Genome Evolution and the Future of Phylogenomics of Non-Avian Reptiles

Abstract

Non-avian reptiles comprise a large proportion of amniote vertebrate diversity, with squamate reptiles—lizards and snakes—recently overtaking birds as the most species-rich tetrapod radiation. Despite displaying an extraordinary diversity of phenotypic and genomic traits, genomic resources in non-avian reptiles have accumulated more slowly than they have in mammals and birds, the remaining amniotes. Here we review the remarkable natural history of non-avian reptiles, with a focus on the physical traits, genomic characteristics, and sequence compositional patterns that comprise key axes of variation across amniotes. We argue that the high evolutionary diversity of non-avian reptiles can fuel a new generation of whole-genome phylogenomic analyses. A survey of phylogenetic investigations in non-avian reptiles shows that sequence capture-based approaches are the most commonly used, with studies of markers known as ultraconserved elements (UCEs) especially well represented. However, many other types of markers exist and are increasingly being mined from genome assemblies in silico, including some with greater information potential than UCEs for certain investigations. We discuss the importance of high-quality genomic resources and methods for bioinformatically extracting a range of marker sets from genome assemblies. Finally, we encourage herpetologists working in genomics, genetics, evolutionary biology, and other fields to work collectively towards building genomic resources for non-avian reptiles, especially squamates, that rival those already in place for mammals and birds. Overall, the development of this cross-amniote phylogenomic tree of life will contribute to illuminate interesting dimensions of biodiversity across non-avian reptiles and broader amniotes.

New chromosome-scale genomes provide insights into marine adaptations of sea snakes (Hydrophis: Elapidae)

“…Non-avian reptiles have emerged as an important group for studying karyotype evolution (reviewed in [ 36 ]). Our study contributes to this expanding literature by examining syntenic changes over a much more recent timeframe than most previous analyses of the group.…”

Clinging on the brink: Whole genomes reveal human‐induced population declines and severe inbreeding in the Critically Endangered Emirati Leaf‐toed Gecko (Asaccus caudivolvulus)

“…Despite the exponential growth in the availability of reference genome data in recent years, squamate reptiles fall behind other taxonomic groups in terms of reference genome availability. To date, reference genomes are available for less than 1% of squamate reptiles whereas this is the case for 9% and 6% of mammals and birds respectively (Card et al., 2023). Within squamates, geckos are particularly underrepresented with only 10 available reference genomes (Card et al., 2023) for a group of 2291 species (Uetz et al., 2023).…”

“…To date, reference genomes are available for less than 1% of squamate reptiles whereas this is the case for 9% and 6% of mammals and birds respectively (Card et al., 2023). Within squamates, geckos are particularly underrepresented with only 10 available reference genomes (Card et al., 2023) for a group of 2291 species (Uetz et al., 2023). The lack of genomic resources for geckos can have profound implications in conservation and management strategies for endangered species within this group.…”

Reptile Evolution and Genetics: An Overview

“…One relevant paper concerns genome evolution and phylogenomic [ 9 ] and evidences the advancement of whole genome sequencing in the general framework of the karyology and composition of non-avian reptiles. This study shows that genomic resources in non-avian reptiles have now accumulated more slowly than in other amniotic groups despite the extraordinary diversity of phenotypic and genomic traits.…”