Genetic structure and recent population expansion in the commercially harvested deep-sea decapod, Metanephrops challengeri (Crustacea: Decapoda)

Verry, Alexander J. F.; Walton, Kerry; Tuck, Ian; Ritchie, Peter A.

doi:10.1080/00288330.2019.1707696

Cited by 4 publications

(5 citation statements)

References 72 publications

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“…The STF appears to permit only a unidirectional gene flow from SCI_6A to SCI_3, while greatly restricting particle movement from SCI_3 to SCI_6A. These results are concordant with previous studies in the species using a single COI marker that suggested this marked genetic differentiation between scampi from the Auckland Islands (SCI_6A) and those east of the main islands of New Zealand is likely due to the STF 30,54 . Our results also suggest that the TF also likely plays a role in facilitating gene flow from the west to the east (Fig.…”

Section: Discussionsupporting

confidence: 89%

“…The genetic differentiation among SCIs was more subtle than might be expected for this species given their extensive spatial distribution and constrained capacity for dispersal due to their abbreviated pelagic larval phase, restricted post-larval benthic dispersal and low fecundity 26,29,31,33,52,53 . Significant genetic differences among eastern SCIs (SCI_1, SCI_2 & www.nature.com/scientificreports/ SCI_3) were found when utilizing a single mitochondrial marker 54 , but this differentiation was not apparent in this current study. The difference could potentially be due to the lower effective population size in mitochondrial DNA (haploid, and female inherited) versus nuclear DNA (diploid, and inherited from males and females), or due to the genome-wide analyses providing a more accurate evaluation of the stock structure, compared to the stochastically-variable results from a single mitochondrial gene 4,55 .…”

Section: Discussioncontrasting

confidence: 70%

“…1), although it is perhaps surprising that there is such little genetic divergence between SCI_6A and SCI_7, given the apparent geographic isolation of the sampled region in SCI_7. This suggests that genetic drift among SCIs may be limited due to the large effective population sizes 54 , or more likely that the two areas are linked through a contiguous distribution of this species that permits stepping stone gene connectivity when supported by hydrodynamic dispersal of larvae (Fig. 4; Table S9).…”

Section: Discussionmentioning

confidence: 99%

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Genetic and particle modelling approaches to assessing population connectivity in a deep sea lobster

Reis

Norrie

Jeffs

et al. 2022

Sci Rep

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The emergence of high resolution population genetic techniques, such as genotyping-by-sequencing (GBS), in combination with recent advances in particle modelling of larval dispersal in marine organisms, can deliver powerful new insights to support fisheries conservation and management. In this study, we used this combination to investigate the population connectivity of a commercial deep sea lobster species, the New Zealand scampi, Metanephrops challengeri, which ranges across a vast area of seafloor around New Zealand. This species has limited dispersal capabilities, including larvae with weak swimming abilities and short pelagic duration, while the reptant juvenile/adult stages of the lifecycle are obligate burrow dwellers with limited home ranges. Ninety-one individuals, collected from five scampi fishery management areas around New Zealand, were genotyped using GBS. Using 983 haplotypic genomic loci, three genetically distinct groups were identified: eastern, southern and western. These groups showed significant genetic differentiation with clear source-sink dynamics. The direction of gene flow inferred from the genomic data largely reflected the hydrodynamic particle modelling of ocean current flow around New Zealand. The modelled dispersal during pelagic larval phase highlights the strong connectivity among eastern sampling locations and explains the low genetic differentiation detected among these sampled areas. Our results highlight the value of using a transdisciplinary approach in the inference of connectivity among populations for informing conservation and fishery management.

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Section: Discussionsupporting

confidence: 89%

Section: Discussioncontrasting

confidence: 70%

Section: Discussionmentioning

confidence: 99%

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Genetic and particle modelling approaches to assessing population connectivity in a deep sea lobster

Reis

Norrie

Jeffs

et al. 2022

Sci Rep

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“…Over the last four decades, we have assembled extensive knowledge on the genetic characterization of marine organisms, mainly concerning the spatial distribution and structuring of populations (e.g., Knutsen et al, 2007;Plank et al, 2010;Robalo et al, 2013;Riginos et al, 2019;Verry et al, 2020). With this information, it is now possible and relevant to understand how these patterns behave through time.…”

Section: Introductionmentioning

confidence: 99%

Time matters: genetic composition and evaluation of effective population size in temperate coastal fish species

Francisco

Robalo

2020

PeerJ

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Background Extensive knowledge on the genetic characterization of marine organisms has been assembled, mainly concerning the spatial distribution and structuring of populations. Temporal monitoring assesses not only the stability in genetic composition but also its trajectory over time, providing critical information for the accurate forecast of changes in genetic diversity of marine populations, particularly important for both fisheries and endangered species management. We assessed fluctuations in genetic composition among different sampling periods in the western Portuguese shore in three fish species. Methods White seabream Diplodus sargus, sand smelt Atherina presbyter and shanny Lipophrys pholis were chosen, because of their genetic patterns in distinct ecological environments, insight into historical and contemporary factors influencing population effective size (Ne), and degree of commercial exploitation. Samples were obtained near Lisbon between 2003 and 2014 and screened for genetic variation with mitochondrial and nuclear markers. Analyses included genealogies, genetic diversities, temporal structures and contemporary Ne. Results For mtDNA no temporal structure was detected, while for nDNA significant differences were recorded between some sampling periods for the shanny and the sand smelt. Haplotype networks revealed deep genealogies, with various levels of diversification. The shanny revealed a smaller Ne/generation when compared to the other species, which, in turn, revealed no evidence of genetic drift for most study periods. These results highlight the fact that temporal variations in genetic pool composition should be considered when evaluating the population structure of fish species with long distance dispersal, which are more vulnerable to recruitment fluctuations.

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“…The Wairarapa Eddy has been shown to retain Jasus edwardsii (spiny rock lobster) larvae for up to 12 months (Chiswell & Booth 1999). Converging oceanic inflows such as the Subtropical Convergence Zone can act as significant barriers to migration (Verry et al 2020).…”

Section: New Zealand Setting Geography and Geologymentioning

confidence: 99%

A Nation-wide Phylogenetic and Phylogeographic Investigation of the Endemic New Zealand Oyster Borers, Haustrum scobina and Haustrum albomarginatum

O’Mahony¹

2021

Preprint

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The endemic New Zealand sea snails Haustrum scobina and Haustrum albomarginatum are rocky shore intertidal dogwhelks of the Muricidae family. They have direct developing young and are carnivores. Their radula is used to drill into the shells of their prey, and they are commonly referred to as oyster borers. The taxonomic status of these species is still unresolved and therefore the name Haustrum scobina sensu lato is used. The overall goal of this thesis research was to investigate the phylogeny and phylogeography of Haustrum scobina sensu lato using mitochondrial DNA sequences. Comparisons made to phylogeographic studies of ecologically similar species such as Cominella spp. provide an opportunity to identify the common environmental determinates of population migration route, genetic differentiation and speciation whenever similar patterns are found. A nation-wide collection of samples was used to generate 277 new sequences from a 610 bp portion of the cytochrome c oxidase subunit I (COI) gene. This enabled the formation of a dataset of 654 DNA sequences, which was comprised of the 277 new sequences, 16 retrieved from a published study that deposited them in GenBank, and 361 from a previous unpublished thesis study. An unexpectedly diverse phylogeny of 58 COI haplotypes from 31 sample sites was recovered. These formed three clusters using K-means clustering by pairwise mutational distance. The in-group species did not form reciprocal monophyly groups, and the expected closest outgroup species (Haustrum haustorium) appeared to be as similar to the in-group clusters as they were to each other. A dataset of 27 DNA sequences from an 827 bp portion of the large sub-unit 28S nuclear rRNA gene was produced with the intention of corroborating the findings from the analyses of the COI dataset. This consisted of 26 new sequences and one sequence from a published study that deposited the sequence on GenBank. The expected taxonomic arrangement of Haustrum scobina sensu lato could not be matched by COI sequences due to incongruence with the 28S phylogeny and shell morphology. The 28S dataset and shell morphology indicated there are two species in Haustrum scobina sensu lato. These are most likely Haustrum scobina and Haustrum albomarginatum, but they could not clearly be identified in the COI data. As a result, the phylogeographic certainty was limited when using the COI dataset because of the lack of clarity between the haplotypes of the two putative species. Possible reasons for the complicated COI dataset are discussed. Phylogenetic analysis of both the 28S and COI datasets did not support the expected conclusion that members of Haustrum scobina sensu lato are each other’s closest relatives. Haustrum haustorium was the expected immediate outgroup species but formed a polytomy with the in-group. A decrease in COI haplotype diversity was observed in southern samples when they were compared to the samples collected at northern locations. Taranaki sites shared a haplotype with multiple South Island sites that had no haplotype diversity. This suggested post-glacial re-colonisation of southern sites after displacement by ice-age conditions from these locations, a hypothesis consistent with results from studies of the Cominella genus. Association between Purau Bay in Lyttleton Harbour, Titahi Bay, Port Ahuriri and Kawau Island with no associated haplotypes between these locations suggested human-mediated translocation events. A genetic disjunction was also apparent between the south Wellington/Wairarapa coast and the eastern Wairarapa coast. This pattern was consistent with one study of Cominella maculosa and other studies have attributed similar patterns of other species in the region to recent uplift events affecting coastal community composition. The phylogeny of Haustrum scobina sensu lato will require further investigation before it can be used to more confidently resolve the phylogeographic history of the species.

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Genetic structure and recent population expansion in the commercially harvested deep-sea decapod, Metanephrops challengeri (Crustacea: Decapoda)

Cited by 4 publications

References 72 publications

Genetic and particle modelling approaches to assessing population connectivity in a deep sea lobster

Genetic and particle modelling approaches to assessing population connectivity in a deep sea lobster

Time matters: genetic composition and evaluation of effective population size in temperate coastal fish species

A Nation-wide Phylogenetic and Phylogeographic Investigation of the Endemic New Zealand Oyster Borers, Haustrum scobina and Haustrum albomarginatum

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