Phylogeography of the scalloped spiny-lobster Panulirus homarus rubellus in the southwest Indian Ocean

Reddy, Maggie M.; Macdonald, Angus H. H.; Groeneveld, Johan C.; Schleyer, Michael H.

doi:10.1163/1937240x-00002284

Cited by 22 publications

(15 citation statements)

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“…In our study, pairwise differentiation estimates ( F ST ) analysis using 7988 SNP loci, showed low but statistically significant ( p < 0.05) differentiation between Ashuwaymiyah and other locations, except for Al Ashkharah and Mirbat (Table 3 ). Earlier reports showed that P. homarus possesses a genetic structure at the large Indo-Pacific scale [ 36 ] and relatively small scales, within both the north west Indian Ocean and south west Indian Ocean [ 38 , 58 ].…”

Section: Discussionmentioning

confidence: 99%

“…Characterisation of stock boundaries and identification of population divergence will greatly support managers in deciding whether two populations should be managed together, or as separate stocks [ 27 , 33 ]. Many recent works of P. homarus have studied sub-species resolution, phylogeography throughout its wide range [ 34 – 37 ] or dispersal capabilities [ 38 ]. However, the fine-scale genetic structure of the species in many regions is still remains unrevealed [ 38 ].…”

Section: Introductionmentioning

confidence: 99%

“…Many recent works of P. homarus have studied sub-species resolution, phylogeography throughout its wide range [ 34 – 37 ] or dispersal capabilities [ 38 ]. However, the fine-scale genetic structure of the species in many regions is still remains unrevealed [ 38 ].…”

Section: Introductionmentioning

confidence: 99%

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Genome-wide SNP analyses reveal high gene flow and signatures of local adaptation among the scalloped spiny lobster (Panulirus homarus) along the Omani coastline

et al. 2018

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BackgroundThe scalloped spiny lobster (Panulirus homarus) is a popular seafood commodity worldwide and an important export item from Oman. Annual catches in commercial fisheries are in serious decline, which has resulted in calls for the development of an integrated stock management approach. In Oman, the scalloped spiny lobster is currently treated as a single management unit (MU) or stock and there is an absence of information on the genetic population structure of the species that can inform management decisions, particularly at a fine-scale level. This work is the first to identify genome-wide single nucleotide polymorphisms (SNPs) for P. homarus using Diversity Arrays Technology sequencing (DArT-seq) and to elucidate any stock structure in the species.ResultsAfter stringent filtering, 7988 high utility SNPs were discovered and used to assess the genetic diversity, connectivity and structure of P. homarus populations from Al Ashkharah, Masirah Island, Duqm, Ras Madrakah, Haitam, Ashuwaymiyah, Mirbat and Dhalkut landing sites. Pairwise FST estimates revealed low differentiation among populations (pairwise FST range = − 0.0008 - 0.0021). Analysis of genetic variation using putatively directional FST outliers (504 SNPs) revealed higher and significant pairwise differentiation (p < 0.01) for all locations, with Ashuwaymiyah being the most diverged population (Ashuwaymiyah pairwise FST range = 0.0288–0.0736). Analysis of population structure using Discriminant Analysis of Principal Components (DAPC) revealed a broad admixture among P. homarus, however, Ashuwaymiyah stock appeared to be potentially under local adaptive pressures. Fine scale analysis using Netview R provided further support for the general admixture of P. homarus.ConclusionsFindings here suggested that stocks of P. homarus along the Omani coastline are admixed. Yet, fishery managers need to treat the lobster stock from Ashuwaymiyah with caution as it might be subject to local adaptive pressures. We emphasize further study with larger number of samples to confirm the genetic status of the Ashuwaymiyah stock. The approach utilised in this study has high transferability in conservation and management of other marine stocks with similar biological and ecological attributes.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5044-8) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Genome-wide SNP analyses reveal high gene flow and signatures of local adaptation among the scalloped spiny lobster (Panulirus homarus) along the Omani coastline

et al. 2018

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“…The scalloped spiny lobster Panulirus homarus is widespread in the Indo-West Pacific, extending northwards from southeastern Africa to the Arabian Sea, and eastwards to Japan, Indonesia, and northern Australia (Holthuis, 1991). Panulirus homarus comprises several putative subspecies, and its evolutionary history and phylogeography have been popular subjects in the recent literature (Farhadi, Farahmand, Nematollahi, Jeffs, & Lavery, 2013;Farhadi et al, 2017, Lavery et al, 2014Reddy, MacDonald, Groeneveld, & Schleyer, 2014;Singh, Groeneveld, Al-Marzouqi, & Willows-Munro, 2017). Analyses of mitochondrial and nuclear sequences from several genetic markers and microsatellite loci have come to broadly similar conclusions, that at least three or four separate evolutionary lineages exist, occupying distinct geographic ranges.…”

Section: Introductionmentioning

confidence: 99%

Seascape genetics of the spiny lobster Panulirus homarus in the Western Indian Ocean: Understanding how oceanographic features shape the genetic structure of species with high larval dispersal potential

Singh

Groeneveld

Hart-Davis

et al. 2018

Ecology and Evolution

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This study examines the fine‐scale population genetic structure and phylogeography of the spiny lobster Panulirus homarus in the Western Indian Ocean. A seascape genetics approach was used to relate the observed genetic structure based on 21 microsatellite loci to ocean circulation patterns, and to determine the influence of latitude, sea surface temperature (SST), and ocean turbidity (KD490) on population‐level processes. At a geospatial level, the genetic clusters recovered corresponded to three putative subspecies, P. h. rubellus from the SW Indian Ocean, P. h. megasculptus from the NW Indian Ocean, and P. h. homarus from the tropical region in‐between. Virtual passive Lagrangian particles advected using satellite‐derived ocean surface currents were used to simulate larval dispersal. In the SW Indian Ocean, the dispersion of particles tracked over a 4‐month period provided insight into a steep genetic gradient observed at the Delagoa Bight, which separates P. h. rubellus and P. h. homarus. South of the contact zone, particles were advected southwestwards by prevailing boundary currents or were retained in nearshore eddies close to release locations. Some particles released in southeast Madagascar dispersed across the Mozambique Channel and reached the African shelf. Dispersal was characterized by high seasonal and inter‐annual variability, and a large proportion of particles were dispersed far offshore and presumably lost. In the NW Indian Ocean, particles were retained within the Arabian Sea. Larval retention and self‐recruitment in the Arabian Sea could explain the recent genetic divergence between P. h. megasculptus and P. h. homarus. Geographic distance and minimum SST were significantly associated with genetic differentiation in multivariate analysis, suggesting that larval tolerance to SST plays a role in shaping the population structure of P. homarus.

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“…Genetic markers, such as microsatellites, have been successfully applied for the stock identification and fishery management of several marine species Milano et al, 2011;Cuveliers et al, 2012;Corander et al, 2013). However, for the population genetic studies of scalloped spiny lobster mainly sequencing of the control region in the mtDNA has been applied (Gopal et al, 2006;Groeneveld et al, 2007;Reddy et al, 2014). To date, only a few microsatellites markers are known in the tropical scalloped spiny lobster species (Dao et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

Novel genomic microsatellite markers for genetic population and diversity studies of tropical scalloped spiny lobster (Panulirus homarus) and their potential application in related Panulirus species

et al. 2016

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ABSTRACT. Fourteen polymorphic microsatellites with perfect di-, tri-, and tetra-nucleotide repeats were identified for Panulirus homarus using Roche 454 whole-genome sequencing method. Microsatellites were efficiently co-amplified in four multiplexes and a singleplex, providing consistent and easily interpretable genotypes. The number of alleles per locus ranged from 2 to 11 with the observed and expected heterozygosity ranging between 0.000-0.532 and 0.031-0.836, respectively. A significant deviation from Hardy-Weinberg equilibrium was observed for majority of the loci, probably due to homozygote excess. Genetic linkage disequilibrium analysis between all the possible pairs of the loci showed significant departure from the null hypothesis in the loci pairs Pho-G11-Pho-G33 and Pho-G33-Pho-G57. High success in primer cross-species amplification of these microsatellite markers indicates their utility for genetic studies of different Panulirus species.

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Phylogeography of the scalloped spiny-lobster Panulirus homarus rubellus in the southwest Indian Ocean

Cited by 22 publications

References 63 publications

Genome-wide SNP analyses reveal high gene flow and signatures of local adaptation among the scalloped spiny lobster (Panulirus homarus) along the Omani coastline

Genome-wide SNP analyses reveal high gene flow and signatures of local adaptation among the scalloped spiny lobster (Panulirus homarus) along the Omani coastline

Seascape genetics of the spiny lobster Panulirus homarus in the Western Indian Ocean: Understanding how oceanographic features shape the genetic structure of species with high larval dispersal potential

Novel genomic microsatellite markers for genetic population and diversity studies of tropical scalloped spiny lobster (Panulirus homarus) and their potential application in related Panulirus species

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