Perna perna metadata and genotypic data
Data files
Sep 12, 2023 version files 76.22 KB
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Perna_perna_metadata_and_genotypic_data.csv
70.57 KB
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README.md
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Abstract
Studies investigating gene flow in sessile or sedentary marine species typically draw conclusions about larval dispersal by investigating genetic structure of adults. Here, we generated microsatellite data from adults, recruits, settlers and planktonic larvae of the brown mussel, Perna perna, from the south-east coast of South Africa, and identified a consistent mismatch in genetic structure between the adults and all earlier life stages. While adults could be assigned to two major geographical groups (western and eastern), most of the early-stage mussels were strongly affiliated with the eastern group. This result suggests that few of the early-stage individuals present in the western portion of the sampling range will become part of the adult population. Our findings highlight the importance of post-settlement processes as key drivers of population structure and caution against the exclusive use of genetic data generated from adults to assess population connectivity facilitated by the dispersal of planktonic propagules.
Genotypic data based on four microsatellite loci for 607 individuals spanning adult, recruit, settler and larvae of the brown mussel, Perna perna. Samples were collected on the south-east coast of South Africa. Fieldwork was conducted between March 2016 and February 2017. The total number of samples collected per life-history stage was 344 adults from eight sites, 86 recruits and 99 settlers collected from four of these sites, and 78 larvae from five adjacent nearshore sites. All associated metadata for 607 individuals are included in the dataset.
For the generation of genotypic data, genomic DNA from adults, recruits and settlers was extracted using the CTAB protocol (Doyle and Doyle 1987; Doyle 1991). This extraction method was not suitable for larvae as too little DNA was recovered due to their small size (~150 µm in size), and a modified one-step incubation/denaturation protocol (Badenhorst and Roodt-Wilding 2007) was used instead. Samples were genotyped using four polymorphic microsatellite loci designed by Coelho et al. (Coelho et al. 2012), with a fluorescently labelled M13 primer incorporated into the PCR product (Schuelke 2000). For each specimen, PCR products were pseudo-multiplexed (pooled) and genotyped on an ABI 3130xl Genetic Analyzer (Applied Biosystems). The software Geneious was used to fit the ladder, call peaks, bin alleles and produce a table of genotypes. Since this is diploid data, there are two alleles per locus. This is coded such that each allele is in a separate column. Missing data is depicted as 0 (zero).
Description of the data and file structure
This is a .csv file containing metadata (columns A to I) and genotypic data (columns J to Q) for 607 Perna perna individuals, consisting of four different life-history stages (adults, recruits, settlers and larvae). These specimens were sampled along the western edge of the region where the ranges of the species’ two evolutionary lineages overlap (Ntuli et al. 2020). Fieldwork was conducted between March 2016 and February 2017. The total number of samples collected per life-history stage was 344 adults from eight sites, 86 recruits and 99 settlers collected from four of these sites, and 78 larvae from five adjacent nearshore sites. Larvae were collected from the surface waters between 900 and 2400 m from the shore using a submersible 2.2 KC Denmark 23.580 plankton net during two consecutive spawning periods (McQuaid and Lawrie 2005; Porri et al. 2006, 2008).
The genotypic data was based on four polymorphic microsatellite loci (P02, P05, P08 and P29) from markers designed by Coelho et al. 2012. The software Geneious was used to fit the ladder, call peaks, bin alleles and produce a table of genotypes. This is diploid data which means there are two alleles per locus. This is coded such that each allele is in a separate column. Missing data is depicted as 0 (zero). Refer to table below that contains information on each column in the data file.
Table 1.
| Column name | Description | Units | Code explanation | Data format | Missing data code |
|---|---|---|---|---|---|
| Individual ID | Specimen identification for Perna perna individual | n/a | n/a | Text | No missing data |
| Species name | Perna perna | n/a | n/a | Text | No missing data |
| Life-history stage | Life-history stage for that Perna perna specimen, which is either adult, recruit, settler or larval | n/a | n/a | Text | No missing data |
| Location | Sampling location | n/a | n/a | Text | No missing data |
| Site name | Site in South Africa where samples were collected | n/a | n/a | Text | No missing data |
| Site code | Site code for the site where samples were collected | n/a | 1A: Cape St Francis adult site1R: Cape St Francis recruit site1S: Cape St Francis settler site1L: Cape St Francis larval site2A: Jeffreys Bay adult site3A: Kini Bay adult site4L: Sardinia Bay larval site5A: Skoenmakerskop adult site5R: Skoenmakerskop recruit site5S: Skoenmakerskop settler site6A: Algoa Bay adult site6L: Algoa Bay larval site7A: Cape Padrone adult site7L: Cape Padrone larval site8A: Cannon Rocks adult site8R: Cannon Rocks recruit site8S: Cannon Rocks settler site8L: Cannon Rocks larval site9A: Kenton-on-Sea adult site9R: Kenton-on-Sea recruit site9S: Kenton-on-Sea settler site | Text | No missing data |
| Collection date | Date sample was collected | Date format | n/a | date-month-year | No missing data |
| Latitude | Latitude GPS coordinate where sample was collected | GPS format | n/a | Decimal degrees | No missing data |
| Longitude | Longitude GPS coordinate where sample was collected | GPS format | n/a | Decimal degrees | No missing data |
| P02_1 | First allele for locus P02 | numerical | n/a | numerical | 0 |
| P02_2 | Second allele for locus P02 | numerical | n/a | numerical | 0 |
| P05_1 | First allele for locus P05 | numerical | n/a | numerical | 0 |
| P05_2 | Second allele for locus P05 | numerical | n/a | numerical | 0 |
| P08_1 | First allele for locus P08 | numerical | n/a | numerical | 0 |
| P08_2 | Second allele for locus P08 | numerical | n/a | numerical | 0 |
| P29_1 | First allele for locus P29 | numerical | n/a | numerical | 0 |
| P29_2 | Second allele for locus P29 | numerical | n/a | numerical | 0 |
Sharing/Access information
There are no links to other publicly accessible locations for the data and data was not derived from another source.
Code/Software
Sample collection and data generation
Adult, recruit, settler and larval specimens of Perna perna were sampled along the western edge of the region where the ranges of the species’ two evolutionary lineages overlap. Fieldwork was conducted between March 2016 and February 2017. The total number of samples collected per life-history stage was 344 adults from eight sites, 86 recruits and 99 settlers collected from four of these sites, and 78 larvae from five adjacent nearshore sites. Larvae were collected from the surface waters between 900 and 2400 m from the shore using a submersible 2.2 KC Denmark 23.580 plankton net during two consecutive spawning periods.
Genomic DNA from adults, recruits and settlers was extracted using the CTAB protocol (Doyle and Doyle 1987; Doyle 1991). Larval specimens were extracted using a modified one-step incubation/denaturation protocol (Badenhorst and Roodt-Wilding 2007). Samples were genotyped using four polymorphic microsatellite loci designed by Coelho et al. (Coelho et al. 2012), with a fluorescently labelled M13 primer incorporated into the PCR product (Schuelke 2000). For each specimen, PCR products were pseudo-multiplexed (pooled) and genotyped on an ABI 3130xl Genetic Analyzer (Applied Biosystems). Geneious was used for peak calling, bin alleles and produce a table of genotypes. Since this is diploid data, there are two alleles per locus, coded in separate columns. Missing data is depicted with 0 (zero). Tests for genotyping errors, null alleles and allelic dropouts were performed in MICRO-CHECKER v 2.2.3 (Van Oosterhout et al. 2004).