Meeting Abstract
Different genomic regions vary in mode of inheritance, rates of recombination, and effective population size, which may result in contrasting patterns of genetic diversity and evolutionary history. For species with genetic sex determination, distinct patterns of inheritance among the autosomes, sex chromosomes, and mitochondria may provide particular insight into patterns of demography and sex-biased gene flow. Here, we sampled genetic variation from nuclear and mitochondrial RADseq loci from three pairs of rattlesnake lineages (genus Crotalus, and interpreted these data using a chromosome-level reference genome for the Prairie Rattlesnake (Crotalus viridis) to compare and contrast patterns of variation, population genetic structure, and differentiation among genomic regions. Within populations, we find that sex chromosomes and mitochondria exhibit patterns of genetic diversity different from autosomes, including nucleotide diversity (π) and -based effective population size estimates. We also find that between-population comparisons of differentiation (FST) and estimates of demographic history provide consistent evidence for allopatric divergence followed by secondary contact with gene flow across genomic regions. Our results illustrate the power of interpreting population genetic variation in the context of chromosomal genome assemblies for understanding the early stages of speciation, and demonstrate consistent and sex-biased signals of gene flow in secondary contact in rattlesnakes.
