DOI: 10.5061/dryad.rv15dv4kc
title: Phylogenetic relationships and species delimitation of bunchgrass lizards of the genus Sceloporus from Mexico with the description of a new species

description:  Molecular data continue to serve as an invaluable tool to assess
 species limits and patterns of cryptic diversity, particularly in areas
 harboring high levels of biodiversity. The Sceloporus scalaris group,
 known as bunchgrass lizards, contains 13 described and one undescribed
 species distributed throughout high elevation biotas of Mexico. However,
 recent studies suggest that diversity in the group may be substantially
 underestimated. We collect new sequence data from four independent loci to
 determine the evolutionary distinctiveness and phylogenetic relationships
 of an isolated population of bunchgrass lizard in the Sierra San Juan
 (SSJ) in the Mexican state of Nayarit. Concatenation and coalescent-based
 phylogenetic and species delimitation analyses suggest that this
 population represents a distinct evolutionary lineage allied to the S.
 scalaris group. We describe the new SSJ population as a new species to
 better account for its morphological and evolutionary distinctiveness.
 Divergence within the species occurred during the Neogene and Quaternary,
 most likely due to range shifts associated with mountain uplift and
 glacial-interglacial cycles. Our results provide additional evidence that
 supports the importance of the Mexican highlands as a biodiversity hotspot
 which maintains cryptic lineages awaiting discovery.
description: # Phylogenetic relationships and species delimitation of bunchgrass
 lizards of the genus Sceloporus from Mexico with the description of a new
 species Dataset DOI: [10.5061/dryad.rv15dv4kc](10.5061/dryad.rv15dv4kc) ##
 Description of the data and file structure New sequence data were
 generated for 10 individual *Sceloporus* samples from the putative new
 species. New sequences were obtained from four loci (ND4, EXPH5, KIF24,
 R35). These new sequences were combined with sequence data from Grummer et
 al. (2014) available on GenBank to infer the phylogenetic position of the
 new taxon. We provide program input files for the phylogenetic analyses
 performed in this study.  ### Files and variables #### File:
 All\_nDNA\_ND4\_Concatenated\_SVDq.nex **Description:** Concatenated mtDNA
 + nDNA alignment used for SVDquartets and RAxML analyses. #### File:
 All\_nDNAOnly\_Concatenated.nex **Description:** Concatenated nDNA
 alignment used for SVDquartets and RAxML analyses. #### File:
 EXPH5\_Phry\_starBEAST.nex **Description:** EXPH5 alignment used for
 starBEAST analysis. Note that the sequence data were analytically phased. 
 #### File: KIF24\_starBEAST.nex **Description:** KIF24 alignment used for
 starBEAST analysis. Note that the sequence data were analytically phased. 
 #### File: Taxon\_Speciesname\_BEAST.txt **Description:** Map file used
 for starBEAST. This file was used to allocate individual sequences to
 species.  #### File: ND4\_Phry\_starBEAST.nex **Description:** ND4
 alignment used for starBEAST analysis. #### File: R35\_Phry\_starBEAST.nex
 **Description:** R35 alignment used for starBEAST analysis. Note that the
 sequence data were analytically phased.  #### File:
 All\_nDNA\_ND4\_Concatenated.phy **Description:** Concatenated mtDNA +
 nDNA file used for phylogenetic analysis. #### File:
 S\_Scalaris\_AlignedSeqs.Imap.txt **Description:** Imap file used in
 BPP. This file was used to allocate individual sequences to species. ####
 File: S\_Scalaris\_AlignedSeqs.txt **Description:** Sequence file used in
 BPP. File includes both mtDNA and nDNA loci. #### File:
 S\_Scalaris\_AlignedSeqs\_nDNAONLY.Imap.txt **Description:** nDNA only
 Imap file used in BPP. This file was used to allocate individual sequences
 to species. #### File: S\_Scalaris\_AlignedSeqs\_nDNAONLY.txt
 **Description:** nDNA only sequence file used in BPP. This file excludes
 the mtDNA data.