DOI: 10.5061/dryad.59zw3r2mg
title: Data from: Demographic expansion and panmixia in a St. Martin endemic, Anolis pogus, coincides with the decline of a competitor

description: 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.
description: # Demographic expansion and panmixia in a St. Martin endemic, Anolis
 pogus, coincides with the decline of a competitor Dataset DOI:
 [10.5061/dryad.59zw3r2mg](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 &gt;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 ###### Content Description: 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). ###### Required programs: *
 Trimmomatic v0.39 * bwa v0.7.19 * angsd v0.940 ##### analyses_master.sh
 ###### Content Description: 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. ###### Required programs: * PCAngsd v1.36.3 * NGSadmix v32 *
 ngsPSMC * ngs-tools v1.8.6 * ngsRelate v2 * BCFtools v1.22 * angsd v0.940
 ##### genomics_script.R ###### Content Description: 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. ###### Required programs: * R version 4.3.3
 ##### AbundanceModel_clean.R ###### Content Description: Script for
 abundance modeling using random forest and GLM. All required libraries are
 called in the script. The required input file is AbundanceSurveys.csv.
 ###### Required programs: * R version 4.3.3 ## Access information Other
 publicly accessible locations of the data: * Raw sequence data are
 available at NCBI SRA