An official website of the United States government
INTRODUCTION The Anthropocene is marked by an accelerated loss of biodiversity, widespread population declines, and a global conservation crisis. Given limited resources for conservation intervention, an approach is needed to identify threatened species from among the thousands lacking adequate information for status assessments. Such prioritization for intervention could come from genome sequence data, as genomes contain information about demography, diversity, fitness, and adaptive potential. However, the relevance of genomic data for identifying at-risk species is uncertain, in part because genetic variation may reflect past events and life histories better than contemporary conservation status. RATIONALE The Zoonomia multispecies alignment presents an opportunity to systematically compare neutral and functional genomic diversity and their relationships to contemporary extinction risk across a large sample of diverse mammalian taxa. We surveyed 240 species spanning from the “Least Concern” to “Critically Endangered” categories, as published in the International Union for Conservation of Nature’s Red List of Threatened Species. Using a single genome for each species, we estimated historical effective population sizes ( N e ) and distributions of genome-wide heterozygosity. To estimate genetic load, we identified substitutions relative to reconstructed ancestral sequences, assuming that mutations at evolutionarily conserved sites and in protein-coding sequences, especially in genes essential for viability in mice, are predominantly deleterious. We examined relationships between the conservation status of species and metrics of heterozygosity, demography, and genetic load and used these data to train and test models to distinguish threatened from nonthreatened species. RESULTS Species with smaller historical N e are more likely to be categorized as at risk of extinction, suggesting that demography, even from periods more than 10,000 years in the past, may be informative of contemporary resilience. Species with smaller historical N e also carry proportionally higher burdens of weakly and moderately deleterious alleles, consistent with theoretical expectations of the long-term accumulation and fixation of genetic load under strong genetic drift. We found weak support for a causative link between fixed drift load and extinction risk; however, other types of genetic load not captured in our data, such as rare, highly deleterious alleles, may also play a role. Although ecological (e.g., physiological, life-history, and behavioral) variables were the best predictors of extinction risk, genomic variables nonrandomly distinguished threatened from nonthreatened species in regression and machine learning models. These results suggest that information encoded within even a single genome can provide a risk assessment in the absence of adequate ecological or population census data. CONCLUSION Our analysis highlights the potential for genomic data to rapidly and inexpensively gauge extinction risk by leveraging relationships between contemporary conservation status and genetic variation shaped by the long-term demographic history of species. As more resequencing data and additional reference genomes become available, estimates of genetic load, estimates of recent demographic history, and accuracy of predictive models will improve. We therefore echo calls for including genomic information in assessments of the conservation status of species. Genomic information can help predict extinction risk in diverse mammalian species. Across 240 mammals, species with smaller historical N e had lower genetic diversity, higher genetic load, and were more likely to be threatened with extinction. Genomic data were used to train models that predict whether a species is threatened, which can be valuable for assessing extinction risk in species lacking ecological or census data. [Animal silhouettes are from PhyloPic]
more »
« less
Cryptic extinction risk in a western Pacific lizard radiation
Abstract Cryptic ecologies, the Wallacean Shortfall of undocumented species’ geographical ranges and the Linnaean Shortfall of undescribed diversity, are all major barriers to conservation assessment. When these factors overlap with drivers of extinction risk, such as insular distributions, the number of threatened species in a region or clade may be underestimated, a situation we term ‘cryptic extinction risk’. The genusLepidodactylusis a diverse radiation of insular and arboreal geckos that occurs across the western Pacific. Previous work onLepidodactylusshowed evidence of evolutionary displacement around continental fringes, suggesting an inherent vulnerability to extinction from factors such as competition and predation. We sought to (1) comprehensively review status and threats, (2) estimate the number of undescribed species, and (3) estimate extinction risk in data deficient and candidate species, inLepidodactylus. From our updated IUCN Red List assessment, 60% of the 58 recognized species are threatened (n = 15) or Data Deficient (n = 21), which is higher than reported for most other lizard groups. Species from the smaller and isolated Pacific islands are of greatest conservation concern, with most either threatened or Data Deficient, and all particularly vulnerable to invasive species. We estimated 32 undescribed candidate species and linear modelling predicted that an additional 18 species, among these and the data deficient species, are threatened with extinction. Focusing efforts to resolve the taxonomy and conservation status of key taxa, especially on small islands in the Pacific, is a high priority for conserving this remarkably diverse, yet poorly understood, lizard fauna. Our data highlight how cryptic ecologies and cryptic diversity combine and lead to significant underestimation of extinction risk.
more »
« less
- Award ID(s):
- 1657648
- PAR ID:
- 10470899
- Publisher / Repository:
- Springer Link
- Date Published:
- Journal Name:
- Biodiversity and Conservation
- Volume:
- 31
- Issue:
- 8-9
- ISSN:
- 0960-3115
- Page Range / eLocation ID:
- 2045 to 2062
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
We describe a new species of Lepidodactylus from Umboi Island, just to the west of New Britain. It is a member of the Lepidodactylus guppyi Group and can be distinguished from all other Melanesian Lepidodactylus by aspects of digital scalation, digital webbing, enlarged femoral/precloacal scales, and color pattern. It is genetically distinct from its closest congeners, and genetic and morphological data indicate that the new species is most similar among named species to Lepidodactylus guppyi from the Solomon Islands, but it diverged from this species and other close relatives approximately 8 MYA or longer at a time prior to the existence of the island that it now occupies. The new species is known from only three individuals collected on a single tree, and efforts to find more animals in what seemed good habitat nearby were unsuccessful. This duplicates the pattern of apparent rarity seen for many Lepidodactylus species. Sufficient habitat exists on Umboi Island for arboreal geckos, suggesting that the species is not actually endangered but is ecologically cryptic. However, lack of needed information leads us to assess this species’ conservation status as Data Deficient.more » « less
-
The diversity of nemerteans along the Pacific coast of the United States is regarded as well characterized, but there remain many cryptic, undescribed, and “orphan” species (those known only in their larval form). Recent sampling of nemerteans in Oregon and Washington has begun to fill in these taxonomic gaps, but nemertean diversity in California has received relatively little attention over the past 60 years. During the summers of 2019 and 2020, nemertean specimens were collected from 20 locations in the Bodega Bay region of northern California, USA, including rocky intertidal shores, sandy beaches, mudflats, and other habitats. Based on morphological assessment and DNA sequence analysis (partial Cytochrome Oxidase I and 16S rRNA genes), our surveys identified 34 nemertean species. Only 13 of these (38%) can be confidently assigned to described species. Another 11 represent species that are new to science, including members of the generaRiserius,Nipponnemertes,Poseidonemertes,Zygonemertes,Nemertellina,Oerstedia, and three species of uncertain affiliation. The remaining ten species include undescribed or cryptic species of uncertain status that have been found previously along the Pacific Coast of North America. Our surveys also document extensions of known geographic ranges for multiple species, including the first records in California ofAntarctonemertes phyllospadicola,Cephalothrix hermaphroditica, andMaculaura oregonensis. This is the first report of the genusNemertellinain the northeast Pacific andRiseriusin California. Overall, our findings highlight how much remains to be learned about the diversity and distribution of nemerteans in the northeast Pacific.more » « less
-
Several species of geckos of the genus Lepidodactylus are endemic to the Solomon Islands and very poorly known. I redescribe one of these, L. flaviocularis, from Guadalcanal, based on examination of a second, newly obtained specimen and quantification of diagnostically useful features of the digits. I also describe a closely related new species from nearby Makira Island in the southern Solomon Islands. Both species are distinguished by their large number of undivided subdigital lamellae, extensive toe webbing, and a continuous row of enlarged precloacal/femoral scales. The new species is distinguished from L. flaviocularis by a number of scalational features and the color of the circumorbial scales. Both species are inhabitants of interior forest, and it remains uncertain whether they are naturally rare, rare due to interactions with invasive species, or simply have cryptic ecological habits, though the last seems most likely. Current evidence for both species is consistent with the taxon-cycle hypothesis, which posits ecological displacement to inland habitats of ancient island inhabitants by newer colonizers, but this remains to be critically tested. The limited pool of specimens available for both species necessitates assessing the IUCN conservation status of each as Data Deficient.more » « less
-
Abstract Systematic assessments of species extinction risk at regular intervals are necessary for informing conservation action1,2. Ongoing developments in taxonomy, threatening processes and research further underscore the need for reassessment3,4. Here we report the findings of the second Global Amphibian Assessment, evaluating 8,011 species for the International Union for Conservation of Nature Red List of Threatened Species. We find that amphibians are the most threatened vertebrate class (40.7% of species are globally threatened). The updated Red List Index shows that the status of amphibians is deteriorating globally, particularly for salamanders and in the Neotropics. Disease and habitat loss drove 91% of status deteriorations between 1980 and 2004. Ongoing and projected climate change effects are now of increasing concern, driving 39% of status deteriorations since 2004, followed by habitat loss (37%). Although signs of species recoveries incentivize immediate conservation action, scaled-up investment is urgently needed to reverse the current trends.more » « less
- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1007/s10531-022-02412-x
