Low but significant genetic differentiation underlies biologically meaningful phenotypic divergence in a large Atlantic salmon population

Aykanat, Tutku; Johnston, Susan E.; Orell, Panu; Niemelä, Eero; Erkinaro, Jaakko; Primmer, Craig R.

doi:10.1111/mec.13383

Cited by 50 publications

(90 citation statements)

References 117 publications

(183 reference statements)

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“…The differences with our study could be due to the different resolution of the molecular markers used or to real differences in connectivity mediated by a longer larval duration among others. Therefore, genome-wide SNP genotyping could provide much greater power than traditional markers to detect genetic differentiation and thus, to define barriers to the dispersion of studied organisms5152.…”

Section: Discussionmentioning

confidence: 99%

Population genomics of an endemic Mediterranean fish: differentiation by fine scale dispersal and adaptation

Carreras

Ordóñez

Zane

et al. 2017

Sci Rep

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The assessment of the genetic structuring of biodiversity is crucial for management and conservation. For species with large effective population sizes a low number of markers may fail to identify population structure. A solution of this shortcoming can be high-throughput sequencing that allows genotyping thousands of markers on a genome-wide approach while facilitating the detection of genetic structuring shaped by selection. We used Genotyping-by-Sequencing (GBS) on 176 individuals of the endemic East Atlantic peacock wrasse (Symphodus tinca), from 6 locations in the Adriatic and Ionian seas. We obtained a total of 4,155 polymorphic SNPs and we observed two strong barriers to gene flow. The first one differentiated Tremiti Islands, in the northwest, from all the other locations while the second one separated east and south-west localities. Outlier SNPs potentially under positive selection and neutral SNPs both showed similar patterns of structuring, although finer scale differentiation was unveiled with outlier loci. Our results reflect the complexity of population genetic structure and demonstrate that both habitat fragmentation and positive selection are on play. This complexity should be considered in biodiversity assessments of different taxa, including non-model yet ecologically relevant organisms.

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Section: Discussionmentioning

confidence: 99%

Population genomics of an endemic Mediterranean fish: differentiation by fine scale dispersal and adaptation

Carreras

Ordóñez

Zane

et al. 2017

Sci Rep

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“…() and Aykanat et al . (). Although the 7k SNP array was originally optimized for use with Norwegian aquaculture S. salar strains and markers are not all expected to be informative in the Teno system, most selected SNPs were from the final dataset of Aykanat et al .…”

Section: Methodsmentioning

confidence: 97%

“…() ( N = 2874) and therefore had been already filtered for high information content (minor allele frequency, f MA > 0·05). Here, information content was further increased by preferentially selecting SNPs that exhibited heterozygosity ( H O ) > 0·2 in the in the dataset (Aykanat et al ., ), though shift in H O distribution in the selected SNPs was not significantly different from zero (Mann–Whitney U = 118760, N 1,2 = 152,2874, P > 0·05). The number of SNPs on a chromosome was roughly proportional to the length of the chromosome (Fig.…”

Section: Methodsmentioning

confidence: 99%

“…S1, Supporting Information) and SNPs were selected to have linkage disequilibrium (LD) < 0·1 with physically adjacent SNPs ( r 2 , Hill & Robertson, ). Pairwise LD was estimated from genotype information for the Teno River main‐stem subpopulation 1 ( N = 347; Aykanat et al ., ), using the r2fast function in GenABEL package 1.8.0 (Aulchenko et al ., ) implemented in R (http://www.r-project.org).…”

Section: Methodsmentioning

confidence: 99%

“…Thus, a simple, inexpensive diagnostic assay for screening sea age genetic status of large numbers of individuals would be useful for management. Also, in the main stem of the Teno River of northern Finland, two cryptic subpopulations of S. salar have recently been identified that exhibit substantial phenotypic differentiation in size and age at maturity (Aykanat et al ., ). This is in addition to previously identified genetically distinct populations in various Teno River tributaries (Vähä et al ., ).…”

Section: Introductionmentioning

confidence: 97%

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From population genomics to conservation and management: a workflow for targeted analysis of markers identified using genome‐wide approaches in Atlantic salmon Salmo salar

Aykanat

Lindqvist

Pritchard

et al. 2016

Journal of Fish Biology

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A genotyping assay for the Ion Torrent Ion PGM platform was developed for fast and cost-effective targeted genotyping of key single nucleotide polymorphisms (SNPs) earlier identified using a genome-wide SNP array in Atlantic salmon Salmo salar. The method comprised a simple primer design step for multiplex-polymerase chain reaction (PCR), followed by two rounds of Ion Torrent Ion PGM sequencing to empirically evaluate marker efficiency in large multiplexes and to optimise or exclude them when necessary. Of 282 primer pairs initially tested, 217 were successfully amplified, indicating good amplification success (>75%). These markers included the sdy partial gene product to determine genetic sex, as well as three additional modules comprising SNPs for assessing neutral genetic variation (N = 150), examining functional genetic variation associated with sea age at maturity (N = 5), and for performing genetic subpopulation assignment (N = 61). The assay was primarily developed to monitor long-term genetic changes in S. salar from the Teno River, but modules are likely suitable for application in a wide range of S. salar populations. Furthermore, the fast and versatile assay development pipeline offers a strategy for developing targeted sequencing assays in any species.

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Contrasting genetic metrics and patterns among naturalized rainbow trout (Oncorhynchus mykiss) in two Patagonian lakes differentially impacted by trout aquaculture

Canales‐Aguirre

Seeb

et al. 2017

Ecology and Evolution

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Different pathways of propagation and dispersal of non‐native species into new environments may have contrasting demographic and genetic impacts on established populations. Repeated introductions of rainbow trout (Oncorhynchus mykiss) to Chile in South America, initially through stocking and later through aquaculture escapes, provide a unique setting to contrast these two pathways. Using a panel of single nucleotide polymorphisms, we found contrasting genetic metrics and patterns among naturalized trout in Lake Llanquihue, Chile's largest producer of salmonid smolts for nearly 50 years, and Lake Todos Los Santos (TLS), a reference lake where aquaculture has been prohibited by law. Trout from Lake Llanquihue showed higher genetic diversity, weaker genetic structure, and larger estimates for the effective number of breeders (N b) than trout from Lake TLS. Trout from Lake TLS were divergent from Lake Llanquihue and showed marked genetic structure and a significant isolation‐by‐distance pattern consistent with secondary contact between documented and undocumented stocking events in opposite shores of the lake. Multiple factors, including differences in propagule pressure, origin of donor populations, lake geomorphology, habitat quality or quantity, and life history, may help explain contrasting genetic metrics and patterns for trout between lakes. We contend that high propagule pressure from aquaculture may not only increase genetic diversity and N b via demographic effects and admixture, but also may impact the evolution of genetic structure and increase gene flow, consistent with findings from artificially propagated salmonid populations in their native and naturalized ranges.

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Low but significant genetic differentiation underlies biologically meaningful phenotypic divergence in a large Atlantic salmon population

Cited by 50 publications

References 117 publications

Population genomics of an endemic Mediterranean fish: differentiation by fine scale dispersal and adaptation

Population genomics of an endemic Mediterranean fish: differentiation by fine scale dispersal and adaptation

From population genomics to conservation and management: a workflow for targeted analysis of markers identified using genome‐wide approaches in Atlantic salmon Salmo salar

Contrasting genetic metrics and patterns among naturalized rainbow trout (Oncorhynchus mykiss) in two Patagonian lakes differentially impacted by trout aquaculture

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