Genetic signals of artificial and natural dispersal linked to colonization of South America by non-native Chinook salmon (Oncorhynchus tshawytscha)

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 (Nb) 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.Fil: Gomez Uchida, Daniel. Núcleo Milenio Invasal; Chile. Universidad de Concepción; ChileFil: Cañas Rojas, Diego. Núcleo Milenio Invasal; Chile. Universidad de Concepción; ChileFil: Riva Rossi, Carla Marcela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto de Diversidad y Evolución Austral; ArgentinaFil: Ciancio Blanc, Javier Ernesto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Centro para el Estudio de Sistemas Marinos; ArgentinaFil: Pascual, Miguel Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto Patagónico para el Estudio de los Ecosistemas Continentales; ArgentinaFil: Ernst, Billy. Universidad de Concepción; Chile. Núcleo Milenio Invasal; ChileFil: Aedo, Eduardo. Universidad Austral de Chile; ChileFil: Musleh, Selim S.. Universidad de Concepción; Chile. Núcleo Milenio Invasal; ChileFil: Valenzuela Aguayo, Francisca. Universidad de Concepción; ChileFil: Quinn, Thomas P.. Núcleo Milenio Invasal; Chile. University of Washington; Estados UnidosFil: Seeb, James E.. Núcleo Milenio Invasal; Chile. University of Washington; Estados UnidosFil: Seeb, Lisa W.. Núcleo Milenio Invasal; Chile. University of Washington; Estados Unido

Development of Genomic Resources for Pacific Herring through Targeted Transcriptome Pyrosequencing

Pacific herring (Clupea pallasii) support commercially and culturally important fisheries but have experienced significant additional pressure from a variety of anthropogenic and environmental sources. In order to provide genomic resources to facilitate organismal and population level research, high-throughput pyrosequencing (Roche 454) was carried out on transcriptome libraries from liver and testes samples taken in Prince William Sound, the Bering Sea, and the Gulf of Alaska. Over 40,000 contigs were identified with an average length of 728 bp. We describe an annotated transcriptome as well as a workflow for single nucleotide polymorphism (SNP) discovery and validation. A subset of 96 candidate SNPs chosen from 10,933 potential SNPs, were tested using a combination of Sanger sequencing and high-resolution melt-curve analysis. Five SNPs supported between-ocean-basin differentiation, while one SNP associated with immune function provided high differentiation between Prince William Sound and Kodiak Island within the Gulf of Alaska. These genomic resources provide a basis for environmental physiology studies and opportunities for marker development and subsequent population structure analysis

Temporal Genetic Variance and Propagule-Driven Genetic Structure Characterize Naturalized Rainbow Trout (Oncorhynchus mykiss) from a Patagonian Lake Impacted by Trout Farming

Knowledge about the genetic underpinnings of invasions—a theme addressed by invasion genetics as a discipline—is still scarce amid well documented ecological impacts of non-native species on ecosystems of Patagonia in South America. One of the most invasive species in Patagonia’s freshwater systems and elsewhere is rainbow trout (Oncorhynchus mykiss). This species was introduced to Chile during the early twentieth century for stocking and promoting recreational fishing; during the late twentieth century was reintroduced for farming purposes and is now naturalized. We used population- and individual-based inference from single nucleotide polymorphisms (SNPs) to illuminate three objectives related to the establishment and naturalization of Rainbow Trout in Lake Llanquihue. This lake has been intensively used for trout farming during the last three decades. Our results emanate from samples collected from five inlet streams over two seasons, winter and spring. First, we found that significant intra- population (temporal) genetic variance was greater than inter-population (spatial) genetic variance, downplaying the importance of spatial divergence during the process of naturalization. Allele frequency differences between cohorts, consistent with variation in fish length between spring and winter collections, might explain temporal genetic differences. Second, individual-based Bayesian clustering suggested that genetic structure within Lake Llanquihue was largely driven by putative farm propagules found at one single stream during spring, but not in winter. This suggests that farm broodstock might migrate upstream to breed during spring at that particular stream. It is unclear whether interbreeding has occurred between “pure” naturalized and farm trout in this and other streams. Third, estimates of the annual number of breeders (N[subscript]b) were below 73 in half of the collections, suggestive of genetically small and recently founded populations that might experience substantial genetic drift. Our results reinforce the notion that naturalized trout originated recently from a small yet genetically diverse source and that farm propagules might have played a significant role in the invasion of Rainbow Trout within a single lake with intensive trout farming. Our results also argue for proficient mitigation measures that include management of escapes and strategies to minimize unintentional releases from farm facilities

Single nucleotide polymorphisms unravel hierarchical divergence and signatures of selection among Alaskan sockeye salmon (Oncorhynchus nerka) populations

<p>Abstract</p> <p>Background</p> <p>Disentangling the roles of geography and ecology driving population divergence and distinguishing adaptive from neutral evolution at the molecular level have been common goals among evolutionary and conservation biologists. Using single nucleotide polymorphism (SNP) multilocus genotypes for 31 sockeye salmon (<it>Oncorhynchus nerka</it>) populations from the Kvichak River, Alaska, we assessed the relative roles of geography (discrete boundaries or continuous distance) and ecology (spawning habitat and timing) driving genetic divergence in this species at varying spatial scales within the drainage. We also evaluated two outlier detection methods to characterize candidate SNPs responding to environmental selection, emphasizing which mechanism(s) may maintain the genetic variation of outlier loci.</p> <p>Results</p> <p>For the entire drainage, Mantel tests suggested a greater role of geographic distance on population divergence than differences in spawn timing when each variable was correlated with pairwise genetic distances. Clustering and hierarchical analyses of molecular variance indicated that the largest genetic differentiation occurred between populations from distinct lakes or subdrainages. Within one population-rich lake, however, Mantel tests suggested a greater role of spawn timing than geographic distance on population divergence when each variable was correlated with pairwise genetic distances. Variable spawn timing among populations was linked to specific spawning habitats as revealed by principal coordinate analyses. We additionally identified two outlier SNPs located in the major histocompatibility complex (MHC) class II that appeared robust to violations of demographic assumptions from an initial pool of eight candidates for selection.</p> <p>Conclusions</p> <p>First, our results suggest that geography and ecology have influenced genetic divergence between Alaskan sockeye salmon populations in a hierarchical manner depending on the spatial scale. Second, we found consistent evidence for diversifying selection in two loci located in the MHC class II by means of outlier detection methods; yet, alternative scenarios for the evolution of these loci were also evaluated. Both conclusions argue that historical contingency and contemporary adaptation have likely driven differentiation between Kvichak River sockeye salmon populations, as revealed by a suite of SNPs. Our findings highlight the need for conservation of complex population structure, because it provides resilience in the face of environmental change, both natural and anthropogenic.</p

Divergent life-history races do not represent Chinook salmon coast-wide: the importance of scale in Quaternary biogeography

The dynamic Quaternary geology of the Pacific Ring of Fire created substantial challenges for biogeography. Fish life history and population genetic variation were shaped by climate change, repeated formation and subsidence of ice sheets, sea-level change, volcanism and tectonics, isostatic rebound, and now human activities. It is widely recognized in Chinook salmon (Oncorhynchus tshawytscha) that parallel evolution and phenotypic plasticity have obscured range-wide patterns of life-history segregation with evolutionary lineage, yet the idea of the lineages themselves persists. We employed a large, internationally standardized, microsatellite data set to explore population structure at coast-wide scale and test for two divergent lineages, whether or not related to life history. We found at least 27 distinct lineages. However, relationships among groups were poorly resolved - essentially a star phylogeny. We found pervasive isolation by distance among groups, complicating cluster analysis. Only in the interior Columbia River (east of the Cascade Mountains) is there a deep genetic bifurcation that supports both the two-lineage hypothesis and the life-history segregation hypothesis. This broad-scale perspective helps reconcile different views of Chinook salmon phylogeography and life-history distribution.Keywords: Wire tag recoveries, North America, British Columbia, Reproductive isolation, Genetic popoulation structure, Columbia River Basin, Oncorhynchus Tshawytscha, Mitochondrial DNA variation, Pacific Salmon, Sockeye salmonThis is the publisher’s final pdf. The published article is copyrighted by NRC Research Press and can be found at: http://www.nrcresearchpress.com

snp4b convert input

single nucleotide polymorphism (SNP) genotype data in CONVERT format. Linked SNPs converted to haplotypes and uninformative SNPs removed (as described in paper)

convert input3SNP

Single nucleotide polymorphism (SNP) genotype data in CONVERT format. Includes all loci in raw format

Data from: Congruent population structure across paralogous and non-paralogous loci in Salish Sea chum salmon (Oncorhynchus keta)

Whole genome duplications are major evolutionary events with a lasting impact on genome structure. Duplication events complicate genetic analyses as paralogous sequences are difficult to distinguish; consequently paralogs are often excluded from studies. The effects of an ancient whole genome duplication (approximately 88MYA) are still evident in salmonids through the persistence of numerous paralogous gene sequences and partial tetrasomic inheritance. We use restriction site-associated DNA sequencing (RADseq) on ten collections of chum salmon from the Salish Sea in the USA and Canada to investigate genetic diversity and population structure in both tetrasomic and re-diploidized regions of the genome. We use a pedigree and high-density linkage map to identify paralogous loci and to investigate genetic variation across the genome. By applying multivariate statistical methods, we show that it is possible to characterize paralogous genetic loci and that they display similar patterns of population structure as the diploidized portion of the genome. We find genetic associations with the adaptively important trait of run timing in both sets of loci. By including paralogous loci in genome scans, we can observe evolutionary signals in genomic regions that have routinely been excluded from population genetic studies in other polyploid-derived species