Genome-wide SNP analyses reveal population structure of Portunus pelagicus along Vietnam coastline

Dang, Binh T.; Rahman, Muhammad Arifur; Tran, Sang; Glenner, Henrik

doi:10.1371/journal.pone.0224473

Cited by 12 publications

(8 citation statements)

References 83 publications

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“…The patterns across populations fit the overall population structure interpretations (see below), with both higher diversity and homozygosity in populations believed to be of mixed origin (SA & NWIO, where high F IS may be due to a Wahlund effect), and lower diversity and F IS in the isolated, remnant population (MI). Similar raised F IS has been observed in other crustacean studies, including on P. ornatus [ 45 ], P. homarus within NWIO [ 12 ] and the widely distributed blue swimmer crab, Portunus pelagicus [ 46 ].…”

Section: Discussionsupporting

confidence: 87%

Genome-wide SNPs in the spiny lobster Panulirus homarus reveal a hybrid origin for its subspecies

2022

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Background Evolutionary divergence and speciation often occur at a slower rate in the marine realm due to the higher potential for long-distance reproductive interaction through larval dispersal. One common evolutionary pattern in the Indo-Pacific, is divergence of populations and species at the peripheries of widely-distributed organisms. However, the evolutionary and demographic histories of such divergence are yet to be well understood. Here we address these issues by coupling genome-wide SNP data with mitochondrial DNA sequences to test the patterns of genetic divergence and possible secondary contact among geographically distant populations of the highly valuable spiny lobster Panulirus homarus species complex, distributed widely through the Indo-Pacific, from South Africa to the Marquesas Islands. Result After stringent filtering, 2020 SNPs were used for population genetic and demographic analyses, revealing strong regional structure (FST = 0.148, P < 0001), superficially in accordance with previous analyses. However, detailed demographic analyses supported a much more complex evolutionary history of these populations, including a hybrid origin of a North-West Indian Ocean (NWIO) population, which has previously been discriminated morphologically, but not genetically. The best-supported demographic models suggested that the current genetic relationships among populations were due to a complex series of past divergences followed by asymmetric migration in more recent times. Conclusion Overall, this study suggests that alternating periods of marine divergence and gene flow have driven the current genetic patterns observed in this lobster and may help explain the observed wider patterns of marine species diversity in the Indo-Pacific.

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Section: Discussionsupporting

confidence: 87%

Genome-wide SNPs in the spiny lobster Panulirus homarus reveal a hybrid origin for its subspecies

2022

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“…The ability to interrogate population diversity using thousands of SNPs, and to identify loci which may be under the influence of selection versus neutral loci (Davey et al., 2011; Gagnaire et al., 2015) enables examination of adaptive divergence in response to environmental factors. There is a growing body of literature documenting genetic structure either due to neutral variation or due to adaptation to environment, at finer spatial scales than expected from species dispersal potentials, among them: ocean currents (Benestan et al., 2016; Coscia et al., 2020; Dang et al., 2019; Gilg & Hilbish, 2003; Lal et al., 2017; Paterno et al., 2017; Riginos et al., 2019; Schunter et al., 2011; Teske et al., 2016; Truelove et al., 2017; Van Wyngaarden et al., 2018; Xuereb et al., 2018), temperature (Carreras et al., 2020; Chu et al., 2014; Coscia et al., 2020; Hoey & Pinsky, 2018; Sandoval‐Castillo et al., 2018; Wang et al., 2013), and salinity (Sjöqvist et al., 2015).…”

Section: Introductionmentioning

confidence: 99%

Genetic differentiation and signatures of local adaptation revealed by RADseq for a highly dispersive mud crab Scylla olivacea (Herbst, 1796) in the Sulu Sea

Mendiola

Ravago-Gotanco

2021

Ecology and Evolution

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Connectivity of marine populations is shaped by complex interactions between biological and physical processes across the seascape. The influence of environmental features on the genetic structure of populations has key implications for the dynamics and persistence of populations, and an understanding of spatial scales and patterns of connectivity is crucial for management and conservation. This study employed a seascape genomics approach combining larval dispersal modeling and population genomic analysis using single nucleotide polymorphisms (SNPs) obtained from RADseq to examine environmental factors influencing patterns of genetic structure and connectivity for a highly dispersive mud crab Scylla olivacea (Herbst, 1796) in the Sulu Sea. Dispersal simulations reveal widespread but asymmetric larval dispersal influenced by persistent southward and westward surface circulation features in the Sulu Sea. Despite potential for widespread dispersal across the Sulu Sea, significant genetic differentiation was detected among eight populations based on 1,655 SNPs (FST = 0.0057, p < .001) and a subset of 1,643 putatively neutral SNP markers (FST = 0.0042, p < .001). Oceanography influences genetic structure, with redundancy analysis (RDA) indicating significant contribution of asymmetric ocean currents to neutral genetic variation (Radj2 = 0.133, p = .035). Genetic structure may also reflect demographic factors, with divergent populations characterized by low effective population sizes (Ne < 50). Pronounced latitudinal genetic structure was recovered for loci putatively under selection (FST = 0.2390, p < .001), significantly correlated with sea surface temperature variabilities during peak spawning months for S. olivacea (Radj2 = 0.692–0.763; p < .050), suggesting putative signatures of selection and local adaptation to thermal clines. While oceanography and dispersal ability likely shape patterns of gene flow and genetic structure of S. olivacea across the Sulu Sea, the impacts of genetic drift and natural selection influenced by sea surface temperature also appear as likely drivers of population genetic structure. This study contributes to the growing body of literature documenting population genetic structure and local adaptation for highly dispersive marine species, and provides information useful for spatial management of the fishery resource.

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“…Following northeast and southwest monsoon driven currents in the Vietnam coastline (Figure 1), fish larvae may be transported along the coast from the Gulf of Tonkin up to the Gulf of Thailand and vice versa. However, upwelling and anticyclonic/cyclonic eddies along the south and central coasts [6], together with tidal and Mekong river discharge (6000-12000 m 3 /s) [7] were considered as the genetic barriers to the dispersal of marine planktonic larvae [10]. The resulting of the current study does not strongly support this hypothesis.…”

Section: Genetics Differentiation Among Populationsmentioning

confidence: 80%

“…This hypothesis has been examined in several studies on population genetics in Vietnam, such as giant clams Tridacna spp. [8], sardine fish Sardinella gibbosa [9], and swimming crab Portunus pelagicus [10].…”

Section: Introductionmentioning

confidence: 99%

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Genetic Diversity and Population Structure of Lethrinus Lentjan (Lethrinidae) in Vietnam Based on SNP Markers

Truong¹,

Tran²,

Vu³

et al. 2022

ECS Trans.

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Lethrinus lentjan (Lacepède, 1802) is an important commercial species for marine fisheries in subtropical and tropical regions of the Indian and Indo-Pacific oceans. Although heavily exploited, their genetic diversity and population structuring along the Vietnam coastline are unclear. Here, we used a panel of single nucleotide polymorphisms (SNPs) generated from restriction site-associated DNA sequencing (RADseq). After removing 405 outlier loci, 1,506 putatively neutral SNPs from 62 individuals were used to assess the genetic population structure of L. lentjan. Observed/expected heterozygosity (Ho/He) within sites ranged from 0.170/0.202 (Southeast) to 0.188/0.213 (Central). Pairwise FST values, Structure and Discriminant Analysis of Principal Components (DAPC) analysis indicate the lack of spatial genetic structure, suggesting the presence of a single panmictic population. Larval dispersal by ocean currents may facilitated high gene flow of L. lentjan along the Vietnamese coastline, and Mekong River outflow may not act as the natural barrier.

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Genome-wide SNP analyses reveal population structure of Portunus pelagicus along Vietnam coastline

Cited by 12 publications

References 83 publications

Genome-wide SNPs in the spiny lobster Panulirus homarus reveal a hybrid origin for its subspecies

Genome-wide SNPs in the spiny lobster Panulirus homarus reveal a hybrid origin for its subspecies

Genetic differentiation and signatures of local adaptation revealed by RADseq for a highly dispersive mud crab Scylla olivacea (Herbst, 1796) in the Sulu Sea

Genetic Diversity and Population Structure of Lethrinus Lentjan (Lethrinidae) in Vietnam Based on SNP Markers

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