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

Abstract

Endangered species that exist in small isolated populations are at elevated risk of losing adaptive variation due to genetic drift. Analyses that estimate short‐term effective population sizes, characterize historical demographic processes, and project the trajectory of genetic variation into the future are useful for predicting how levels of genetic diversity may change. Here, we use data from two independent types of genetic markers (single nucleotide polymorphisms [SNPs] and microsatellites) to evaluate genetic diversity in 17 populations spanning the geographic range of the endangered eastern massasauga rattlesnake ( Sistrurus catenatus ). First, we use SNP data to confirm previous reports that these populations exhibit high levels of genetic structure (overall Fst = 0.25). Second, we show that most populations have contemporary Ne estimates <50. Heterozygosity–fitness correlations in these populations provided no evidence for a genetic cost to living in small populations, though these tests may lack power. Third, model‐based demographic analyses of individual populations indicate that all have experienced declines, with the onset of many of these declines occurring over timescales consistent with anthropogenic impacts (<200 years). Finally, forward simulations of the expected loss of variation in relatively large (Ne = 50) and small (Ne = 10) populations indicate they will lose a substantial amount of their current standing neutral variation (63% and 99%, respectively) over the next 100 years. Our results argue that drift has a significant and increasing impact on levels of genetic variation in isolated populations of this snake, and efforts to assess and mitigate associated impacts on adaptive variation should be components of the management of this endangered reptile.

Comparative phylogeography of mainland and insular species of Neotropical molossid bats (Molossus)

“…Nadeau et al () proposed that a deeper genetic coverage could ameliorate the effect of a small number of individuals. In addition, other studies with next generation sequencing have conducted similar population genetic and demographic analyses using different population sizes (from 5 to 27 individuals) and found consistent results (Sovic, Fries, Martin, & Gibbs, ). Robison, Coffman, Hickerson, and Gutenkunst () also found accurate parameter and demographic estimates for populations with more ancient demographic events (in the order of 0.5 N e generations ago) in small numbers of sampled individuals.…”

Using niche centrality within the scope of the nearly neutral theory of evolution to predict genetic diversity in a tropical conifer species‐pair

“…Population genetics theory directly relates genetic diversity to the effective population size, which is not necessarily a straight-forward parameter to determine (Charlesworth, 2009;Charlesworth et al, 1993;Sovic et al, 2018). In many biogeographic and conservation genetic studies, population size/area is often used as a proxy for effective population size (Frankham, 1996;Leimu & Fischer, 2008); however, better options have been offered by modern approaches based on the nearly neutral theory of evolution (NTT; Ohta, 1973).…”

“…Traditional conservation surveys use basic estimates of genetic diversity, like the mean number of alleles (A) or the expected heterozygosity (H E ), determined from SSR markers (Diniz-Filho et al, 2015;Eckert et al, 2008). While these markers are particularly sensitive to rapid demographic changes, particularly bottlenecks (Milligan et al, 2018;Sovic et al, 2018), estimates performed with SSRs could be inflated because of their hypervariable nature; indeed, they may not represent actual values of within-species genetic diversity (Estoup et al, 2002). Besides, their type of mutations (indels) and (often) non-coding nature does not allow determining π N /π S (Charlesworth et al, 2003;Kirk & Freeland, 2011;Lazrek et al, 2009).…”

Comprehensive genotyping of Brazilian Cassava (Manihot esculentaCrantz) Germplasm Bank: insights into diversification and domestication

“…Observed heterozygosity was higher for genetic groups having less effective population size (Table 1) and this indicates a good measure of the capability of the identified genetic groups to respond to selection, given that the amount of allelic variation left is important for long-term response to selection and survival of populations. In addition, allelic diversity is generally more sensitive to drift than heterozygosity (Allendorf 1986;Sovic et al 2019), This is made possible in a clonally propagated crop like cassava by incorporated seedlings into clonal stocks to provide new genotypes and additional allelic variation (McKey et al 2010). We generally observed high heterozygosity across identified genetic groups, indicating a high proportion of genetic variance (allelic variation) across locus in our populations.…”

“…Minor allele frequency (MAF) were computed using PLINK v2.0 (Purcell et al 2007), while fixation index ( AB ) was estimated using Weir and Cockerham's estimator (Weir and Cockerham 1984). Observed heterozygosity was estimated using GENEPOP software version 4.7.5 (Rousset 2008) And effective population size C , was estimated at an allele frequency of 0.02 using LDNe method (Waples and Do 2008), as described by (Sovic et al 2019) and implemented in the software NeEstimate version 2 (Do et al 2014).…”