10.5061/DRYAD.31ZCRJDMD
van der Zee, Jurjan
0000-0002-1449-2945
University of Groningen
Christianen, Marjolijn
Wageningen University & Research
Bérubé, Martine
University of Groningen
Nava, Mabel
Sea Turtle Conservation Bonaire
Schut, Kaj
Sea Turtle Conservation Bonaire
Humber, Frances
BlueVentures
Alfaro-Núñez, Alonzo
University of Copenhagen
Becking, Leontine
Wageningen University & Research
Palsbøll, Per
University of Groningen
Green turtle ddRAD raw sequencing data
Dryad
dataset
2021
FOS: Biological sciences
Chelonia mydas
double-digest restriction site-associated DNA sequencing (ddRAD-seq)
marine population genetics
Dutch Research Council
https://ror.org/04jsz6e67
NWO-ALW 858.14.090
2021-10-25T00:00:00Z
2021-10-25T00:00:00Z
en
https://doi.org/10.5281/zenodo.5513679
25179269306 bytes
4
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
The occasional westward transport of warm water of the Agulhas Current,
‘Agulhas leakage’, around southern Africa has been suggested to facilitate
tropical marine connectivity between the Atlantic and Indian oceans, but
the ‘Agulhas leakage’ hypothesis doesn’t explain the signatures of
eastward gene flow observed in many tropical marine fauna. We investigated
an alternative hypothesis: the establishment of a warm-water corridor
during comparatively warm interglacial periods. The ‘warm-water corridor’
hypothesis was investigated by studying the population genomic structure
of Atlantic and Southwest Indian Ocean green turtles (N = 27) using 12,035
genome-wide single nucleotide polymorphisms (SNPs) obtained via ddRAD
sequencing. Model-based and multivariate clustering suggested a
hierarchical population structure with two main Atlantic and Southwest
Indian Ocean clusters, and a Caribbean and East Atlantic sub-cluster
nested within the Atlantic cluster. Coalescent-based model selection
supported a model where Southwest Indian Ocean and Caribbean populations
diverged from the East Atlantic population during the transition from the
last interglacial period (130 – 115 thousand years ago; kya) to the last
glacial period (115 – 90 kya). The onset of the last glaciation appeared
to isolate Atlantic and Southwest Indian Ocean green turtles into three
refugia, which subsequently came into secondary contact in the Caribbean
and Southwest Indian Ocean when global temperatures increased after the
Last Glacial Maximum. Our findings support the establishment of a
warm-water corridor facilitating tropical marine connectivity between the
Atlantic and Southwest Indian Ocean during warm interglacials.
The dataset consists of 16 gzipped FASTQ files containing raw ddRAD-seq
Illumina sequencing data obtained from green turtles (Chelonia mydas). A
zipped archive containing the Python and R scripts used to perform the
simulation analysis is also provided, but can also be found on GitHub:
https://github.com/jpvdz/green-turtle-sims.
Please see the published manuscript and accompanying supplementary
material for a detailed description of the methods and steps required to
analyze the raw data. Please see the README.md in the zipped archive
containing the simulation scripts, or on GitHub
(https://github.com/jpvdz/green-turtle-sims) for instructions on how to
run the simulation analysis.