Conservation Genomics of the Eastern Indigo Snake (Drymarchon couperi)

Abstract

The eastern indigo snake (Drymarchon couperi) is a federally threatened species endemic to the southeastern Coastal Plain, where it has been extirpated from southern Alabama and the Florida panhandle. To date, genetic data has had a limited role in conservation management of wild populations and the breeding colony. In this dissertation, I develop a genomic toolkit to survey variation in wild and captive populations of eastern indigo snakes. First, I assemble the first reference genome for the species and use it to reconstruct the species’ demographic history. The final assembled genome size is approximately 1.8Gb and is highly complete (BUSCO = 97%). Further, demographic reconstructions suggest that eastern indigo snake population sizes started to decline 500,000 years ago and have been consistently small for the last 100,000 years. Second, I assess population structure, diversity, and connectivity of wild populations from across the range of the eastern indigo snake. I identified three populations in southeastern Georgia, one in southern Florida, and an admixed population in northern Florida. Populations have low genetic diversity and small effective population sizes, consistent with a threatened species, and connectivity is restricted to adjacent populations. In my third chapter, I compare genetic diversity between the breeding colony and wild populations, and find that genetic diversity in the breeding colony has increased between 2013 and 2023. Genetic diversity in the most recent cohorts captures variation found in the Georgia populations and north Florida admixed population, suggesting effective management of the colony. Lastly, I evaluate the accuracy of the breeding colony studbook using genomic kinship and pedigree reconstruction. Genomic data identified first-degree relationships between captive-bred individuals absent in the studbook pedigree likely attributable to cryptic relatedness detected among wild-caught founder individuals collected from geographically proximate localities. This work exemplifies the broad utility of genomic data for conservation management of threatened species and provides a replicable framework for integrating genomics into the management of other species.