Combining microsatellite, otolith shape and parasites community analyses as a holistic approach to assess population structure of Dentex dentex

Marengo, Michel; Baudouin, Marie; Viret, A.; Laporte, Martin; Berrebi, Patrick; Vignon, Matthias; Marchand, Bernard; Durieux, Eric

doi:10.1016/j.seares.2017.07.003

Cited by 20 publications

(8 citation statements)

References 112 publications

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“…This larval dispersal may be, however, more limited than expected [ 70 ] by distance, for example. The IBD at the limit of significance and the holistic approach of Marengo et al [ 25 ] would support this hypothesis. Among the three markers chosen for the holistic method, only the genetic nuclear markers did not detect any structure.…”

Section: Discussionmentioning

confidence: 93%

“…No Fst value is significant between the different stations and the other methods employed do not show any differentiation among populations. This absence of structure at this local Corsican scale has also been investigated with a multi-method approach [ 25 ] using a combination of markers that have different spatial and temporal scales of integration: microsatellite DNA markers, otolith shape analysis and parasites communities. However, although no genetic structure was found using microsatellites, a complex population structure is suggested in this study with the other marker distinguishing different “ecological population units” around Corsica.…”

Section: Discussionmentioning

confidence: 99%

“…First, sequences from the mitochondrial DNA (mtDNA) cytochrome oxidase (COI) locus were used for barcoding purposes to check for any taxonomic inconsistencies when an individual’s species is determined; subsequently, mtDNA D-loop sequences and multi-locus microsatellite genotype data were employed to refine the intra-specific common dentex population genetic structure within the study area. A recent study [ 25 ] established that there is no genetic structure around Corsica. To a lesser extent, we aim to define the species structure in the Mediterranean Sea and one site in the Atlantic Ocean.…”

Section: Introductionmentioning

confidence: 99%

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Absence of spatial genetic structure in common dentex (Dentex dentex Linnaeus, 1758) in the Mediterranean Sea as evidenced by nuclear and mitochondrial molecular markers

et al. 2018

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The common dentex, Dentex dentex, is a fish species which inhabits marine environments in the Mediterranean and Northeast Atlantic regions. This is an important species from an ecological, economic and conservation perspective, however critical information on its population genetic structure is lacking. Most samples were obtained from the Mediterranean Sea (17 sites) with an emphasis around Corsica (5 sites), plus one Atlantic Ocean site. This provided an opportunity to examine genetic structuring at local and broader scales to provide science based data for the management of fishing stocks in the region. Two mitochondrial regions were examined (D-loop and COI) along with eight microsatellite loci. The COI data was combined with publicly available sequences and demonstrated past misidentification of common dentex. All markers indicated the absence of population genetic structure from the Bay of Biscay to the eastern Mediterranean Sea. Bayesian approaches, as well as the statistical tests performed on the allelic frequencies from microsatellite loci, indicated low differentiation between samples; there was only a slight (p = 0.05) indication of isolation by distance. Common dentex is a marine fish species with a unique panmictic population in the Mediterranean and likely in the Atlantic Ocean as well.

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Section: Discussionmentioning

confidence: 93%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Absence of spatial genetic structure in common dentex (Dentex dentex Linnaeus, 1758) in the Mediterranean Sea as evidenced by nuclear and mitochondrial molecular markers

et al. 2018

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“…Redundancy analysis (RDA) was conducted as a multilocus geno- constituted the explanatory matrix, and the db-MEMs related to spatial components constituted the conditioning matrix controlling for autocorrelation. The function "rda" was used to compute the RDAs on the model (see Laporte et al, 2016;Le Luyer et al, 2017;Marengo et al, 2017 for examples of similar methodology). An analysis of variance (ANOVA; 1,000 permutations) was then performed to assess the global significance of the RDAs, and the percentage of variance explained (PVE) was computed with the function "RsquareAdj".…”

Section: Putative Adaptive Mutations: Geneenvironment Associationsmentioning

confidence: 99%

Adaptive and maladaptive genetic diversity in small populations: Insights from the Brook Charr (Salvelinus fontinalis) case study

et al. 2020

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Investigating the relative importance of neutral versus selective processes governing the accumulation of genetic variants is a key goal in both evolutionary and conservation biology. This is particularly true in the context of small populations, where genetic drift can counteract the effect of selection. Using Brook Charr (Salvelinus fontinalis) from Québec, Canada, as a case study, we investigated the importance of demographic versus selective processes governing the accumulation of both adaptive and maladaptive mutations in closed versus open and connected populations to assess gene flow effect. This was achieved by using 14,779 high‐quality filtered SNPs genotyped among 1,416 fish representing 50 populations from three life history types: lacustrine (closed populations), riverine and anadromous (connected populations). Using the PROVEAN algorithm, we observed a considerable accumulation of putative deleterious mutations across populations. The absence of correlation between the occurrence of putatively beneficial or deleterious mutations and local recombination rate supports the hypothesis that genetic drift might be the main driver of the accumulation of such variants. However, despite a lower genetic diversity observed in lacustrine than in riverine or anadromous populations, lacustrine populations do not exhibit more deleterious mutations than the two other history types, suggesting that the negative effect of genetic drift in lacustrine populations may be mitigated by that of relaxed purifying selection. Moreover, we also identified genomic regions associated with anadromy, as well as an overrepresentation of transposable elements associated with variation in environmental variables, thus supporting the importance of transposable elements in adaptation.

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“…Increasingly, both genotypic and phenotypic traits are being used in combination to characterise fish populations 16 – 19 . While genotypic differences definitively confirm that populations are reproductively isolated from each other, phenotypic variation can arise when groups of fish inhabit different environments for a substantial part of the life cycle and may not necessarily have a genetic basis.…”

Section: Introductionmentioning

confidence: 99%

Combining genetic markers with stable isotopes in otoliths reveals complexity in the stock structure of Atlantic bluefin tuna (Thunnus thynnus)

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Rodríguez-Ezpeleta

Fraile

et al. 2020

Sci Rep

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Atlantic bluefin tuna (Thunnus thynnus) from the two main spawning populations in the Mediterranean and Gulf of Mexico occur together in the western, central and eastern Atlantic. Stock composition of catches from mixing areas is uncertain, presenting a major challenge to the sustainable management of the fisheries. This study combines genetic and chemical markers to develop an integrated method of population assignment. Stable isotope signatures (δ13C and δ18O) in the otolith core of adults from the two main spawning populations (adult baselines) showed less overlap than those of yearlings (12–18 months old) from western and eastern nursery areas suggesting that some exchange occurs towards the end of the yearling phase. The integrated model combined δ18O with four genetic markers (SNPs) to distinguish the adult baselines with greater accuracy than chemical or genetic markers alone. When used to assign individuals from the mixing areas to their population of origin, the integrated model resolved some (but not all) discrepancies between the chemistry and genetic methods. Some individuals in the mixing area had otolith δ18O values and genetic profiles which when taken together, were not representative of either population. These fish may originate from another Atlantic spawning area or may represent population contingents that move away from the main spawning areas during the first year of life. This complexity in stock structure is not captured by the current two-stock model.

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Combining microsatellite, otolith shape and parasites community analyses as a holistic approach to assess population structure of Dentex dentex

Cited by 20 publications

References 112 publications

Absence of spatial genetic structure in common dentex (Dentex dentex Linnaeus, 1758) in the Mediterranean Sea as evidenced by nuclear and mitochondrial molecular markers

Absence of spatial genetic structure in common dentex (Dentex dentex Linnaeus, 1758) in the Mediterranean Sea as evidenced by nuclear and mitochondrial molecular markers

Adaptive and maladaptive genetic diversity in small populations: Insights from the Brook Charr (Salvelinus fontinalis) case study

Combining genetic markers with stable isotopes in otoliths reveals complexity in the stock structure of Atlantic bluefin tuna (Thunnus thynnus)

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