Influence of environmental conditions at spawning sites and migration routes on adaptive variation and population connectivity in Chinook salmon

Whole genome resequencing identifies local adaptation associated with environmental variation for redband trout

Aquatic ectotherms are predicted to harbour genomic signals of local adaptation resulting from selective pressures driven by the strong influence of climate conditions on body temperature. We investigated local adaptation in redband trout (Oncorhynchus mykiss gairdneri) using genome scans for 547 samples from 11 populations across a wide range of habitats and thermal gradients in the interior Columbia River. We estimated allele frequencies for millions of single nucleotide polymorphism loci (SNPs) across populations using low-coverage whole genome resequencing, and used population structure outlier analyses to identify genomic regions under divergent selection between populations. Twelve genomic regions showed signatures of local adaptation, including two regions associated with genes known to influence migration and developmental timing in salmonids (GREB1L, ROCK1, SIX6). Genotype-environment association analyses indicated that diurnal temperature variation was a strong driver of local adaptation, with signatures of selection driven primarily by divergence of two populations in the northern extreme of the subspecies range. We also found evidence for adaptive differences between high-elevation desert vs. montane habitats at a smaller geographical scale. Finally, we estimated vulnerability of redband trout to future climate change using ecological niche modelling and genetic offset analyses under two climate change scenarios. These analyses predicted substantial habitat loss and strong genetic shifts necessary for adaptation to future habitats, with the greatest vulnerability predicted for high-elevation desert populations. Our results provide new insight into the complexity of local adaptation in salmonids, and important predictions regarding future responses of redband trout to climate change.

Revealing Population Connectivity of the Estuarine Tapertail Anchovy Coilia nasus in the Changjiang River Estuary and Its Adjacent Waters Using Otolith Microchemistry

The estuarine tapertail anchovy, Coilia nasus, is a migratory fish with high economic value in China. We collected fish from the Changjiang River (the Yangtze River) estuary, the Qiantang River estuary, and the southern Yellow Sea, and studied their relationships using otolith elemental and stable isotopic microchemistry signatures to assess the population connectivity of C. nasus. Results show that, in addition to Ca, other elements were present in the otolith core. The δ18O, Na/Ca, Fe/Ca, and Cu/Ca values of the Qiantang population were significantly higher than those of the others, whereas its δ13C and Ba/Ca values were found to be significantly lower. Otolith multi-element composition and stable isotope ratios differed significantly between the Qiantang and Changjiang estuary groups (p < 0.05); however, no difference was observed between the latter and the Yellow Sea group. Cluster analysis, linear discriminant analysis, and a self-organizing map strongly suggest possible connectivity between the fish populations of the Changjiang estuary and Yellow Sea, while the population of the Qiantang River estuary appears to be independent. Notably, results suggest a much closer connectivity between the fish populations of the Changjiang River and the Yellow Sea.