Data from: Gene flow creates fuzzy species boundaries in fence lizards
Data files
Sep 14, 2026 version files 41.62 MB
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files.tar.gz
41.62 MB
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README.md
5.60 KB
Abstract
Species delimitation is a fundamental challenge in systematic biology, particularly for geographically variable taxa with hierarchical population structure and gene flow. Migration-aware coalescent models provide a powerful framework for investigating lineage divergence and accurately defining species boundaries. In this study, we combine statistical evaluations of gene flow with phylogenetic and population structure analyses to delimit species of fence lizards within the Sceloporus undulatus complex, a group characterized by extensive population subdivision, mitochondrial DNA introgression, and nuclear gene flow. We find that the undulatus complex exhibits uneven variation in genetic, morphological, and ecological traits, resulting in variable distinctiveness among groups. In some cases, species boundaries are recognized by clear genetic discontinuities without gene flow. In others, shallow divergence, paraphyly, and gene flow produce leaky boundaries and fuzzy species limits. Mitochondrial introgression is extensive and concentrated at species boundaries, while nuclear gene flow occurs between only a few species and at much lower levels than within species. Analyses of morphological and ecological data reveal substantial overlap among populations and only modest differentiation among species, highlighting their limited utility for diagnosing species in this group. By integrating estimates of gene flow with phylogenetic and population structure analyses, this study provides a robust and biologically meaningful revised taxonomic framework for the undulatus complex that aligns species with independently evolving lineages.
Dataset DOI: 10.5061/dryad.547d7wmnx
AUTHORS:
ADAM D. LEACHÉ, HAYDEN R. DAVIS, EDÚ B. GUERRA, ARACELY HERRERA, JULIO LEMOS-ESPINAL, MATTHEW K. FUJITA, TANNER C. MYERS, SONAL SINGHAL
CONTACT:
leache@uw.edu
DATE:
April 7, 2026
DESCRIPTION:
This dataset contains genetic and morphological data used in the study. The directory structure is organized by analysis type, including multispecies coalescent modeling (MSCM), admixture analyses, phylogenetic inference (IQ-TREE), and morphological datasets.
DIRECTORY STRUCTURE OVERVIEW
files.tar.gz contains the following top-level directories and files:
- MSCM/
Contains files used for multispecies coalescent analysis with BPP, including both broadscale and finescale datasets. - admixture/
Contains SNP datasets and population assignment files used for admixture analyses. - iqtree/
Contains sequence alignments used for phylogenetic inference with IQ-TREE. - morphology/
Contains morphological datasets used for statistical analyses. - distances.csv
Pairwise distances (genetic, morphological, ecological, and migration rates) between populations and species. Header includes:- comp=comparison type (species (s) or population (p))
- group1=comparison group 1
- group2=comparison group 2
- morph.dist=morphological distance value
- fst=fixation index value
- eco.dist=ecological distance value
- M=migration rate
Population and species abbreviation key for files containing group names:
Eastern (undulatus; und) - West (W), East (E)
Mexico (edbelli; ed) - Southern (S), Northern (N), Texas-New Mexico (TXNM)
Front Range (erythrocheilus; ery) - Northern (N), Southeast (SE), Southwest (SW)
Central (consobrinus; con) - Southwest (SW), Northwest (NW), Southeast (SE), Northeast (NE), Arkansas-Louisiana (ARLA)
Western (tristichus; tri) - Northeast (NE), Northern (N), Western Arizona (WAZ), Southwest (SW), cowlesi (COW), Central New Mexico (CNM)
MSCM DIRECTORY
MSCM/ contains input files for BPP analyses.
MSCM/broadscale/
Broadscale species-level analyses.
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bidirectional_tests/
Contains pairwise migration rate test configurations.Subdirectories (con_ed, con_ery, con_tri, tri_ed, tri_ery, und_con):
Each contains:- bpp.ctl: Control file specifying BPP model parameters.
- imap.txt: Individual-to-population assignment file.
Files:
- data.txt: Sequence data used for all bidirectional tests.
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species_tree/
Species tree inference using BPP.Files:
- bpp.ctl: Control file for species tree analysis.
- data.txt: Sequence alignment input.
- imap.txt: Population assignment file.
MSCM/finescale/
Fine-scale population-level analyses.
Subdirectories:
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central/, east/, frontrange/, mexico/, west/
Each represents a species.Common files:
- data.txt: Sequence data for the region.
- imap.txt: Sample-to-population mapping.
Control files (*.ctl):
Multiple BPP control files specifying alternative model configurations or population comparisons (file names indicate comparison structure).
ADMIXTURE DIRECTORY
admixture/ contains SNP datasets and input files for admixture analyses.
Top-level:
- full_data.vcf: Combined SNP dataset across all individuals.
Subdirectories (consobrinus, edbelli, erythrocheilus, tristichus, undulatus, undulatus_complex):
Each represents a focal species.
Files:
- all.recode.vcf: Filtered SNP dataset for the focal group.
- keep.txt: Population assignment file used in define included samples in admixture analysis.
IQTREE DIRECTORY
iqtree/ contains sequence alignments used for phylogenetic inference.
Files:
- ddRADseq.phy: Concatenated ddRADseq alignment in PHYLIP format.
- mtDNA.phy: Mitochondrial DNA alignment in PHYLIP format.
MORPHOLOGY DIRECTORY
morphology/ contains morphological datasets.
Files:
- raw_data.csv: Raw morphological measurements for all specimens. Headers are as follows:
- Label=sample name
- SNP=nuclear group assignment
- sex=male or female
- SVL=snout-vent length (mm)
- HL=head length (mm)
- HW= head width (mm)
- FL=femur length (mm)
- TL=toe length (mm)
- DS=dorsal scales (count)
- LAM=lamellae (count)
- FEMS=femoral pores (count)
- FEMSCALES=femoral scales (count)
- populations.csv: Processed dataset with population-level assignments. Headers are as follows:
- Label=sample name
- SNP=nuclear group assignment
- Pop=population assignment
- SVL=snout-vent length (mm)
- HL=head length (mm)
- HW= head width (mm)
- FL=femur length (mm)
- TL=toe length (mm)
- DS=dorsal scales (count)
- LAM=lamellae (count)
- FEMS=femoral pores (count)
- FEMSCALES=femoral scales (count)
FILE FORMATS
- .vcf: Variant Call Format (genomic SNP data)
- .phy: PHYLIP format (sequence alignments)
- .txt: Plain text files (assignments, configuration files, or data matrices)
- .ctl: BPP control files specifying model parameters
- .csv: Comma-separated values (tabular data)
SOFTWARE REQUIREMENTS
Analyses were conducted using:
- BPP (for MSC and MSCM analyses)
- ADMIXTURE (for population structure analyses)
- IQ-TREE (for phylogenetic inference)
NOTES
- File naming conventions reflect taxon names and/or comparison types.
- Control files (*.ctl) define alternative model configurations and should be interpreted alongside the associated data.txt and imap.txt files.
- All paths in control files are relative to their respective directories.