0000000001320632
AUTHOR
Anti Vasemägi
Genome-wide divergence patterns support fine-scaled genetic structuring associated with migration tendency in brown trout
Brown trout (Salmo trutta) exhibit highly diverse life histories varying from resident, slow-growing, and early maturing to migratory, fast-growing, and late maturing, even within single watersheds. We sampled 11 locations within the transboundary Finnish–Russian River Koutajoki watershed to evaluate genomic differences among mainstem and headwater sites, of which some are isolated by migration barriers. Restriction site associated sequencing (RADSeq) revealed that the most headwater localities supported unique, isolated populations with generally lower heterozygosity compared with the mainstem populations. The sampled migratory adults in the three main stems showed signals of admixture de…
Comparing RADseq and microsatellites for estimating genetic diversity and relatedness : Implications for brown trout conservation
The conservation and management of endangered species requires information on their genetic diversity, relatedness and population structure. The main genetic markers applied for these questions are microsatellites and single nucleotide polymorphisms (SNPs), the latter of which remain the more resource demanding approach in most cases. Here, we compare the performance of two approaches, SNPs obtained by restriction-site-associated DNA sequencing (RADseq) and 16 DNA microsatellite loci, for estimating genetic diversity, relatedness and genetic differentiation of three, small, geographically close wild brown trout (Salmo trutta) populations and a regionally used hatchery strain. The genetic di…
Prediction of harmful variants on mitochondrial genes : Test of habitat-dependent and demographic effects in a euryhaline fish
Both effective population size and life history may influence the efficacy of purifying selection, but it remains unclear if the environment affects the accumulation of weakly deleterious nonsynonymous polymorphisms. We hypothesize that the reduced energetic cost of osmoregulation in brackish water habitat may cause relaxation of selective constraints at mitochondrial oxidative phosphorylation (OXPHOS) genes. To test this hypothesis, we analyzed 57 complete mitochondrial genomes of Pungitius pungitius collected from brackish and freshwater habitats. Based on inter- and intraspecific comparisons, we estimated that 84% and 68% of the nonsynonymous polymorphisms in the freshwater and brackish …
The era of reference genomes in conservation genomics
Progress in genome sequencing now enables the large-scale generation of reference genomes. Various international initiatives aim to generate reference genomes representing global biodiversity. These genomes provide unique insights into genomic diversity and architecture, thereby enabling comprehensive analyses of population and functional genomics, and are expected to revolutionize conservation genomics.
Association Mapping Based on a Common-Garden Migration Experiment Reveals Candidate Genes for Migration Tendency in Brown Trout
A better understanding of the environmental and genetic contribution to migratory behavior and the evolution of traits linked to migration is crucial for fish conservation and fisheries management. Up to date, a few genes with unequivocal influence on the adoption of alternative migration strategies have been identified in salmonids. Here, we used a common garden set-up to measure individual migration distances of generally highly polymorphic brown trout Salmo trutta from two populations. Fish from the assumedly resident population showed clearly shorter migration distances than the fish from the assumed migratory population at the ages of 2 and 3 years. By using two alternative analytical …
Comparison of migratory and resident populations of brown trout reveals candidate genes for migration tendency
Candidate genes associated with migration have been identified in multiple taxa: including salmonids, many of whom perform migrations requiring a series of physiological changes associated with the freshwater–saltwater transition. We screened over 5,500 SNPs for signatures of selection related to migratory behavior of brown trout Salmo trutta by focusing on ten differentially migrating freshwater populations from two watersheds (the Koutajoki and the Oulujoki). We found eight outlier SNPs potentially associated with migratory versus resident life history using multiple (≥3) outlier detection approaches. Comparison of three migratory versus resident population pairs in the Koutajoki watershe…
Comparison of Migratory and Resident Populations of Brown Trout Reveals Candidate Genes for Migration Tendency
Abstract Candidate genes associated with migration have been identified in multiple taxa: including salmonids, many of whom perform migrations requiring a series of physiological changes associated with the freshwater–saltwater transition. We screened over 5,500 SNPs for signatures of selection related to migratory behavior of brown trout Salmo trutta by focusing on ten differentially migrating freshwater populations from two watersheds (the Koutajoki and the Oulujoki). We found eight outlier SNPs potentially associated with migratory versus resident life history using multiple (≥3) outlier detection approaches. Comparison of three migratory versus resident population pairs in the Koutajoki…
Supplemental Material for Lemopoulos et al., 2019
Beagle file for the ANGSD pipeline. Genotype probabilities of 116 brown trout. 7520 SNPs are identified and mapped to corresponding location in the Atlantic salmon genome.
Management of human-induced contemporary evolution to maintain and restore genetic diversity in brown trout
Maintaining genetic diversity and integrity of animal populations is a key challenge in conservation. While ecological population declines can be reversed, loss of genetic diversity and original trait distribution is often a one-way road. Migratory brown trout is critically endangered in Finland due to extensive modification of river ecosystems and unrestricted fishing on feeding areas. In addition to being too intense in general, fishing creates challenges by being selective for a number of traits in fish. We have shown that recreational angling, for example, is selective for certain personality traits and can cause inherited behavioural changes in the offspring of brown trout. Only a few …
Genetic causes and consequences of Brown trout migratory behaviour
Salmonids are among the most famous and economically important migrating organisms, but unfortunately also often endangered because of multiple human activities. As many other salmonids, brown trout exhibits diverse life history types related to migration strategies. Resident brown trout stay in rivers for their entire life. In contrast, migratory trout undergo a physiological and morphological transformation called smoltification before leaving their natal rivers to enter either sea, lakes or larger river sections. While the phenotypic variation between resident and migratory ecotypes is well documented, little is known about the intraspecific genetic variation associated with these differ…