The evolutionary origins of the parthenogenetic lizard Aspidoscelis tesselatus

Singhal, Sonal 1 ; Grundler, Maggie 2 ; Rivera, Danielle 3 ; Fisher, Sam3; Hall, Alexander3; Currie, Kathleen3; Nieto Montes de Oca, Adrián4; Roelke, Corey3; Leaché, Adam 5 ; Fujita, Matthew3

Published Sep 30, 2026 on Dryad. https://doi.org/10.5061/dryad.d2547d8k0

Data files

Sep 30, 2026 version files 432.41 MB

all_species.dp10_missing0.5.vcf.gz

371.65 MB
msci.ctl

1.54 KB
msci.imap_haplotype.txt

637 B
msci.loci.txt

19.90 MB
README.md

5.28 KB
TableS1.csv

39.03 KB
tesselatus_parents.dadi.snp_dadi.txt

721.46 KB
tesselatus_parents.dp20_missing0.9.phased.vcf.gz

40.09 MB

Abstract

Most vertebrate species reproduce sexually. The whiptail lizards (Aspidoscelis) are a notable exception; at least 11 of the 45 recognized species are parthenogenetic. Here, we focus on one such species (Aspidoscelis tesselatus) as a case study to understand how parthenogenetic species originate and evolve. Using genome-wide sequence data and ecological niche modelling, we find that A. tesselatus likely arose from a single hybrid speciation event between A. scalaris and A. marmoratus less than 500,000 years ago. The geographic ranges of A. tesselatus and its parental species overlap currently, and niche modelling shows this zone of sympatry was even broader during the period when A. tesselatus likely formed. We additionally show evidence that A. tesselatus has a dynamic genome post-formation, with de novo mutations, introgression, and double-strand break associated events all contributing to variation within the species. These results show that asexual lineages can continue to be shaped by ongoing genomic and ecological dynamics, illuminating the processes that influence transitions in reproductive mode.

Dataset DOI: 10.5061/dryad.d2547d8k0

Description of the data and file structure

The following data are shared.

variant data
- all_species.dp10_missing0.5.vcf.gz: the 'all species' variant dataset including variant & invariant sites
  - This dataset was generated using ipyrad v0.9.95
  - This dataset includes 292,060 single-nucleotide variants across 13,545 loci
  - This dataset includes species Aspidoscelis tesselatus, A. scalaris, A. dixoni, A. gularis, A. septemvittatus, and A. marmoratus
  - This dataset includes 159 individuals; metadata on individuals is available in Table_S1.csv
  - This is a standard Variant Call Format (VCF) file following the specifications outlined here
- tesselatus_parents.dp20_missing0.9.phased.vcf.gz: the 'tesselatus & parents' variant dataset including variant & invariant sites
  - This dataset was generated using ipyrad v0.9.95
  - This dataset includes 7,386 variants across 2,618 loci
  - This dataset includes species Aspidoscelis tesselatus, A. scalaris, A. septemvittatus, and A. marmoratus
  - This dataset includes 158 individuals; metadata on individuals is available in Table_S1.csv
  - This is a standard Variant Call Format (VCF) file following the specifications outlined here
MSC-I files
- msci.ctl: the run file used to run MSC-I
  - MSC-Iis a program offered through the bpp package
  - The format of this file follows the guidelines outlined in the manual
- msci.imap_haplotype.txt: the population - individual mapping file used to run MSC-I
  - we ran this program using 14 individuals (5 for Aspidoscelis tesselatus; 5 for A. marmoratus; 4 for A. scalaris)
  - This file shows how these individuals; haplotypes map to the key populations
  - metadata on individuals is available in Table_S1.csv
  - The format of this file follows the guidelines outlined in the manual
- msci.loci.txt: the locus info used to run MSC-I
  - we ran this program for 2000 phased loci, this file includes the locus information
  - The format of this file follows the guidelines outlined in the manual
Table S1.csv: the supplemental table containing all sample information; see details on this file below
tesselatus_parents.dadi.snp_dadi.txt: the input file for dadi
- this is the variant data used to infer the joint site frequency spectrum (jSFS) used in demographic model fitting with dadi
- using the variant data in tesselatus_parents.dp20_missing0.9.phased.vcf.gz, we randomly sampled 1 variable site per 100 base pairs to create this file
- the format of these data follow the standard "SNP data format" outlined here
- outgroup information should not be trusted here; we used the folded jSFS for all model fitting we thinned

Files and variables

File: TableS1.csv

Description: Samples (n = 227) included in the analysis

Columns:

Sample_Name: the name of the sample as recorded by the field collector
Name_in_DataFiles: for a small number of samples, the name recorded in data files is slightly different, recognizing that a specific tissue was used to collect data for these sampled
Institution: for those samples that are vouchered, the institution where the voucher resides; institution codes follow (Sabaj, 2020)
Voucher: voucher number for those samples that are vouchered; not all samples are vouchered
Latitude: location of where sample was found in decimal degrees
Longitude: location of where sample was found in decimal degrees
Locality: geographic location of where sample was found in plain text
BioSample_Accession: the accession ID for where ddRAD genomic data for the sample can be found on the Short Read Archive hosted by NCBI
Species: the original species ascribed to the sample by the field collector
Lineage: the most likely operational taxonomic unit (OTU) based on the genetic clustering results presented in Figure 2 of Singhal et al. 2026

Code/software

Code & scripts are on our github: https://github.com/singhal/whiptails

Access information

Other publicly accessible locations of the data:

https://github.com/singhal/whiptails
The BioProject for this study is PRJNA1415884

Data was derived from the following sources:

GBIF data for Aspidoscelis marmoratus: https://doi.org/10.15468/dl.pned5t
GBIF data for Aspidoscelis scalaris: https://doi.org/10.15468/dl.52pmzs
GBIF data for Aspidoscelis tesselatus: https://doi.org/10.15468/dl.9bdtns