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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 (iHS and Rsb) and one FST based 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 the iHS, Rsb and FST based 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.

The phylogenetic resolution provided by genome-wide data has demonstrated the usefulness of RAD sequencing to tackle long-standing taxonomic questions. Cnidarians have recently become a model group in this regard, yet species delimitation analyses have been mostly performed in octocorals. In this study, we used RAD sequencing to test the species hypotheses in a wide-spread complex of sea anemones (genus Anthothoe), contrasting this new line of evidence with their current classification. The alternative hypotheses were tested using a Bayes Factors delimitation method, and the most probable species tree was then evaluated under different biogeographic scenarios. Our results decisively rejected the current morphology-informed delimitation model and infer the presence of several cryptic species associated with distinct marine ecoregions. This spatial pattern was remarkably consistent throughout the study, highlighting the role of geographic distribution as a powerful explanatory variable of lineages diversification. The southern Gondwana pattern with episodic, jump dispersal events is the biogeographic historical representation that best fits the Anthothoe species tree. The high population differentiation possibly amplified by the occurrence of asexual reproduction makes it difficult to identify genes responsible for local adaptation, however, these seem to be mainly associated with cellular and metabolic processes. We propose a new set of species hypotheses for the Southern Hemispheric Anthothoe clade, based on the pronounced genomic divergence observed among lineages. Although the link between the genetic and phenotypic differentiation remains elusive, newer sequencing technologies are bringing us closer to understanding the evolution of sea anemone diversity and, therefore, how to appropriately classify them. Fil: Spano, Carlos A.. Universidad de Concepción; Chile Fil: Häussermann, Vreni. Pontificia Universidad Católica de Valparaíso; Chile. Huinay Scientific Field Station; Chile Fil: Acuña, Fabian Horacio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Marinas y Costeras. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Instituto de Investigaciones Marinas y Costeras; Argentina Fil: Griffiths, Charles. University Of Cape Town; Sudáfrica Fil: Seeb, Lisa W.. University Of Washington. School Of Aquatic And Fisheries Sciences; Estados Unidos Fil: Gomez-Uchida, Daniel. Universidad de Concepción; Chile

Numerous empirical studies have reported lack of migration–drift equilibrium in wild populations. Determining the causes of nonequilibrium population structure is challenging because different evolutionary processes acting at a variety of spatiotemporal scales can produce similar patterns. Studies of contemporary populations in northern latitudes suggest that nonequilibrium population structure is probably caused by recent colonization of the region after the last Pleistocene ice age ended ~13 000 years ago. The chum salmon's (Oncorhynchus keta) range was fragmented by dramatic environmental changes during the Pleistocene. We investigated the population structure of chum salmon on the North Alaska Peninsula (NAP) and, using both empirical data and simulations, evaluated the effects of colonization timing and founder population heterogeneity on patterns of genetic differentiation. We screened 161 single nucleotide polymorphisms and found evidence of nonequilibrium population structure when the slope of the isolation-by-distance relationship was examined at incremental spatial scales. In addition, simulations suggested that this pattern closely matched models of recent colonization of the NAP by secondary contact. Our results agree with geological and archaeological data indicating that the NAP was a dynamic landscape that may have been more recently colonized than during the last deglaciation because of dramatic changes in coastal hydrology over the last several thousand years.

Salmonids are an important cultural and ecological resource exhibiting near worldwide distribution between their native and introduced range. Previous research has generated linkage maps and genomic resources for several species as well as genome assemblies for two species. We first leveraged improvements in mapping and genotyping methods to create a dense linkage map for Chinook salmon Oncorhynchus tshawytscha by assembling family data from different sources. We successfully mapped 14 620 SNP loci including 2336 paralogs in subtelomeric regions. This improved map was then used as a foundation to integrate genomic resources for gene annotation and population genomic analyses. We anchored a total of 286 scaffolds from the Atlantic salmon genome to the linkage map to provide a framework for the placement 11 728 Chinook salmon ESTs. Previously identified thermotolerance QTL were found to colocalize with several candidate genes including HSP70, a gene known to be involved in thermal response, as well as its inhibitor. Multiple regions of the genome with elevated divergence between populations were also identified, and annotation of ESTs in these regions identified candidate genes for fitness related traits such as stress response, growth and behaviour. Collectively, these results demonstrate the utility of combining genomic resources with linkage maps to enhance evolutionary inferences.

We genotyped nuclear and mitochondrial single nucleotide polymorphisms (SNPs) in six paired archived and contemporary collections of Alaskan sockeye salmon ( Oncorhynchus nerka ) to evaluate the stability of allele frequencies over 25–42 years (4.9–8.4 generations). First, our results show that temporal changes were dramatically (between 40- and 250-fold) smaller than spatial differences in allele frequencies when based on nuclear SNPs. Second, the magnitude of temporal change was consistent with a model of genetic drift: (i) SNPs with high levels of differentiation (large θ) and candidates for diversifying selection were not more likely to show significant temporal changes than small-θ SNPs; and (ii) the fraction of single-locus significant tests was consistent with theoretical predictions relating sample size and the annual number of breeders (Nb). Third, estimates of Nbwere bound by infinitely large upper 95% confidence intervals, except for one paired collection with unique life-history attributes of both a smoltification phase and generation time shorter than the other paired collections. Use of multigenerational SNP data sets seems a safe practice in management of Alaska sockeye salmon that could be extended to other large, wild aquatic populations.

The Southern Darwin’s frog Rhinoderma darwinii is a charismatic, mouth-brooding amphibian endemic to temperate forests of South America with a Vulnerable conservation status according to the IUCN Red List. We developed microsatellite markers from next generation sequence data that will aid genetic monitoring during and after re-introduction efforts. Using bioinformatics we characterized 3,521 perfect microsatellite repeats and designed primers for 35 of them. From these, 23 were polymorphic and amplified reliably. Number of alleles varied between 2 and 15, allele sizes varied between 84 and 299 bp, and observed heterozygosities varied between 0.105 and 0.904. These microsatellites represent a valuable resource to aid recovery of threatened Southern Darwin’s frog populations.

By pooling or removing samples of small size, we investigated how results from microsatellite analyses of spatial genetic structure in darkblotched rockfish (Sebastes crameri) were affected. Genotypes from six and seven microsatellite loci from 1206 specimens collected offshore from Washington to California were employed in the analy- ses. Sample sizes varied greatly among locations (n = 11-114). When adjacent samples of n 100) and further in- creased the correlation, although this strategy did not raise overall FST. These results indicate that under genetic isola- tion by distance, excessive pooling might not enhance the overall genetic differentiation among populations. The regression slope in isolation by distance plots was robust throughout all treatments, and its value suggests limited dis- persal distance on this species. Resume : Nous avons etudie comment les resultats d'analyses des microsatellites sur la structure genetique spatiale chez le sebaste tachete (Sebastes crameri) sont affectes par la fusion et le retrait d'echantillons de petite taille. Des genotypes de six et sept locus microsatellites chez 1206 specimens recoltes du Washington a la Californie ont servi aux analyses. Les tailles des echantillons varient considerablement selon les sites (n = 11-114). Lorsque des echantillons adjacents de n < 25 sont fusionnes a l'aide d'une distance genetique absolue (FST ≤ 0), la correlation entre les distances genetique et geographique calculees dans les donnees originales double presque et le FST (intervalle de confiance de 95 %) global augmente de 0,001 (0,000-0,002) a 0,002 (0,001-0,003). Le retrait des echantillons de n <

We deep-sequenced the transcriptome of Chinook salmon (Oncorhynchus tshawytscha) that yielded 2.5 million high-quality reads (combined for four fish) with an average length of 378 bp. De novo assembly resulted in 44,264 contigs with an average length of 567 bp and an average depth of 29 reads. Nearly half (42 %) of the contigs were annotated through alignment against protein, gene ontology (GO) and taxonomic databases using BLASTX. Overrepresented GO categories included metabolism (32 %), biosynthesis (11 %), transport (7 %), transcription (5 %) and other important pathways (response to stress, lipid metabolism and reproduction: 3 %). We identified 3,793 putative single nucleotide polymorphisms (SNPs) in silico, of which 718 were annotated. We characterized a sample of 54 annotated SNPs within contigs with transition-to-transversion ratios

Landscape genetics holds promise for the forecasting of spatial patterns of genetic diversity based on key environmental features. Yet, the degree to which inferences based on single species can be extended to whole communities is not fully understood. We used a pristine and spatially structured community of three landlocked salmonids (Salvelinus fontinalis, Salmo salar, and Salvelinus alpinus) from Gros Morne National Park (Newfoundland, Canada) to test several predictions on the interacting effects of landscape and life history variation on genetic diversity, neutral divergence, and gene flow (m, migration rate). Landscape factors consistently influenced multispecies genetic patterns: (i) waterfalls created strong dichotomies in genetic diversity and divergence between populations above and below them in all three salmonids; (ii) contemporary m decreased with waterway distance in all three species, while neutral genetic divergence (h) increased with waterway distance, albeit in only two taxa; (iii) river flow generally produced downstream-biased m between populations when waterfalls separated these, but not otherwise. In contrast, we expected differential life history to result in a hierarchy of neutral divergence (S. salar > S. fontinalis > S. alpinus) based on disparities in dispersal abilities and population size from previous mark-recapture studies. Such hierarchy additionally matched varying degrees of spatial genetic structure among species revealed through individual-based analyses. We conclude that, whereas key landscape attributes hold power to predict multispecies genetic patterns in equivalent communities, they are likely to interact with species-specific life history attributes such as dispersal, demography, and ecology, which will in turn affect holistic conservation strategies.

We report the variance effective population size (Ne) 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 Ne estimate (Ne) plus 95% confidence interval was (Ne) = 9157 [6495-12 215], showing that the breeding population number could be 3-4 orders of magnitude smaller than the census population size (N) = 24 376 210). Our estimates resemble closely those found for fishes with similar life history, suggesting that the small (Ne)/(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 (Ne)/(N) ratios have been commonly associated with potential loss of genetic variation, our estimates need careful consideration in rockfish management and conservation.