FBIP: scallop population genetics

Rouvay Roodt-Wilding1, Mahlatse Kgatla2

1 Stellenbosch University, Department of Genetics, Private Bag X1, Matieland , 7602, Stellenbosch; 2 SANBI, 2 Cussonia Avenue, Brummeria, 0184, Pretoria, South Africa

Corresponding author(s): Rouvay Roodt-Wilding (roodt@sun.ac.za)

Received {date}; Revised {date}; Accepted {date}; Published {date}

Citation: Combination of authors, year of data paper publication (in parentheses), Title, Journal Name, Volume, Issue number (in parentheses), and doi of the data paper.

Resource Citation

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

Abstract

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.

Keywords: Occurrence, Specimen

Project details

Project title: Scallop population genetics
Personnel: Rouvay Roodt-Wilding
Funding: Foundational Biodiversity Information Programme
Study area descriptions/descriptor: South Africa, Western Cape, False Bay
Design description: 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.

Data published through GBIF: http://ipt.sanbi.org.za/iptsanbi/resource?r=fbip_scallop_population_genetics

Taxonomic coverage

General taxonomic coverage description: All scallops identified to species
Taxonomic ranks
Species: Pecten  sulcicostatus

Spatial coverage

General spatial coverage: South Africa, Western Cape, False Bay
Coordinates: 34°11'27.6''S and 34°11'27.6''S Latitude; 18°38'27.6''E and 18°38'27.6''E Longitude 

Temporal coverage: October 31, 2014

Methods

Method step description: 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.
Study extent description: False Bay, 20-40m depth
Sampling description: -Study populations and specimen collection.
-Establishment of genomic resources and molecular marker development.
-Population genetic analyses.

Datasets

Dataset description
Object name: Darwin Core Archive FBIP: scallop population genetics
Character encoding: UTF-8
Format name: Darwin Core Archive format
Format version: 1.0
Distribution: http://ipt.sanbi.org.za/iptsanbi/archive.do?r=fbip_scallop_population_genetics
Publication date of data: 2019-09-26
Language: English
Licences of use: Creative Commons Attribution (CC-BY) 4.0 License

Metadata language: English
Date of metadata creation: 2019-05-07
Hierarchy level: Dataset