DOI: 10.5061/dryad.rxwdbrvhh
title: Contrasting the depths of divergence between gene-tree and coalescent estimates in the North American Racers (Colubridae: Coluber constrictor)

description: The North American racers (Coluber constrictor) are widely distributed
 across the Nearctic and numerous studies have demonstrated extensive
 variation in morphology, ecology, and population genetic structure. Here
 we take an integrative approach to understand lineage diversification
 within this taxon by combining genomic sequence capture data, mtDNA
 sequence data, morphometrics, and ecological niche models. Both the
 genomic data and mtDNA phylogeographic analyses support five lineages
 distributed across the range of this species. However, demographic model
 selection based on these two datasets strongly conflict in both the model
 of divergence and estimates of timing of lineage divergence. While mtDNA
 and concatenated genomic data suggest a Miocene origin of these distinct
 groups, coalescent-based demographic models of sequence capture data
 suggest lineage diversification occurred at ~33 kya in allopatry without
 gene flow. Using linear morphological measurements of head shape we
 demonstrate that lineages distributed largely east and west of the
 Mississippi River are distinguishable. Furthermore, ecological niche
 modelling demonstrates that lineages distributed in subtropical habitats
 have environmental niche space that is significantly differentiated from
 lineages distributed across the continent. Taken together, these results
 suggest that ecology is an important axis of lineage divergence within
 this group and that more fine-scale analyses may find even greater
 differentiation across the populations identified here.
description: Genomic data were generated via sequence capture using the
 squamate specific SqCL probe set. mtDNA data were mined from these
 sequence capture data. The locality information used for ecological niche
 models were obtained from VertNet as georeferenced museum specimen
 vouchers.
description: # Contrasting the depths of divergence between gene-tree and coalescent
 estimates in the North American Racers (Colubridae: Coluber constrictor)
 [https://doi.org/10.5061/dryad.rxwdbrvhh](https://doi.org/10.5061/dryad.rxwdbrvhh) Data contained here are files needed to reconstruct ecological niche models and the assembled genomic and mtDNA data sets used in this study. ## Description of the data and file structure Locality information used for ecological niche models. Each of these files are named according to the lineage that the locality data belongs to. Within each file are the vouchered museum specimen numbers, latitude and longitude, and description of the collection locality. Central_Georeferenced_Coluber_From_VertNet_thinned_08032021.csv East_Georeferenced_Coluber_From_VertNet_thinned_08032021.csv Florida_Georeferenced_Coluber_From_VertNet_thinned_08022021.csv south_texas_Georeferenced_Coluber_From_VertNet_thinned.csv Western_Georeferenced_Coluber_From_VertNet_thinned_08212023.csv Genetic data used in this study. Concatenated, phased genomic data in phylip format, this file can be used to reconstruct the maximum likelihood concatenated tree presented in the paper and the alignment can be viewed in a text editor or commonly used Geneious software: conc_Coluber_phased_with_outgroups.phy mtDNA cytb alignment in fasta format, this file can be used to reconstruct the maximum likelihood gene tree presented in the paper and the alignment can be viewed in a text editor or commonly used Geneious software: Final_cytb_Coluber_alignment.fasta Variant calling format file with one SNP per locus, this file was used for population structure analyses and can be manipulated in R (e.g., with the vcfR library) or using command line tools (e.g., vcftools): Coluber_constricotr_SeqCap_1_SNP_per_locus.vcf All assembled fasta files. These loci do not contain the outgroups, have been filtered by nucleotide diversity to remove potentially paralogous loci, and are filtered for missing data with a 30% missingness threshold. This zipped directory contains 3,417 fasta files. These alignments can be sued to reconstruct the demographic history of Coluber constrictor, as was done in this paper using PipeMaster: Coluber_fasta_files_no_og_filtered_by_pi_M30.zip