Tag Archives: Extinct in the wild

Genomes of two Extinct-in-the-Wild reptiles from Christmas Island reveal distinct evolutionary histories and conservation insights

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Type: Journal Article

Reference: Dodge, T. O., Farquharson, K. A., Ford, C., Cavanagh, L., Schubert, K., Schumer, M., Belov, K, & Hogg, C. J. (2022). Genomes of two Extinct‐in‐the‐Wild reptiles from Christmas Island reveal distinct evolutionary histories and conservation insights. Molecular Ecology Resources. doi:10.1111/1755-0998.13780

Abstract

Genomics can play important roles in biodiversity conservation, especially for Extinct-in-the-Wild species where genetic factors greatly influence risk of total extinction and probability of successful reintroductions. The Christmas Island blue-tailed skink (Cryptoblepharus egeriae) and Lister’s gecko (Lepidodactylus listeri) are two endemic reptile species that went extinct in the wild shortly following the introduction of a predatory snake. After a decade of management, captive populations have expanded from 66 skinks and 43 geckos to several thousand individuals; however, little is known about patterns of genetic variation in these species. Here, we use PacBio HiFi long-read and Hi-C sequencing to generate highly contiguous reference genomes for both reptiles, including the XY chromosome pair in the skink. We then analyze patterns of genetic diversity to infer ancient demography and more recent histories of inbreeding. We observe high genome-wide heterozygosity in the skink (0.007 heterozygous sites per base-pair) and gecko (0.005), consistent with large historical population sizes. However, nearly 10% of the blue-tailed skink reference genome falls within long (>1Mb) runs of homozygosity (ROH), resulting in homozygosity at all major histocompatibility complex (MHC) loci. In contrast, we detect a single ROH in Lister’s gecko. We infer from the ROH lengths that related skinks may have established the captive populations. Despite a shared recent extinction in the wild, our results suggest important differences in these species’ histories and implications for management. We show how reference genomes can contribute evolutionary and conservation insights, and we provide resources for future population-level and comparative genomic studies in reptiles.

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Addressing Threats and Ecosystem Intactness to Enable Action for Extinct in the Wild Species

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Type: Journal Article

Reference: Dalrymple, S.E., Abeli, T., Ewen, J.G., Gilbert, T.C., Hogg, C.J., Lloyd, N.A., Moehrenschlager, A., Rodríguez, J.P., & Smith, D. (2023). Addressing Threats and Ecosystem Intactness to Enable Action for Extinct in the Wild Species. Diversity 15, 268. doi.org/10.3390/d15020268

Abstract

The species listed as Extinct in the Wild (EW) in the IUCN Red List of Threatened Species consist of 84 plants and animals that have been lost from their indigenous range. EW species are therefore restricted to ex situ conservation facilities and often have populations founded with few individuals. Our analysis demonstrates that 60% of EW species are associated with ecoregions that have very low proportions of intact habitat. Furthermore, threats such as invasive species, pollution, and climate change affect just over half of EW species and compound the obstacles facing their reinstatement to the wild. Despite these bleak assessments, there are various options for EW recovery. We present five scenarios that encapsulate the circumstances facing EW species and suggest potential conservation action for each of these situations. We illustrate these scenarios using case studies of EW species that demonstrate how the various options of ex situ management, reintroduction, and assisted colonisation to new habitat can be used to address the very exacting requirements of EW species. Our aim is to present a broad review of the obstacles facing the recovery of EW species whilst inspiring action to prevent the extinction of the most imperilled species on the planet.

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