Population genetic structure in the redefined vermilion rockfish (Sebastes miniatus) indicates limited larval dispersal and reveals natural management units

2009 ◽  
Vol 66 (9) ◽  
pp. 1569-1581 ◽  
Author(s):  
John R. Hyde ◽  
Russell D. Vetter
Keyword(s):  
Larval Dispersal ◽  
Sequence Data ◽  
Isolation By Distance ◽  
Dispersal Distance ◽  
Unintended Consequences ◽  
Management Units ◽  
Distance Analysis ◽  
Mitochondrial Cytochrome B ◽  
Genetic Barriers ◽  
Ecological Province

Recent studies have revealed that the vermilion rockfish Sebastes miniatus is a cryptic species pair. The splitting of this species impacts stock size estimates and draws attention to the unintended consequences of current management policies. Differences in exploitation level between the species necessitated an evaluation of population structure and connectivity among regional management segments of the fishery. Analysis of gene flow and calculations of larval dispersal values were accomplished using 782 bp of DNA sequence data from the mitochondrial cytochrome b gene of 684 vermilion rockfish sampled from 16 sites between Kyuquot Sound, Canada, and San Quintin, Mexico. Significant genetic heterogeneity was found among sample sites (ΦST = 0.0742, p < 0.001 and FST = 0.0899, p < 0.001). Isolation by distance analysis produced a significant correlation, suggesting low average larval dispersal distance. Analysis of molecular variance showed significant partitioning of genetic variance across the biogeographic boundary at Point Conception (ΦCT = 0.0923, p < 0.001 and FCT = 0.0135, p < 0.001) with additional genetic barriers found at Cape Mendocino, Punta Colnett, Santa Monica Bay, and along the coast of Washington. These genetic barriers conform to oceanographic compartments previously proposed for the California Current Ecological Province and suggest natural management units for this species.

scholarly journals Probability of successful larval dispersal declines fivefold over 1 km in a coral reef fish

2011 ◽  
Vol 279 (1735) ◽  
pp. 1883-1888 ◽  
Author(s):  
Peter M. Buston ◽  
Geoffrey P. Jones ◽  
Serge Planes ◽  
Simon R. Thorrold
Keyword(s):  
Larval Dispersal ◽  
Isolation By Distance ◽  
Dispersal Distance ◽  
Population Connectivity ◽  
Marine Ecology ◽  
Sea Anemones ◽  
Marine Population ◽  
Amphiprion Percula ◽  
Distance Distributions ◽  
Dispersal Distances

A central question of marine ecology is, how far do larvae disperse? Coupled biophysical models predict that the probability of successful dispersal declines as a function of distance between populations. Estimates of genetic isolation-by-distance and self-recruitment provide indirect support for this prediction. Here, we conduct the first direct test of this prediction, using data from the well-studied system of clown anemonefish ( Amphiprion percula ) at Kimbe Island, in Papua New Guinea. Amphiprion percula live in small breeding groups that inhabit sea anemones. These groups can be thought of as populations within a metapopulation. We use the x- and y -coordinates of each anemone to determine the expected distribution of dispersal distances (the distribution of distances between each and every population in the metapopulation). We use parentage analyses to trace recruits back to parents and determine the observed distribution of dispersal distances. Then, we employ a logistic model to (i) compare the observed and expected dispersal distance distributions and (ii) determine the relationship between the probability of successful dispersal and the distance between populations. The observed and expected dispersal distance distributions are significantly different ( p < 0.0001). Remarkably, the probability of successful dispersal between populations decreases fivefold over 1 km. This study provides a framework for quantitative investigations of larval dispersal that can be applied to other species. Further, the approach facilitates testing biological and physical hypotheses for the factors influencing larval dispersal in unison, which will advance our understanding of marine population connectivity.

Population Subdivision and Molecular Sequence Variation: Theory and Analysis of Drosophila ananassae Data

Genetics ◽  
2003 ◽  
Vol 165 (3) ◽  
pp. 1385-1395
Author(s):  
Claus Vogl ◽  
Aparup Das ◽  
Mark Beaumont ◽  
Sujata Mohanty ◽  
Wolfgang Stephan
Keyword(s):  
Sequence Data ◽  
Isolation By Distance ◽  
Allele Frequencies ◽  
Drosophila Ananassae ◽  
Population Subdivision ◽  
Variation Theory ◽  
Peripheral Populations ◽  
Molecular Variation ◽  
Data Set ◽  
Evolutionary Forces

Abstract Population subdivision complicates analysis of molecular variation. Even if neutrality is assumed, three evolutionary forces need to be considered: migration, mutation, and drift. Simplification can be achieved by assuming that the process of migration among and drift within subpopulations is occurring fast compared to mutation and drift in the entire population. This allows a two-step approach in the analysis: (i) analysis of population subdivision and (ii) analysis of molecular variation in the migrant pool. We model population subdivision using an infinite island model, where we allow the migration/drift parameter 0398; to vary among populations. Thus, central and peripheral populations can be differentiated. For inference of 0398;, we use a coalescence approach, implemented via a Markov chain Monte Carlo (MCMC) integration method that allows estimation of allele frequencies in the migrant pool. The second step of this approach (analysis of molecular variation in the migrant pool) uses the estimated allele frequencies in the migrant pool for the study of molecular variation. We apply this method to a Drosophila ananassae sequence data set. We find little indication of isolation by distance, but large differences in the migration parameter among populations. The population as a whole seems to be expanding. A population from Bogor (Java, Indonesia) shows the highest variation and seems closest to the species center.

scholarly journals Investigation of the molecular signatures of selection on ATP synthase genes in the marine bivalve Limecola balthica

2019 ◽  
Vol 32 ◽  
pp. 3 ◽  
Author(s):  
Eric Pante ◽  
Vanessa Becquet ◽  
Amélia Viricel ◽  
Pascale Garcia
Keyword(s):  
Atp Synthase ◽  
Sequence Data ◽  
Nuclear Gene ◽  
Cellular Respiration ◽  
Marine Bivalve ◽  
Gamma Subunit ◽  
Genetic Barriers ◽  
Different Populations ◽  
Peptide Interaction ◽  
Evolutionarily Stable

We used transcriptomic sequence data to describe patterns of divergence and selection across different populations of a marine bivalve (Limecola balthica). Our analyses focused on a nuclear gene (atp5c1) that was previously detected in an FST scan as highly structured among populations separated by the Finistère Peninsula in France. This gene encodes the gamma subunit of the FO/F1 ATP synthase, a multi-protein complex that is paramount to cellular respiration and energy production. Analysis of non-synonymous to synonymous mutation ratios revealed that 65% of the gene is highly conserved (dN/dS ≤ 0.1, min = 0), while 6% of the gene is likely under positive selection (dN/dS ≥ 1, max = 2.03). All replacement mutations are clustered on a 46 residues portion of the protein, within an inter-peptide interaction zone. Comparative genomics suggests that these mutations are evolutionarily stable, and we hypothesize that they are involved in inter-population genetic incompatibilities with other subunits of the ATP synthase complex. The protein stability of the gamma subunit conferred by southern variants was inferred to be higher under warmer temperatures, suggesting that environmental conditions may contribute to the strength of genetic barriers in L. balthica.

Significant population genetic structure detected for a new and highly restricted species of Atriplex (Chenopodiaceae) from Western Australia, and implications for conservation management

2012 ◽  
Vol 60 (1) ◽  
pp. 32 ◽  
Author(s):  
Laurence J. Clarke ◽  
Duncan I. Jardine ◽  
Margaret Byrne ◽  
Kelly Shepherd ◽  
Andrew J. Lowe
Keyword(s):  
Genetic Variation ◽  
New Species ◽  
Genetic Structure ◽  
Western Australia ◽  
Sequence Data ◽  
Isolation By Distance ◽  
Conservation Strategies ◽  
New Taxon ◽  
Near Surface ◽  
Two Populations

Atriplex sp. Yeelirrie Station (L. Trotter & A. Douglas LCH 25025) is a highly restricted, potentially new species of saltbush, known from only two sites ~30 km apart in central Western Australia. Knowledge of genetic structure within the species is required to inform conservation strategies as both populations occur within a palaeovalley that contains significant near-surface uranium mineralisation. We investigate the structure of genetic variation within populations and subpopulations of this taxon using nuclear microsatellites. Internal transcribed spacer sequence data places this new taxon within a clade of polyploid Atriplex species, and the maximum number of alleles per locus suggests it is hexaploid. The two populations possessed similar levels of genetic diversity, but exhibited a surprising level of genetic differentiation given their proximity. Significant isolation by distance over scales of less than 5 km suggests dispersal is highly restricted. In addition, the proportion of variation between the populations (12%) is similar to that among A. nummularia populations sampled at a continent-wide scale (several thousand kilometres), and only marginally less than that between distinct A. nummularia subspecies. Additional work is required to further clarify the exact taxonomic status of the two populations. We propose management recommendations for this potentially new species in light of its highly structured genetic variation.

A widespread distribution for Arostrilepis tenuicirrosa (Eucestoda: Hymenolepididae) in Myodes voles (Cricetidae: Arvicolinae) from the Palearctic based on molecular and morphological evidence: historical and biogeographic implications

2013 ◽  
Vol 58 (4) ◽  
Author(s):  
Kurt Galbreath ◽  
Kristina Ragaliauskaite ◽  
Leonas Kontrimavichus ◽  
Arseny Makarikov ◽  
Eric Hoberg
Keyword(s):  
Sequence Data ◽  
Molecular Data ◽  
Intraspecific Diversity ◽  
Myodes Glareolus ◽  
Morphological Evidence ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Biogeographic History ◽  
Mitochondrial Cytochrome B ◽  
The Republic

AbstractHymenolepidid cestodes in Myodes glareolus from Lithuania and additional specimens originally attributed to Arostrilepis horrida from the Republic of Belarus are now referred to A. tenuicirrosa. Our study includes the first records of A. tenuicirrosa from the European (western) region of the Palearctic, and contributes to the recognition of A. horrida (sensu lato) as a complex of cryptic species distributed broadly across the Holarctic. Specimens of A. tenuicirrosa from Lithuania were compared to cestodes representing apparently disjunct populations in the eastern Palearctic based on structural characters of adult parasites and molecular sequence data from nuclear (ITS2) and mitochondrial (cytochrome b) genes. Morphological and molecular data revealed low levels of divergence between eastern and western populations. Phylogeographic relationships among populations and host biogeographic history suggests that limited intraspecific diversity within A. tenuicirrosa may reflect a Late Pleistocene transcontinental range expansion from an East Asian point of origin.

Dependence of sustainability on the configuration of marine reserves and larval dispersal distance

2001 ◽  
Vol 4 (2) ◽  
pp. 144-150 ◽  
Author(s):  
Botsford ◽  
Hastings ◽  
Gaines
Keyword(s):  
Larval Dispersal ◽  
Marine Reserves ◽  
Dispersal Distance

Evidence of genetic differentiation in cigar wrasse Cheilio inermis (Labridae) within the western Indian Ocean

Genome ◽  
2020 ◽  
Vol 63 (10) ◽  
pp. 493-502
Author(s):  
Sisanda Mayekiso ◽  
Gavin Gouws ◽  
Monica Mwale ◽  
Ofer Gon
Keyword(s):  
Indian Ocean ◽  
Genetic Differentiation ◽  
Larval Dispersal ◽  
Sequence Data ◽  
Allelic Diversity ◽  
Nuclear Gene ◽  
Western Indian Ocean ◽  
Parental Origin ◽  
Pelagic Larvae ◽  
Atpase 6

Patterns of genetic structure and connectivity of the monotypic cigar wrasse Cheilio inermis within western Indian Ocean (WIO) are poorly understood. Whether the species exists as a single panmictic population across the WIO is unclear. Sequence data were generated from two mitochondrial genes (cytochrome b and ATPase 6) and one nuclear intron (S7 intron I). High levels of haplotype and allelic diversity (h = 0.88–0.98; A = 0.95–0.98), along with low nucleotide diversities were observed across all markers. The pairwise ΦST values indicated differentiation of Tanga from the four WIO localities (Inhaca, Nosy Bé, Gazi, and Shimoni), as well as differentiation between the northernmost WIO localities. AMOVAs indicated high differentiation among defined locality groups, whereas nuclear gene analysis found little differentiation among groups. The observed genetic differentiation in C. inermis could be caused by oceanic barriers, and by limited larval dispersal with the pelagic larvae possibly settling near their parental origin and promoting differentiation.

Modeling no-take marine reserves in regulated fisheries: assessing the role of larval dispersal

2008 ◽  
Vol 65 (11) ◽  
pp. 2509-2523 ◽  
Author(s):  
Carey R. McGilliard ◽  
Ray Hilborn
Keyword(s):  
Larval Dispersal ◽  
Marine Reserves ◽  
Dispersal Distance ◽  
Maximum Sustainable Yield ◽  
Catch Per Unit Effort ◽  
Long Distance ◽  
Total Allowable Catch ◽  
Dispersal Distances ◽  
The Impact

We explored the effects of larval dispersal distance on the impact of no-take marine reserves (NTMRs) implemented in fisheries with catch regulations. NTMRs exist in many fisheries with harvest regulated by annual catch limits. In these fisheries, catch is taken from outside NTMRs, potentially resulting in reduced abundance outside NTMRs and an overall reduction in catch. We used a spatial model with two life stages (larvae and adults) to evaluate the effects of larval dispersal distance for fisheries managed by a total allowable catch (TAC) and an NTMR. We examined effects of the timing of density-dependent mortality in relation to larval movement. Abundance reached similar values for populations with long and short larval dispersal distances. Catch declined substantially for stocks with short larval dispersal distances. When larval dispersal distances were long, catch declined to values below maximum sustainable yield (MSY), but stabilized. Catch per unit effort (CPUE) declined to 9% of CPUE at MSY for stocks with short distance larval dispersal after the implementation of an NTMR; with long distance larval dispersal, CPUE declined to approximately 50% or less of the CPUE at MSY. The CPUE did not reflect trends in abundance after the implementation of an NTMR.

Significant population genetic structuring but a lack of phylogeographic structuring in the endemic Tasmanian tree frog (Litoria burrowsae)

2014 ◽  
Vol 62 (3) ◽  
pp. 238 ◽  
Author(s):  
Z. Y. Zhang ◽  
S. Cashins ◽  
A. Philips ◽  
C. P. Burridge
Keyword(s):  
Population Genetic ◽  
Nuclear Dna ◽  
Isolation By Distance ◽  
Global Climate ◽  
Haplotype Diversity ◽  
Habitat Destruction ◽  
Phylogeographic Structure ◽  
Tree Frog ◽  
Genetic Structuring ◽  
Management Units

Conservation of frogs is of global concern, owing to declines resulting from habitat destruction, global climate change, and disease. Knowledge of genetic variation in frog species is therefore desirable for the identification of management units. Here we surveyed mitochondrial DNA sequence variation in the Tasmanian endemic hylid frog Litoria burrowsae, which is infected by chytrid fungus, Batrachochytrium dendrobatidis, and may be declining. Neither phylogeographic structure nor deep phylogenetic divergence was detected in the species, although its populations were highly differentiated with respect to haplotype frequencies. The low-haplotype diversity in L. burrowsae suggests a recent bottleneck in the species, and population genetic structuring may reflect isolation by distance as well as founder effects associated with range expansion. Three putative management units were identified that require verification based on nuclear DNA variation and adaptation to local environments.

scholarly journals Genetic variation and population dispersal of Yangtze voles Microtus fortis calamorum in the Dongting Lake region

2012 ◽  
Vol 58 (2) ◽  
pp. 211-220 ◽  
Author(s):  
Zongming Guo ◽  
Pengfei Song ◽  
Cong GUO ◽  
Zhaobin Song ◽  
Yong Wang ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Isolation By Distance ◽  
Geographic Distance ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
Dongting Lake ◽  
Distance Analysis ◽  
Population Dispersal ◽  
Lake Region ◽  
Nonparametric Correlation

Abstract To understand genetic variation and population dispersal in the Yangtze vole Microtus fortis calamorum distributed in the Dongting Lake region, 144 individuals were collected from six habitat patches. The mitochondrial DNA control region was sequenced and 17 haplotypes were observed. Of the six investigated populations, haplotype and nucleotide diversities of those from larger patches were higher than those from smaller patches. Nonparametric correlation analysis showed that patch size had a positive correlation with haplotype diversity (r = 0.943, P &lt; 0.01). A neighbour-joining tree of the 17 haplotypes showed no geographic genetic structure among the six populations. Analysis of isolation by distance showed that genetic differentiation among the six populations was not positively related to geographic distance. Analysis of mismatch distribution indicated that the voles had passed through a population expansion. The pattern of haplotype distribution in the Changsha population suggests that the population was established by a founder effect [Current Zoology 58 (2): 211–220, 2012].

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