Similarity of contemporary and historical gene flow among highly fragmented populations of an endangered rattlesnake

Abstract

Populations of endangered taxa in recently fragmented habitats often show high levels of genetic structure, but the role that contemporary versus historical processes play in generating this pattern is unclear. The eastern massasauga rattlesnake (Sistrurus c. catenatus) is an endangered snake that presently occurs throughout central and eastern North America in a series of populations that are isolated because of habitat fragmentation and destruction. Here, we use data from 19 species-specific microsatellite DNA loci to assess the levels of genetic differentiation, genetic effective population size, and contemporary and historical levels of gene flow for 19 populations sampled across the range of this snake. Eastern massasaugas display high levels of genetic differentiation (overall θ(Fst) = 0.21) and a Bayesian clustering method indicates that each population represents a unique genetic cluster even at regional spatial scales. There is a twofold variation in genetically effective population sizes but little genetic evidence that populations have undergone recent or historical declines in size. Finally, both contemporary and historical migration rates among populations were low and similar in magnitude even for populations located <7 km apart. A test of alternate models of population history strongly favours a model of long-term drift-migration equilibrium over a recent isolation drift-only model. These results suggest that recent habitat fragmentation has had little effect on the genetic characteristics of these snakes, but rather that this species has historically existed in small isolated populations that may be resistant to the long-term negative effects of inbreeding.

Genetic diversity and spatial structure of the Rufous‐throated Antbird (Gymnopithys rufigula), an Amazonian obligate army‐ant follower

“…BayesAss uses a Bayesian approach and MCMC sampling to estimate migration ( m ) over the last few generations (Wilson & Rannala, 2003). Following Chiucchi and Gibbs (2010) and Converse et al. (2015), we assumed that meant roughly five generations.…”

“…To be able to compare migration estimations resulted from Migrate‐N (M =  m /μ) to those resulting from BayesAss ( m ), we multiplied M values by a commonly assumed microsatellite mutation rate of 5 × 10 −4 (Chiucchi & Gibbs, 2010; Converse et al., 2015). …”

The influence of contemporary and historic landscape features on the genetic structure of the sand dune endemic, Cirsium pitcheri (Asteraceae)

“…The TwoPhased Model of mutation was run for 10 5 simulations with 95% single-step mutations and 5% multi-step mutations and a variance of 12 as recommended by Piry et al (1999) and Chiucchi and Gibbs (2010). As these first tests are best for detecting bottlenecks in the 0.2-0.4 N e generations, we also employed the mode-shift test for detecting more recent bottlenecks (Cornuet and Luikart, 1997;Luikart et al, 1998;Chiucchi and Gibbs, 2010).…”

“…BOTTLENECK v1.2.0 was used to test for evidence of recent and past bottlenecks (Cornuet and Luikart, 1997) using a Wilcoxon's signs test to look for evidence of heterozygous excess and deficiency using both the Infinite Allele Model and the Two-Phased Model of mutation, a variant of the strict Stepwise Mutation Model (Luikart et al, 1998). The TwoPhased Model of mutation was run for 10 5 simulations with 95% single-step mutations and 5% multi-step mutations and a variance of 12 as recommended by Piry et al (1999) and Chiucchi and Gibbs (2010). As these first tests are best for detecting bottlenecks in the 0.2-0.4 N e generations, we also employed the mode-shift test for detecting more recent bottlenecks (Cornuet and Luikart, 1997;Luikart et al, 1998;Chiucchi and Gibbs, 2010).…”

“…No significant bottleneck was detected using either the Stepwise Mutation Model or Two-Phased Model of mutation models in BOTTLENECK v1.2.0 (Cornuet and Luikart, 1997; Table 1). However, three populations (NLM-WI2, NLM-UP3 and LH-HSP1) did show a mode-shift in distribution, from the L shape expected under mutation-drift equilibrium (data not shown) suggesting evidence of a recent bottleneck (Cornuet and Luikart, 1997;Luikart et al, 1998;Chiucchi and Gibbs, 2010).…”