New Nuclear SNP Markers Unravel the Genetic Structure and Effective Population Size of Albacore Tuna (Thunnus alalunga)

Laconcha, Urtzi; Iriondo, Mikel; Arrizabalaga, Haritz; Manzano, Carmen; Markaide, Pablo; Montes, Iratxe; Zarraonaindia, Iratxe; Velado, I.; Bilbao, Eider; Goñi, Nicolás; Santiago, Josu; Domingo, Andrés; Karakulak, F. Saadet; Oray, I. K.; Estonba, Andone

doi:10.1371/journal.pone.0128247

Cited by 44 publications

(51 citation statements)

References 85 publications

(115 reference statements)

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“…Divergence in T. rotula was similar to other phytoplankton species sampled over large distances, such as across the Baltic Sea and the NE Atlantic (maximum F ST = 0.099) (21,22) but below the maximum F ST (0.76) observed among allopatrically separated populations of the pennate diatom P. pungens (17). Divergence in T. rotula was comparable to population divergence observed in globally distributed, highly migratory marine macrofauna (maximum F ST = 0.175) (40)(41)(42). Thus, F ST observed here for T. rotula is within the range expected for cosmopolitan high-dispersal marine organisms, but lower than those exhibiting strong patterns of allopatry.…”

Section: Resultssupporting

confidence: 69%

Evidence for environmental and ecological selection in a microbe with no geographic limits to gene flow

Whittaker

Rynearson

2017

Proc. Natl. Acad. Sci. U.S.A.

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The ability for organisms to disperse throughout their environment is thought to strongly influence population structure and thus evolution of diversity within species. A decades-long debate surrounds processes that generate and support high microbial diversity, particularly in the ocean. The debate concerns whether diversification occurs primarily through geographic partitioning (where distance limits gene flow) or through environmental selection, and remains unresolved due to lack of empirical data. Here we show that gene flow in a diatom, an ecologically important eukaryotic microbe, is not limited by global-scale geographic distance. Instead, environmental and ecological selection likely play a more significant role than dispersal in generating and maintaining diversity. We detected significantly diverged populations (FST> 0.130) and discovered temporal genetic variability at a single site that was on par with spatial genetic variability observed over distances of 15,000 km. Relatedness among populations was decoupled from geographic distance across the global ocean and instead, correlated significantly with water temperature and whole-community chlorophylla. Correlations with temperature point to the importance of environmental selection in structuring populations. Correlations with whole-community chlorophylla, a proxy for autotrophic biomass, suggest that ecological selection via interactions with other plankton may generate and maintain population genetic structure in marine microbes despite global-scale dispersal. Here, we provide empirical evidence for global gene flow in a marine eukaryotic microbe, suggesting that everything holds the potential to be everywhere, with environmental and ecological selection rather than geography or dispersal dictating the structure and evolution of diversity over space and time.

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Section: Resultssupporting

confidence: 69%

Evidence for environmental and ecological selection in a microbe with no geographic limits to gene flow

Whittaker

Rynearson

2017

Proc. Natl. Acad. Sci. U.S.A.

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“…Moreover, it has also been suggested to play an important role in invasive processes of aquatic organisms (Vera, Díez‐del‐Molino, & García‐Marín, 2016b). Adaptive variants maintained by balancing selection have been reported in different species, such as those in immune‐related genes in three‐spined stickleback (Feulner et al., 2013; Guo et al., 2015) and in ribosomal structure and regulation genes in the albacore tuna (Laconcha et al., 2015). Seven of the eight outlier loci identified as being influenced by balancing selection in the current study were detected in the BAS‐BLS comparison, a result consistent with parallel adaptation to low salinities.…”

Section: Discussionmentioning

confidence: 99%

Parallel evolution and adaptation to environmental factors in a marine flatfish: Implications for fisheries and aquaculture management of the turbot (Scophthalmus maximus)

Prado

Vera

Hermida

et al. 2018

Evolutionary Applications

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Unraveling adaptive genetic variation represents, in addition to the estimate of population demographic parameters, a cornerstone for the management of aquatic natural living resources, which, in turn, represent the raw material for breeding programs. The turbot (Scophthalmus maximus) is a marine flatfish of high commercial value living on the European continental shelf. While wild populations are declining, aquaculture is flourishing in southern Europe. We evaluated the genetic structure of turbot throughout its natural distribution range (672 individuals; 20 populations) by analyzing allele frequency data from 755 single nucleotide polymorphism discovered and genotyped by double‐digest RAD sequencing. The species was structured into four main regions: Baltic Sea, Atlantic Ocean, Adriatic Sea, and Black Sea, with subtle differentiation apparent at the distribution margins of the Atlantic region. Genetic diversity and effective population size estimates were highest in the Atlantic populations, the area of greatest occurrence, while turbot from other regions showed lower levels, reflecting geographical isolation and reduced abundance. Divergent selection was detected within and between the Atlantic Ocean and Baltic Sea regions, and also when comparing these two regions with the Black Sea. Evidence of parallel evolution was detected between the two low salinity regions, the Baltic and Black seas. Correlation between genetic and environmental variation indicated that temperature and salinity were probably the main environmental drivers of selection. Mining around the four genomic regions consistently inferred to be under selection identified candidate genes related to osmoregulation, growth, and resistance to diseases. The new insights are useful for the management of turbot fisheries and aquaculture by providing the baseline for evaluating the consequences of turbot releases from restocking and farming.

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“…Genetic differentiation between Atlantic and Indo-Pacific groups has also been described for two other circumtropical members of the genus Thunnus : albacore ( T. alalunga ; Albaina et al. 2013; Laconcha et al. 2015) and bigeye tuna ( T. obesus ; Chow et al.…”

Section: Discussionmentioning

confidence: 99%

Genomic Differentiation and Demographic Histories of Atlantic and Indo-Pacific Yellowfin Tuna (Thunnus albacares) Populations

Barth

Damerau

Matschiner

et al. 2017

Genome Biology and Evolution

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Recent developments in the field of genomics have provided new and powerful insights into population structure and dynamics that are essential for the conservation of biological diversity. As a commercially highly valuable species, the yellowfin tuna (Thunnus albacares) is intensely exploited throughout its distribution in tropical oceans around the world, and is currently classified as near threatened. However, conservation efforts for this species have so far been hampered by limited knowledge of its population structure, due to incongruent results of previous investigations. Here, we use whole-genome sequencing in concert with a draft genome assembly to decipher the global population structure of the yellowfin tuna, and to investigate its demographic history. We detect significant differentiation of Atlantic and Indo-Pacific yellowfin tuna populations as well as the possibility of a third diverged yellowfin tuna group in the Arabian Sea. We further observe evidence for past population expansion as well as asymmetric gene flow from the Indo-Pacific to the Atlantic.

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New Nuclear SNP Markers Unravel the Genetic Structure and Effective Population Size of Albacore Tuna (Thunnus alalunga)

Cited by 44 publications

References 85 publications

Evidence for environmental and ecological selection in a microbe with no geographic limits to gene flow

Evidence for environmental and ecological selection in a microbe with no geographic limits to gene flow

Parallel evolution and adaptation to environmental factors in a marine flatfish: Implications for fisheries and aquaculture management of the turbot (Scophthalmus maximus)

Genomic Differentiation and Demographic Histories of Atlantic and Indo-Pacific Yellowfin Tuna (Thunnus albacares) Populations

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