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  • 1
    Online Resource
    Online Resource
    Mixed-stock analyses of migratory, non-native Chinook salmon at sea and assignment to natal sites in fresh water at their introduced range in South America
    Springer Science and Business Media LLC ; 2020
    In:  Biological Invasions Vol. 22, No. 11 ( 2020-11), p. 3175-3182
    Details
    In: Biological Invasions, Springer Science and Business Media LLC, Vol. 22, No. 11 ( 2020-11), p. 3175-3182
    Type of Medium: Online Resource
    ISSN: 1387-3547 , 1573-1464
    URL: Article
    DOI: 10.1007/s10530-020-02319-0
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2020
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    SSG: 12
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  • 2
    Online Resource
    Online Resource
    An empirical comparison of SNPs and microsatellites for parentage and kinship assignment in a wild sockeye salmon ( Oncorhynchus nerka ) population
    Wiley ; 2011
    In:  Molecular Ecology Resources Vol. 11, No. s1 ( 2011-03), p. 150-161
    Details
    In: Molecular Ecology Resources, Wiley, Vol. 11, No. s1 ( 2011-03), p. 150-161
    Abstract: Because of their high variability, microsatellites are still considered the marker of choice for studies on parentage and kinship in wild populations. Nevertheless, single nucleotide polymorphisms (SNPs) are becoming increasing popular in many areas of molecular ecology, owing to their high‐throughput, easy transferability between laboratories and low genotyping error. An ongoing discussion concerns the relative power of SNPs compared to microsatellites—that is, how many SNP loci are needed to replace a panel of microsatellites? Here, we evaluate the assignment power of 80 SNPs ( H E  = 0.30, 80 independent alleles) and 11 microsatellites ( H E  = 0.85, 192 independent alleles) in a wild population of about 400 sockeye salmon with two commonly used software packages (Cervus3, Colony2) and, for SNPs only, a newly developed software (SNPPIT). Assignment success was higher for SNPs than for microsatellites, especially for parent pairs, irrespective of the method used. Colony2 assigned a larger proportion of offspring to at least one parent than the other methods, although Cervus and SNPPIT detected more parent pairs. Identification of full‐sib groups without parental information from relatedness measures was possible using both marker systems, although explicit reconstruction of such groups in Colony2 was impossible for SNPs because of computation time. Our results confirm the applicability of SNPs for parentage analyses and refute the predictability of assignment success from the number of independent alleles.
    Type of Medium: Online Resource
    ISSN: 1755-098X , 1755-0998
    URL: Issue
    URL: Article
    DOI: 10.1111/men.2011.11.issue-s1
    DOI: 10.1111/j.1755-0998.2010.02961.x
    Language: English
    Publisher: Wiley
    Publication Date: 2011
    detail.hit.zdb_id: 2406833-0
    SSG: 12
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  • 3
    Online Resource
    Online Resource
    Recombination patterns reveal information about centromere location on linkage maps
    Wiley ; 2016
    In:  Molecular Ecology Resources Vol. 16, No. 3 ( 2016-05), p. 655-661
    Details
    In: Molecular Ecology Resources, Wiley, Vol. 16, No. 3 ( 2016-05), p. 655-661
    Abstract: Linkage mapping is often used to identify genes associated with phenotypic traits and for aiding genome assemblies. Still, many emerging maps do not locate centromeres – an essential component of the genomic landscape. Here, we demonstrate that for genomes with strong chiasma interference, approximate centromere placement is possible by phasing the same data used to generate linkage maps. Assuming one obligate crossover per chromosome arm, information about centromere location can be revealed by tracking the accumulated recombination frequency along linkage groups, similar to half‐tetrad analyses. We validate the method on a linkage map for sockeye salmon ( Oncorhynchus nerka ) with known centromeric regions. Further tests suggest that the method will work well in other salmonids and other eukaryotes. However, the method performed weakly when applied to a male linkage map (rainbow trout; O. mykiss ) characterized by low and unevenly distributed recombination – a general feature of male meiosis in many species. Further, a high frequency of double crossovers along chromosome arms in barley reduced resolution for locating centromeric regions on most linkage groups. Despite these limitations, our method should work well for high‐density maps in species with strong recombination interference and will enrich many existing and future mapping resources.
    Type of Medium: Online Resource
    ISSN: 1755-098X , 1755-0998
    URL: Issue
    URL: Article
    DOI: 10.1111/men.2016.16.issue-3
    DOI: 10.1111/1755-0998.12484
    Language: English
    Publisher: Wiley
    Publication Date: 2016
    detail.hit.zdb_id: 2406833-0
    SSG: 12
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  • 4
    Online Resource
    Online Resource
    Paralogs are revealed by proportion of heterozygotes and deviations in read ratios in genotyping‐by‐sequencing data from natural populations
    Wiley ; 2017
    In:  Molecular Ecology Resources Vol. 17, No. 4 ( 2017-07), p. 656-669
    Details
    In: Molecular Ecology Resources, Wiley, Vol. 17, No. 4 ( 2017-07), p. 656-669
    Abstract: Whole‐genome duplications have occurred in the recent ancestors of many plants, fish, and amphibians, resulting in a pervasiveness of paralogous loci and the potential for both disomic and tetrasomic inheritance in the same genome. Paralogs can be difficult to reliably genotype and are often excluded from genotyping‐by‐sequencing (GBS) analyses; however, removal requires paralogs to be identified which is difficult without a reference genome. We present a method for identifying paralogs in natural populations by combining two properties of duplicated loci: (i) the expected frequency of heterozygotes exceeds that for singleton loci, and (ii) within heterozygotes, observed read ratios for each allele in GBS data will deviate from the 1:1 expected for singleton (diploid) loci. These deviations are often not apparent within individuals, particularly when sequence coverage is low; but, we postulated that summing allele reads for each locus over all heterozygous individuals in a population would provide sufficient power to detect deviations at those loci. We identified paralogous loci in three species: Chinook salmon ( Oncorhynchus tshawytscha ) which retains regions with ongoing residual tetrasomy on eight chromosome arms following a recent whole‐genome duplication, mountain barberry ( Berberis alpina ) which has a large proportion of paralogs that arose through an unknown mechanism, and dusky parrotfish ( Scarus niger ) which has largely rediploidized following an ancient whole‐genome duplication. Importantly, this approach only requires the genotype and allele‐specific read counts for each individual, information which is readily obtained from most GBS analysis pipelines.
    Type of Medium: Online Resource
    ISSN: 1755-098X , 1755-0998
    URL: Issue
    URL: Article
    DOI: 10.1111/men.2017.17.issue-4
    DOI: 10.1111/1755-0998.12613
    Language: English
    Publisher: Wiley
    Publication Date: 2017
    detail.hit.zdb_id: 2406833-0
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  • 5
    Online Resource
    Online Resource
    Genetic Relationships Among Salvelinus Species Inferred from Allozyme Data
    Canadian Science Publishing ; 1994
    In:  Canadian Journal of Fisheries and Aquatic Sciences Vol. 51, No. S1 ( 1994-12-19), p. 182-197
    Details
    In: Canadian Journal of Fisheries and Aquatic Sciences, Canadian Science Publishing, Vol. 51, No. S1 ( 1994-12-19), p. 182-197
    Abstract: We studied phylogenetic relationships in the genus Salvelinus with emphasis on S. alpinus, S. malma, and S. confluentus. Sixty allozyme loci were resolved in 422 individuals representing six species from a worldwide distribution. We used phenetic (UPGMA), phylogenetic (Fitch and Margoliash), and maximum-likelihood techniques to derive estimates of Salvelinus phylogeny. Three almost identical topologies were produced, but we chose the Fitch and Margoliash topology as the best phylogenetic estimate. The distances used to construct this tree assume that gene frequencies are affected only by genetic drift, which we argued was the dominant speciation force in Salvelinus. This topology was also the shortest. Jackknifing the Fitch and Margoliash tree resolved the branching order among the three Salvelinus subgenera: S. [Baione], S. [Cristivomer] , and S. [Salvelinus]. It also revealed two sister groups within the Salvelinus subgenus: S. leucomaenis – S. confluentus and S. alpinus – S. malma.
    Type of Medium: Online Resource
    ISSN: 0706-652X , 1205-7533
    URL: Article
    DOI: 10.1139/f94-304
    Language: English
    Publisher: Canadian Science Publishing
    Publication Date: 1994
    detail.hit.zdb_id: 7966-2
    detail.hit.zdb_id: 1473089-3
    SSG: 21,3
    SSG: 12
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  • 6
    Online Resource
    Online Resource
    Allele frequency stability in large, wild exploited populations over multiple generations: insights from Alaska sockeye salmon ( Oncorhynchus nerka )
    Canadian Science Publishing ; 2012
    In:  Canadian Journal of Fisheries and Aquatic Sciences Vol. 69, No. 5 ( 2012-05), p. 916-929
    Details
    In: Canadian Journal of Fisheries and Aquatic Sciences, Canadian Science Publishing, Vol. 69, No. 5 ( 2012-05), p. 916-929
    Abstract: 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 (N b ). Third, estimates of N b were 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.
    Type of Medium: Online Resource
    ISSN: 0706-652X , 1205-7533
    URL: Article
    DOI: 10.1139/f2012-029
    Language: English
    Publisher: Canadian Science Publishing
    Publication Date: 2012
    detail.hit.zdb_id: 7966-2
    detail.hit.zdb_id: 1473089-3
    SSG: 21,3
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  • 7
    Online Resource
    Online Resource
    Conserved islands of divergence associated with adaptive variation in sockeye salmon are maintained by multiple mechanisms
    Wiley ; 2023
    In:  Molecular Ecology
    Details
    In: Molecular Ecology, Wiley
    Abstract: Local adaptation is facilitated by loci clustered in relatively few regions of the genome, termed genomic islands of divergence. The mechanisms that create and maintain these islands and how they contribute to adaptive divergence is an active research topic. Here, we use sockeye salmon as a model to investigate both the mechanisms responsible for creating islands of divergence and the patterns of differentiation at these islands. Previous research suggested that multiple islands contributed to adaptive radiation of sockeye salmon. However, the low‐density genomic methods used by these studies made it difficult to fully elucidate the mechanisms responsible for islands and connect genotypes to adaptive variation. We used whole genome resequencing to genotype millions of loci to investigate patterns of genetic variation at islands and the mechanisms that potentially created them. We discovered 64 islands, including 16 clustered in four genomic regions shared between two isolated populations. Characterisation of these four regions suggested that three were likely created by structural variation, while one was created by processes not involving structural variation. All four regions were small ( 〈  600 kb), suggesting low recombination regions do not have to span megabases to be important for adaptive divergence. Differentiation at islands was not consistently associated with established population attributes. In sum, the landscape of adaptive divergence and the mechanisms that create it are complex; this complexity likely helps to facilitate fine‐scale local adaptation unique to each population.
    Type of Medium: Online Resource
    ISSN: 0962-1083 , 1365-294X
    URL: Article
    DOI: 10.1111/mec.17126
    RVK:
    WA 15000
    Language: English
    Publisher: Wiley
    Publication Date: 2023
    detail.hit.zdb_id: 2020749-9
    detail.hit.zdb_id: 1126687-9
    SSG: 12
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  • 8
    Online Resource
    Online Resource
    Retention of a chromosomal inversion from an anadromous ancestor provides the genetic basis for alternative freshwater ecotypes in rainbow trout
    Wiley ; 2019
    In:  Molecular Ecology Vol. 28, No. 6 ( 2019-03), p. 1412-1427
    Details
    In: Molecular Ecology, Wiley, Vol. 28, No. 6 ( 2019-03), p. 1412-1427
    Abstract: Migratory behaviour patterns in animals are controlled by a complex genetic architecture. Rainbow trout ( Oncorhynchus mykiss ) is a salmonid fish that spawns in streams but exhibits three primary life history pathways: stream‐resident (fluvial), lake‐migrant (adfluvial) and ocean‐migrant (anadromous). Previous studies examining fluvial and anadromous O .  mykiss have identified several genes associated with life history divergence including the presence of an inversion complex within chromosome 5 (Omy05) that appears to maintain a suite of linked genes controlling migratory behaviour. However, adfluvial trout are migratory without being anadromous, and the genetic basis for this life history has not been investigated from evolutionary perspectives. We sampled wild, native nonanadromous rainbow trout occupying connected stream and lake habitats in a southwest Alaskan watershed to determine whether these fish exhibit genetic divergence between fluvial and adfluvial ecotypes, and whether that divergence parallels that documented in fluvial and anadromous O. mykiss . Data from restriction site‐associated DNA (RAD) sequencing revealed an association between frequencies of both the Omy05 inversion complex and other single nucleotide polymorphisms (SNPs) with habitat type (stream or lake), supporting the genetic divergence of fluvial and adfluvial individuals in sympatry. The presence of a genetic basis for migration into lakes, analogous to that documented for anadromy, indicates that the adfluvial ecotype must be recognized separately from the fluvial form of O .  mykiss even though neither is anadromous. These results highlight the genetic architecture underlying migration and the importance of chromosomal inversions in promoting and sustaining intraspecific diversity.
    Type of Medium: Online Resource
    ISSN: 0962-1083 , 1365-294X
    URL: Issue
    URL: Article
    DOI: 10.1111/mec.2019.28.issue-6
    DOI: 10.1111/mec.15037
    RVK:
    WA 15000
    Language: English
    Publisher: Wiley
    Publication Date: 2019
    detail.hit.zdb_id: 2020749-9
    detail.hit.zdb_id: 1126687-9
    SSG: 12
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  • 9
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    Online Resource
    Transforming ecology and conservation biology through genome editing
    Wiley ; 2020
    In:  Conservation Biology Vol. 34, No. 1 ( 2020-02), p. 54-65
    Details
    In: Conservation Biology, Wiley, Vol. 34, No. 1 ( 2020-02), p. 54-65
    Abstract: Article impact statement : Novel applications of CRISPR technology have the potential to make significant contributions to ecology and conservation.
    Type of Medium: Online Resource
    ISSN: 0888-8892 , 1523-1739
    URL: Issue
    URL: Article
    DOI: 10.1111/cobi.v34.1
    DOI: 10.1111/cobi.13292
    Language: English
    Publisher: Wiley
    Publication Date: 2020
    detail.hit.zdb_id: 2020041-9
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  • 10
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    Temporally Isolated Lineages of Pink Salmon Reveal Unique Signatures of Selection on Distinct Pools of Standing Genetic Variation
    Oxford University Press (OUP) ; 2014
    In:  Journal of Heredity Vol. 105, No. 6 ( 2014), p. 835-845
    Details
    In: Journal of Heredity, Oxford University Press (OUP), Vol. 105, No. 6 ( 2014), p. 835-845
    Type of Medium: Online Resource
    ISSN: 0022-1503 , 1465-7333
    URL: Article
    DOI: 10.1093/jhered/esu063
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2014
    detail.hit.zdb_id: 1466720-4
    detail.hit.zdb_id: 2518163-4
    SSG: 12
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