DOI: 10.5061/dryad.7hs34mj
title: Data from: The multispecies coalescent over-splits species in the case of geographically widespread taxa

description: Many recent species delimitation studies rely exclusively on limited
 analyses of genetic data analyzed under the multispecies coalescent (MSC)
 model, and results from these studies often are regarded as conclusive
 support for taxonomic changes. However, most MSC-based species
 delimitation methods have well-known and often unmet assumptions.
 Uncritical application of these genetic-based approaches (without due
 consideration of sampling design, the effects of a priori group
 designations, isolation by distance, cytoplasmic–nuclear mismatch, and
 population structure) can lead to over-splitting of species. Here, we
 argue that in many common biological scenarios, researchers must be
 particularly cautious regarding these limitations, especially in cases of
 well-studied, geographically variable, and parapatrically-distributed
 species complexes. We consider these points with respect to a historically
 controversial species group, the American milksnakes (Lampropeltis
 triangulum complex), using genetic data from a recent analysis (Ruane et
 al. 2014; Syst. Biol. 63:231-250). We show that over-reliance on the
 program BPP, without adequate consideration of its assumptions and of
 sampling limitations, resulted in over-splitting of species in this study.
 Several of the hypothesized species of milksnakes instead appear to
 represent arbitrary slices of continuous geographic clines. We conclude
 that the best available evidence supports three, rather than seven,
 species within this complex. More generally, we recommend that
 coalescent-based species delimitation studies incorporate thorough
 analyses of geographic variation and carefully examine putative contact
 zones among delimited species before making taxonomic changes.
description: # Data from: The multispecies coalescent over-splits species in the case
 of geographically widespread taxa Dataset DOI:
 [10.5061/dryad.7hs34mj](10.5061/dryad.7hs34mj) ## Description of the data
 and file structure This repository contains data files for: **Chambers EA
 & Hillis DM. (2020) The multispecies coalescent over-splits species in
 the case of geographically widespread taxa.** ***Systematic Biology
 69(1):184–193***, **[DOI](https://doi.org/10.1093/sysbio/syz042).** This
 paper re-examines species delimitation in the American milksnake species
 complex (*Lampropeltis triangulum*). All raw data and input files can be
 found on Dryad. ## DRYAD FILES: DATA FILES --- ### Naming Conventions *
 **TAXONOMY**: Files are named according to taxonomic groups contained with
 them. * **trigentalt** Includes samples belonging to triangulum, gentilis,
 and alterna. * **trigent** Includes samples belonging to L. triangulum and
 gentilis. * **DATASETS**: Files for analyses are named according the
 number of individuals within them. * **complex89** Refers to when 89
 individuals from the L. triangulum species complex were analyzed. *
 **all124** Refers to when all 124 individuals were analyzed. ### Data
 Structure Supplementary data files are organized in directories
 corresponding to which part of the analysis they correspond to: *
 `BEAST.zip` contains files associated with reconstructing gene trees and
 genetic distance matrices * `BPP.zip` contains files associated with BPP
 analyses * `PHASE.zip` contains files associated with phasing haplotypes *
 `Structurama.zip` contains files associated with Structurama analyses ```
 Chambersetal_PNAS_SuppMaterials/ |-- BEAST/ | | |-- Cytb_tree/ # Files
 relevant to generating cytb tree | | | |-- Cytb_full_trigentalt.xml # xml
 output file for cytb tree | | | |-- Cytb_full_trigentalt.trees # tree file
 for cytb tree | | | |-- Cytb_full_trigentalt.ops # ops file for cytb tree
 | | | |-- Cytb_full_trigentalt.nex # Nexus file for cytb tree | | | |--
 Cytb_full_trigentalt.log # log file for cytb tree | | | |--
 Cytb_full_trigentalt_MJruleconsensus.tre # majority rule consensus tree
 file for cytb tree | | | |-- Cytb_full_trigentalt_MaxCladeCred.trees.pdf #
 max clade credibility tree file for cytb tree (pdf) | | | |--
 Cytb_full_trigentalt_MaxCladeCred.trees # max clade credibility tree file
 for cytb tree (tree format) | | | |-- Nuclear_trees/ # Files relevant to
 generating nuclear locus tree | | | |-- Input_output_files/ # Input and
 output files for generating nuclear trees | | | | |-- COMPLETE 2CL3.nex #
 Nexus input file for nuclear gene 2CL3 | | | | |-- COMPLETE 2CL3.trees #
 Output tree file for nuclear gene 2CL3 | | | | |-- COMPLETE 2CL4.nex #
 Nexus input file for nuclear gene 2CL4 | | | | |-- COMPLETE 2CL4.trees #
 Output tree file for nuclear gene 2CL4 | | | | |-- COMPLETE 2CL8.nex #
 Nexus input file for nuclear gene 2CL8 | | | | |-- COMPLETE 2CL8.trees #
 Output tree file for nuclear gene 2CL8 | | | | |-- COMPLETE CL4.nex #
 Nexus input file for nuclear gene CL4 | | | | |-- COMPLETE CL4.trees #
 Output tree file for nuclear gene CL4 | | | | |-- COMPLETE GAD15.nex #
 Nexus input file for nuclear gene GAD15 | | | | |-- COMPLETE GAD15.trees #
 Output tree file for nuclear gene GAD15 | | | | |-- COMPLETE LATCL.nex #
 Nexus input file for nuclear gene LATCL | | | | |-- COMPLETE LATCL.trees #
 Output tree file for nuclear gene LATCL | | | | |-- COMPLETE NAV56.nex #
 Nexus input file for nuclear gene NAV56 | | | | |-- COMPLETE NAV56.trees #
 Output tree file for nuclear gene NAV56 | | | | |-- COMPLETE NT3.nex #
 Nexus input file for nuclear gene NT3 | | | | |-- COMPLETE NT3.trees #
 Output tree file for nuclear gene NT3 | | | | |-- COMPLETE PRLR.nex #
 Nexus input file for nuclear gene PRLR | | | | |-- COMPLETE PRLR.trees #
 Output tree file for nuclear gene PRLR | | | | |-- COMPLETE SPTBN1.nex #
 Nexus input file for nuclear gene SPTBN1 | | | | |-- COMPLETE SPTBN1.trees
 # Output tree file for nuclear gene SPTBN1 | | | | |-- COMPLETE VIM56.nex
 # Nexus input file for nuclear gene VIM56 | | | | |-- COMPLETE VIM56.trees
 # Output tree file for nuclear gene VIM56 | | | |--
 Max_clade_credibility_trees/ # Maximum clade credibility output trees from
 nuclear tree analysis | | | | |-- COMPLETE_2CL3_output.trees # Max clade
 cred tree for nuclear gene 2CL3 | | | | |-- COMPLETE_2CL4_output.trees #
 Max clade cred tree for nuclear gene 2CL4 | | | | |--
 COMPLETE_2CL8_output.trees # Max clade cred tree for nuclear gene 2CL8 | |
 | | |-- COMPLETE_CL4_output.trees # Max clade cred tree for nuclear gene
 CL4 | | | | |-- COMPLETE_GAD15_output.trees # Max clade cred tree for
 nuclear gene GAD15 | | | | |-- COMPLETE_LATCL_output.trees # Max clade
 cred tree for nuclear gene LATCL | | | | |-- COMPLETE_NAV56_output.trees #
 Max clade cred tree for nuclear gene NAV56 | | | | |--
 COMPLETE_NT3_output.trees # Max clade cred tree for nuclear gene NT3 | | |
 | |-- COMPLETE_PRLR_output.trees # Max clade cred tree for nuclear gene
 PRLR | | | | |-- COMPLETE_SPTBN1_output.trees # Max clade cred tree for
 nuclear gene SPTBN1 | | | | |-- COMPLETE_VIM56_output.trees # Max clade
 cred tree for nuclear gene VIM56 | | | |-- MJrule_consensus_trees/ #
 Majority rule consensus output trees from nuclear tree analysis | | | |
 |-- 2CL3_consensus.tre # Consensus tree for nuclear gene 2CL3 (tree file
 format) | | | | |-- 2CL4_consensus.tre # Consensus tree for nuclear gene
 2CL4 (tree file format) | | | | |-- 2CL8_consensus.tre # Consensus tree
 for nuclear gene 2CL8 (tre file format) | | | | |-- 2CL8_consensus.trees #
 Consensus tree for nuclear gene 2CL8 (trees file format) | | | | |--
 CL4_consensus.tre # Consensus tree for nuclear gene CL4 (tree file format)
 | | | | |-- GAD15_consensus.tre # Consensus tree for nuclear gene GAD15
 (tree file format) | | | | |-- LATCL_consensus.tre # Consensus tree for
 nuclear gene LATCL (tree file format) | | | | |-- NAV56_consensus.tre #
 Consensus tree for nuclear gene NAV56 (tree file format) | | | | |--
 NT3_consensus.tre # Consensus tree for nuclear gene NT3 (tree file format)
 | | | | |-- PRLR_consensus.tre # Consensus tree for nuclear gene PRLR
 (tree file format) | | | | |-- SPTBN1_consensus.tre # Consensus tree for
 nuclear gene SPTBN1 (tree file format) | | | | |-- VIM56_consensus.tre #
 Consensus tree for nuclear gene VIM56 (tree file format) | | | | |--
 Consens_2CL3.pdf # Consensus tree for nuclear gene 2CL3 (PDF file format)
 | | | | |-- Consens_2CL4.pdf # Consensus tree for nuclear gene 2CL4 (PDF
 file format) | | | | |-- Consens_2CL8.pdf # Consensus tree for nuclear
 gene 2CL8 (PDF file format) | | | | |-- Consens_CL4.pdf # Consensus tree
 for nuclear gene CL4 (PDF file format) | | | | |-- Consens_GAD15.pdf #
 Consensus tree for nuclear gene GAD15 (PDF file format) | | | | |--
 Consens_LATCL.pdf # Consensus tree for nuclear gene LATCL (PDF file
 format) | | | | |-- Consens_NAV56.pdf # Consensus tree for nuclear gene
 NAV56 (PDF file format) | | | | |-- Consens_NT3.pdf # Consensus tree for
 nuclear gene NT3 (PDF file format) | | | | |-- Consens_PRLR.pdf #
 Consensus tree for nuclear gene PRLR (PDF file format) | | | | |--
 Consens_SPTBN1.pdf # Consensus tree for nuclear gene SPTBN1 (PDF file
 format) | | | | |-- Consens_VIM56.pdf # Consensus tree for nuclear gene
 VIM56 (PDF file format) | | | | |-- Consensus_gene_trees.pdf # Consensus
 tree for all nuclear genes (PDF file format) | |-- BPP/ # All input and
 output files relevant to BPP analysis | |-- Unguided_BPP/ # Files relevant
 to running BPP unguided (no guide tree) on all individuals | | |--
 allspecies.Imap.txt # Imap population assignment for BPP | | |--
 Lampropeltis.txt # Input data in Phylip format | | |-- unguided_mcmc.txt #
 MCMC output from BPP | | |-- unguided_out.txt # Output log from BPP | |
 |-- unguided.bpp.ctl # Input control file for BPP | |--
 Unguided_trigentanalysis/ # Files relevant to running BPP unguided (no
 guide tree) on only triangulum and gentilis | | |-- trigent1alt.Imap.txt #
 Population assignment for first grouping of tri and gent | | |--
 trigent2alt.Imap.txt # Population assignment for second grouping of tri
 and gent | | |-- trigent3alt.Imap.txt # Population assignment for third
 grouping of tri and gent | | |-- trigent4alt.Imap.txt # Population
 assignment for fourth grouping of tri and gent | | |--
 trigent5alt.Imap.txt # Population assignment for fifth grouping of tri and
 gent | | |-- trigentalt.txt # Population assignment for Ruane et al.
 (2014) grouping of tri and gent | | |-- unguided_trigent_1_alt.bpp.ctl #
 BPP control file for for first grouping of tri and gent | | |--
 unguided_trigent_2_alt.bpp.ctl # BPP control file for for second grouping
 of tri and gent | | |-- unguided_trigent_3_alt.bpp.ctl # BPP control file
 for for third grouping of tri and gent | | |--
 unguided_trigent_4_alt.bpp.ctl # BPP control file for for fourth grouping
 of tri and gent | | |-- unguided_trigent_5_alt.bpp.ctl # BPP control file
 for for fifth grouping of tri and gent | |-- PHASE/ # All input and output
 files relevant to phasing data | |-- all124/ # Phasing for all individuals
 in analysis (n=124) | | |-- PHASE_input/ # Input files for phasing | | |
 |-- 2CL3.inp # PHASE input file for nuclear gene 2CL3 | | | |-- 2CL4.inp #
 PHASE input file for nuclear gene 2CL4 | | | |-- 2CL8.inp # PHASE input
 file for nuclear gene 2CL8 | | | |-- CL4.inp # PHASE input file for
 nuclear gene CL4 | | | |-- GAD15.inp # PHASE input file for nuclear gene
 GAD15 | | | |-- LATCL.inp # PHASE input file for nuclear gene LATCL | | |
 |-- NAV56.inp # PHASE input file for nuclear gene NAV56 | | | |-- NT3.inp
 # PHASE input file for nuclear gene NT3 | | | |-- PRLR.inp # PHASE input
 file for nuclear gene PRLR | | | |-- SPTBN1.inp # PHASE input file for
 nuclear gene SPTBN1 | | | |-- VIM56.inp # PHASE input file for nuclear
 gene VIM56 | | |-- PHASE_output/ # Output files for phasing | | | |--
 2CL3.inp # Input file provided to PHASE for nuclear gene 2CL3 | | | |--
 2CL3.out # Output file generated by PHASE for nuclear gene 2CL3 | | | |--
 2CL3.out_freqs # Haplotype frequency estimates for nuclear gene 2CL3 | | |
 |-- 2CL3.out_hbg # Haplotype block groupings for nuclear gene 2CL3 | | |
 |-- 2CL3.out_monitor # Progress monitor for phasing nuclear gene 2CL3 | |
 | |-- 2CL3.out_pairs # Pairwise probabilities for nuclear gene 2CL3 | | |
 |-- 2CL3.out_probs # Per-ind haplotype probabilities for nuclear gene 2CL3
 | | | |-- 2CL3.out_recom # Recombination rate estimates for nuclear gene
 2CL3 | | | |-- 2CL4.inp # Input file provided to PHASE for nuclear gene
 2CL4 | | | |-- 2CL4.out # Output file generated by PHASE for nuclear gene
 2CL4 | | | |-- 2CL4.out_freqs # Haplotype frequency estimates for nuclear
 gene 2CL4 | | | |-- 2CL4.out_hbg # Haplotype block groupings for nuclear
 gene 2CL4 | | | |-- 2CL4.out_monitor # Progress monitor for phasing
 nuclear gene 2CL4 | | | |-- 2CL4.out_pairs # Pairwise probabilities for
 nuclear gene 2CL4 | | | |-- 2CL4.out_probs # Per-ind haplotype
 probabilities for nuclear gene 2CL4 | | | |-- 2CL4.out_recom #
 Recombination rate estimates for nuclear gene 2CL4 | | | |-- 2CL8.inp #
 Input file provided to PHASE for nuclear gene 2CL8 | | | |-- 2CL8.out #
 Output file generated by PHASE for nuclear gene 2CL8 | | | |--
 2CL8.out_freqs # Haplotype frequency estimates for nuclear gene 2CL8 | | |
 |-- 2CL8.out_hbg # Haplotype block groupings for nuclear gene 2CL8 | | |
 |-- 2CL8.out_monitor # Progress monitor for phasing nuclear gene 2CL8 | |
 | |-- 2CL8.out_pairs # Pairwise probabilities for nuclear gene 2CL8 | | |
 |-- 2CL8.out_probs # Per-ind haplotype probabilities for nuclear gene 2CL8
 | | | |-- 2CL8.out_recom # Recombination rate estimates for nuclear gene
 2CL8 | | | |-- CL4.inp # Input file provided to PHASE for nuclear gene CL4
 | | | |-- CL4.out # Output file generated by PHASE for nuclear gene CL4 |
 | | |-- CL4.out_freqs # Haplotype frequency estimates for nuclear gene CL4
 | | | |-- CL4.out_hbg # Haplotype block groupings for nuclear gene CL4 | |
 | |-- CL4.out_monitor # Progress monitor for phasing nuclear gene CL4 | |
 | |-- CL4.out_pairs # Pairwise probabilities for nuclear gene CL4 | | |
 |-- CL4.out_probs # Per-ind haplotype probabilities for nuclear gene CL4 |
 | | |-- CL4.out_recom # Recombination rate estimates for nuclear gene CL4
 | | | |-- GAD15.inp # Input file provided to PHASE for nuclear gene GAD15
 | | | |-- GAD15.out # Output file generated by PHASE for nuclear gene
 GAD15 | | | |-- GAD15.out_freqs # Haplotype frequency estimates for
 nuclear gene GAD15 | | | |-- GAD15.out_hbg # Haplotype block groupings for
 nuclear gene GAD15 | | | |-- GAD15.out_monitor # Progress monitor for
 phasing nuclear gene GAD15 | | | |-- GAD15.out_pairs # Pairwise
 probabilities for nuclear gene GAD15 | | | |-- GAD15.out_probs # Per-ind
 haplotype probabilities for nuclear gene GAD15 | | | |-- GAD15.out_recom #
 Recombination rate estimates for nuclear gene GAD15 | | | |-- LATCL.inp #
 Input file provided to PHASE for nuclear gene LATCL | | | |-- LATCL.out #
 Output file generated by PHASE for nuclear gene LATCL | | | |--
 LATCL.out_freqs # Haplotype frequency estimates for nuclear gene LATCL | |
 | |-- LATCL.out_hbg # Haplotype block groupings for nuclear gene LATCL | |
 | |-- LATCL.out_monitor # Progress monitor for phasing nuclear gene LATCL
 | | | |-- LATCL.out_pairs # Pairwise probabilities for nuclear gene LATCL
 | | | |-- LATCL.out_probs # Per-ind haplotype probabilities for nuclear
 gene LATCL | | | |-- LATCL.out_recom # Recombination rate estimates for
 nuclear gene LATCL | | | |-- NAV56.inp # Input file provided to PHASE for
 nuclear gene NAV56 | | | |-- NAV56.out # Output file generated by PHASE
 for nuclear gene NAV56 | | | |-- NAV56.out_freqs # Haplotype frequency
 estimates for nuclear gene NAV56 | | | |-- NAV56.out_hbg # Haplotype block
 groupings for nuclear gene NAV56 | | | |-- NAV56.out_monitor # Progress
 monitor for phasing nuclear gene NAV56 | | | |-- NAV56.out_pairs #
 Pairwise probabilities for nuclear gene NAV56 | | | |-- NAV56.out_probs #
 Per-ind haplotype probabilities for nuclear gene NAV56 | | | |--
 NAV56.out_recom # Recombination rate estimates for nuclear gene NAV56 | |
 | |-- NT3.inp # Input file provided to PHASE for nuclear gene NT3 | | |
 |-- NT3.out # Output file generated by PHASE for nuclear gene NT3 | | |
 |-- NT3.out_freqs # Haplotype frequency estimates for nuclear gene NT3 | |
 | |-- NT3.out_hbg # Haplotype block groupings for nuclear gene NT3 | | |
 |-- NT3.out_monitor # Progress monitor for phasing nuclear gene NT3 | | |
 |-- NT3.out_pairs # Pairwise probabilities for nuclear gene NT3 | | | |--
 NT3.out_probs # Per-ind haplotype probabilities for nuclear gene NT3 | | |
 |-- NT3.out_recom # Recombination rate estimates for nuclear gene NT3 | |
 | |-- PRLR.inp # Input file provided to PHASE for nuclear gene PRLR | | |
 |-- PRLR.out # Output file generated by PHASE for nuclear gene PRLR | | |
 |-- PRLR.out_freqs # Haplotype frequency estimates for nuclear gene PRLR |
 | | |-- PRLR.out_hbg # Haplotype block groupings for nuclear gene PRLR | |
 | |-- PRLR.out_monitor # Progress monitor for phasing nuclear gene PRLR |
 | | |-- PRLR.out_pairs # Pairwise probabilities for nuclear gene PRLR | |
 | |-- PRLR.out_probs # Per-ind haplotype probabilities for nuclear gene
 PRLR | | | |-- PRLR.out_recom # Recombination rate estimates for nuclear
 gene PRLR | | | |-- SPTBN1.inp # Input file provided to PHASE for nuclear
 gene SPTBN1 | | | |-- SPTBN1.out # Output file generated by PHASE for
 nuclear gene SPTBN1 | | | |-- SPTBN1.out_freqs # Haplotype frequency
 estimates for nuclear gene SPTBN1 | | | |-- SPTBN1.out_hbg # Haplotype
 block groupings for nuclear gene SPTBN1 | | | |-- SPTBN1.out_monitor #
 Progress monitor for phasing nuclear gene SPTBN1 | | | |--
 SPTBN1.out_pairs # Pairwise probabilities for nuclear gene SPTBN1 | | |
 |-- SPTBN1.out_probs # Per-ind haplotype probabilities for nuclear gene
 SPTBN1 | | | |-- SPTBN1.out_recom # Recombination rate estimates for
 nuclear gene SPTBN1 | | | |-- VIM56.inp # Input file provided to PHASE for
 nuclear gene VIM56 | | | |-- VIM56.out # Output file generated by PHASE
 for nuclear gene VIM56 | | | |-- VIM56.out_freqs # Haplotype frequency
 estimates for nuclear gene VIM56 | | | |-- VIM56.out_hbg # Haplotype block
 groupings for nuclear gene VIM56 | | | |-- VIM56.out_monitor # Progress
 monitor for phasing nuclear gene VIM56 | | | |-- VIM56.out_pairs #
 Pairwise probabilities for nuclear gene VIM56 | | | |-- VIM56.out_probs #
 Per-ind haplotype probabilities for nuclear gene VIM56 | | | |--
 VIM56.out_recom # Recombination rate estimates for nuclear gene VIM56 | |
 |-- seqPHASE_input/ # Input files for helper tool seqPHASE | | | |--
 lampropeltis_2CL3_heterozygotes.fasta # Heterozygous sites from nuclear
 gene 2CL3 | | | |-- lampropeltis_2CL3_homozygotes.fasta # Homozygous sites
 from nuclear gene 2CL3 | | | |-- lampropeltis_2CL4_heterozygotes.fasta #
 Heterozygous sites from nuclear gene 2CL4 | | | |--
 lampropeltis_2CL4_homozygotes.fasta # Homozygous sites from nuclear gene
 2CL4 | | | |-- lampropeltis_2CL8_heterozygotes.fasta # Heterozygous sites
 from nuclear gene 2CL8 | | | |-- lampropeltis_2CL8_homozygotes.fasta #
 Homozygous sites from nuclear gene 2CL8 | | | |--
 lampropeltis_CL4_heterozygotes.fasta # Heterozygous sites from nuclear
 gene CL4 | | | |-- lampropeltis_CL4_homozygotes.fasta # Homozygous sites
 from nuclear gene CL4 | | | |-- lampropeltis_GAD15_heterozygotes.fasta #
 Heterozygous sites from nuclear gene GAD15 | | | |--
 lampropeltis_GAD15_homozygotes.fasta # Homozygous sites from nuclear gene
 GAD15 | | | |-- lampropeltis_LATCL_heterozygotes.fasta # Heterozygous
 sites from nuclear gene LATCL | | | |--
 lampropeltis_LATCL_homozygotes.fasta # Homozygous sites from nuclear gene
 LATCL | | | |-- lampropeltis_NAV56_heterozygotes.fasta # Heterozygous
 sites from nuclear gene NAV56 | | | |--
 lampropeltis_NAV56_homozygotes.fasta # Homozygous sites from nuclear gene
 NAV56 | | | |-- lampropeltis_NT3_heterozygotes.fasta # Heterozygous sites
 from nuclear gene NT3 | | | |-- lampropeltis_NT3_homozygotes.fasta #
 Homozygous sites from nuclear gene NT3 | | | |--
 lampropeltis_PRLR_heterozygotes.fasta # Heterozygous sites from nuclear
 gene PRLR | | | |-- lampropeltis_PRLR_homozygotes.fasta # Homozygous sites
 from nuclear gene PRLR | | | |-- lampropeltis_SPTBN1_heterozygotes.fasta #
 Heterozygous sites from nuclear gene SPTBN1 | | | |--
 lampropeltis_SPTBN1_homozygotes.fasta # Homozygous sites from nuclear gene
 SPTBN1 | | | |-- lampropeltis_VIM56_heterozygotes.fasta # Heterozygous
 sites from nuclear gene VIM56 | | | |--
 lampropeltis_VIM56_homozygotes.fasta # Homozygous sites from nuclear gene
 VIM56 | |-- complex89/ # Phasing for only individuals within complex
 (n=89) | | |-- PHASE_input/ # Input files to PHASE for complex individuals
 | | | |-- lampropeltis_2CL3.inp # PHASE input file for complex inds for
 nuclear gene 2CL3 | | | |-- lampropeltis_2CL4.inp # PHASE input file for
 complex inds for nuclear gene 2CL4 | | | |-- lampropeltis_2CL8.inp # PHASE
 input file for complex inds for nuclear gene 2CL8 | | | |--
 lampropeltis_CL4.inp # PHASE input file for complex inds for nuclear gene
 CL4 | | | |-- lampropeltis_GAD15.inp # PHASE input file for complex inds
 for nuclear gene GAD15 | | | |-- lampropeltis_LATCL.inp # PHASE input file
 for complex inds for nuclear gene LATCL | | | |-- lampropeltis_NAV56.inp #
 PHASE input file for complex inds for nuclear gene NAV56 | | | |--
 lampropeltis_NT3.inp # PHASE input file for complex inds for nuclear gene
 NT3 | | | |-- lampropeltis_PRLR.inp # PHASE input file for complex inds
 for nuclear gene PRLR | | | |-- lampropeltis_SPTBN1.inp # PHASE input file
 for complex inds for nuclear gene SPTBN1 | | | |-- lampropeltis_VIM56.inp
 # PHASE input file for complex inds for nuclear gene VIM56 | | | |--
 triangulum_2CL3.inp # PHASE input file for triangulum only for nuclear
 gene 2CL3 | | | |-- triangulum_2CL4.inp # PHASE input file for triangulum
 only for nuclear gene 2CL4 | | | |-- triangulum_2CL8.inp # PHASE input
 file for triangulum only for nuclear gene 2CL8 | | | |--
 triangulum_CL4.inp # PHASE input file for triangulum only for nuclear gene
 CL4 | | | |-- triangulum_GAD15.inp # PHASE input file for triangulum only
 for nuclear gene GAD15 | | | |-- triangulum_LATCL.inp # PHASE input file
 for triangulum only for nuclear gene LATCL | | | |-- triangulum_NAV56.inp
 # PHASE input file for triangulum only for nuclear gene NAV56 | | | |--
 triangulum_NT3.inp # PHASE input file for triangulum only for nuclear gene
 NT3 | | | |-- triangulum_PRLR.inp # PHASE input file for triangulum only
 for nuclear gene PRLR | | | |-- triangulum_SPTBN1.inp # PHASE input file
 for triangulum only for nuclear gene SPTBN1 | | | |-- triangulum_VIM56.inp
 # PHASE input file for triangulum only for nuclear gene VIM56 | | | |--
 triangulum_2CL3.const # PHASE input file for triangulum only for nuclear
 gene 2CL3 to keep phase fixed | | | |-- triangulum_2CL4.const # PHASE
 input file for triangulum only for nuclear gene 2CL4 to keep phase fixed |
 | | |-- triangulum_2CL8.const # PHASE input file for triangulum only for
 nuclear gene 2CL8 to keep phase fixed | | | |-- triangulum_CL4.const #
 PHASE input file for triangulum only for nuclear gene CL4 to keep phase
 fixed | | | |-- triangulum_GAD15.const # PHASE input file for triangulum
 only for nuclear gene GAD15 to keep phase fixed | | | |--
 triangulum_LATCL.const # PHASE input file for triangulum only for nuclear
 gene LATCL to keep phase fixed | | | |-- triangulum_NAV56.const # PHASE
 input file for triangulum only for nuclear gene NAV56 to keep phase fixed
 | | | |-- triangulum_NT3.const # PHASE input file for triangulum only for
 nuclear gene NT3 to keep phase fixed | | | |-- triangulum_PRLR.const #
 PHASE input file for triangulum only for nuclear gene PRLR to keep phase
 fixed | | | |-- triangulum_SPTBN1.const # PHASE input file for triangulum
 only for nuclear gene SPTBN1 to keep phase fixed | | | |--
 triangulum_VIM56.const # PHASE input file for triangulum only for nuclear
 gene VIM56 to keep phase fixed | | | |-- triangulum_2CL3.known # PHASE
 input file for triangulum only for nuclear gene 2CL3 for known phased info
 | | | |-- triangulum_2CL4.known # PHASE input file for triangulum only for
 nuclear gene 2CL4 for known phased info | | | |-- triangulum_2CL8.known #
 PHASE input file for triangulum only for nuclear gene 2CL8 for known
 phased info | | | |-- triangulum_CL4.known # PHASE input file for
 triangulum only for nuclear gene CL4 for known phased info | | | |--
 triangulum_GAD15.known # PHASE input file for triangulum only for nuclear
 gene GAD15 for known phased info | | | |-- triangulum_LATCL.known # PHASE
 input file for triangulum only for nuclear gene LATCL for known phased
 info | | | |-- triangulum_NAV56.known # PHASE input file for triangulum
 only for nuclear gene NAV56 for known phased info | | | |--
 triangulum_NT3.known # PHASE input file for triangulum only for nuclear
 gene NT3 for known phased info | | | |-- triangulum_PRLR.known # PHASE
 input file for triangulum only for nuclear gene PRLR for known phased info
 | | | |-- triangulum_SPTBN1.known # PHASE input file for triangulum only
 for nuclear gene SPTBN1 for known phased info | | | |--
 triangulum_VIM56.known # PHASE input file for triangulum only for nuclear
 gene VIM56 for known phased info | | |-- PHASE_output/ # Output files from
 phasing for complex only | | | |-- lampropeltis_2CL3.inp # Input file
 provided to PHASE for nuclear gene 2CL3 for all inds in complex | | | |--
 lampropeltis_2CL3.out # Output file generated by PHASE for nuclear gene
 2CL3 for all inds in complex | | | |-- lampropeltis_2CL3.out_freqs #
 Haplotype frequency estimates for nuclear gene 2CL3 for all inds in
 complex | | | |-- lampropeltis_2CL3.out_hbg # Haplotype block groupings
 for nuclear gene 2CL3 for all inds in complex | | | |--
 lampropeltis_2CL3.out_monitor # Progress monitor for phasing nuclear gene
 2CL3 for all inds in complex | | | |-- lampropeltis_2CL3.out_pairs #
 Pairwise probabilities for nuclear gene 2CL3 for all inds in complex | | |
 |-- lampropeltis_2CL3.out_probs # Per-ind haplotype probabilities for
 nuclear gene 2CL3 for all inds in complex | | | |--
 lampropeltis_2CL3.out_recom # Recombination rate estimates for nuclear
 gene 2CL3 for all inds in complex | | | |-- lampropeltis_2CL4.inp # Input
 file provided to PHASE for nuclear gene 2CL4 for all inds in complex | | |
 |-- lampropeltis_2CL4.out # Output file generated by PHASE for nuclear
 gene 2CL4 for all inds in complex | | | |-- lampropeltis_2CL4.out_freqs #
 Haplotype frequency estimates for nuclear gene 2CL4 for all inds in
 complex | | | |-- lampropeltis_2CL4.out_hbg # Haplotype block groupings
 for nuclear gene 2CL4 for all inds in complex | | | |--
 lampropeltis_2CL4.out_monitor # Progress monitor for phasing nuclear gene
 2CL4 for all inds in complex | | | |-- lampropeltis_2CL4.out_pairs #
 Pairwise probabilities for nuclear gene 2CL4 for all inds in complex | | |
 |-- lampropeltis_2CL4.out_probs # Per-ind haplotype probabilities for
 nuclear gene 2CL4 for all inds in complex | | | |--
 lampropeltis_2CL4.out_recom # Recombination rate estimates for nuclear
 gene 2CL4 for all inds in complex | | | |-- lampropeltis_2CL8.inp # Input
 file provided to PHASE for nuclear gene 2CL8 for all inds in complex | | |
 |-- lampropeltis_2CL8.out # Output file generated by PHASE for nuclear
 gene 2CL8 for all inds in complex | | | |-- lampropeltis_2CL8.out_freqs #
 Haplotype frequency estimates for nuclear gene 2CL8 for all inds in
 complex | | | |-- lampropeltis_2CL8.out_hbg # Haplotype block groupings
 for nuclear gene 2CL8 for all inds in complex | | | |--
 lampropeltis_2CL8.out_monitor # Progress monitor for phasing nuclear gene
 2CL8 for all inds in complex | | | |-- lampropeltis_2CL8.out_pairs #
 Pairwise probabilities for nuclear gene 2CL8 for all inds in complex | | |
 |-- lampropeltis_2CL8.out_probs # Per-ind haplotype probabilities for
 nuclear gene 2CL8 for all inds in complex | | | |--
 lampropeltis_2CL8.out_recom # Recombination rate estimates for nuclear
 gene 2CL8 for all inds in complex | | | |-- lampropeltis_CL4.inp # Input
 file provided to PHASE for nuclear gene CL4 for all inds in complex | | |
 |-- lampropeltis_CL4.out # Output file generated by PHASE for nuclear gene
 CL4 for all inds in complex | | | |-- lampropeltis_CL4.out_freqs #
 Haplotype frequency estimates for nuclear gene CL4 for all inds in complex
 | | | |-- lampropeltis_CL4.out_hbg # Haplotype block groupings for nuclear
 gene CL4 for all inds in complex | | | |-- lampropeltis_CL4.out_monitor #
 Progress monitor for phasing nuclear gene CL4 for all inds in complex | |
 | |-- lampropeltis_CL4.out_pairs # Pairwise probabilities for nuclear gene
 CL4 for all inds in complex | | | |-- lampropeltis_CL4.out_probs # Per-ind
 haplotype probabilities for nuclear gene CL4 for all inds in complex | | |
 |-- lampropeltis_CL4.out_recom # Recombination rate estimates for nuclear
 gene CL4 for all inds in complex | | | |-- lampropeltis_GAD15.inp # Input
 file provided to PHASE for nuclear gene GAD15 for all inds in complex | |
 | |-- lampropeltis_GAD15.out # Output file generated by PHASE for nuclear
 gene GAD15 for all inds in complex | | | |-- lampropeltis_GAD15.out_freqs
 # Haplotype frequency estimates for nuclear gene GAD15 for all inds in
 complex | | | |-- lampropeltis_GAD15.out_hbg # Haplotype block groupings
 for nuclear gene GAD15 for all inds in complex | | | |--
 lampropeltis_GAD15.out_monitor # Progress monitor for phasing nuclear gene
 GAD15 for all inds in complex | | | |-- lampropeltis_GAD15.out_pairs #
 Pairwise probabilities for nuclear gene GAD15 for all inds in complex | |
 | |-- lampropeltis_GAD15.out_probs # Per-ind haplotype probabilities for
 nuclear gene GAD15 for all inds in complex | | | |--
 lampropeltis_GAD15.out_recom # Recombination rate estimates for nuclear
 gene GAD15 for all inds in complex | | | |-- lampropeltis_LATCL.inp #
 Input file provided to PHASE for nuclear gene LATCL for all inds in
 complex | | | |-- lampropeltis_LATCL.out # Output file generated by PHASE
 for nuclear gene LATCL for all inds in complex | | | |--
 lampropeltis_LATCL.out_freqs # Haplotype frequency estimates for nuclear
 gene LATCL for all inds in complex | | | |-- lampropeltis_LATCL.out_hbg #
 Haplotype block groupings for nuclear gene LATCL for all inds in complex |
 | | |-- lampropeltis_LATCL.out_monitor # Progress monitor for phasing
 nuclear gene LATCL for all inds in complex | | | |--
 lampropeltis_LATCL.out_pairs # Pairwise probabilities for nuclear gene
 LATCL for all inds in complex | | | |-- lampropeltis_LATCL.out_probs #
 Per-ind haplotype probabilities for nuclear gene LATCL for all inds in
 complex | | | |-- lampropeltis_LATCL.out_recom # Recombination rate
 estimates for nuclear gene LATCL for all inds in complex | | | |--
 lampropeltis_NAV56.inp # Input file provided to PHASE for nuclear gene
 NAV56 for all inds in complex | | | |-- lampropeltis_NAV56.out # Output
 file generated by PHASE for nuclear gene NAV56 for all inds in complex | |
 | |-- lampropeltis_NAV56.out_freqs # Haplotype frequency estimates for
 nuclear gene NAV56 for all inds in complex | | | |--
 lampropeltis_NAV56.out_hbg # Haplotype block groupings for nuclear gene
 NAV56 for all inds in complex | | | |-- lampropeltis_NAV56.out_monitor #
 Progress monitor for phasing nuclear gene NAV56 for all inds in complex |
 | | |-- lampropeltis_NAV56.out_pairs # Pairwise probabilities for nuclear
 gene NAV56 for all inds in complex | | | |-- lampropeltis_NAV56.out_probs
 # Per-ind haplotype probabilities for nuclear gene NAV56 for all inds in
 complex | | | |-- lampropeltis_NAV56.out_recom # Recombination rate
 estimates for nuclear gene NAV56 for all inds in complex | | | |--
 lampropeltis_NT3.inp # Input file provided to PHASE for nuclear gene NT3
 for all inds in complex | | | |-- lampropeltis_NT3.out # Output file
 generated by PHASE for nuclear gene NT3 for all inds in complex | | | |--
 lampropeltis_NT3.out_freqs # Haplotype frequency estimates for nuclear
 gene NT3 for all inds in complex | | | |-- lampropeltis_NT3.out_hbg #
 Haplotype block groupings for nuclear gene NT3 for all inds in complex | |
 | |-- lampropeltis_NT3.out_monitor # Progress monitor for phasing nuclear
 gene NT3 for all inds in complex | | | |-- lampropeltis_NT3.out_pairs #
 Pairwise probabilities for nuclear gene NT3 for all inds in complex | | |
 |-- lampropeltis_NT3.out_probs # Per-ind haplotype probabilities for
 nuclear gene NT3 for all inds in complex | | | |--
 lampropeltis_NT3.out_recom # Recombination rate estimates for nuclear gene
 NT3 for all inds in complex | | | |-- lampropeltis_PRLR.inp # Input file
 provided to PHASE for nuclear gene PRLR for all inds in complex | | | |--
 lampropeltis_PRLR.out # Output file generated by PHASE for nuclear gene
 PRLR for all inds in complex | | | |-- lampropeltis_PRLR.out_freqs #
 Haplotype frequency estimates for nuclear gene PRLR for all inds in
 complex | | | |-- lampropeltis_PRLR.out_hbg # Haplotype block groupings
 for nuclear gene PRLR for all inds in complex | | | |--
 lampropeltis_PRLR.out_monitor # Progress monitor for phasing nuclear gene
 PRLR for all inds in complex | | | |-- lampropeltis_PRLR.out_pairs #
 Pairwise probabilities for nuclear gene PRLR for all inds in complex | | |
 |-- lampropeltis_PRLR.out_probs # Per-ind haplotype probabilities for
 nuclear gene PRLR for all inds in complex | | | |--
 lampropeltis_PRLR.out_recom # Recombination rate estimates for nuclear
 gene PRLR for all inds in complex | | | |-- lampropeltis_SPTBN1.inp #
 Input file provided to PHASE for nuclear gene SPTBN1 for all inds in
 complex | | | |-- lampropeltis_SPTBN1.out # Output file generated by PHASE
 for nuclear gene SPTBN1 for all inds in complex | | | |--
 lampropeltis_SPTBN1.out_freqs # Haplotype frequency estimates for nuclear
 gene SPTBN1 for all inds in complex | | | |-- lampropeltis_SPTBN1.out_hbg
 # Haplotype block groupings for nuclear gene SPTBN1 for all inds in
 complex | | | |-- lampropeltis_SPTBN1.out_monitor # Progress monitor for
 phasing nuclear gene SPTBN1 for all inds in complex | | | |--
 lampropeltis_SPTBN1.out_pairs # Pairwise probabilities for nuclear gene
 SPTBN1 for all inds in complex | | | |-- lampropeltis_SPTBN1.out_probs #
 Per-ind haplotype probabilities for nuclear gene SPTBN1 for all inds in
 complex | | | |-- lampropeltis_SPTBN1.out_recom # Recombination rate
 estimates for nuclear gene SPTBN1 for all inds in complex | | | |--
 lampropeltis_VIM56.inp # Input file provided to PHASE for nuclear gene
 VIM56 for all inds in complex | | | |-- lampropeltis_VIM56.out # Output
 file generated by PHASE for nuclear gene VIM56 for all inds in complex | |
 | |-- lampropeltis_VIM56.out_freqs # Haplotype frequency estimates for
 nuclear gene VIM56 for all inds in complex | | | |--
 lampropeltis_VIM56.out_hbg # Haplotype block groupings for nuclear gene
 VIM56 for all inds in complex | | | |-- lampropeltis_VIM56.out_monitor #
 Progress monitor for phasing nuclear gene VIM56 for all inds in complex |
 | | |-- lampropeltis_VIM56.out_pairs # Pairwise probabilities for nuclear
 gene VIM56 for all inds in complex | | | |-- lampropeltis_VIM56.out_probs
 # Per-ind haplotype probabilities for nuclear gene VIM56 for all inds in
 complex | | | |-- lampropeltis_VIM56.out_recom # Recombination rate
 estimates for nuclear gene VIM56 for all inds in complex | | | |--
 triangulum_2CL3.inp # Input file provided to PHASE for nuclear gene 2CL3
 for only triangulum | | | |-- triangulum_2CL3.out # Output file generated
 by PHASE for nuclear gene 2CL3 for only triangulum | | | |--
 triangulum_2CL3.out_freqs # Haplotype frequency estimates for nuclear gene
 2CL3 for only triangulum | | | |-- triangulum_2CL3.out_hbg # Haplotype
 block groupings for nuclear gene 2CL3 for only triangulum | | | |--
 triangulum_2CL3.out_monitor # Progress monitor for phasing nuclear gene
 2CL3 for only triangulum | | | |-- triangulum_2CL3.out_pairs # Pairwise
 probabilities for nuclear gene 2CL3 for only triangulum | | | |--
 triangulum_2CL3.out_probs # Per-ind haplotype probabilities for nuclear
 gene 2CL3 for only triangulum | | | |-- triangulum_2CL3.out_recom #
 Recombination rate estimates for nuclear gene 2CL3 for only triangulum | |
 | |-- triangulum_2CL4.inp # Input file provided to PHASE for nuclear gene
 2CL4 for only triangulum | | | |-- triangulum_2CL4.out # Output file
 generated by PHASE for nuclear gene 2CL4 for only triangulum | | | |--
 triangulum_2CL4.out_freqs # Haplotype frequency estimates for nuclear gene
 2CL4 for only triangulum | | | |-- triangulum_2CL4.out_hbg # Haplotype
 block groupings for nuclear gene 2CL4 for only triangulum | | | |--
 triangulum_2CL4.out_monitor # Progress monitor for phasing nuclear gene
 2CL4 for only triangulum | | | |-- triangulum_2CL4.out_pairs # Pairwise
 probabilities for nuclear gene 2CL4 for only triangulum | | | |--
 triangulum_2CL4.out_probs # Per-ind haplotype probabilities for nuclear
 gene 2CL4 for only triangulum | | | |-- triangulum_2CL4.out_recom #
 Recombination rate estimates for nuclear gene 2CL4 for only triangulum | |
 | |-- triangulum_2CL8.inp # Input file provided to PHASE for nuclear gene
 2CL8 for only triangulum | | | |-- triangulum_2CL8.out # Output file
 generated by PHASE for nuclear gene 2CL8 for only triangulum | | | |--
 triangulum_2CL8.out_freqs # Haplotype frequency estimates for nuclear gene
 2CL8 for only triangulum | | | |-- triangulum_2CL8.out_hbg # Haplotype
 block groupings for nuclear gene 2CL8 for only triangulum | | | |--
 triangulum_2CL8.out_monitor # Progress monitor for phasing nuclear gene
 2CL8 for only triangulum | | | |-- triangulum_2CL8.out_pairs # Pairwise
 probabilities for nuclear gene 2CL8 for only triangulum | | | |--
 triangulum_2CL8.out_probs # Per-ind haplotype probabilities for nuclear
 gene 2CL8 for only triangulum | | | |-- triangulum_2CL8.out_recom #
 Recombination rate estimates for nuclear gene 2CL8 for only triangulum | |
 | |-- triangulum_CL4.inp # Input file provided to PHASE for nuclear gene
 CL4 for only triangulum | | | |-- triangulum_CL4.out # Output file
 generated by PHASE for nuclear gene CL4 for only triangulum | | | |--
 triangulum_CL4.out_freqs # Haplotype frequency estimates for nuclear gene
 CL4 for only triangulum | | | |-- triangulum_CL4.out_hbg # Haplotype block
 groupings for nuclear gene CL4 for only triangulum | | | |--
 triangulum_CL4.out_monitor # Progress monitor for phasing nuclear gene CL4
 for only triangulum | | | |-- triangulum_CL4.out_pairs # Pairwise
 probabilities for nuclear gene CL4 for only triangulum | | | |--
 triangulum_CL4.out_probs # Per-ind haplotype probabilities for nuclear
 gene CL4 for only triangulum | | | |-- triangulum_CL4.out_recom #
 Recombination rate estimates for nuclear gene CL4 for only triangulum | |
 | |-- triangulum_GAD15.inp # Input file provided to PHASE for nuclear gene
 GAD15 for only triangulum | | | |-- triangulum_GAD15.out # Output file
 generated by PHASE for nuclear gene GAD15 for only triangulum | | | |--
 triangulum_GAD15.out_freqs # Haplotype frequency estimates for nuclear
 gene GAD15 for only triangulum | | | |-- triangulum_GAD15.out_hbg #
 Haplotype block groupings for nuclear gene GAD15 for only triangulum | | |
 |-- triangulum_GAD15.out_monitor # Progress monitor for phasing nuclear
 gene GAD15 for only triangulum | | | |-- triangulum_GAD15.out_pairs #
 Pairwise probabilities for nuclear gene GAD15 for only triangulum | | |
 |-- triangulum_GAD15.out_probs # Per-ind haplotype probabilities for
 nuclear gene GAD15 for only triangulum | | | |--
 triangulum_GAD15.out_recom # Recombination rate estimates for nuclear gene
 GAD15 for only triangulum | | | |-- triangulum_LATCL.inp # Input file
 provided to PHASE for nuclear gene LATCL for only triangulum | | | |--
 triangulum_LATCL.out # Output file generated by PHASE for nuclear gene
 LATCL for only triangulum | | | |-- triangulum_LATCL.out_freqs # Haplotype
 frequency estimates for nuclear gene LATCL for only triangulum | | | |--
 triangulum_LATCL.out_hbg # Haplotype block groupings for nuclear gene
 LATCL for only triangulum | | | |-- triangulum_LATCL.out_monitor #
 Progress monitor for phasing nuclear gene LATCL for only triangulum | | |
 |-- triangulum_LATCL.out_pairs # Pairwise probabilities for nuclear gene
 LATCL for only triangulum | | | |-- triangulum_LATCL.out_probs # Per-ind
 haplotype probabilities for nuclear gene LATCL for only triangulum | | |
 |-- triangulum_LATCL.out_recom # Recombination rate estimates for nuclear
 gene LATCL for only triangulum | | | |-- triangulum_NAV56.inp # Input file
 provided to PHASE for nuclear gene NAV56 for only triangulum | | | |--
 triangulum_NAV56.out # Output file generated by PHASE for nuclear gene
 NAV56 for only triangulum | | | |-- triangulum_NAV56.out_freqs # Haplotype
 frequency estimates for nuclear gene NAV56 for only triangulum | | | |--
 triangulum_NAV56.out_hbg # Haplotype block groupings for nuclear gene
 NAV56 for only triangulum | | | |-- triangulum_NAV56.out_monitor #
 Progress monitor for phasing nuclear gene NAV56 for only triangulum | | |
 |-- triangulum_NAV56.out_pairs # Pairwise probabilities for nuclear gene
 NAV56 for only triangulum | | | |-- triangulum_NAV56.out_probs # Per-ind
 haplotype probabilities for nuclear gene NAV56 for only triangulum | | |
 |-- triangulum_NAV56.out_recom # Recombination rate estimates for nuclear
 gene NAV56 for only triangulum | | | |-- triangulum_NT3.inp # Input file
 provided to PHASE for nuclear gene NT3 for only triangulum | | | |--
 triangulum_NT3.out # Output file generated by PHASE for nuclear gene NT3
 for only triangulum | | | |-- triangulum_NT3.out_freqs # Haplotype
 frequency estimates for nuclear gene NT3 for only triangulum | | | |--
 triangulum_NT3.out_hbg # Haplotype block groupings for nuclear gene NT3
 for only triangulum | | | |-- triangulum_NT3.out_monitor # Progress
 monitor for phasing nuclear gene NT3 for only triangulum | | | |--
 triangulum_NT3.out_pairs # Pairwise probabilities for nuclear gene NT3 for
 only triangulum | | | |-- triangulum_NT3.out_probs # Per-ind haplotype
 probabilities for nuclear gene NT3 for only triangulum | | | |--
 triangulum_NT3.out_recom # Recombination rate estimates for nuclear gene
 NT3 for only triangulum | | | |-- triangulum_PRLR.inp # Input file
 provided to PHASE for nuclear gene PRLR for only triangulum | | | |--
 triangulum_PRLR.out # Output file generated by PHASE for nuclear gene PRLR
 for only triangulum | | | |-- triangulum_PRLR.out_freqs # Haplotype
 frequency estimates for nuclear gene PRLR for only triangulum | | | |--
 triangulum_PRLR.out_hbg # Haplotype block groupings for nuclear gene PRLR
 for only triangulum | | | |-- triangulum_PRLR.out_monitor # Progress
 monitor for phasing nuclear gene PRLR for only triangulum | | | |--
 triangulum_PRLR.out_pairs # Pairwise probabilities for nuclear gene PRLR
 for only triangulum | | | |-- triangulum_PRLR.out_probs # Per-ind
 haplotype probabilities for nuclear gene PRLR for only triangulum | | |
 |-- triangulum_PRLR.out_recom # Recombination rate estimates for nuclear
 gene PRLR for only triangulum | | | |-- triangulum_SPTBN1.inp # Input file
 provided to PHASE for nuclear gene SPTBN1 for only triangulum | | | |--
 triangulum_SPTBN1.out # Output file generated by PHASE for nuclear gene
 SPTBN1 for only triangulum | | | |-- triangulum_SPTBN1.out_freqs #
 Haplotype frequency estimates for nuclear gene SPTBN1 for only triangulum
 | | | |-- triangulum_SPTBN1.out_hbg # Haplotype block groupings for
 nuclear gene SPTBN1 for only triangulum | | | |--
 triangulum_SPTBN1.out_monitor # Progress monitor for phasing nuclear gene
 SPTBN1 for only triangulum | | | |-- triangulum_SPTBN1.out_pairs #
 Pairwise probabilities for nuclear gene SPTBN1 for only triangulum | | |
 |-- triangulum_SPTBN1.out_probs # Per-ind haplotype probabilities for
 nuclear gene SPTBN1 for only triangulum | | | |--
 triangulum_SPTBN1.out_recom # Recombination rate estimates for nuclear
 gene SPTBN1 for only triangulum | | | |-- triangulum_VIM56.inp # Input
 file provided to PHASE for nuclear gene VIM56 for only triangulum | | |
 |-- triangulum_VIM56.out # Output file generated by PHASE for nuclear gene
 VIM56 for only triangulum | | | |-- triangulum_VIM56.out_freqs # Haplotype
 frequency estimates for nuclear gene VIM56 for only triangulum | | | |--
 triangulum_VIM56.out_hbg # Haplotype block groupings for nuclear gene
 VIM56 for only triangulum | | | |-- triangulum_VIM56.out_monitor #
 Progress monitor for phasing nuclear gene VIM56 for only triangulum | | |
 |-- triangulum_VIM56.out_pairs # Pairwise probabilities for nuclear gene
 VIM56 for only triangulum | | | |-- triangulum_VIM56.out_probs # Per-ind
 haplotype probabilities for nuclear gene VIM56 for only triangulum | | |
 |-- triangulum_VIM56.out_recom # Recombination rate estimates for nuclear
 gene VIM56 for only triangulum | | |-- seqPHASE_input/ # Input files for
 helper tool seqPHASE for complex inds only | | | |--
 complex89_2CL3_heterozygotes.fasta # Heterozygous sites from nuclear gene
 2CL3 for complex inds only | | | |-- complex89_2CL3_homozygotes.fasta #
 Homozygous sites from nuclear gene 2CL3 for complex inds only | | | |--
 complex89_2CL4_heterozygotes.fasta # Heterozygous sites from nuclear gene
 2CL4 for complex inds only | | | |-- complex89_2CL4_homozygotes.fasta #
 Homozygous sites from nuclear gene 2CL4 for complex inds only | | | |--
 complex89_2CL8_heterozygotes.fasta # Heterozygous sites from nuclear gene
 2CL8 for complex inds only | | | |-- complex89_2CL8_homozygotes.fasta #
 Homozygous sites from nuclear gene 2CL8 for complex inds only | | | |--
 complex89_CL4_heterozygotes.fasta # Heterozygous sites from nuclear gene
 CL4 for complex inds only | | | |-- complex89_CL4_homozygotes.fasta #
 Homozygous sites from nuclear gene CL4 for complex inds only | | | |--
 complex89_GAD15_heterozygotes.fasta # Heterozygous sites from nuclear gene
 GAD15 for complex inds only | | | |-- complex89_GAD15_homozygotes.fasta #
 Homozygous sites from nuclear gene GAD15 for complex inds only | | | |--
 complex89_LATCL_heterozygotes.fasta # Heterozygous sites from nuclear gene
 LATCL for complex inds only | | | |-- complex89_LATCL_homozygotes.fasta #
 Homozygous sites from nuclear gene LATCL for complex inds only | | | |--
 complex89_NAV56_heterozygotes.fasta # Heterozygous sites from nuclear gene
 NAV56 for complex inds only | | | |-- complex89_NAV56_homozygotes.fasta #
 Homozygous sites from nuclear gene NAV56 for complex inds only | | | |--
 complex89_NT3_heterozygotes.fasta # Heterozygous sites from nuclear gene
 NT3 for complex inds only | | | |-- complex89_NT3_homozygotes.fasta #
 Homozygous sites from nuclear gene NT3 for complex inds only | | | |--
 complex89_PRLR_heterozygotes.fasta # Heterozygous sites from nuclear gene
 PRLR for complex inds only | | | |-- complex89_PRLR_homozygotes.fasta #
 Homozygous sites from nuclear gene PRLR for complex inds only | | | |--
 complex89_SPTBN1_heterozygotes.fasta # Heterozygous sites from nuclear
 gene SPTBN1 for complex inds only | | | |--
 complex89_SPTBN1_homozygotes.fasta # Homozygous sites from nuclear gene
 SPTBN1 for complex inds only | | | |-- complex89_VIM56_heterozygotes.fasta
 # Heterozygous sites from nuclear gene VIM56 for complex inds only | | |
 |-- complex89_VIM56_homozygotes.fasta # Homozygous sites from nuclear gene
 VIM56 for complex inds only | |-- Structurama/ # All input and output
 files relevant to Structurama analysis | |-- all124_structurama_mt.in #
 Input file for Structurama for all 124 individuals | |--
 all124identifiers.txt # Identifiers for Structurama for all 124
 individuals | |-- complex89_structurama_mt.in # Input file for Structurama
 for complex individuals | |-- complex89identifiers.txt # Identifiers for
 Structurama for complex individuals | |-- Output_files/ # Structurama
 output files | | |-- all124/ # Structurama output files for all 124
 individuals | | | |-- all124_mt.out# Output Structurama file for run 1 for
 all 124 individuals | | | |-- all124_mt_post.txt # Posterior sample file
 from MCMC run 1 for all 124 individuals | | | |-- all124_mt2_post.txt#
 Output Structurama file for run 2 for all 124 individuals | | | |--
 all124_mt2.out # Posterior sample file from MCMC run 2 for all 124
 individuals | | | |-- all124_mt3_post.txt# Output Structurama file for run
 3 for all 124 individuals | | | |-- all124_mt3.out # Posterior sample file
 from MCMC run 3 for all 124 individuals | | | |-- all124_mt4.out# Output
 Structurama file for run 4 for all 124 individuals | | | |--
 all124_mt4.post.txt # Posterior sample file from MCMC run 4 for all 124
 individuals | | | |-- all124_mt5_post.txt# Output Structurama file for run
 5 for all 124 individuals | | | |-- all124_mt5.out # Posterior sample file
 from MCMC run 5 for all 124 individuals | | | |-- all124_mt6.out# Output
 Structurama file for run 6 for all 124 individuals | | | |--
 all124_mt6.post.txt # Posterior sample file from MCMC run 6 for all 124
 individuals | | | |-- all124_mt7.out# Output Structurama file for run 7
 for all 124 individuals | | | |-- all124_mt7.post.txt # Posterior sample
 file from MCMC run 7 for all 124 individuals | | | |-- all124_mt8.out#
 Output Structurama file for run 8 for all 124 individuals | | | |--
 all124_mt8.post.txt # Posterior sample file from MCMC run 8 for all 124
 individuals | | | |-- all124_mt9.out# Output Structurama file for run 9
 for all 124 individuals | | | |-- all124_mt9.post.txt # Posterior sample
 file from MCMC run 9 for all 124 individuals | | | |-- all124_mt10.out#
 Output Structurama file for run 10 for all 124 individuals | | | |--
 all124_mt10.post.txt # Posterior sample file from MCMC run 10 for all 124
 individuals | | | |-- Run1_all124_124vis_figure.pdf# Output Structurama
 viz for run 1 for all 124 individuals | | | |--
 Run2_all124_124vis_figure.pdf# Output Structurama viz for run 2 for all
 124 individuals | | | |-- Run3_all124_124vis_figure.pdf# Output
 Structurama viz for run 3 for all 124 individuals | | | |--
 Run4_all124_124vis_figure.pdf# Output Structurama viz for run 4 for all
 124 individuals | | | |-- Run5_all124_124vis_figure.pdf# Output
 Structurama viz for run 5 for all 124 individuals | | | |--
 Run6_all124_124vis_figure.pdf# Output Structurama viz for run 6 for all
 124 individuals | | | |-- Run7_all124_124vis_figure.pdf# Output
 Structurama viz for run 7 for all 124 individuals | | | |--
 Run8_all124_124vis_figure.pdf# Output Structurama viz for run 8 for all
 124 individuals | | | |-- Run9_all124_124vis_figure.pdf# Output
 Structurama viz for run 9 for all 124 individuals | | | |--
 Run10_all124_124vis_figure.pdf# Output Structurama viz for run 10 for all
 124 individuals | | |-- complex89/ # Structurama output files for only 89
 complex individuals ||||--complex1mtout# Output Structurama file for run 1
 for complex individuals only ||||--complex1mtpost.txt # Posterior sample
 file from MCMC run 1 for complex individuals only ||||--complex2mtout#
 Output Structurama file for run 2 for complex individuals only
 ||||--complex2mtpost.txt # Posterior sample file from MCMC run 2 for
 complex individuals only ||||--complex3mtout# Output Structurama file for
 run 3 for complex individuals only ||||--complex3outpost.txt # Posterior
 sample file from MCMC run 3 for complex individuals only
 ||||--complex4mtout# Output Structurama file for run 4 for complex
 individuals only ||||--complex4mtpost.txt # Posterior sample file from
 MCMC run 4 for complex individuals only ||||--complex5mtout# Output
 Structurama file for run 5 for complex individuals only
 ||||--complex5mtpost.txt # Posterior sample file from MCMC run 5 for
 complex individuals only ||||--complex6mtout# Output Structurama file for
 run 6 for complex individuals only ||||--complex6mtpost.txt # Posterior
 sample file from MCMC run 6 for complex individuals only
 ||||--complex7mtout# Output Structurama file for run 7 for complex
 individuals only ||||--complex7mtpost.txt # Posterior sample file from
 MCMC run 7 for complex individuals only ||||--complex8mtout# Output
 Structurama file for run 8 for complex individuals only
 ||||--complex8mtpost.txt # Posterior sample file from MCMC run 8 for
 complex individuals only ||||--complex9mtout# Output Structurama file for
 run 9 for complex individuals only ||||--complex9mtpost.txt # Posterior
 sample file from MCMC run 9 for complex individuals only
 ||||--complex10mtout# Output Structurama file for run 10 for complex
 individuals only ||||--complex10mtpost.txt # Posterior sample file from
 MCMC run 10 for complex individuals only ||||--Run1mt_k6_figure.pdf#
 Output Structurama viz for run 1 for complex individuals only
 ||||--Run2mt_k6_figure.pdf# Output Structurama viz for run 2 for complex
 individuals only ||||--Run3mt_k6_figure.pdf# Output Structurama viz for
 run 3 for complex individuals only ||||--Run4mt_k4_figure.pdf# Output
 Structurama viz for run 4 for complex individuals only
 ||||--Run5mt_k4_figure.pdf# Output Structurama viz for run 5 for complex
 individuals only ||||--Run6mt_k4_figure.pdf# Output Structurama viz for
 run 6 for complex individuals only ||||--Run7mt_k5_figure.pdf# Output
 Structurama viz for run 7 for complex individuals only
 ||||--Run8mt_k6_figure.pdf# Output Structurama viz for run 8 for complex
 individuals only ||||--Run9mt_k5_figure.pdf# Output Structurama viz for
 run 9 for complex individuals only ||||--Run10mt_k7_figure.pdf# Output
 Structurama viz for run 10 for complex individuals only | |--
 Structurama_code.R # Script to process Structurama files ``` ### Files and
 variables #### File: FigS1_Structurama.pdf **Description:** Supplementary
 Figure. Results from Structurama analyses. #### File:
 FigS2_consensustrees.pdf **Description:** Supplementary Figure.
 Majority-rule consensus gene trees for 11 nuclear genes. #### File:
 FigS3_cytbtree.pdf **Description:** Supplementary Figure. Maximum clade
 credibility cytb gene tree. #### File: TableS1.pdf
 **Description:** Supplementary Table. Results from BPP analyses for
 alternative splits of *L. gentilis* and* L. triangulum*. #### File:
 TableS2.pdf **Description:** Supplementary Table. Taxonomy of Lampropeltis
 species. #### File: Online Appendix 1.pdf **Description:** Appendix 1.
 Details for Structurama analyses. #### File: Online Appendix 2.pdf
 **Description:** Appendix 2. Details for gene tree reconstruction. ####
 File: Online Appendix 3.pdf **Description:** Appendix 3. Details for BPP
 analyses. #### File: ChambersHillis_SuppFiles.zip
 **Description:** Compressed version of all supplementary files.