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]
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Cryptic extinction risk in a western Pacific lizard radiation
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 genus
- Award ID(s):
- 1657648
- NSF-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
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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
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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1007/s10531-022-02412-x
