It's about time: Insights into temporal genetic patterns in oceanic zooplankton from biodiversity indices

Abstract

Large population sizes and high dispersal potential should lead to temporal genetic stability in marine species; however, the magnitude of allele frequency shifts through time have varied greatly in prior studies. We investigated temporal variation in the genetic composition of populations of two planktonic copepod species at an open ocean time series site in the North Pacific Subtropical Gyre (Station ALOHA, 22.45°N, 158°W). We sequenced fragments of the mitochondrial genes cytochrome c oxidase subunit II (Haloptilus longicornis) and subunit I (Pleuromamma xiphias) from approximately 500 individuals of each species collected on 11 cruises from September 2012 to October 2013 (12–15 generations). Conventional population genetic analyses found no evidence for significant temporal variation across cruises, including results of non-hierarchical analysis of molecular variance, pairwise ΦST values among cruises, and isolation-by-time Mantel tests. Generalized entropies were able to characterize the turnover of rare haplotypic variants through time using q = 0 (haplotype richness), the shifting frequencies of the less common haplotypes using q = 1 (Shannon differentiation), and the general stability of the most abundant haplotypes using q = 2 (Jost's D). With q = 1, mild seasonality was detected in the composition of P. xiphias haplotypes from three summertime cruises, in which both copepodites and adults were included in the analyses. These results highlight the complementary insights that F-statistics and generalized entropy contribute to characterizing the nuances of population genetic composition through time. This approach may prove particularly useful for unlocking patterns in genomic datasets for marine species.