Data from: The challenges of detecting subtle population structure and its importance for the conservation of emperor penguins

Understanding the boundaries of breeding populations is of great
importance for conservation efforts and estimates of extinction risk for
threatened species. However, determining these boundaries can be difficult
when population structure is subtle. Emperor penguins are highly reliant
on sea ice, and some populations may be in jeopardy as climate change
alters sea-ice extent and quality. An understanding of emperor penguin
population structure is therefore urgently needed. Two previous studies
have differed in their conclusions, particularly whether the Ross Sea, a
major stronghold for the species, is isolated or not. We assessed emperor
penguin population structure using 4,596 genome-wide single nucleotide
polymorphisms (SNPs), characterized in 110 individuals (10–16 per colony)
from eight colonies around Antarctica. In contrast to a previous
conclusion that emperor penguins are panmictic around the entire
continent, we find that emperor penguins comprise at least four
metapopulations, and that the Ross Sea is clearly a distinct
metapopulation. Using larger sample sizes and a thorough assessment of the
limitations of different analytical methods, we have shown that population
structure within emperor penguins does exist and argue that its
recognition is vital for the effective conservation of the species. We
discuss the many difficulties that molecular ecologists and managers face
in the detection and interpretation of subtle population structure using
large SNP data sets, and argue that subtle structure should be taken into
account when determining management strategies for threatened species,
until accurate estimates of demographic connectivity among populations can
be made.