Are Genomic Updates of Well-Studied Species Worth the Investment for Conservation? A Case Study of the Critically Endangered Magdalena River Turtle

Abstract

As genomic-scale data sets become economically feasible for most organisms, a key question for conservation biology is whether the increased resolution offered by new genomic approaches justifies repeating earlier studies based on traditional markers, rather than investing those same time and monetary resources in less-known species. Genomic studies offer clear advantages when the objective is to identify adaptive loci that may be critical to conservation policy-makers. However, the answer is far less certain for the population and landscape studies based on neutral loci that dominate the conservation genetics research agenda. We used RADseq to revisit earlier molecular studies of the IUCN Critically Endangered Magdalena River turtle (Podocnemis lewyana), documenting the conservation insights gained by increasing the number of neutral markers by several orders of magnitude. Earlier research indicated that P. lewyana has the lowest genetic diversity known for any chelonian, and little or no population differentiation among independent rivers. In contrast, the RADseq data revealed discrete population structure with isolation-by-distance within river segments and identified precise population breaks clearly delineating management units. It also confirmed that the species does not have extremely low heterozygosity and that effective population sizes are probably sufficient to maintain long-term evolutionary potential. Contrary to earlier inferences from more limited population genetic markers, our genomic data suggest that management strategies should shift from active genetic rescue to more passive protection without extreme interventions. We conclude with a list of examples of conservation studies in other vertebrates indicating that for many systems a genomic update is worth the investment.

A brief history of population genetic research in California and an evaluation of its utility for conservation decision-making

“…While there is nothing inherently wrong with such estimates, the predominance of microsatellite studies, combined with their very high estimates of genetic variation, suggest that great caution should be used when comparing them to studies conducted using other marker types. In a conservation context, these inherent differences could have considerable consequences for prioritization of populations based on levels of standing genetic variation if study-specific differences, such as marker type, are not accounted for— Gallego-García et al (2021) is a case in point for endangered turtles. A results of studies across marker types is to standardize to a mean of 0 and a variance of 1, which at least places them on a comparable scale of variation ( Kort et al 2021 ).…”

“…A similar study in the brown trout, Salmo trutta , revealed that among-population F ST estimates were similar between microsatellites and SNPs, as were the rank order of populations for allelic richness and heterozygosity, while effective population size estimates based on the 2 marker types were uncorrelated ( Lemopoulos et al 2019 ). Similarly, a reexamination of genetic variation in the critically endangered Magdelena River turtle Podocnemis lewyana across its range in Columbia by Gallego-García et al (2021) found that the long-held inference of the species as an extreme outlier for low genetic diversity based on microsatellites did not hold up when thousands of SNPs were examined: P. lewyana diversity was still low, but not lower than other endangered turtles. What these and many other studies demonstrate is the importance of marker type when evaluating raw estimates of genetic diversity for any given species or population.…”

CaliPopGen: A genetic and life history database for the fauna and flora of California

“…We assembled trait data that have previously been shown to correlate with genetic diversity, including those related to reproduction, life cycle, and body size, as well as conservation status (e.g. 23 – 26 ,). Life history data were compiled by first referencing large online repositories, often specific to taxonomic groups, like the TRY plant trait database 27 , and the Royal Botanic Gardens Kew Seed Information Database 28 .…”

Landscape Genomics to Enable Conservation Actions: The California Conservation Genomics Project

“…The CCGP also will provide a platform to explore some of the more vexing questions in conservation biology, such as whether species with limited ranges should be managed or protected in the same way as widely distributed ones, whether species formerly widespread but now limited in geographic scope should be stewarded differently than species that have always had small ranges (Robinson et al 2016), and whether, and when, genome-level data are worth collecting for species that have been previously analyzed with more restricted data sets (Beninde et al 2022;Gallego-García et al 2021). With the rate of extinction in the last century estimated to be 22 times faster than the historical baseline rate (Ceballos et al 2015) rapidly gathering largescale landscape genomic datasets, complemented by highquality reference genomes, is one positive step that can and should be made, to understand biodiversity as it now exists, and doing what we can to ensure resilience in the face of a rapidly changing world.…”