Data from: Demographic expansion and panmixia in a St. Martin endemic, Anolis pogus, coincides with the decline of a competitor
Data files
Jul 09, 2025 version files 12.17 KB
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AbundanceSurveys.csv
4.75 KB
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README.md
4.25 KB
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SampleMetaData.csv
3.17 KB
Abstract
Understanding patterns of differentiation at microgeographic scales can enhance our understanding of evolutionary dynamics and lead to the development of effective conservation strategies. In particular, high levels of landscape heterogeneity can strongly influence species abundances, genetic structure, and demographic trends. The bearded anole, Anolis pogus, is endemic to the topographically complex island of St. Martin and of conservation concern. Here, we examined genetic diversity and inbreeding, assessed which features of the landscape influence population abundances, tested for population genetic structure across St. Martin, and inferred historical demographic trends. We performed WGS on 54 individuals and conducted abundance surveys of 100 plots throughout the island of St. Martin. Genomic data are hosted elsewhere on NCBI SRA (PRJNA1278788). Hosted here are data from abundance surveys as well as metadata for individuals used to generate WGS libraries. Further, Zenodo provides scripts used to analyse the genomic and abundance data. Our data demonstrate that A. pogus is panmictic on the island of St. Martin, lacking any population structure including isolation by distance. We also find that the species has low levels of inbreeding and has likely recently experienced demographic expansion. Overall, these analyses suggest that A. pogus is unlikely to be of immediate conservation concern. Further, we highlight the role of demographic history and ecological interactions in shaping population structure.
Dataset DOI: 10.5061/dryad.59zw3r2mg
Description of the data and file structure
Here, we provide data for a conservation biology study of Anolis pogus in Yuan et al. 2025 Journal of Heredity. This study examined the abundance patterns, population structure, inbreeding levels, and demographic history in this species. Data includes both WGS data for 54 individuals as well as abundance survey data from 112 sites. Here, metadata is provided for our WGS libraries. Raw reads are available elsewhere on NCBI SRA (PRJNA1278788). We also provide our abundance survey data. In Zenodo, we provide scripts for processing raw sequencing data, SNP and genotype likelihood calling, and analyses of demographic history, inbreeding, and population structure. We also provide an R script for the fitting of abundance models based on our survey data.
Files and variables
File: AbundanceSurveys.csv
Description: A .csv file of data from abundance surveys performed across the island of St. Martin. This data consists of 100 survey plots 80 sq. meters in size which were surveyed between 30 November 2018 until 08 February 2019. Standard plots were surveyed for 40 person minutes. Additionally, this data includes 12 absence only sites which were surveyed for >2 hours.
Variables
- Plot #: Numeric Plot ID number.
- Date: The date in which the survey was conducted (YYYY-MM-DD).
- Time: The time in which the survey began (hh:mm).
- Lat: Latitude of survey site (degree decimal).
- Lon: Longitude of survey site (degree decimal).
- Abundance: Abundance count of A. pogus from survey site.
File: SampleMetaData.csv
Description: Metadata for 54 whole genome sequencing libraries of Anolis pogus. Data were paired end sequenced using a NovaSeq X. These raw data associated with this metadata are available on NCBI SRA (PRJNA1278788).
Variables
- ID: Individual library ID.
- Genus: The genus of the sample, in this case all Anolis
- Species: The species of the sample, in this case all pogus
- Sex: The sex of the sample (F = female, M = male, U = unsexed)
- Locality: A descriptive locality where the sample was collected.
- Lat: Latitude of collection location (degree decimal).
- Lon: Longitude of collection location (degree decimal).
Code/software
data_processing.sh
Script for processing raw sequencing data including trimming, QC, alignment, mapping, and SNP soft calling. Required programs are loaded as modules, which may differ from system to system. Reference genome for mapping was the Anolis sagrei genome (AnoSag2.1).
- Trimmomatic v0.39
- bwa v0.7.19
- angsd v0.940
analyses_master.sh
Script for conducting analyses from genotype likelihood data. Analyses included in this script include PCA, admixture analyses, demographic reconstruction, genetic distance, inbreeding and relatedness estimation, and the calculation of the site frequency spectrum.
- PCAngsd v1.36.3
- NGSadmix v32
- ngsPSMC
- ngs-tools v1.8.6
- ngsRelate v2
- BCFtools v1.22
- angsd v0.940
genomics_script.R
Additional script for genomic analyses conducted in R. Input data are generated from metadata files and from .sh scripts described above. All required libraries are called in the script. Analyses included are genetic diversity for mitochondrial data, multiple matrix regression with randomization, visualization of PCA and admixture analyses results, end of analysis pipeline for inbreeding and relatedness analyses, and visualization of ngsPSMC demographic results.
- R version 4.3.3
AbundanceModel_clean.R
Script for abundance modeling using random forest and GLM. All required libraries are called in the script. The required input file is AbundanceSurveys.csv.
- R version 4.3.3
Access information
Other publicly accessible locations of the data:
- Raw sequence data are available at NCBI SRA