Dataset Information

Striking Phenotypic Variation yet Low Genetic Differentiation in Sympatric Lake Trout (Salvelinus namaycush).

ABSTRACT: The study of population differentiation in the context of ecological speciation is commonly assessed using populations with obvious discreteness. Fewer studies have examined diversifying populations with occasional adaptive variation and minor reproductive isolation, so factors impeding or facilitating the progress of early stage differentiation are less understood. We detected non-random genetic structuring in lake trout (Salvelinus namaycush) inhabiting a large, pristine, postglacial lake (Mistassini Lake, Canada), with up to five discernible genetic clusters having distinctions in body shape, size, colouration and head shape. However, genetic differentiation was low (FST = 0.017) and genetic clustering was largely incongruent between several population- and individual-based clustering approaches. Genotype- and phenotype-environment associations with spatial habitat, depth and fish community structure (competitors and prey) were either inconsistent or weak. Striking morphological variation was often more continuous within than among defined genetic clusters. Low genetic differentiation was a consequence of relatively high contemporary gene flow despite large effective population sizes, not migration-drift disequilibrium. Our results suggest a highly plastic propensity for occupying multiple habitat niches in lake trout and a low cost of morphological plasticity, which may constrain the speed and extent of adaptive divergence. We discuss how factors relating to niche conservatism in this species may also influence how plasticity affects adaptive divergence, even where ample ecological opportunity apparently exists.

SUBMITTER: Marin K

PROVIDER: S-EPMC5040267 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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Striking Phenotypic Variation yet Low Genetic Differentiation in Sympatric Lake Trout (Salvelinus namaycush).

Marin Kia K Coon Andrew A Carson Robert R Debes Paul V PV Fraser Dylan J DJ

PloS one 20160928 9

The study of population differentiation in the context of ecological speciation is commonly assessed using populations with obvious discreteness. Fewer studies have examined diversifying populations with occasional adaptive variation and minor reproductive isolation, so factors impeding or facilitating the progress of early stage differentiation are less understood. We detected non-random genetic structuring in lake trout (Salvelinus namaycush) inhabiting a large, pristine, postglacial lake (Mis ...[more]

PMID: 27680019

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Project description:Abstract Kinship‐based methods of population assessment such as close‐kin mark‐recapture require accurate and efficient genotyping methods capable of resolving complex relationships among kin. Inference of such relationships can be difficult using biallelic loci due to the large number of markers required to obtain the necessary power. Sequencing‐based microsatellite panels offer an efficient alternative, combining high polymorphism with efficient next‐generation methods. Here we construct, optimize, and test one such panel for lake trout (Salvelinus namaycush) using a combination of previously‐published loci adapted for sequencing and de novo loci mined from a genome assembly. We performed three rounds of primer optimization, yielding a final panel of 131 loci, followed by testing with two different levels of PCR multiplexing (all primers in one or two groups) and two different reaction volumes (5 and 10 μL). Our results showed that the use of the largest multiplex and smallest reaction volume did not substantially change results, allowing significant cost and time savings. To test panel accuracy, we used both a set of 153 known‐origin samples from origins of management interest and a series of hatchery crosses representing nine families with parent‐offspring, half‐sibling, and largely‐unrelated pairs. Our results indicate that sequencing‐based microsatellite panels can efficiently and accurately provide the information required for a population genetics analyses including population assignment, calculation of between‐population FST, and kinship‐based population estimation techniques. Such techniques are seeing increasing applications for a wide range of taxa; our findings should provide insight and guidance for the development of the necessary molecular resources. Kinship‐based methods of population assessment such as close‐kin mark‐recapture require accurate and efficient genotyping methods capable of resolving complex relationships among kin, but inference of such relationships can be difficult using biallelic loci. Sequencing‐based microsatellite panels offer an efficient alternative, combining high polymorphism with efficient next‐generation methods. Here we construct, optimize, and test one such panel for lake trout (Salvelinus namaycush) using a combination of historical loci adapted for sequencing and de novo loci mined from a genome assembly.

Dataset Information

Striking Phenotypic Variation yet Low Genetic Differentiation in Sympatric Lake Trout (Salvelinus namaycush).

Publications

Striking Phenotypic Variation yet Low Genetic Differentiation in Sympatric Lake Trout (Salvelinus namaycush).

Similar Datasets

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