Eastern Racer

description

Sequence alignments The final assembled dataset consisted of 3417 loci (3348 UCE loci, 61 AHE loci, and eight of the ‘ legacy Sanger’ loci). The mean proportion of loci recovered within each sample was 94 % (range: 65 – 97 %). The mean length of these assembled loci after trimming was 230.2 base pairs (range: 2 – 1731) and the mean number of segregating sites was 3.9 (range: 0 – 30). All raw sequence data have been accessioned on the NCBI Sequence Read Archive (BioProject ID PRJNA 1082780; Supporting Information, Table S 1). The mtDNA sequence assembled from these raw reads ranged in length from 124 to 7083 bp in length and were trimmed to the 1117 bp length of Cytb. Population structure, phylogenetic relationships, and gene divergence times Results from sNMF analyses indicate that K = 5 is the best fit (Fig. 3). These five populations correspond to a population in peninsular Florida, an eastern population in the temperate deciduous forests, a central population within the North American grasslands, a western population isolated across the Rocky Mountains, and a population from south Texas. Hereafter these populations will be referred to as the Florida, eastern, central, western, a

Contrasting the depths of divergence between gene-tree and coalescent estimates in the North American racers (Colubridae: Coluber constrictor)

discussion

DISCUSSION Previous studies have suggested morphological variation and extensive population genetic structure across the distribution of the North American racers (e. g. Ortenburger 1928, Anderson 1996, Burbrink et al. 2008). Here we corroborate much of this lineage divergence using a combination of genomic sequence capture data, mtDNA, morphology, and ecological niche models. We demonstrate that this structure corresponds to several well-known biogeographic barriers across North America. The genome-scale data and mtDNA show similar geographic lineages and largely agree in the phylogenetic relationships among these lineages. However, demographic models based on the genomic data strongly disagree with the best-fit model to the mtDNA in divergence times and topology. Furthermore, comparing divergence times estimated from mtDNA and concatenated genomic data to the divergence times estimated from demographic models suggests that these discrepancies are the result of differences between gene- vs. coalescent-divergence time estimates. Additionally, we find that several of these lineages are distinguishable morphologically, largely across the Mississippi River, and several adjacent popula

Contrasting the depths of divergence between gene-tree and coalescent estimates in the North American racers (Colubridae: Coluber constrictor)