DOI: 10.5061/dryad.44j0zpcs5
title: 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

description: 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. 
description: # 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 Dataset DOI:
 [10.5061/dryad.44j0zpcs5](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](https://www.ncbi.nlm.nih.gov/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](https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1268565)