DOI: 10.5061/dryad.b2rbnzsqs
title: Whole-genome sequencing confirms multiple species of Galapagos giant tortoises

description: Galapagos giant tortoises are endemic to the Galapagos Archipelago, where
 they are found in isolated populations. While these populations are widely
 considered distinguishable in morphology, behavior, and genetics, the
 recent divergence of these taxa has made their status as species
 controversial. Here, we apply multispecies coalescent methods for species
 delimitation to whole genome resequencing data from 38 tortoises across
 all 13 extant taxa to assess support for delimiting these taxa as species.
 In contrast to previous studies based solely on divergence time, we find
 strong evidence to reject the hypothesis that all Galapagos giant
 tortoises belong to a single species. Instead, a conservative
 interpretation of model-based and divergence-based results indicates that
 these taxa form a species complex consisting of a minimum of 9 species,
 with most analyses supporting 13 species. There is mixed support for the
 species status of taxa living on the same island, with some methods
 delimiting them as separate species and others suggesting multiple
 populations of a single species per island. These results make clear that
 Galapagos giant tortoise taxa represent different stages in the process of
 speciation, with some taxa further along in that evolutionary process than
 others. Our study provides insight into the complex process of speciation
 on islands, which is urgently needed given the threatened status of island
 species around the world.
description: # Whole-genome sequencing confirms multiple species of Galapagos giant
 tortoises
 [https://doi.org/10.5061/dryad.b2rbnzsqs](https://doi.org/10.5061/dryad.b2rbnzsqs) ## Description of the data and file structure The Dryad repository contains: * tortoises_1kb_w100kb_phased.txt & tortoiseswithchaco_1kb_w100kb_phased.txt: fasta alignments of 1kb segments of the Galapagos giant tortoise genome separated by 100kb. The file "tortoiseswithchaco_1kb_w100kb_phased.txt" contains the alignments of the Galapagos giant tortoise individuals and the Chaco tortoise individual, while the other file contains only Galapagos giant tortoise individuals. * A01_tortoiseswith_mediumtheta.bpp.ctl: BPP control file to build a phylogenetic tree of Galapagos giant tortoise species with Chaco tortoise outgroup. * A11_*.ctl: BPP control files for running the species delimitation model. Control files are either for running with or without the Chaco tortoise and with different priors for theta. * A00_*.ctl: BPP control files for running parameter estimation. Control files are either for running with or without the Chaco tortoise and with different priors for theta. * FINAL2000* and FINAL5000*: Newick and Phylip files for the 2000 SNP and 5000 SNP data sets used in IQTree for the SNAPP analysis. * Model*.xml: Input files for the SNAPP analysis. * Model*.out: Output from the SNAPP analysis. * * ### Files and variables #### File: A01\_tortoiseswith\_mediumtheta.bpp.ctl **Description:** BPP control file for building a phylogenetic tree ("A01" model in BPP) of Galapagos giant tortoises with the Chaco tortoise outgroup. #### File: A00\_tortoiseswithchaco\_bigtheta.bpp.ctl **Description:** BPP control file for estimating theta and divergence parameters of Galapagos giant tortoises with the Chaco tortoise outgroup, using a large theta prior. #### File: A00\_tortoiseswithchaco\_mediumtheta.bpp.ctl **Description:** BPP control file for estimating theta and divergence parameters of Galapagos giant tortoises with the Chaco tortoise outgroup, using a medium theta prior. #### File: A00\_tortoiseswithchaco\_smalltheta.bpp.ctl **Description:** BPP control file for estimating theta and divergence parameters of Galapagos giant tortoises with the Chaco tortoise outgroup, using a small theta prior. #### File: A00\_tortoises\_bigtheta.bpp.ctl **Description:** BPP control file for estimating theta and divergence parameters of Galapagos giant tortoises using a large theta prior. #### File: A00\_tortoises\_mediumtheta.bpp.ctl **Description:** BPP control file for estimating theta and divergence parameters of Galapagos giant tortoises using a medium theta prior. #### File: A00\_tortoises\_smalltheta.bpp.ctl **Description:** BPP control file for estimating theta and divergence parameters of Galapagos giant tortoises using a small theta prior. #### File: tortoiseswithchaco\_1kb\_w100kb\_phased.txt **Description:** File containing loci sampled from the Galapagos giant tortoise and Chaco tortoise samples consisting of phased loci that are each 1kb long and spaced 100kb apart. #### File: tortoises\_1kb\_w100kb\_phased.txt **Description:** File containing loci sampled from the Galapagos giant tortoise samples consisting of phased loci that are each 1kb long and spaced 100kb apart. #### File: A11\_tortoises\_mediumtheta.bpp.ctl **Description:** BPP control file for species delimitation of Galapagos giant tortoises using a medium theta prior. #### File: A11\_tortoises\_largetheta.bpp.ctl **Description:** BPP control file for species delimitation of Galapagos giant tortoises using a large theta prior. #### File: A11\_tortoises\_smalltheta.bpp.ctl **Description:** BPP control file for species delimitation of Galapagos giant tortoises using a small theta prior. #### File: A11\_tortoiseswithchaco\_mediumtheta.bpp.ctl **Description:** BPP control file for species delimitation of Galapagos giant tortoises with the Chaco tortoise outgroup using a medium theta prior. #### File: A11\_tortoiseswithchaco\_largetheta.bpp.ctl **Description:** BPP control file for species delimitation of Galapagos giant tortoises with the Chaco tortoise outgroup using a large theta prior. #### File: A11\_tortoiseswithchaco\_smalltheta.bpp.ctl **Description:** BPP control file for species delimitation of Galapagos giant tortoises with the Chaco tortoise outgroup using a small theta prior.