Nile tilapia belongs to the second most cultivated group of fish in the world, mainly because of its favorable characteristics for production. Genetic improvement programs and domestication process of Nile tilapia may have modified the genome through selective pressure, leaving signals that can be detected at the molecular level. In this work, signatures of selection were identified using genome-wide SNP data, by two haplotype-based (iHSandRsb) and oneF_STbased method. Whole-genome re-sequencing of 326 individuals from three strains (A, B and C) of farmed tilapia maintained in Brazil and Costa Rica was carried out using Illumina HiSeq 2500 technology. After applying conventional SNP-calling and quality-control filters, ~ 1.3 M high-quality SNPs were inferred and used as input for theiHS,RsbandF_STbased methods. We detected several candidate genes putatively subjected to selection in each strain. A considerable number of these genes are associated with growth (e.g.NCAPG, KLF3, TBC1D1, TTN), early development (e.g.FGFR3, PFKFB3), and immunity traits (e.g.NLRC3,PIGR,MAP1S). These candidate genes represent putative genomic landmarks that could be associated to traits of biological and commercial interest in farmed Nile tilapia.

Pervasive introductions of non-native taxa are behind processes of homogenization of various types affecting the global flora and fauna. Chile’s freshwater ecosystems encompass a diverse and highly endemic fish fauna that might be sensitive to the introduction of non-native species, an ongoing process that started two centuries ago, but has to date received little attention. Using historical (native) and present-day (native and non-native) presence-absence data sets of compositional similarity, our goal was twofold: (1) evaluate patterns of taxonomic homogenization at various spatial scales and (2) identify clusters of widely versus narrowly distributed species to assess their relative role in compositional changes. We expect that non-native species with wide distributions might have a larger influence in taxonomic homogenization than those with narrow distributions. Chile’s fish assemblages have become increasingly homogenized during the last two centuries when evaluating changes in compositional similarity among 201 watersheds (65.3 % of total comparisons showed homogenization) distributed among six defined biotic units. Taxonomic differentiation was significantly more prevalent than taxonomic homogenization within biotic units. Among biotic units, comparisons between historical and current compositional similarity were all significantly different. We identified one cluster of non-native fishes that were distributed across the entire five or six biotic units. This cluster included Brown Trout (Salmo trutta) and Rainbow Trout (Oncorhynchus mykiss) as the two most representative species. A second cluster we identified included fishes such that on average spanned only one or two biotic units. We provide first evidence for an ongoing and large-scale process of taxonomic homogenization among Chile’s watersheds occurring at various scales. Our findings provide taxonomic and biogeographic baseline information for management plans and courses of action for conservation of native fishes, many of which are endemic. We also discuss management guidelines of non-native fishes in Chile. Baseline information of both native and non-native fish taxa might be applicable to other isolated regions elsewhere.

Genetics data have provided unprecedented insights into evolutionary aspects of colonization by non‐native populations. Yet, our understanding of how artificial (human‐mediated) and natural dispersal pathways of non‐native individuals influence genetic metrics, evolution of genetic structure, and admixture remains elusive. We capitalize on the widespread colonization of Chinook salmon Oncorhynchus tshawytscha in South America, mediated by both dispersal pathways, to address these issues using data from a panel of polymorphic SNPs. First, genetic diversity and the number of effective breeders (N_b) were higher among artificial than natural populations. Contemporary gene flow was common between adjacent artificial and natural and adjacent natural populations, but uncommon between geographically distant populations. Second, genetic structure revealed four distinct clusters throughout the Chinook salmon distributional range with varying levels of genetic connectivity. Isolation by distance resulted from weak differentiation between adjacent artificial and natural and between natural populations, with strong differentiation between distant Pacific Ocean and Atlantic Ocean populations, which experienced strong genetic drift. Third, genetic mixture analyses revealed the presence of at least six donor geographic regions from North America, some of which likely hybridized as a result of multiple introductions. Relative propagule pressure or the proportion of Chinook salmon propagules introduced from various geographic regions according to government records significantly influenced genetic mixtures for two of three artificial populations. Our findings support a model of colonization in which high‐diversity artificial populations established first; some of these populations exhibited significant admixture resulting from propagule pressure. Low‐diversity natural populations were likely subsequently founded from a reduced number of individuals.

We report the variance effective population size (N_e) in darkblotched rockfish (Sebastes crameri) utilizing the temporal method for overlapping generations, which requires a combination of age-specific demography and genetic information from cohorts. Following calculations of age-specific survival and reproductive success from fishery data, we genotyped a sample (n = 1087) comprised by 6 cohorts (from 1995 to 2000) across 7 microsatellite loci. Our N_e estimate ($N^e$) plus 95% confidence interval was $N^e$ = 9157 [6495–12 215], showing that the breeding population number could be 3–4 orders of magnitude smaller than the census population size ($N^e$ = 24 376 210). Our estimates resemble closely those found for fishes with similar life history, suggesting that the small $N^e/N^$ ratio for S. crameri is most likely explained by a combination of high variance in reproductive success among individuals, genetic structure, and demographic perturbations such as historical fishing. Because small $N^e/N^$ ratios have been commonly associated with potential loss of genetic variation, our estimates need careful consideration in rockfish management and conservation.