Conservation Genetics and Genomics of Amphibians and Reptiles

Abstract

Amphibians and reptiles as a group are often secretive, reach their greatest diversity often in remote tropical regions, and contain some of the most endangered groups of organisms on earth. Particularly in the past decade, genetics and genomics have been instrumental in the conservation biology of these cryptic vertebrates, enabling work ranging from the identification of populations subject to trade and exploitation, to the identification of cryptic lineages harboring critical genetic variation, to the analysis of genes controlling key life history traits. In this review, we highlight some of the most important ways that genetic analyses have brought new insights to the conservation of amphibians and reptiles. Although genomics has only recently emerged as part of this conservation tool kit, several large-scale data sources, including full genomes, expressed sequence tags, and transcriptomes, are providing new opportunities to identify key genes, quantify landscape effects, and manage captive breeding stocks of at-risk species.

Sorting duplicated loci disentangles complexities of polyploid genomes masked by genotyping by sequencing

“…; Ellegren ; Shaffer et al . ). However, potentially large numbers of paralogous loci in polyploid‐origin genomes challenge genomic analyses; genome assemblies are particularly challenging due to equivocal sequence alignment.…”

Conservation of the endangered Mediterranean tortoise Testudo hermanni hermanni: The contribution of population genetics and historical demography

“…Consequently, a variety of roles have been identified for the implications of genetics in conservation (see DeSalle and Amato, 2004). According to Shaffer et al (2015), one of the most direct roles of genetics in informing amphibian and reptile conservation actions involves identifying and managing the human activities that endanger wild populations. They identify three main topics that we feel are particularly relevant: the trade in threatened species, captive breeding, and the design of natural reserves and parks.…”

“…For the management of populations, effective population size (Ne) is a critical piece of information (Frankham, 2007). Because reptiles and amphibians are often difficult to count in the wild, direct estimates of the number of breeding individuals are rare (Shaffer et al, 2015). The application of genetic methods can not only help to estimate the effective breeding size of a population, but for several species also offers a valuable alternative that allows the historical patterns of population expansion or decline to be inferred (Funk et al, 1999;Phillipsen et al, 2011;Casas-Marce et al, 2013;Kamath et al, 2015).…”

Sequencing smart:De novosequencing and assembly approaches for non-model mammals

“…Through comparative genomics, it is possible to identify how different organisms are related to each other, how they adapt to novel environments, or the genetic basis underlying novel phenotypes. These new findings can be applied to further research, such as in the biomedical and food industries through breeding programs with the development of marker assisted selection and in conservation biology [3][4][5][6][7][8][9][10][11][12] De novo assembly of endangered species, followed by low-coverage population-level sequencing provides unprecedented information about the amount of genetic diversity within populations, past and ongoing gene flow between different populations, and the level of inbreeding in small populations.…”