Phylogenetic relationships and species delimitation of bunchgrass lizards of the genus Sceloporus from Mexico with the description of a new species
Data files
Apr 09, 2025 version files 969.09 KB
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All_nDNA_ND4_Concatenated_SVDq.nex
125.44 KB
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All_nDNA_ND4_Concatenated.phy
124.53 KB
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All_nDNAOnly_Concatenated.nex
93.68 KB
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EXPH5_Phry_starBEAST.nex
83.50 KB
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KIF24_starBEAST.nex
43.39 KB
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ND4_Phry_starBEAST.nex
34.23 KB
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R35_Phry_starBEAST.nex
57.10 KB
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README.md
2.43 KB
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S_Scalaris_AlignedSeqs_nDNAONLY.Imap.txt
4.01 KB
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S_Scalaris_AlignedSeqs_nDNAONLY.txt
179.65 KB
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S_Scalaris_AlignedSeqs.Imap.txt
5.42 KB
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S_Scalaris_AlignedSeqs.txt
211.36 KB
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Taxon_Speciesname_BEAST.txt
4.36 KB
Abstract
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.
Dataset DOI: 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.