Origin of a cryptic lineage in a threatened reptile through isolation and historical hybridization

Abstract

Identifying phylogenetically distinct lineages and understanding the evolutionary processes by which they have arisen are important goals of phylogeography. This information can also help define conservation units in endangered species. Such analyses are being transformed by the availability of genomic-scale data sets and novel analytical approaches for statistically comparing different historical scenarios as causes of phylogeographic patterns. Here, we use genomic-scale restriction-site-associated DNA sequencing (RADseq) data to test for distinct lineages in the endangered Eastern Massasauga Rattlesnake (Sistrurus catenatus). We then use coalescent-based modeling techniques to identify the evolutionary mechanisms responsible for the origin of the lineages in this species. We find equivocal evidence for distinct phylogenetic lineages within S. catenatus east of the Mississippi River, but strong support for a previously unrecognized lineage on the western edge of the range of this snake, represented by populations from Iowa, USA. Snakes from these populations show patterns of genetic admixture with a nearby non-threatened sister species (Sistrurus tergeminus). Tests of historical demographic models support the hypothesis that the genetic distinctiveness of Iowa snakes is due to a combination of isolation and historical introgression between S. catenatus and S. tergeminus. Our work provides an example of how model-based analysis of genomic-scale data can help identify conservation units in rare species.

Genomic signatures of sympatric speciation with historical and contemporary gene flow in a tropical anthozoan (Hexacorallia: Actiniaria)

“…Due to the computational constraints of running SNAPP with biallelic SNP data (i.e., computation time increases linearly as more loci are added but exponentially as more samples are added), and constraints for estimating species trees with missing data (i.e., data has to be present in at least one individual at each locus for each putative species), we followed Sovic et al, () and created new SNP data sets with significantly fewer individuals so that our analyses could be completed over the course of days rather than weeks or months. We used five randomly selected individuals from each genetic cluster delimited by Structure and used E. diaphana as an outgroup as BFD* can only perform model selection on models with n ≥ 2 species (Table ).…”

Genetic signatures of small effective population sizes and demographic declines in an endangered rattlesnake, Sistrurus catenatus

“…Weber, Kay, Fisher, & Hoekstra, 2012) were generated with EcoRI and SbfI restriction enzymes (New England Biolabs, Ipswich, MA) and a modified version of the RADSeq protocol described in DaCosta and Sorenson (2014). For details of the library preparation methods, see the Supplemental Information section of Sovic et al (2016).…”

“…These reflect the amount of genetic diversity (estimated as)maintained in a population at evolutionary equilibrium due to the joint effect of drift and mutation (µ) over a period of approximately 4Ne generations ( = 4Neµ). Likewise, the estimates of Ne using fastsimcoal generated by Sovic et al (2016) and here also represent historical estimates of effective population size over many past generations. These long-term estimates have conservation value in potentially representing a measure of population size that predates human impacts.…”

Local prey community composition and genetic distance predict venom divergence among populations of the northern Pacific rattlesnake (Crotalus oreganus)

“…Following Sovic et al . (), our analyses only included loci with no missing data across all samples to minimize the impact of unscored genotypes on estimates of population‐genetic parameters (Arnold et al ., ).…”

“…We extracted genomic DNA from snake blood using the standard phenol-chloroform protocol and generated double-digest RAD-seq libraries for each individual following the methods of Sovic et al (2016). Briefly, we digested genomic DNA with the EcoRI and SbfI restriction enzymes (New England Biolabs, Ipswich, MA, USA) and electrophoresed each individual's genomic DNA on a single lane of a 2% (w/v) low melt point agarose gel to isolate fragments of between 300 and 450 base pairs.…”