Reassessing a Holocene extinction: multiple lines of evidence do not support the historical presence and recent extirpation of a protected anole on the island of Anguilla

Yuan, Michael 1 ; Bell, Rayna 1 ; Myers, Edward1

Published Jul 01, 2025 on Dryad. https://doi.org/10.5061/dryad.44j0zpcs5

Data files

Jul 01, 2025 version files 19.77 KB

README.md

3.63 KB
SVL_master_QC.csv

16.14 KB

Abstract

Accurate assessment of historical species ranges is important for conservation science and management. Inaccurate historical species ranges can lead to incorrect assumptions about local extinctions, population trends, and potential sites for reintroductions. Yet, historical knowledge is often lacking for many species. Here, we present body size data on the case of the bearded anole, Anolis pogus, which is long believed to have been recently extirpated from the island of Anguilla. Body size data consists of snout-vent length for adult male and female Anolis pogus, A. schwartzi, and A. gingivinus. These data were generated from a mix of field measurements and samples from natural history collections. We then compared these data with the size distributions of anole fossils found on the island of Anguilla. We show that rather than a two-species community, the fossil size data better corresponds to sexual dimorphism in a single-species community consisting only of A. gingivinus. Thus, fossil data do not support the historical presence of A. pogus as previously suggested. We also generated WGS libraries from archival samples of Anolis pogus allegedly collected on Anguilla. We show that all of these museum samples are actually A. schwartzi and originated from a nearby island, St. Eustatius. Thus, there are no existing collections of A. pogus from the island of Anguilla. Scripts for analyzing these genomic data are archived on Zenodo. Raw sequence data are hosted on NCBI's SRA database.

Dataset DOI: 10.5061/dryad.44j0zpcs5

Description of the data and file structure

We have submitted data for body sizes of field-collected and museum specimens from three species of anoles: A. pogus, A. schwartzi, and A. gingivinus. This dataset is used in our analyses comparing known fossil size distributions on Anguilla to potential species. Anole fossils cannot be identified to species, only genus. This work is described in our manuscript "Reassessing a Holocene extinction: multiple lines of evidence do not support the historical presence and recent extirpation of a protected anole on the island of Anguilla". In addition to the body size data, we also provide a script for assembling whole mitochondrial genomes from historical museum samples. We sequenced formalin-fixed livers from the only two A. pogus collected on Anguilla and showed that they are actually incorrectly sorted A. schwartzi from the nearby island of Anguilla. Raw sequence data from these specimens are deposited in NCBI's SRA under bioproject PRJNA1268565.

Files and variables

File: SVL_master_QC.csv

Description: A csv file containing the body size of our anole study species. Body size is measured in mm as snout-vent length, a standardized measure of body size in lizards. Data is presented for 322 individuals of A. pogus (43 male; 27 female), A. gingivinus (90 male; 49 female), and A. schwartzi (78 male; 35 female)

Variables

catalognumber: This variable provides an identification number for individuals sampled in this study. These numbers are either museum IDs (CAS = California Academy of Sciences; USNM = US National Museum of Natural History, Smithsonian Institution) or individual field IDs assigned by the author (MLY). A small number of individuals measured in the field were not given a field ID and are labelled as 'Field Measurement'.
genus: The genus of the individual. Always Anolis.
specificepithet: The species name of the individual, either pogus, schwartzi, or gingivinus.
sex: male or female.
lifestage: Juvenile or Adult. In this dataset, always adults.
island: The island from which the individual was originally collected. All islands are in the Lesser Antilles.
SVL: The snout-vent length of the individual. This measurement is taken from the tip of the snout to the cloacal vent of the animal and is a standardized measure in herpetology to ensure comparable data. SVL is presented in mm.

Code/software

Data can be viewed with any standardized spreadsheet viewing software and is comma-delimited.

Zenodo script:

ANGUILLA-mitochondrial_script.sh

This bash script was used for assembling a reference mitochondrial genome and aligning historical reads to the reference to generate a consensus mitochondrial genome for each individual.
Required programs: MITObim, samtools, picard, bwa (either loaded as modules or in a conda environment).
Slurm commands:
--job-name=mt: name of job.
--partition=high2: partition to assign job to. Should be changed to match the HPC being used.
--mem=80G: total memory allocated to the job.
--time=150:00:00: wall time limit for the job.

Access information

Other publicly accessible locations of the data:

Raw sequence data: SRA bioproject: PRJNA1268565