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\begin{document}

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



\author[1]{Tristram Dodge}%
\author[1]{Katherine Farquharson}%
\author[2]{Claire Ford}%
\author[2]{Lisa Cavanagh}%
\author[3]{Kristen Schubert}%
\author[4]{Molly Schumer}%
\author[1]{Katherine Belov}%
\author[1]{Carolyn J. Hogg}%
\affil[1]{The University of Sydney}%
\affil[2]{Taronga Conservation Society Australia}%
\affil[3]{Parks Australia}%
\affil[4]{Stanford University}%


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  \date{May 24, 2024}


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\begin{abstract}
Genomics can play important roles in biodiversity conservation,
especially for Extinct-in-the-Wild species where genetic factors can
influence total extinction risk 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 after 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 contiguous reference genomes for both species,
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 blue-tailed skink (0.007) and Lister's gecko (0.005), consistent
with large historical population sizes. However, nearly 10\% of the
skink reference genome falls within long runs of homozygosity (ROH),
resulting in homozygosity at all major histocompatibility complex (MHC)
loci, whereas we detect only a single ROH in the 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 species' histories and implications for
management. We show how reference genomes can provide evolutionary and
conservation insights in the absence of resequencing data, and we
provide a resource for future population-level and comparative genomic
studies in reptiles.%
\end{abstract}%



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\textbf{Hosted file}

\verb`CI_reptiles_manuscript_V9_11.21.22 (1).docx`  available at \url{https://authorea.com/users/557855/articles/607316-genomes-of-two-extinct-in-the-wild-reptiles-from-christmas-island-reveal-distinct-evolutionary-histories-and-conservation-insights}

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