DOI: 10.5061/dryad.4qs50
title: Data from: The biogeography of deep time phylogenetic reticulation

description: Most phylogenies are typically represented as purely bifurcating. However,
 as genomic data has become more common in phylogenetic studies, it is not
 unusual to find reticulation among terminal lineages or among internal
 nodes (deep time reticulation; DTR). In these situations, gene flow must
 have happened in the same or adjacent geographic areas for these DTRs to
 have occurred and therefore biogeographic reconstruction should provide
 similar area estimates for parental nodes, provided extinction or
 dispersal has not eroded these patterns. We examine the phylogeny of the
 widely distributed New World kingsnakes (Lampropeltis), determine if DTR
 is present in this group, and estimate the ancestral area for
 reticulation. Importantly, we develop a new method that uses coalescent
 simulations in a machine learning framework to show conclusively that this
 phylogeny is best represented as reticulating at deeper time. Using joint
 probabilities of ancestral area reconstructions on the bifurcating
 parental lineages from the reticulating node, we show that this
 reticulation likely occurred in northwestern Mexico/southwestern US and
 subsequently led to the diversification of the Mexican kingsnakes. This
 region has been previously identified as an area important for
 understanding speciation and secondary contact with gene flow in snakes
 and other squamates. This research shows that phylogenetic reticulation is
 common, even in well-studied groups, and that the geographic scope of
 ancient hybridization is recoverable.
description: Supplementary Fig.
 S1.Work flow for estimating the phylogenetic and biogeographic location of
 reticulation via SnaQ and custom neural network
 simulators.Work flow for estimating
 the phylogenetic and biogeographic location of reticulation via SnaQ and
 custom neural network simulators.FigS1.Flowchart.pdfSupplementary Fig. S2. Slope statistics generated using the capushe R package showing Maximal Jump (A) and AIC (B) against the number of hybrid nodes per Lampropeltis phylogeny from SNaQ.Slope statistics generated using the capushe R package showing Maximal Jump (A) and AIC (B) against the number of hybrid nodes per Lampropeltis phylogeny from SNaQ.FigS2. Slope Stats.pdfSupplementary Fig. S3. Reticulating phylogenies of Lampropeltis from SNaQ for hybrid node numbers from 2-10. Note that hybrid nodes 0,1 are shown in Fig.1Reticulating phylogenies of Lampropeltis from SNaQ for hybrid node numbers from 2-10. Note that hybrid nodes 0,1 are shown in Fig.1FigS3_H2-H10.pdfSupplementary Table. S1. Results from SNaQ showing the pseudolikelihoods (complexity) for each model (number of hybrid nodes) along with penalty used as inputs for the R package capushe.Results from SNaQ showing the pseudolikelihoods (complexity) for each model (number of hybrid nodes) along with penalty used as inputs for the R package capushe.TableS1.likelihoods_lamps_hybrid.txtSupplementary Table. S2. Results from BioGeoBEARS showing AIC for each biogeographic model estimating ancestral area for reticulating phylogenies broken into parental major (Tree 1) and minor sister clades (Tree 2) of Lampropeltis.Results from BioGeoBEARS showing AIC for each biogeographic model estimating ancestral area for reticulating phylogenies broken into parental major (Tree 1) and minor sister clades (Tree 2) of Lampropeltis.Table_S2.BioGeoBears_results.txtData 1. Lampropeltis_NGSGenomic Data for LampropeltisLampropelist_NGS.zipData 2. Georeferenced data for all species of Lampropeltis used for modeling range.Georeferenced data for all species of Lampropeltis used for modeling range.GEOREFERENCED.txtData 3. BioGeoBEARS code for estimating ancestral area in Lampropeltis.BioGeoBEARS code for estimating ancestral area in Lampropeltis.BioGEOBEARS_Tutorial_Lamps .RData 4. Geographic areas used for BioGeoBEARS generated from InfoMAP Bioregions.Geographic areas used for BioGeoBEARS generated from InfoMAP Bioregions.Biogeo_Lamps.txtData 5. Bifurcating tree where the hybrid clade is sister to the major edge used to estimate ancestral area in BioGeoBEARS (Tree 1).Bifurcating tree where the hybrid clade is sister to the major edge used to estimate ancestral area in BioGeoBEARS (Tree 1).Tree1_BeastData 6. Bifurcating tree where the hybrid clade is sister to the minor edge used to estimate ancestral area in BioGeoBEARS (Tree 2).Bifurcating tree where the hybrid clade is sister to the minor edge used to estimate ancestral area in BioGeoBEARS (Tree 2).Tree2_BeastData 7. XML code for estimating a dated phylogeny under the topological constraint where the hybrid clade is sister to the bifurcating major sister clade (Tree 1).XML code for estimating a dated phylogeny under the topological constraint where the hybrid clade is sister to the bifurcating major sister clade (Tree 1).Lamp_concatenated_1.xmlData 8. XML code for estimating a dated phylogeny under the topological constraint where the hybrid clade is sister to the minor sister clade (Tree 2).XML code for estimating a dated phylogeny under the topological constraint where the hybrid clade is sister to the minor sister clade (Tree 2).Lamp_concatenated_2.xml