Data from: Morphological and genomic comparisons of Hawaiian and Japanese Black-footed Albatrosses (Phoebastria nigripes) using double digest RADseq: implications for conservation

Evaluating the genetic and demographic independence of populations of
threatened species is important for determining appropriate conservation
measures, but different technologies can yield different conclusions.
Despite multiple studies, the taxonomic status and extent of gene flow
between the main breeding populations of Black-footed Albatross
(Phoebastria nigripes), a Near-Threatened philopatric seabird, are still
controversial. Here, we employ double digest RADseq to quantify the extent
of genomewide divergence and gene flow in this species. Our genomewide
data set of 9760 loci containing 3455 single nucleotide polymorphisms
yielded estimates of genetic diversity and gene flow that were generally
robust across seven different filtering and sampling protocols and suggest
a low level of genomic variation (θ per site = ~0.00002–0.00028), with
estimates of effective population size (Ne = ~500–15 881) falling far
below current census size. Genetic differentiation was small but
detectable between Japan and Hawaii (FST ≈ 0.038–0.049), with no FST
outliers. Additionally, using museum specimens, we found that effect sizes
of morphological differences by sex or population rarely exceeded 4%.
These patterns suggest that the Hawaiian and Japanese populations exhibit
small but significant differences and should be considered separate
management units, although the evolutionary and adaptive consequences of
this differentiation remain to be identified.