and genome assembly, and its fresh leaves were utilized for genomic DNA isolation. For the survey of the S. xylocarpa genome, the extracted DNA was served as establishing two paired-end (PE) libraries, each with a 300 bp insert. Sequencing of each PE library was conducted to generate ~30 Gb reads via Illumina NovaSeq 6000. For de novo genome assembly of S. xylocarpa , the extracted DNA was subjected to sequencing on a PacBio Sequel II system to yield HiFi long-read data, averaging 17.8 kb in length. For chromosome anchoring, Illumina NovaSeq 6000 was adopted to sequence a prepared Hi-C library [ 51 ], resulting in 150 bp PE reads.

The genome survey was conducted using GenomeScope (v2.0) [ 52 ] based on 60 Gb Illumina reads from two PE libraries. To construct a genome assembly, contigs were derived from de novo assembly of PacBio HiFi long-reads with the assistance of hifiasm (v0.12) [ 53 ]. The resulting contigs were then anchored onto 12 pseudochromosomes by using both HiC-Pro (v2.10.0) [ 54 ] and LACHESIS [ 55 ] with Hi-C datasets. Alignment of Hi-C reads against these resultant contigs was performed using BWA (v0.7.10-r789) [ 56 ].

Genome assembly assessment was processed in term of DNA read mapped rate and annotation completeness. Mapping of Illumina reads to the S. xylocarpa genome assembly was carried out using BWA. CEGMA (v2.5) [ 57 ] and BUSCO (v4.0.6) [ 58 ] were employed to appraise the gene completeness within the S. xylocarpa assembly, with results summarized in Tables S14 and S15 , respectively (see online supplementary material).

Genome annotation

The S. xylocarpa genome was explored for protein-encoding genes searched with a synergistic application of transcriptome-based, sequence similarity-based and de-novo predicting approaches. In the transcriptomic evidence-based prediction method, GeneMarkS-T (v5.1) was utilized to infer the gene models from the transcripts of reference-guided assembly. This process involved alignment of RNA-Seq reads against the S. xylocarpa genome by HISAT2 (v2.0.4) [ 59 ], followed by genome-based assembly with using StringTie (v1.2.3) [ 60 ]. For the homology-based technique, these reference gene models were drawn from four species, namely Actinidia chinensis , A. thaliana , R. simsii , and Nyssa sinensis , using GeMoMa (v1.7) [ 61 ]. For ab initio prediction methods, the de-novo gene models were archived by a combination of Augustus (v2.4) [ 62 ] and SNAP from Korf Lab’s GitHub. Finally, the above three sets of gene models were merged using the EVidenceModeler (v1.1.1) [ 63 ], followed by refinement with PASA (v2.0.2) [ 64 ].

Protein-encoding genes were aligned and annotated with Diamond (v0.9.24) [ 65 ], with searches conducted on NCBI NR (Non-redundant) database, as well as SwissProt/TrEMBL and EggNOG (v5.0) [ 66 ]. Additionally, HMMER (v3.1) was adopted to delineate protein domains by searching against Pfam (v33.1) [ 67 ].

Non-coding RNAs (e.g., miRNA, rRNA, tRNA, snoRNA, and snRNA) were determined in the S. xylocarpa genome, and the utilized methods and databases were summarized in Table S16 (see online supplementary material). Transposon elements (TEs) were identified in the S. xylocarpa genome using a combination of RepeatModeler and RepeatMasker under RepBase database (v19.06). Annotation of terminal repeat retrotransposons (LTR-RTs) in the S. xylocarpa genome was accomplished using both LTRharvest [ 68 ] and LTR_finder [ 69 ]. TRF (v4.09.1) from Benson Lab’s GitHub and MISA (v2.1) were utilized to delineate tandem repeats in the S. xylocarpa assembly.

Phylogenetic analysis and estimation of divergence time

OrthoFinder (v2.5.4) [ 70 ] was applied to delineate orthologous gene clusters between S. xylocarpa and 26 other angiosperms. The low-copy orthologous genes were screened based on three criteria: (i) presence in ≥75% of genomes, (ii) ≤5 copies per orthologous gene group per species, and (iii) selection of the longest copy for phylogenetic analysis. A total of 1291 low-copy orthologous genes were predicted between them, and 13 145 homologous groups were identified in S. xylocarpa . Multiple sequence alignment (MSA) was accomplished using low-copy orthologous proteins via MUSCLE (v3.8.1551) [ 71 ], followed by constructing a well-supported maximum likelihood (ML) tree by IQ-TREE (v1.6.12) under the best-fitting model (JTT + F + R6) [ 72 ]. The MCMCTree program belonging to the PAML (v4.9) [ 73 ] package was utilized to date the divergence times of S. xylocarpa and the remaining 26 angiosperms. Three dated ages were chosen from TimeTree3 as standard normal priors, aligning with the speciation intervals for A. thaliana and Vitis vinifera (109–123 Mya), S. xylocarpa and Souroubea exauriculata (89–118 Mya), and Ardisia humilis with Primula veris (42–79 Mya). CAFE 5 [ 74 ] was employed to deduce the expansion and contraction patterns occurring in orthologous gene families across S. xylocarpa and the 26 other angiosperms.

Whole-genome duplication (WGD) events investigatory and ancestral karyotypes reconstruction

WGD software [ 75 ] was utilized to delineate the distribution of paralog ages, as indicated by synonymous substitutions per synonymous site ( Ks ) values. The MCL package was adopted to reconstruct gene family memberships using all potential paralogs which were deduced via all-vs-all protein BLAST [ 76 ], imposing an e-value of 10 −10 . MAFFT [ 77 ] was exploited for multi-alignment of each family. FastTree [ 78 ] was chosen to delineate a phylogenetic tree per gene families with n*(n-1)/2 ≤ ‘max airwise’. CODEML implemented in the PAML (v4.9) package [ 73 ] was employed to calculate ML-based K s values for each gene pair. Mixture modelling was done for all inferred WGDs with the BGMM (Bayesian Gaussian Mixture Models) method. The WGDI (v0.6.2) [ 79 ] was employed to achieve collinear segment pairs. All syntenic blocks were determined with WGDI under ‘ P -value = 0.05’ and the improved collinearity mode. The K s pipeline in WGDI was adopted to infer the K s value for each anchoring gene pair within a syntenic block, and the block mode was utilized to draw the K s dotplot of all anchor pairs. The KsPeaks pipeline in WGDI was applied to delineate the K s median value for each syntenic block. Finally, the K s distributions were summarized and visualized using the R package ggplot2 (v3.5.0).

The pattern of chromosomal evolution within the order Ericales was reconstructed by utilizing well-defined polyploidization events and established phylogenetic relationships. Initially, we utilized WGDI [ 79 ] based on adjacent conserved collinear blocks to facilitate intra- or inter-genome comparisons, resulting in collinear dotplots annotated with Ks values. By including suitable outgroups and applying maximum parsimony rooted in well-defined phylogenetic relationships, we reconstructed ancestral karyotypes at every node within the phylogenetic tree of the Ericales. Lastly, by juxtaposing the acquired ancestral chromosomes with present-day species and elucidating the chromosomal evolution pattern of the Ericales.

Scanning electron microscopy and determination of lignin content

The drupes of S. xylocarpa at six developmental stages were harvested from trees located at the Xinzhuang campus of Nanjing Forestry University (118.81° N, 32.08° E). The drupes were collected every 1 month from April to September 2022, and the harvested samples were quickly frozen in liquid nitrogen and subsequently transferred to a −80°C refrigerator for storage. The content of lignin at six developmental stages was measured using a JC2203-M kit (JC DTECT Biotechnologies Co., Ltd, Nanjing, China) with triplicate samples per stage.

The fruits in the ripening stage were harvested for their morphological observation. The drupe samples were sliced into 20 μm thick sections consisting of exocarp, mesocarp, and endocarp, using a TU-213 sliding microtome (YAMATO, Saitama, Japan). A 1% aqueous Safranine O solution was utilized to stain the 20 μm-thick slices. The photographs of these qualified samples were acquisited on a BX51 microscope (Olympus, Tokyo, Japan), and processed with STL-IMCS software.

Transcriptome sequencing of pericarps and evolution analysis

The drupes were collected at six developmental stages with three biological replicates from S. xylocarpa trees cultivated at Nanjing Forestry University’s Xinzhuang campus (118.81°N, 32.08°E). Illumina RNA-Seq libraries were prepared from the RNAs that were isolated with RNAprep Pure Plant Kit (Tiangen, Beijing, China) and their sequencing was accomplished on Illumina NovaSeq 6000.

Raw reads were trimmed to remove adaptors, and low-quality reads (the reads with N ratio greater than 10% or whose base with Phread quality score [Q] ≤10 accounts for more than 50% of the whole reads) were discarded. These trimmed reads were mapped against the S. xylocarpa genome using Bowtie2 [ 80 ]. The calculation and normalization of gene expression levels were conducted via the FPKM (Fragments Per Kilobase of exon model per Million mapped fragments) method [ 81 ]. RSEM software [ 82 ] was then used to perform the calculation of FPKM values. Gene expression heatmaps were visualized using TBtools [ 83 ]. BLASTP [ 76 ] was used to identify lignin synthase genes (including PAL , C4H , C3H , F5H , 4CL , CCR , CAD , COMT , and CCoAOMT ) from the protein sequences of S. xylocarpa . The lignin synthase protein sequences of A. thaliana , used as the query, were obtained from Uniprot [ 84 , 85 ] ( Table S17 , see online supplementary material). The protein sequences of lignin synthases from A. thaliana were aligned against all the protein sequence of S. xylocarpa , with an e-value <10 −5 , to obtain the potential lignin synthase protein sequences of S. xylocarpa . The conserved domains and conserved motifs in these candidate lignin synthase of S. xylocarpa were identified and inspected using TBtools and CD-search. To identify MYB candidates in S. xylocarpa , we downloaded the Hidden Markov Model (HMM) profile of MYB (PF00249) and used it as the query ( P  < 0.001) to search the S. xylocarpa protein sequences. A BLASTP search using A. thaliana MYB sequences from TAIR ( https://www.arabidopsis.org/ ) as queries was accomplished with an e-value <10 −5 . The MYB family was finally determined by the protein sequences of the conserved domain. ClustalW was chosen for MSA [ 86 ]. IQ-TREE2 was hired to build ML trees under the ‘-alrt 1000 -B 1000’ parameter [ 87 ].

Genome resequencing and SNP calling

To conduct the population genomic analysis within the S. xylocarpa population, leaves of 20 wild samples were collected from Southeast China for genome resequencing. The natural distribution information for these samples is provided in Table S18 (see online supplementary material). Genome resequencing was conducted on the DNBSEQ-T7 sequencer to generate 150 bp PE reads with an average depth of ~18.6×.

All raw reads were trimmed with the software fastp (v0.12.4) [ 88 ] to eliminate low quality bases and adaptors, and the clean reads were then mapped to the S. xylocarpa genome using bwa-mem (v0.7.17) [ 89 ]. The SAM format files were processed using SAMtools (v1.15.1) [ 90 ] for sorting and merging. Picard (v2.25.0) was used for assigning read group information, including library, lane, and sample identity. GATK (v4.2.0.0) [ 91 , 92 ] was adopted to predict SNPs. Subsequently, all these SNPs were annotated by ANNOVAR [ 93 ] with the ‘—neargene 2000’ option to define the length of upstream and downstream regions’ surrounding genes. The subsequent analyses were conducted using a set of 43 817 152 high-quality SNPs that had been identified. We utilized Plink (v1.90b6.21) for performing PCA (principal component analysis) and evaluating genomic diversity (π) [ 94 ]. We inferred the construction of the neighbour-joining (NJ) phylogenetic tree using Phylip (v3.697) [ 95 ] based on SNPs from genomic resequencing of 20 individuals. Population ancestry information was then calculated by Admixture (v1.3.0) [ 96 ], setting the K values from 1–6 for different numbers of clusters. PopLDdecay was employed to delineate the pattern of LD decay [ 97 ]. Long runs of homozygosity (ROHs) were sought using Plink (v1.90b6.21) within 50-SNP windows, where no heterozygous markers were allowed. ROHs were detected in regions longer than 10 kb with a minimum of 50 SNPs. ROHs were classified into different categories based on their lengths [ 98 ].

Demographic inference and identification of deleterious mutations

The PSMC model was employed with the settings [-N25 -t15 -r5 -p ‘4 + 25*2 + 4 + 6’] to depict ancient demographic history [ 99 ]. The mutation rate (u) was estimated using the formula u = Ks/2 T. The estimated divergence time (T) was about 62 Mya between S. xylocarpa and G. urceolata . The generation time was assumed to be 10 years based on the average time taken from seed to seed, as observed, and thus u = [0.31/ [(2 × 62e 6 )] × 10] = 2.5 e −8 (the substitutions per site per generation). To assess the accumulation of extreme deleterious mutations in the scale tree, the ‘-lof’ parameter of SNPEFF was used to annotate SNPs that lead to loss of function (LOF). XP-CLR (v1.0) was used to estimate the XP-CLR score for detecting signals of selective sweeps in the S. xylocarpa genome between two populations, Nanjing and Ningbo [ 100 ].

The joint site frequency spectrum (SFS) of S. xylocarpa from NB and NJ was utilized for estimating the parameters of evolutionary scenario. Various models of historical events were applied to the joint SFS of NB and NJ ( Fig. S12 , see online supplementary material). For convergence assurance, each model underwent 50 runs with varying starting points and the model with the highest likelihood was selected. The fastsimcoal2 program was adopted to analyse the gene flow between two subpopulations under the parameters [-m -0 -C 10 -n 100 000 -L 40 -s0 -M -q] [ 101 ]. Additionally, environmental adaptation analysis between two genetic groups (NB and NJ) was conducted using latent factor mixed models (LFMM) [ 102 ] and redundancy analysis (RDA) [ 103 ]. Nineteen climatic factors were downloaded from WorldClim ( https://worldclim.org/ ) and 27 soil-related environmental variables were acquired from the National Earth System Science Data Center ( https://www.geodata.cn ).

We acknowledge Shi-Jing Sun at College of Materials Science and Engineering, Nanjing Forestry University for assistance in lignin determination. We also thank Xiao-Gang Xu at College of Life Sciences, Nanjing Forestry University, and Dao-Liang Yan at School of Forestry and Biotechnology Zhejiang A&F University, for help in collecting plant samples. We sincerely thank Wen-Tai Dai from the Institute of Soil Science, Chinese Academy of Sciences, for his assistance in soil data collection. We also appreciate the advice on data analysis provided by Jie-Yu Wang at China National Genebank (CNGB), Shenzhen, Cheng-ao Yang at College of Horticulture, Nanjing Agricultural University, and Yu-Peng Sang at College of Life Sciences, Sichuan University. We also acknowledge the data support from ‘National Earth System Science Data Center ( https://www.geodata.cn )’. This work was financially supported by the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD).

Y.-F.D. and J.-Y.X. conceived and designed the project. X.-F.W., S.Z., Y.-X.L., D.-W.Z., Z.-F.W., and J.G. conducted bioinformatic analyses. Y.-X.L., D.-W.Z., and S.-L.L. performed anatomical experiments and lignin determination. S.-L.L., Y.-F.S., Y.Y., X.-G.Y., and M.Z. collected the plant materials. S.Z., X.-F.W., Y.-X.L., Z.-F.W., and J.-Y.X. drafted the manuscript. All authors contributed to and approved the final manuscript.

Assembled genome, DNA resequencing, and RNA sequencing data for S. xylocarpa are accessible from NGDC (National Genomics Data Center, https://ngdc.cncb.ac.cn/ ) under BioProject no. PRJCA016116, consisting of GWH (genome warehouse) no. GWHCBFM00000000, and GSA (genome sequence archive) no. CRA010572 and CRA016108, respectively. All relevant data can be found within the manuscript and its supporting materials.

The authors declare that there is no conflict of interest.

Supplementary data is available at Horticulture Research online.

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• Published: 10 October 2023

Conservation genomics

Saving endangered species with genomic prediction

• Michael Fletcher 1  

Nature Genetics volume  55 ,  page 1609 ( 2023 ) Cite this article

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The kākāpō is a charismatic parrot endemic to Aotearoa New Zealand with an idiosyncratic lifestyle. Like much of the country’s native flora and fauna, populations of kākāpō were markedly reduced after human settlement and the introduction of non-native mammalian predators, but conservation efforts since 1995 involving intensive intervention (such as active genetic management, hand-rearing of chicks and population transfers to refuge islands) mean that their number stands at 247 as of 2023. Building on past genomics efforts, Guhlin et al. present a species-wide genomic dataset for 169 birds that were alive in 2018. Analysis of these data enabled a more accurate estimation of overall kākāpō genetic diversity and population relatedness, and an improved variant genotyper. Combination with the rich phenotypic data collected by the Kākāpō Recovery Team enabled the identification of loci associated with, and the construction of accurate predictors for, important breeding traits such as offspring survival and growth, despite the small sample size. This work illustrates how the application of such genetic and genomic methods can inform conservation efforts for critically endangered species globally, as well as setting an example of how such cutting-edge science offers meaningful impacts on issues that are prominent in the public eye.

Original reference: Nat. Ecol. Evol . https://doi.org/10.1038/s41559-023-02165-y (2023)

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ORIGINAL RESEARCH article

Conservation genomic study of hopea hainanensis (dipterocarpaceae), an endangered tree with extremely small populations on hainan island, china.

• 1 Hainan University, Haikou, China
• 2 Haikou Marine Geological Survey Center, China Geological Survey, Haikou, Hainan Province, China
• 3 Chinese Research Academy of Environmental Sciences, Beijing, Beijing Municipality, China

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Hopea hainanensis Merrill & Chun is considered a keystone and indicator species in the tropical lowland rainforests of Hainan Island. Due to its high-quality timber, H. hainanensis has been heavily exploited, leading to its classification as a First-Class National Protected Plants in China and a Plant Species with Extremely Small Populations (PSESP). This study analyzed genome-wide single nucleotide polymorphisms (SNPs) obtained through Restriction site-associated DNA sequencing (RAD-seq) from 78 adult trees across 10 H. hainanensis populations on Hainan Island. The nucleotide diversity of the sampled populations ranged from 0.00096 to 0.00138, which is lower than that observed in several other PSESP and endangered tree species. Bayesian unsupervised clustering, principal component analysis, and NJ tree reconstruction identified 3 to 5 genetic clusters in H. hainanensis, most of which were geographically widespread and shared by multiple populations. Demographic history analysis based on pooled samples indicated that the decline of the H. hainanensis population began approximately 20,000 years ago, starting from an ancestral population size of about 10,000 individuals. The reduction of population size accelerated around 4,000 years ago and has continued to the present, resulting in a severely reduced population on Hainan Island. Intensified genetic drift in small and isolated H. hainanensis populations may contribute to moderate differentiation between some of them, as revealed by pairwise Fst. In conclusion, our conservation genomic study confirms severe population decline and extremely low level of nucleotide variation in H. hainanensis on Hainan Island. These findings provide critical insights for the sustainable management and genetic restoration of H. hainanensis on Hainan Island.

Keywords: Hopea hainanensis Merrill & Chun, conservation genomics, Plant Species with Extremely Small Populations, Population decline, Reduced-representation genome sequencing

Received: 03 Jun 2024; Accepted: 09 Aug 2024.

Copyright: © 2024 Tang, Long, Wang, Rao, Long, Yan and Liu. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY) . The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Liang Tang, Hainan University, Haikou, China Jun-qiao Long, Haikou Marine Geological Survey Center, China Geological Survey, Haikou, 571127, Hainan Province, China Hai-ying Wang, Hainan University, Haikou, China Li Yan, Haikou Marine Geological Survey Center, China Geological Survey, Haikou, 571127, Hainan Province, China Yong-bo Liu, Chinese Research Academy of Environmental Sciences, Beijing, Beijing Municipality, China

Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.

Identification and micropropagation of Homalomena pendula , an endangered medicinal plant

• Original Article
• Published: 12 August 2024
• Volume 158 , article number  40 , ( 2024 )

Cite this article

• Le Nguyen Thoi Trung 2 , 6 ,
• Nguyen Hoang An 1 ,
• Phan Thi Thao Nguyen 1 ,
• Ho Nhat Quang 1 ,
• Hoang Tan Quang 3 ,
• Ton Nu Minh Thi 4 ,
• Hoang Xuan Thao 5 ,
• Tran Nam Thang 6 &
• Truong Thi Bich Phuong   ORCID: orcid.org/0000-0002-8049-8499 1  

The large-leaved Homalomena (LLH, Homalomena pendula ) represents an endangered medicinal plant species within Vietnam, primarily attributed to its recognized tonic properties. Despite its imminent threat of extinction within Vietnamese ecosystems, the development of a robust protocol for molecular species identification and large-scale propagation of LLH remains absent. Consequently, we present the first conservation endeavor for LLH based on plant micropropagation techniques, with plant materials validated through anatomical observations and DNA barcoding ( rbc L). Our investigation yielded five rbc L sequences specific to LLH, serving as the current best barcode for LLH identification and thereby facilitating forthcoming taxonomic endeavors. Optimization of in vitro culture conditions revealed that the Murashige and Skoog (MS) medium supplemented with 2 mg/L 6-benzylaminopurine, 0.5 mg/L α-naphthaleneacetic acid, and 60 g/L mashed potato, alongside the incorporation of 0.5 mg/L indole-3-butyric acid to the basal MS medium, yielded optimal outcomes for shoot proliferation and root development, respectively. After successful micropropagation, acclimatization of rooted plantlets to a substrate comprising soil, coconut coir, and rice husk (in a 1:1:1 ratio) culminated in a 100% survival rate among the plants.

Key message

The first established protocol for species identification and micropropagation of H. pendula .

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Acknowledgements

The authors acknowledge the partial support of Hue University under the Core Research Program, Grant No. NCM.DHH.2020.12. We also thank Mr. Tong Van Bao Thanh for his help in taking pictures of LLH plantlets.

The authors did not receive support from any organization for the submitted work.

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Conceptualization, methodology, project administration, writing—original draft preparation, and validation: Trung LNT. Investigation (DNA barcoding): Quang HT and Thi TNM. Investigation (macro- and micro-anatomical observations and micropropagation): Trung LNT, Thang TN, Quang HN, Thao HX. Formal analysis: An NH and Nguyen PTT. Supervision, funding acquisition, and writing—review and editing: Phuong TTB. All authors have read and approved the final manuscript.

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Trung, L.N.T., An, N.H., Nguyen, P.T.T. et al. Identification and micropropagation of Homalomena pendula , an endangered medicinal plant. Plant Cell Tiss Organ Cult 158 , 40 (2024). https://doi.org/10.1007/s11240-024-02835-0

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Wetland plant once nearly extinct may have recovered enough to come off the endangered species list

In this September 2020 photo provided by Western Pennsylvania Conservancy, a northeastern bulrush stands in a vernal pool in Tioga State Forest in Tioga County, Pa. The plant was in danger of extinction but recovery efforts have led the U.S. Fish and Wildlife Service to propose that it be removed from the federal endangered species list. (Mary Ann Furedi/Western Pennsylvania Conservancy via AP)

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BOSTON (AP) — The federal wildlife service on Tuesday proposed that a wetland plant once in danger of going extinct be taken off the endangered species list due to its successful recovery.

The U.S. Fish and Wildlife Service is asking that the northeastern bulrush be delisted . The plant is a leafy perennial herb with a cluster of flowers found in the Northeast from Vermont to Virginia. The federal service’s proposal opens a 60 day comment period.

The plant was listed as endangered in 1991 when there were only 13 known populations left in seven states. It now has 148 populations in eight states, often in vernal pools, swamps and small wetlands.

“Our important partnerships with state agencies, conservation organizations and academic researchers have helped us better understand and conserve northeastern bulrush through long-term population monitoring, habitat conservation, and increased surveys in prime habitat areas,” said Wendi Weber, northeast regional director for the U.S. Fish and Wildlife Service.

Detailed surveys of the plant’s unique behavior have aided the recovery effort. The bulrush can disappear for years and reemerge when conditions are right.

Several states also worked to reduce invasive species that encroach on wetlands and protect land where the bulrush is found. Vermont, for example, has purchased two parcels for the bulrush.

In 2014, a coalition of soil and water conservation groups and a wetlands organization launched a successful pilot program to establish a new northeastern bulrush population in New York.

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Endangered skates saved from extinction by hatching in captivity

The Maugean skate ( Zearaja maugeana ) is only found in one habitat in Australia, which is under threat from human activity. Now the species has been saved from extinction by hatching in captivity

By James Woodford

13 August 2024

Newly hatched Maugean skates

Jayson Semmens/University of Tasmania

One of the world’s most endangered species of marine fish has been saved from extinction, thanks to researchers who captured wild specimens and helped them reproduce in captivity.

The Maugean skate ( Zearaja maugeana ) is only found in Macquarie harbour on the extremely isolated and rugged south-west coast of Tasmania, Australia. The area is already a naturally low-oxygen environment, making it difficult for fish to thrive, but human impacts, especially salmon farming and river flow changes as a result of hydroelectric dams, have made the situation worse.

Largest ever animal may have been Triassic ichthyosaur super-predator

Jayson Semmens at the University of Tasmania says while no-one knows the exact population of these skates, a collapse between 2014 and 2021 saw it halve. There may now be just over 1000 individuals, he says, and of greatest concern is that they are now predominantly adults, meaning that juveniles aren’t reaching maturity.

As a marine heatwave tightened its grip last year in this region, off south-eastern Australia, Semmens and his colleagues decided to undertake a radical intervention to try to safeguard the skates from extinction.

In December 2023, the team collected 50 eggs and saw over half of them successfully hatch in captivity. They also collected four adults, two of which died within a fortnight. The two survivors were kept separate, so the team was shocked when the remaining female laid eggs.

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Semmens says this is because the skates are able to store sperm, to fertilise eggs later. “She’s been laying on average every four days, two eggs every time,” he says. “We have over a hundred eggs from her now and the vast majority of them are looking like they’re going to be viable.”

Can genetically modifying a rare marsupial save it from extinction?

In order to maximise the genetic variability of the captive-reared juveniles, the team is considering capturing other females that have already been inseminated, obtaining eggs and then releasing the females back to the wild.

But team member David Moreno , also at the University of Tasmania, says captive breeding isn’t the full solution, so the researchers are also working to reverse environmental issues in Macquarie harbour, including a trial of pumping oxygen into the water.

There is no quick fix and even if the captive -reared individuals are able to be released immediately, it would be four to five years before they reached maturity and could start contributing to the population.

The stakes are high if the recovery effort fails. “This would be the first extinction of a ray or shark species in modern history,” says Moreno. “So it is a really big line in the sand.”

• conservation

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