Hawksbill turtle ddRAD raw sequencing data

Pleistocene environmental changes are generally assumed to have
dramatically affected species’ demography via changes in habitat
availability, but this is challenging to investigate due to our limited
knowledge of how Pleistocene ecosystems changed through time. Here, we
tracked changes in shallow marine habitat availability resulting from
Pleistocene sea level fluctuations throughout the last glacial cycle (120
– 14 thousand years ago; kya) and assessed correlations with past changes
in genetic diversity inferred from genome-wide SNPs, obtained via ddRAD
sequencing, in Caribbean hawksbill turtles, which feed in coral reefs
commonly found in shallow tropical waters. We found sea level regression
resulted in an average 75% reduction in shallow marine habitat
availability during the last glacial cycle. Changes in shallow marine
habitat availability correlated strongly with past changes in hawksbill
turtle genetic diversity, which gradually declined to ~1/4th of
present-day levels during the Last Glacial Maximum (LGM; 26 – 19 kya).
Shallow marine habitat availability and genetic diversity rapidly
increased after the LGM, signifying a population expansion in response to
warming environmental conditions. Our results suggest a positive
correlation between Pleistocene environmental changes, habitat
availability and species’ demography, and that demographic changes in
hawksbill turtles were potentially driven by feeding habitat availability.
However, we also identified challenges associated with disentangling the
potential environmental drivers of past demographic changes, which
highlight the need for integrative approaches. Our conclusions underline
the role of habitat availability on species’ demography and biodiversity,
and that the consequences of ongoing habitat loss should not be
underestimated.