scholarly journals Fine-scale seascape genomics of an exploited marine species, the common cockle Cerastoderma edule, using a multi-modelling approach

2019 ◽  
Author(s):  
Ilaria Coscia ◽  
Sophie B. Wilmes ◽  
Joseph E. Ironside ◽  
Alice Goward-Brown ◽  
Enda O’Dea ◽  
...  
Keyword(s):  
Larval Dispersal ◽  
Spatial Genetic Structure ◽  
Marine Species ◽  
Larval Transport ◽  
Fine Scale ◽  
Nucleotide Polymorphisms ◽  
Cerastoderma Edule ◽  
Larval Behaviour ◽  
Outlier Loci ◽  
Commercially Important

ABSTRACTPopulation dynamics of marine species that are sessile as adults are driven by oceanographic dispersal of larvae from spawning to nursery grounds. This is mediated by life-history traits such as the timing and frequency of spawning, larval behaviour and duration, and settlement success. Here, we use 1725 single nucleotide polymorphisms (SNPs) to study the fine scale spatial genetic structure in the commercially important cockle species Cerastoderma edule and compare it to environmental variables and current-mediated larval dispersal within a modelling framework. Hydrodynamic modelling employing the NEMO Atlantic Margin Model (AMM15) was used to simulate larval transport and estimate connectivity between populations during spawning months (April - September), factoring in larval duration and seasonal variability of ocean currents. Results at neutral loci reveal the existence of three separate genetic clusters (mean FST=0.021) within a relatively fine spatial scale in the northwest Atlantic. Environmental association (EA) analysis indicates that oceanographic currents and geographical distance between the populations explain over 20% of the variance observed at neutral loci, while genetic variance (71%) at outlier loci was explained by sea surface temperatures extremes. These results fill an important knowledge gap in the management of a commercially important, overexploited species, and bring us closer to understanding the role of larval dispersal in connecting populations at a fine geographical scale.

scholarly journals Biotic and abiotic factors shaping the genome of cockle (Cerastoderma edule) in the Northeast Atlantic: a baseline for sustainable management of its wild resources

2020 ◽  
Author(s):  
Manuel Vera ◽  
Francesco Maroso ◽  
Sophie-B. Wilmes ◽  
Miguel Hermida ◽  
Andrés Blanco ◽  
...  
Keyword(s):  
Sustainable Management ◽  
Larval Dispersal ◽  
Population Genomics ◽  
Abiotic Factors ◽  
Atlantic Coast ◽  
Conservation Strategies ◽  
Marine Bivalve ◽  
Cerastoderma Edule ◽  
Northeast Atlantic ◽  
Outlier Loci

AbstractKnowledge on how environmental factors shape the genome of marine species is crucial for sustainable management of fisheries and wild populations. The edible cockle (Cerastoderma edule) is a marine bivalve distributed along the Northeast Atlantic coast of Europe and is an important resource from both commercial and ecological perspectives. We performed a population genomics screening using 2b-RAD genotyping on 9,309 SNPs localised in the cockle’s genome on a sample of 536 specimens pertaining to 14 beds in the Northeast Atlantic to ascertain its genetic structure regarding environmental variation. Larval dispersal modelling considering species behaviour and interannual variability in ocean conditions was carried out, as an essential background to compare genetic information with. Cockle populations in the Northeast Atlantic were shown to be panmictic and displayed low but significant geographical differentiation across populations (FST = 0.0240; P < 0.001), albeit not across generations. We identified 441 outlier SNPs related to divergent selection, sea surface temperature being the main environmental driver following a latitudinal axis. Two main genetic groups were identified, northwards and southwards of French Brittany, in accordance with our modelling, which demonstrated a barrier for larval dispersal linked to the Ushant front. Further genetic subdivision was observed using outlier loci and considering larval behaviour. The northern group was divided into the Irish/Celtic Seas and the English Channel/North Sea, while the southern group was divided into three subgroups. This information represents the baseline for management of cockles, designing conservation strategies, founding broodstock for depleted beds, and producing suitable seed for aquaculture production.

scholarly journals Spatial Autocorrelation Analysis Using MIG-seq Data Indirectly Estimated the Gamete and Larval Dispersal Range of the Blue Coral, Heliopora coerulea, Within Reefs

2021 ◽  
Vol 8 ◽  
Author(s):  
Daniel Frikli Mokodongan ◽  
Hiroki Taninaka ◽  
La Sara ◽  
Taisei Kikuchi ◽  
Hideaki Yuasa ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Spatial Autocorrelation ◽  
Larval Dispersal ◽  
Population Genetic ◽  
Spatial Genetic Structure ◽  
Spatial Autocorrelation Analysis ◽  
Nucleotide Polymorphisms ◽  
Autocorrelation Analysis ◽  
Distance Method ◽  
Genome Wide

Spatial autocorrelation analysis is a well-established technique for detecting spatial structures and patterns in ecology. However, compared to inter-population genetic structure, much less studies examined spatial genetic structure (SGS) within a population by means of spatial autocorrelation analysis. More SGS analysis that compares the robustness of genome-wide single nucleotide polymorphisms (SNPs) and traditional population genetic markers in detecting SGS, and direct comparison between the estimated dispersal range based on SGS and the larval dispersal range of corals directly surveyed in the field would be important. In this study, we examined the SGS of a reef-building coral species, Heliopora coerulea, in two different reefs (Shiraho and Akaishi) using genome-wide SNPs derived from Multiplexed inter-simple sequence repeat (ISSR) genotyping by sequencing (MIG-seq) analysis and nine microsatellite loci for comparison. Microsatellite data failed to reveal significant spatial patterns when using the same number of samples as MIG-seq, whereas MIG-seq analysis revealed significant spatial autocorrelation patterns up to 750 m in both Shiraho and Akaishi reefs based on the maximum significant distance method. However, detailed spatial genetic analysis using fine-scale distance classes (25–200 m) found an x-intercept of 255–392 m in Shiraho and that of 258–330 m in Akaishi reef. The latter results agreed well with a previously reported direct field observation of larval dispersal, indicating that the larvae of H. coerulea settled within a 350 m range in Shiraho reef within one generation. Overall, our results empirically demonstrate that the x-intercept of the spatial correlogram agrees well with the larval dispersal distance that is most frequently found in field observations, and they would be useful for deciding effective conservation management units for maintenance and/or recovery within an ecological time scale.

scholarly journals Fine‐scale seascape genomics of an exploited marine species, the common cockle Cerastoderma edule , using a multimodelling approach

2020 ◽  
Vol 13 (8) ◽  
pp. 1854-1867 ◽  
Author(s):  
Ilaria Coscia ◽  
Sophie B. Wilmes ◽  
Joseph E. Ironside ◽  
Alice Goward‐Brown ◽  
Enda O’Dea ◽  
...  
Keyword(s):  
Marine Species ◽  
Fine Scale ◽  
Cerastoderma Edule ◽  
The Common ◽  
Common Cockle

Genome-Wide Single Nucleotide Polymorphisms are Robust in Resolving Fine-Scale Population Genetic Structure of the Small Brown Planthopper, Laodelphax striatellus (Fallén) (Hemiptera: Delphacidae)

2019 ◽  
Vol 112 (5) ◽  
pp. 2362-2368
Author(s):  
Yan Liu ◽  
Lei Chen ◽  
Xing-Zhi Duan ◽  
Dian-Shu Zhao ◽  
Jing-Tao Sun ◽  
...  
Keyword(s):  
Population Structure ◽  
Discriminant Analysis ◽  
Genetic Structure ◽  
Population Genetic ◽  
Brown Planthopper ◽  
Fine Scale ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Small Brown Planthopper ◽  
Scale Population

Abstract Deciphering genetic structure and inferring migration routes of insects with high migratory ability have been challenging, due to weak genetic differentiation and limited resolution offered by traditional genotyping methods. Here, we tested the ability of double digest restriction-site associated DNA sequencing (ddRADseq)-based single nucleotide polymorphisms (SNPs) in revealing the population structure relative to 13 microsatellite markers by using four small brown planthopper populations as subjects. Using ddRADseq, we identified 230,000 RAD loci and 5,535 SNP sites, which were present in at least 80% of individuals across the four populations with a minimum sequencing depth of 10. Our results show that this large SNP panel is more powerful than traditional microsatellite markers in revealing fine-scale population structure among the small brown planthopper populations. In contrast to the mixed population structure suggested by microsatellites, discriminant analysis of principal components (DAPC) of the SNP dataset clearly separated the individuals into four geographic populations. Our results also suggest the DAPC analysis is more powerful than the principal component analysis (PCA) in resolving population genetic structure of high migratory taxa, probably due to the advantages of DAPC in using more genetic variation and the discriminant analysis function. Together, these results point to ddRADseq being a promising approach for population genetic and migration studies of small brown planthopper.

scholarly journals Stirred but not shaken: population and recruitment genetics of the scallop (Pecten fumatus) in Bass Strait, Australia

2016 ◽  
Vol 73 (9) ◽  
pp. 2333-2341 ◽  
Author(s):  
Jennifer R. Ovenden ◽  
Bree J. Tillett ◽  
Michael Macbeth ◽  
Damien Broderick ◽  
Fiona Filardo ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Population Genetic Structure ◽  
Population Genetic ◽  
Allelic Variation ◽  
Open Water ◽  
Marine Species ◽  
Population Connectivity ◽  
Valuable Insight ◽  
Fine Scale ◽  
Scale Population

Abstract We report population genetic structure and fine-scale recruitment processes for the scallop beds (Pecten fumatus) in Bass Strait and the eastern coastline of Tasmania in southern Australia. Conventional population pairwise FST analyses are compared with novel discriminant analysis of principal components (DAPC) to assess population genetic structure using allelic variation in 11 microsatellite loci. Fine-scale population connectivity was compared with oceanic features of the sampled area. Disjunct scallop beds were genetically distinct, but there was little population genetic structure between beds connected by tides and oceanic currents. To identify recruitment patterns among and within beds, pedigree analyses determined the distribution of parent–offspring and sibling relationships in the sampled populations. Beds in northeastern Bass Strait were genetically distinct to adjacent beds (FST 0.003–0.005) and may not contribute to wider recruitment based on biophysical models of larval movement. Unfortunately, pedigree analyses lacked power to further dissect fine-scale recruitment processes including self-recruitment. Our results support the management of disjunct populations as separate stocks and the protection of source populations among open water beds. The application of DAPC and parentage analyses in the current study provided valuable insight into their potential power to determine population connectivity in marine species with larval dispersal.

scholarly journals Fine-scale spatial genetic structure of sycamore maple (Acer pseudoplatanus L.)

2011 ◽  
Vol 131 (3) ◽  
pp. 739-746 ◽  
Author(s):  
Madhav Pandey ◽  
Oliver Gailing ◽  
Hans H. Hattemer ◽  
Reiner Finkeldey
Keyword(s):  
Genetic Structure ◽  
Spatial Genetic Structure ◽  
Acer Pseudoplatanus ◽  
Fine Scale ◽  
Sycamore Maple

scholarly journals Spatial population genomics of a recent mosquito invasion

2020 ◽  
Author(s):  
Thomas L Schmidt ◽  
T. Swan ◽  
Jessica Chung ◽  
Stephan Karl ◽  
Samuel Demok ◽  
...  
Keyword(s):  
Gene Flow ◽  
Population Genomics ◽  
Isolation By Distance ◽  
Spatial Genetic Structure ◽  
Nucleotide Polymorphisms ◽  
Discrete Events ◽  
Long Distance ◽  
Population Genomic ◽  
Asian Tiger ◽  
Study Designs

AbstractPopulation genomic approaches can characterise dispersal across a single generation through to many generations in the past, bridging the gap between individual movement and intergenerational gene flow. These approaches are particularly useful when investigating dispersal in recently altered systems, where they provide a way of inferring long-distance dispersal between newly established populations and their interactions with existing populations. Human-mediated biological invasions represent such altered systems which can be investigated with appropriate study designs and analyses. Here we apply temporally-restricted sampling and a range of population genomic approaches to investigate dispersal in a 2004 invasion of Aedes albopictus (the Asian tiger mosquito) in the Torres Strait Islands (TSI) of Australia. We sampled mosquitoes from 13 TSI villages simultaneously and genotyped 373 mosquitoes at genome-wide single nucleotide polymorphisms (SNPs): 331 from the TSI, 36 from Papua New Guinea (PNG), and 4 incursive mosquitoes detected in uninvaded regions. Within villages, spatial genetic structure varied substantially but overall displayed isolation by distance and a neighbourhood size of 232–577. Close kin dyads revealed recent movement between islands 31–203 km apart, and deep learning inferences showed incursive Ae. albopictus had travelled to uninvaded regions from both adjacent and non-adjacent islands. Private alleles and a coancestry matrix indicated direct gene flow from PNG into nearby islands. Outlier analyses also detected four linked alleles introgressed from PNG, with the alleles surrounding 12 resistance-associated cytochrome P450 genes. By treating dispersal as both an intergenerational process and a set of discrete events, we describe a highly interconnected invasive system.

scholarly journals Are patterns of fine-scale spatial genetic structure consistent between sites within tropical tree species?

PLoS ONE ◽  
2018 ◽  
Vol 13 (3) ◽  
pp. e0193501
Author(s):  
James R. Smith ◽  
Jaboury Ghazoul ◽  
David F. R. P. Burslem ◽  
Akira Itoh ◽  
Eyen Khoo ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Tree Species ◽  
Spatial Genetic Structure ◽  
Tropical Tree ◽  
Fine Scale ◽  
Tropical Tree Species
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