DOI: 10.5061/dryad.dv41ns1wm
title: Resolving spatial complexities of hybridization in the context of the gray zone of speciation in North American ratsnakes (Pantherophis obsoletus complex)

description: Inferring the history of divergence between species in a framework that
 permits the presence of gene flow has been crucial for characterizing the
 “gray zone” of speciation, which is the period of time where lineages have
 diverged but have not yet achieved strict reproductive isolation. However,
 estimates of both divergence times and rates of gene flow often ignore
 spatial information, for example when considering the location and width
 of hybrid zones with respect to changes in environment between lineages.
 To connect phylogeographic estimates of lineage structure, migration,
 historical demography, and timing of divergence with hybrid zone dynamics,
 we used population genomic data from the North American ratsnake complex
 (Pantherophis obsoletus). We examined the spatial context of
 diversification by linking migration and timing of divergence to the
 location and widths of hybrid zones. Artificial neural network approaches
 were applied to understand how landscape features and past climate have
 influenced population genetic structure among these lineages. We found
 that rates of migration between lineages were associated with the overall
 width of hybrid zones. Timing of divergence was not related to migration
 rate or hybrid zone width across species pairs but may be related to the
 number of alleles weakly introgressing through hybrid zones. This research
 underscores how incomplete reproductive isolation can be better understood
 by considering differential allelic introgression and the effects of
 historical and contemporary landscape features on the formation of
 lineages as well as overall genomic estimates of migration rates through
 time.
description: <strong>Supporting Information Material 1</strong>:
 Supplemental Methods and Results Data S1. All
 <i>Pantherophis obsoletus</i> samples with locality
 information sequenced. Data S2. R code for estimating
 groupings, admixture and locus clines, and RDA and ANN estimates of
 ecological and spatial predictors of genetic variation.
 Data S3. VCF files for use with R code. Data
 S4. Locality and sample data formatted for use with R.
 Data S5. Unfiltered Fasta files. Geographic
 Localities R scripts
 <strong>Supporting Information Material 1</strong>:
 Additional Methods Table S1 – Priors and summary stats
 for PipeMaster; estimates of migration, timing of divergence, and
 historical demography Table S2 – PHRAPL Results
 (<i>open with R read.table() or Excel</i>)
 Fig. S1 – Delimiting populations using sparse nonnegative matrix
 factorization (SNMF) and spatial Principal Component analysis (sPCA)
 showing the location of four geographically distinct lineages.
 Fig. S2 – DAPC and TESS estimates of population structure over K
 = 2 to 5. Fig. S3 – PipeMaster model fit of observed
 data to simulations under IM, IMD, and IMD-LGM  models for
 PC1-PC10. Fig. S4 – Expansion times estimated from
 PipeMaster for all adjacent taxon pairs. Fig. S5–
 Results from PipeMaster after removing hybrids showing estimates and
 directionality of gene flow (A), divergence times between groups and taxon
 pairs and the Mississippi River (<i>P.alleghaniensis/
 P.spiloides</i> vs <i>P.obsoletus/P.bairdi</i>) (B), and
 changes in population sizes over time (C). Fig. S6 –
 Prediction of cline width under neutrality (black line through time) given
 divergence times for each species pair: A) <i>Pantherophis
 alleghaniensis/P. spiloides</i>, B) <i>P. spiloides/P.
 obsoletus</i>, and C) <i>P. obsoletus/P. bairdi.
 </i>Colored vertical lines represent times of divergence between
 species pairs and horizontal colored lines indicate actual cline
 widths.