DOI: 10.5061/dryad.xpnvx0kd9
title: Ecological divergence and the history of gene flow in the Nearctic milksnakes (Lampropeltis triangulum complex)

description: Many phylogeographic studies on species with large ranges have found
 genetic-geographic structure associated with changes in habitat and
 physical barriers to gene flow. These studies may conclude absence of
 population structure, lineage structure that indicates unique species have
 been discovered, or suggest more research is needed prior to delimitation.
 Comparative risks of delimiting species incorrectly or failing to delimit
 species are usually not weighed and a more detailed return to these
 problems with more data often does not occur. With genomic data and better
 modeling capabilities we can more clearly delimit species by understanding
 causes of speciation with respect to biogeography and migration between
 lineages, the location of hybrid zones in relationship to the ecology of
 parental lineages, and differential introgression of genes between taxa.
 Here we examine the origins of three Nearctic milksnakes (Lampropeltis
 elapsoides, L. triangulum, and L. gentilis) using genomic-scale data to
 better understand the diversification of these taxa previously delimited
 based on a smaller genetic dataset. Methods that reject pure isolation by
 distance in favor of environmentally driven reduction in gene flow clearly
 indicate that all three lineages should continue to be recognized as
 unique species. These results underscore conspicuous environmental changes
 that occur between the sister-taxa forming due to changes in habitat from
 the Great Plains (GP) to the forested regions of the Eastern Nearctic
 (ENA). This area has been recognized for turnover of reptile and amphibian
 species but with few phylogeographic studies examining
 environmental-genetic structure in this region. We show that the two
 species meeting at the GP/ENA, L. triangulum and L. gentilis, likely
 formed in the mid-Pleistocene and have maintained partial reproductive
 isolation over much of this time, exchanging fewer than one
 migrant/generation, and formed a hybrid zone with differential
 introgression of loci. We also show that when L. triangulum and L.
 gentilis are each in contact with the much older L. elapsoides, some
 limited gene flow has occurred. We conclude that phylogenetic reticulation
 in this genus, and likely for many other taxa, is common across throughout
 time. Furthermore, the application of the biological species concept to
 the whole genome will give rise to grave misunderstandings of the
 complexities of how species form and remain unique even in the face of
 gene flow.
description: <b><i>Electronic Supplementary
 Figures</i></b> Fig. S1. Illustration of
 the six historical demographic models: IM - Isolation with migration model
 with constant population size; IMD - isolation with migration model with
 one demographic change in each species; IMBott - isolation with migration
 model with two demographic changes in each species generating a
 demographic bottleneck history; IM-sc - Isolation with a secondary contact
 migration (following the last glacial maximum) model with constant
 population size; IMD-sc - isolation with secondary contact (following the
 last glacial maximum) migration model with one demographic change in each
 species; IMBott-sc - isolation with a secondary contact migration
 (following the last glacial maximum) model with two demographic changes in
 each species generating a demographic bottleneck history.
 Fig. S2. Population cluster estimation using TESS3r for K = 4,
 showing groupings corresponding to <i>L. annulata
 </i>(purple), <i>L. gentilis</i> (green), <i>L.
 triangulum </i>(red) and <i>L. elapsoides</i>
 (blue). Fig. S3. DAPC estimates of population structure
 considering lowest BIC over different GBS sequence assembly filtering
 strategies with average missing data per individual, number of
 individuals, and number of loci ranging from 17-48%, 129-159,137-3391,
 respectively. Fig S4.  TESS3r estimates of population
 structure considering lowest BIC over different GBS sequence assembly
 filtering strategies with average missing data per individual, number of
 individuals, and number of loci ranging from 17-48%, 129-159,137-3391,
 respectively. Fig. S5. Predictions of group membership
 given ancestral coefficients, where <i>L. gentilis</i> (blue),
 <i>L. triangulum </i>(green) and <i>L.
 elapsoides</i> (red) are overwhelmingly supported relative to evenly
 distributed coefficients (yellow) estimated from TESS3r among all three
 taxa at southern end of the Mississippi River in Louisiana.
 Fig. S6. Fit of observed data to different historical demographic
 models over principal component space. Fig. S7. Using
 40 loci between <i>Lampropeltis triangulum </i>and <i>L.
 elapsoides</i> and nine loci for <i>Lampropeltis triangulum
 </i>and<i> L. gentilis </i>falling below neutral cline
 widths showing (A) DAPC spatial predictions for two groups, (B)
 discriminant function distributions of those groups, and (C) distributions
 of ancestral coefficients from TESS3r. Fig. S8 –
 Estimation of cline width and Fst for each locus for both species-pair
 comparisons: <i>L. gentilis</i> x <i>L. triangulum
 </i>and <i>L.triangulum </i> x <i>L.
 elapsoides</i>.  
 <b><i>Electronic Supplementary
 Data</i></b> Data. D1. List of samples and
 localities used for this research. Data. D2. Fasta
 files generated for <i>Lampropeltis triangulum, L.
 gentilis</i> and <i>L. elapsoides</i> from
 ipyrad. Data. D3. VCF file generated for
 <i>Lampropeltis triangulum, L. gentilis</i> and <i>L.
 elapsoides</i> from ipyrad. Data. D4. R code for
 estimating lineage structure, cline widths from admixture proportions,
 cline widths for loci, and redundancy analyses (RDA) and artificial neural
 networks (ANN) to examine the effect of space and ecology on genetic
 structure of <i>Lampropeltis triangulum, L. gentilis</i> and
 <i>L. elapsoides.</i> Data. D5. Priors used
 for simulation of historical demographic parameters in PipeMaster for
 <i>Lampropeltis triangulum, L. gentilis</i> and <i>L.
 elapsoides.</i>
description: Please visit this link to view the most updated version of this
 data submission: https://doi.org/10.5061/dryad.g79cnp5qm