FBIP: scallop population genetics

Registros biológicos
Última versión publicado por South African National Biodiversity Institute el sep 26, 2019 South African National Biodiversity Institute
Fecha de publicación:
26 de septiembre de 2019
Licencia:
CC-BY 4.0

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Descripción

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.

Registros

Los datos en este recurso de registros biológicos han sido publicados como Archivo Darwin Core(DwC-A), el cual es un formato estándar para compartir datos de biodiversidad como un conjunto de una o más tablas de datos. La tabla de datos del core contiene 37 registros.

Este IPT archiva los datos y, por lo tanto, sirve como repositorio de datos. Los datos y los metadatos del recurso están disponibles para su descarga en la sección descargas. La tabla versiones enumera otras versiones del recurso que se han puesto a disposición del público y permite seguir los cambios realizados en el recurso a lo largo del tiempo.

Versiones

La siguiente tabla muestra sólo las versiones publicadas del recurso que son de acceso público.

¿Cómo referenciar?

Los usuarios deben citar este trabajo de la siguiente manera:

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

Derechos

Los usuarios deben respetar los siguientes derechos de uso:

El publicador y propietario de los derechos de este trabajo es South African National Biodiversity Institute. Esta obra está bajo una licencia Creative Commons de Atribución/Reconocimiento (CC-BY 4.0).

Registro GBIF

Este recurso ha sido registrado en GBIF con el siguiente UUID: b5899cfd-0acd-4179-8ca2-bb6fb1873941.  South African National Biodiversity Institute publica este recurso y está registrado en GBIF como un publicador de datos avalado por South African Biodiversity Information Facility.

Palabras clave

Occurrence; Specimen

Contactos

Rouvay Roodt-Wilding
  • Proveedor De Los Metadatos
  • Originador
  • Punto De Contacto
Associate Professor
Stellenbosch University
Department of Genetics, Private Bag X1, Matieland 
7602 Stellenbosch
Western Cape
0218085831
Mahlatse Kgatla
  • Proveedor De Contenido
FBIP Data Specialist
SANBI
2 Cussonia Avenue, Brummeria
0184 Pretoria
Gauteng
ZA
0128435196

Cobertura geográfica

South Africa, Western Cape, False Bay

Coordenadas límite Latitud Mínima Longitud Mínima [-34,191, 18,641], Latitud Máxima Longitud Máxima [-34,191, 18,641]

Cobertura taxonómica

All scallops identified to species

Especie Pecten sulcicostatus

Cobertura temporal

Fecha Inicial 2014-10-31

Datos del proyecto

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.

Título Scallop population genetics
Identificador IBSG13052118234
Fuentes de Financiación Foundational Biodiversity Information Programme
Descripción del área de estudio South Africa, Western Cape, False Bay
Descripción del diseño 16S rRNA mitochondrial sequences were generated for Pecten sulcicostatus specimens collected at False Bay by scuba. Samples were collected from live specimens in their natural habitat using non-lethal methods.

Personas asociadas al proyecto:

Rouvay Roodt-Wilding
  • Investigador Principal

Métodos de muestreo

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

Área de Estudio False Bay, 20-40m depth

Descripción de la metodología paso a paso:

  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.

Metadatos adicionales