Whole-genome sequencing confirms multiple species of Galapagos giant tortoises

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 delimiti..., , , # 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 ...