DOI: 10.5061/dryad.r7989
title: Data from: Cryptic diversity and discordance in single-locus species delimitation methods within horned lizards (Phrynosomatidae: Phrynosoma)

description: Biodiversity reduction and loss continues to progress at an alarming rate,
 and thus there is widespread interest in utilizing rapid and efficient
 methods for quantifying and delimiting taxonomic diversity. Single-locus
 species-delimitation methods have become popular, in part due to the
 adoption of the DNA barcoding paradigm. These techniques can be broadly
 classified into tree-based and distance-based methods depending on whether
 species are delimited based on a constructed genealogy. Although the
 relative performance of these methods has been tested repeatedly with
 simulations, additional studies are needed to assess congruence with
 empirical data. We compiled a large data set of mitochondrial ND4
 sequences from horned lizards (Phrynosoma) to elucidate congruence using
 four tree-based (single-threshold GMYC, multiple-threshold GMYC, bPTP,
 mPTP) and one distance-based (ABGD) species delimitation models. We were
 particularly interested in cases with highly uneven sampling and/or large
 differences in intraspecific diversity. Results showed a high degree of
 discordance among methods, with multiple-threshold GMYC and bPTP
 suggesting an unrealistically high number of species (29 and 26 species
 within the P. douglasii complex alone). The single-threshold GMYC model
 was the most conservative, likely a result of difficulty in locating the
 inflection point in the genealogies. mPTP and ABGD appeared to be the most
 stable across sampling regimes and suggested the presence of additional
 cryptic species that warrant further investigation. These results suggest
 that the mPTP model may be preferable in empirical data sets with highly
 uneven sampling or large differences in effective population sizes of
 species.
description: Phrynos_ND4_220_OGsMultiple sequence alignment of unique ND4 haplotypes (220).Phrynos_ND4_GMYC_OGs_fixed.fastaPhrynos_ND4_Unique_Haplotypes_ABGDMultiple sequence alignment for ABGD analysis of unique haplotypes with singletons removed.Phrynos_ND4_GMYC_OGs_fixed_ABGD.fastaPhrynos_ND4_EvenSampling_149Multiple sequence alignment of 149 ND4 haplotypes (even sampling) after pruning P. platyrhinos sequences.Phrynos_ND4_GMYC_OGs_fixed_EvenSampling.fastaPhrynos_ND4_EvenSampling_ABGDMultiple sequence alignment for ABGD analysis on the evenly sampled data set with singletons removed.Phrynos_ND4_GMYC_OGs_fixed_EvenSampling_ABGD.fastaPhrynosoma_ND4_all_OGsMultiple sequence alignment of all ND4 sequences (368) including duplicate haplotypes.Phrynosoma_ND4_363_ABGDMultiple sequence alignment of 363 ND4 haplotypes (including duplicates) with singletons removed.RAxML_bestTree_220ML tree from RAxML analysis of 220 haplotypes.RAxML_bestTree_fixed.Phrynos_mPTPRAxML_bipartitions_220ML tree from RaxML analysis of 220 haplotypes with bootstrap support on nodes.RAxML_bipartitions_fixed.Phrynos_mPTPRAxML_bestTree_149ML tree from RaxML analysis of 149 haplotypes on the evenly sampled data set.RAxML_bestTree.Phrynos_fixed_EvenSampling_PTPRAxML_bipartitions_149ML tree from RAxML analysis of 149 haplotypes on the evenly sampled data set. Nodes are annotated with bootstrap proportions.RAxML_bipartitions.Phrynos_fixed_EvenSampling_PTPMCCTree_CAHeights_220BEAST MCC tree based on 220 unique haplotypes. Node heights annotated using common ancestor heights.Phrynos_BEAST_GMYC_fixed_MeanHeights_220BEAST MCC tree based on 220 unique haplotypes. Node heights annotated using mean heights.Phrynos_BEAST_MCC_fixed_220_MedianHeightsBEAST MCC tree based on 220 unique haplotypes. Node heights annotated using median heights.Phrynos_GMYC_fixed_EvenSampling_MCCBEAST MCC tree based on 149 unique haplotypes with even sampling. Node heights annotated using mean heights.Phrynos_BEAST_368_CaHeightsBEAST MCC tree based on 368 haplotypes (including duplicates). Node heights annotated using common ancestor heights.Phrynos_BEAST_368_MeanHeightsBEAST MCC tree based on 368 haplotypes (including duplicates). Node heights annotated using mean heights.Phrynos_BEAST_368_MedianHeightsBEAST MCC tree based on 368 haplotypes (including duplicates). Node heights annotated using median heights.RAxML_bestTree_368ML tree from RAxML analysis of 368 sequences (including duplicates).RAxML_bestTree.Phrynos_368_RAxMLRAxML_bipartitions_368ML tree from RAxML analysis of 368 sequences (including duplicates). Nodes annotated with bootstrap proportions.RAxML_bipartitions.Phrynos_368_RAxML