FBIP: scallop population genetics

Enregistrements de données

Les données de cette ressource occurrence ont été publiées sous forme d'une Archive Darwin Core (Darwin Core Archive ou DwC-A), le format standard pour partager des données de biodiversité en tant qu'ensemble d'un ou plusieurs tableurs de données. Le tableur de données du cœur de standard (core) contient 37 enregistrements.

Cet IPT archive les données et sert donc de dépôt de données. Les données et métadonnées de la ressource sont disponibles pour téléchargement dans la section téléchargements. Le tableau des versions liste les autres versions de chaque ressource rendues disponibles de façon publique et permet de tracer les modifications apportées à la ressource au fil du temps.

Versions

Le tableau ci-dessous n'affiche que les versions publiées de la ressource accessibles publiquement.

Comment citer

Les chercheurs doivent citer cette ressource comme suit:

Roodt-Wilding R (2019): FBIP: scallop population genetics. v1.0. South African National Biodiversity Institute. Dataset/Occurrence. http://ipt.sanbi.org.za/iptsanbi/resource?r=fbip_scallop_population_genetics&v=1.0

Droits

Les chercheurs doivent respecter la déclaration de droits suivante:

L’éditeur et détenteur des droits de cette ressource est South African National Biodiversity Institute. Ce travail est sous licence Creative Commons Attribution (CC-BY) 4.0.

Enregistrement GBIF

Cette ressource a été enregistrée sur le portail GBIF, et possède l'UUID GBIF suivante : b5899cfd-0acd-4179-8ca2-bb6fb1873941.  South African National Biodiversity Institute publie cette ressource, et est enregistré dans le GBIF comme éditeur de données avec l'approbation du South African Biodiversity Information Facility.

Mots-clé

Occurrence; Specimen

Contacts

Couverture géographique

South Africa, Western Cape, False Bay

Couverture taxonomique

All scallops identified to species

Couverture temporelle

Données sur le projet

The study focused on genomic resource development for Pecten sulcicostatus followed by the quantification of genetic diversity within a single natural population, namely the False Bay Pecten sulcicostatus population. The data set represents a list of tissue samples and DNA extracts taken from live specimens and their haplotype for the 16S gene. The 16S rRNA sequences generated in this project have been submitted to GenBank to allow other researchers to access this information.

Les personnes impliquées dans le projet:

Méthodes d'échantillonnage

-Study populations and specimen collection. -Establishment of genomic resources and molecular marker development. -Population genetic analyses.

Description des étapes de la méthode:

1. Study populations and specimen collection (6 months: January 2014 - June 2014): This study will focus on the broad geographic distribution of Pecten sulcicostatus within its natural distribution range, taking into account the three marine bio-geographical provinces of South Africa and major barriers to gene flow. Specimens will be collected from False bay, representing the western geographical distribution extreme (west of the Agulhas upwelling; a major bio-geographical barrier to many marine species around the South African coast); Mossel bay (south coast sampling location, between the Agulhas upwelling and thermal front at Algoa bay); Algoa bay, representing a secondary bio-geographical barrier (thermal front) and East London, representing the eastern geographical distribution extreme (east of the thermal front at Algoa bay). Fifty specimens will be collected from each of the four sampling locations, 200 specimens in total. Establishment of genomic resources and molecular marker development (5 months: February 2014 - June 2014): The FIASCO/454 microsatellite-marker isolation technique that has been shown to be a high-throughput, time- and cost-effective protocol for marker development in uncharacterized species will be employed: Firstly, a genomic library enriched for microsatellite repeat motifs will be generated via the FIASCO protocol. This will be followed by next generation, pyrosequencing (454 – GS FLX system) to determine the nucleotide composition and sequence of the genomic fragments. Raw sequence data will be subject to quality control and individual reads will be assembled into contigs to eliminate sequence redundancy. Using appropriate algorithms, contigs and singleton reads will be screened for repetitive microsatellite motifs. Primers will be designed and optimized for PCR amplification of each microsatellite locus. Polymorphism will be tested by means of polyacrylamide gel electrophoresis. Finally, primers for polymorphic loci will be labelled with fluorescent dyes for genotyping using capillary electrophoresis and optimized into multiplex reactions for diagnostic standardization. Population genetic analyses (6 months: July 2014 - December 2014): Each individual within the study cohort will be genotyped for each of the developed microsatellite markers. The genotype data will be employed to evaluate panmixia, population differentiation and the compartmentalization of intra- and interspecific genetic diversity. In order to evaluate intraspecific genetic diversity the following estimates will be calculated for each population: heterozygosity, number of alleles, effective number of alleles and information (Shannon-Weaver) index. In order to assess interspecific population diversity, pairwise Fst and analogous statistics will be estimated, as well as the following analyses: analysis of molecular variance (AMOVA) and principle coordinate analysis (PCoA). To further evaluate the genetic relationship amongst populations, population-trees (using genetic distance estimates and phylogenetic clustering algorithms) will be constructed and a Bayesian clustering algorithm will be implemented to evaluate the number of distinct genetic populations. Contemporary population size and evidence for population expansions or contractions will also be investigated to obtain a understanding of how demographic factors may influence genetic diversity.

Métadonnées additionnelles