Whole‐genome resequencing confirms reproductive isolation between sympatric demes of brown trout (<i>Salmo trutta</i>) detected with allozymes

Saha, Atal; Andersson, Anastasia; Kurland, Sara; Keehnen, Naomi; Kutschera, Verena E.; Hössjer, Ola; Ekman, Diana; Karlsson, Sten; Kardos, Marty; Ståhl, Gunnar; Allendorf, Fred W.; Ryman, Nils; Laikre, Linda

doi:10.1111/mec.16252

Cited by 12 publications

(24 citation statements)

References 83 publications

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“…Our present 96 SNPs were selected from 3,782 SNPs variable in Danish brown trout (Bekkevold et al, 2019). The 96 SNPs are distributed across the genome, with 1-3 SNPs on each of the 40 chromosomes (Saha et al, 2021).…”

Section: Genotypingmentioning

confidence: 99%

“…To quantify changes in genetic diversity over time we used three indicators suggested for national monitoring and management of genetic resources in aquatic environments in Sweden . We also applied the three indicators proposed for the CBD context by Laikre et al (2020) and elaborated by Hoban et al (2020Hoban et al ( , 2021b and Laikre et al (2021;Figure 2). These indicators are pragmatic and designed to be applicable at a global scale by all nations with indicators 1 and 2 possible to apply using proxies in the absence of genetic data (Figure 2; Hoban et al, 2020Hoban et al, , 2021bLaikre et al, 2021).…”

Section: Indicatorsmentioning

confidence: 99%

“…The species is suitable also because of its tendency to form genetically distinct populations over even restricted areas (Bekkevold et al, 2020), thus enabling monitoring of the between population diversity component. We were particularly interested in mapping the potential occurrence of multiple, genetically distinct populations in the same small lake (so-called cryptic sympatry; Andersson, 2021). Such hidden biodiversity has only been documented in two cases for brown trout (Ryman et al, 1979;Andersson et al, 2017a;Saha et al, 2021) but may be more common than currently recognized because of limited statistical power in detecting them using typically applied sample sizes (Jorde et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

“…We were particularly interested in mapping the potential occurrence of multiple, genetically distinct populations in the same small lake (so-called cryptic sympatry; Andersson, 2021). Such hidden biodiversity has only been documented in two cases for brown trout (Ryman et al, 1979;Andersson et al, 2017a;Saha et al, 2021) but may be more common than currently recognized because of limited statistical power in detecting them using typically applied sample sizes (Jorde et al, 2018). Finally, the brown trout carries a key ecological role in these lakes where it is a top predator and often the only fish species; its cultural and socio-economic value is also high (Frank et al, 2011;Marco-Rius et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

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Mapping and monitoring genetic diversity of an alpine freshwater top predator by applying newly proposed indicators

Andersson

Karlsson

Ryman

et al. 2021

Preprint

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Genetic diversity is the basis for population adaptation and long-term survival, yet rarely considered in biodiversity monitoring. One key issue is the need for useful and straightforward indicators of genetic diversity. To test newly proposed indicators, we monitored genetic diversity over 40 years (1970-2010) in metapopulations of brown trout inhabiting 27 small mountain lakes representing 10 water systems in central Sweden. Three of the indicators were previously proposed for broad, international use for the Convention on Biological Diversity (CBD) context, while three others were recently elaborated for national use by a Swedish science-management effort and applied for the first time here. The Swedish indicators use molecular genetic data to monitor genetic diversity within and between populations and assess the effective population size (Ne). We used a panel of 96 SNPs and identified 29 discrete populations retained over time. Over 40 percent of the lakes harbored more than one population indicating that brown trout biodiversity hidden as cryptic, sympatric populations are more common than recognized. The Ne indicator showed values below the threshold (Ne≤500) in 20 populations with five showing Ne<100. Although statistically significant genetic diversity reductions occurred in several populations, they were mostly within proposed threshold limits. Metapopulation structure appears to buffer against diversity loss; when applying the indicators to metapopulations most indicators suggest an acceptable genetic status in all but one system. The CBD indicators agreed with the national ones but provided less detail. We propose that all indicators applied here are appropriate for monitoring genetic diversity within species.

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Section: Genotypingmentioning

confidence: 99%

Section: Indicatorsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Mapping and monitoring genetic diversity of an alpine freshwater top predator by applying newly proposed indicators

Andersson

Karlsson

Ryman

et al. 2021

Preprint

Self Cite

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show abstract

“…current systems, fronts, gyres and eddies) or environmental gaps limiting dispersal (Blanco‐González et al, 2016 ; Nielsen et al, 2004 ; Vera et al, 2016 ; Xuereb et al, 2018 ), but also natural local selection in response to environmental variation (Clucas et al, 2019 ; Jiménez‐Mena et al, 2020 ; Vilas et al, 2015 ). Furthermore, historical vicariance, not yet erased by gene flow, and reproductive isolation can be other factors explaining differentiation (Gagnaire et al, 2015 ; Riginos et al, 2016 ; Saha et al, 2021 ). Distinguishing between neutral and adaptive genetic variation in the marine landscape has become a central issue in conservation biology, allowing for interpreting genetic variation in both historical/demographic and adaptive terms (Bernatchez, 2016 ; Nielsen et al, 2009 ).…”

Section: Introductionmentioning

confidence: 99%

Genomic survey of edible cockle (Cerastoderma edule) in the Northeast Atlantic: A baseline for sustainable management of its wild resources

Vera

Maroso

Wilmes

et al. 2022

Evolutionary Applications

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Knowledge on correlations between environmental factors and genome divergence between populations of marine species is crucial for sustainable management of fisheries and wild populations. The edible cockle (Cerastoderma edule) is a marine bivalve distributed along the Northeast Atlantic coast of Europe and is an important resource from both commercial and ecological perspectives. We performed a population genomics screening using 2b‐RAD genotyping on 9309 SNPs localized in the cockle's genome on a sample of 536 specimens pertaining to 14 beds in the Northeast Atlantic Ocean to analyse the genetic structure with regard to environmental variables. Larval dispersal modelling considering species behaviour and interannual/interseasonal variation in ocean conditions was carried out as an essential background to which compare genetic information. Cockle populations in the Northeast Atlantic displayed low but significant geographical differentiation between populations (FST = 0.0240; p < 0.001), albeit not across generations. We identified 742 and 36 outlier SNPs related to divergent and balancing selection in all the geographical scenarios inspected, and sea temperature and salinity were the main environmental correlates suggested. Highly significant linkage disequilibrium was detected at specific genomic regions against the very low values observed across the whole genome. Two main genetic groups were identified, northwards and southwards of French Brittany. Larval dispersal modelling suggested a barrier for larval dispersal linked to the Ushant front that could explain these two genetic clusters. Further genetic subdivision was observed using outlier loci and considering larval advection. The northern group was divided into the Irish/Celtic Seas and the English Channel/North Sea, while the southern group was divided into three subgroups. This information represents the baseline for the management of cockles, designing conservation strategies, founding broodstock for depleted beds and producing suitable seed for aquaculture production.

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Genomic dynamics of brown trout populations released to a novel environment

Kurland

Rafati

Ryman

et al. 2022

Ecology and Evolution

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Population translocations occur for a variety of reasons, from displacement due to climate change to human-induced transfers. Such actions have adverse effects on genetic variation and understanding their microevolutionary consequences requires monitoring. Here, we return to an experimental release of brown trout (Salmo trutta) in order to monitor the genomic effects of population translocations. In 1979, fish from each of two genetically (F ST = 0.16) and ecologically separate populations were simultaneously released, at one point in time, to a lake system previously void of brown trout. Here, whole-genome sequencing of pooled DNA (Pool-seq) is used to characterize diversity within and divergence between the introduced populations and fish inhabiting two lakes downstream of the release sites, sampled 30 years later (c. 5 generations). Present results suggest that while extensive hybridization has occurred, the two introduced populations are unequally represented in the lakes downstream of the release sites. One population, which is ecologically resident in its original habitat, mainly contributes to the lake closest to the release site. The other population, migratory in its natal habitat, is genetically more represented in the lake further downstream. Genomic regions putatively under directional selection in the new habitat are identified, where allele frequencies in both established populations are more similar to the introduced population stemming from a resident population than the migratory one. Results suggest that the microevolutionary consequences of population translocations, for example, hybridization and adaptation, can be rapid and that Pool-seq can be used as an initial tool to monitor genome-wide effects.

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Whole‐genome resequencing confirms reproductive isolation between sympatric demes of brown trout (Salmo trutta) detected with allozymes

Abstract: This is an open access article under the terms of the Creat ive Commo ns Attri butio n-NonCo mmerc ial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.

Cited by 12 publications

References 83 publications

Mapping and monitoring genetic diversity of an alpine freshwater top predator by applying newly proposed indicators

Mapping and monitoring genetic diversity of an alpine freshwater top predator by applying newly proposed indicators

Genomic survey of edible cockle (Cerastoderma edule) in the Northeast Atlantic: A baseline for sustainable management of its wild resources

Genomic dynamics of brown trout populations released to a novel environment

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