Genomic Signatures of Freshwater Adaptation in Pacific Herring (Clupea pallasii)

Abstract

Pacific herring (Clupea pallasii) is an essential target of commercial fishing in the North Pacific Ocean. Previous studies have suggested the existence of marine and lake ecological forms of this species within its range. The lake ecological form of herring has a shortened life cycle, spending the winter and spawning in brackish waters near the shoreline without long migrations for feeding; it also has a relatively smaller body size than the marine form. Genetic-based studies have shown that brackish water Pacific herring not only can be distinguished as a separate lake ecological form but possibly has its genetic legacy. Here, as part of an ongoing study, using ddRAD-sequencing data for marine and lake ecological forms from a total of 54 individuals and methods of comparative bioinformatics, we describe genomic signatures of freshwater adaptivity in Pacific herring. In total, 253 genes containing discriminating SNPs were found, and part of those genes was organized into genome clusters, also known as “genomic islands of divergence”. Moreover, the Tajima’s D test showed that these loci are under directional selection in the lake populations of the Pacific herring. Yet, most discriminating loci between the lake and marine ecological forms of Pacific herring do not intersect (by gene name) with those in other known marine fish species with known freshwater/brackish populations. However, some are associated with the same physiological trait—osmoregulation.

Conservation genetics and potential geographic distribution modeling of Corybas taliensis, a small ‘sky Island’ orchid species in China

“…The negative Tajima’s D values for C. taliensis might indicate genes with an excess of low-frequency variation, suggesting that the populations might have experienced expansion after a recent bottleneck, the higher medians of N 1a , N 3b , N 1 , N 2 and N 3 than of N 0 in DIYABC support the population expansion (Table 4 ), or that the genes targeted are under positive selective pressure [ 57 , 58 ]. However, if not impossible, it is very difficult to distinguish between population growth and selection if only intraspecific polymorphism is studied.…”