Drivers of neutral and adaptive differentiation in pike (<i>Esox lucius</i>) populations from contrasting environments

Sunde, Johanna; Yıldırım, Yeşerin; Tibblin, Petter; Bekkevold, Dorte; Skov, Christian; Nordahl, Oscar; Larsson, Per; Forsman, Anders

doi:10.1111/mec.16315

Cited by 19 publications

(18 citation statements)

References 178 publications

(223 reference statements)

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“…Levels of overall genetic diversity observed in the localities using the NL and OL datasets ( H O = 0.073 and H O = 0.061, respectively, Table 1 ) were lower than the reported for other TEP marine organisms using microsatellite data ( García-De León et al, 2018 ; Reguera-Rouzaud et al, 2021 ), but they are comparable with values obtained using genomic data. This is the case of the genus Jasus ( J. cavereorum H O = 0.012 and J. paulensis H O = 0.087) ( Silva et al, 2021 ), Symphodus tinca , S. ocellatus ( Torrado et al, 2020 ), and for the freshwater species Esox lucius ( Sunde et al, 2022 ). A proper evaluation of the lower values of heterozygosity is necessary to avoid reaching erroneous conclusions.…”

Section: Discussionmentioning

confidence: 97%

Genomic assessment reveals signal of adaptive selection in populations of the Spotted rose snapper Lutjanus guttatus from the Tropical Eastern Pacific

Mar‐Silva

Díaz‐Jaimes

Domínguez-Mendoza

et al. 2023

PeerJ

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Background The lack of barriers in the marine environment has promoted the idea of panmixia in marine organisms. However, oceanographic conditions and habitat characteristics have recently been linked to genetic structure in marine species. The Tropical Eastern Pacific (TEP) is characterized by dynamic current systems and heterogeneous oceanographic conditions. The Gulf of Panama (part of the equatorial segment for the TEP) is influenced by a complex current system and heterogeneous environment, which has been shown to limit the gene flow for shoreline species. Next Generation Sequencing (NGS) has contributed to detect genetic differences in previously reported panmictic species by the assessment of loci associated with selection and to understand how selection acts affects marine populations. Lutjanus guttatus is a species distributed in the TEP for which previous studies using mitochondrial data recovered a panmictic pattern along its distributional range. In this study, we used SNP data of L. guttatus individuals sampled along its range to evaluate population genetic structure and investigate whether oceanographic factors influence the species’ genetic architecture. Finally, we assessed the role of adaptive selection by evaluating the contribution of outlier and neutral loci to genetic divergence. Methods The RADcap method was used to obtain 24 million paired reads for 123 individuals of L. guttatus covering nearly all its distributional area. Genetic variation was assessed using both spatial and non-spatial methods by comparing three different data sets: (i) a Combined Loci (CL dataset = 2003 SNPs); a search for putative loci under selection allowed the evaluation of (ii) Neutral Loci (NL dataset = 1858 SNPs) and (iii) Outlier Loci (OL dataset = 145 SNPs). We used the estimating effective migration surface (EEMS) approach to detect possible barriers to gene flow. Results Genetic differences were found in the OL dataset, showing two clusters (Northern and Southern), whereas NL showed no differences. This result may be related to the Selection-Migration balance model. The limit between the Northern and Southern groups was in the Gulf of Panama, which has been previously identified as a barrier to gene flow for other species, mainly due to its heterogeneous oceanographic conditions. The results suggest that selection plays an important role in generating genetic differences in Lutjanus guttatus. A migration corridor was detected that coincides with the Costa Rica Coastal Current that flows from Central America to the Gulf of California, allowing the homogenization of the northern population. In the Southern cluster, a migration corridor was observed with the OL from Panama to Colombia, which could be associated with the currents found in the Gulf of Panama. Genetic variation found in the OL of Lutjanus guttatus highlights the usefulness of NGS data in evaluating the role of selection in population differentiation.

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Section: Discussionmentioning

confidence: 97%

Genomic assessment reveals signal of adaptive selection in populations of the Spotted rose snapper Lutjanus guttatus from the Tropical Eastern Pacific

Mar‐Silva

Díaz‐Jaimes

Domínguez-Mendoza

et al. 2023

PeerJ

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“…The number of groups ranged from 2 to 11, with 1000 permutations, and the maximum Φ CT value (genetic diversity between groups) was calculated to determine the best way to group the population. A genetic distance matrix (Sunde et al, 2022 ) was created based on pairwise genetic divergences between populations. For geographic distance, the straight‐line distances between populations were calculated in terms of longitude and latitude.…”

Section: Methodsmentioning

confidence: 99%

Genetic population structure and demographic history of the endemic fish Paralichthys olivaceus of the Northwest Pacific Ocean

Sun

Yang

Huang

et al. 2022

Ecology and Evolution

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The Northwest Pacific marginal waters comprising the South China Sea, East China Sea, Yellow Sea, and the Sea of Japan have unique geomorphic features. The Japanese flounder Paralichthys olivaceus , which is endemic to the Northwest Pacific, has high nutritional, economic, and ecological value. To allow the examination of the demographic history and population structure of the most common P. olivaceus species range over the five marginal seas (East China Sea, Yellow Sea, Bohai Sea, Northwest Pacific Ocean, and the Sea of Japan), the mitochondrial DNA control region of 91 individuals from six populations in China was sequenced. These sequences were combined with 233 sequences from four populations distributed in the Northwestern Pacific Ocean for analysis. Higher levels of nucleotide diversity (0.032 ± 0.016) and haplotype diversity (0.996 ± 0.001) were observed. The peripheral Fuqing population in the East China Sea had the relatively lowest genetic diversity and highest differentiation. Furthermore, when the results of the isolation by distance test, spatial analysis of molecular variation and geographic barrier analysis are also considered, there is a clear need to prioritize resource conservation and enhancement measures in this area. The phylogenetic trees, structure assignment test, and haplotypes network revealed no significant differences in the genealogical structure among ten populations. Mismatch distribution analysis, Bayesian skyline plots, and neutrality tests suggested that P. olivaceus experienced population expansion during the Pleistocene. Ocean currents and climate change play important roles in shaping the geographical distribution and genetic population structure of P. olivaceus .

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“…An increasing number of studies have provided evidence of differentiation resulting from such ecological and behavioural barriers (e.g. Bergek & Björklund, 2007;Momigliano et al, 2017;Nordahl et al, 2019;Rundle et al, 2000;Sunde et al, 2021;Vonlanthen et al, 2009). Hence, knowledge of cryptic barriers is crucial to avoid loss of unique genetic and phenotypic variation within and among subpopulations (Hutchinson, 2008;Schindler et al, 2010;Stephenson, 1999).…”

Section: Introductionmentioning

confidence: 99%

“…Separation of anadromous perch into different freshwater systems during spawning raises the question whether this, as in other anadromous species (e.g. pike (Nordahl et al, 2019;Sunde et al, 2020Sunde et al, , 2021 and salmonids (Fraser et al, 2011)), has resulted in genetic differentiation between spawning localities. Spatial genetic differentiation in perch is influenced by several factors, such as dispersal, home range, and reproductive homing.…”

Section: Introductionmentioning

confidence: 99%

Reproductive homing and fine‐scaled genetic structuring of anadromous Baltic Sea perch (Perca fluviatilis)

Hall

Koch‐Schmidt

Larsson

et al. 2022

Fisheries Management Eco

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To investigate the population dynamics of anadromous Baltic Sea perch Perca fluviatilis (Linnaeus), we studied the migratory behaviour (arrival to spawning location) and population structure (genetic structure and differentiation) of three closely located (<50 km) populations. Spawning migration lasted for 32-80 days, and passive integrated transponder tag (PIT-tag) data indicated that anadromous perch displayed reproductive homing. Populations were differentiated, despite low levels of gene flow (3%-5%), and differentiation increased with increasing geographic distance. This finescaled spatial structuring was likely, at least partly, explained by homing behaviour.Analyses of temporal within-stream substructuring yielded inconclusive results, so further studies are required to evaluate this. Taken together, our findings highlight the potential for fine-scaled genetic structuring in anadromous perch and indicate that multiple mechanisms, such as isolation by distance, homing, and reproductive timing could contribute to this pattern. This illustrates the importance of considering cryptic barriers to accurately identify reproductive units, and points to the need for local management of anadromous perch.

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Drivers of neutral and adaptive differentiation in pike (Esox lucius) populations from contrasting environments

Abstract: This is an open access article under the terms of the Creat ive Commo ns Attri bution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Cited by 19 publications

References 178 publications

Genomic assessment reveals signal of adaptive selection in populations of the Spotted rose snapper Lutjanus guttatus from the Tropical Eastern Pacific

Genomic assessment reveals signal of adaptive selection in populations of the Spotted rose snapper Lutjanus guttatus from the Tropical Eastern Pacific

Genetic population structure and demographic history of the endemic fish Paralichthys olivaceus of the Northwest Pacific Ocean

Reproductive homing and fine‐scaled genetic structuring of anadromous Baltic Sea perch (Perca fluviatilis)

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