DOI: 10.5061/dryad.tqjq2bw54
title: Perna perna metadata and genotypic data

description: 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.
description: Sample collection and data
 generation Adult, recruit, settler and
 larval specimens of <em>Perna</em>
 <em>perna</em> 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). 
description: # Perna perna metadata and genotypic data 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 site<br>1R: Cape St Francis recruit site<br>1S:
 Cape St Francis settler site<br>1L: Cape St Francis larval
 site<br>2A: Jeffreys Bay adult site<br>3A: Kini Bay adult
 site<br>4L: Sardinia Bay larval site<br>5A: Skoenmakerskop
 adult site<br>5R: Skoenmakerskop recruit site<br>5S:
 Skoenmakerskop settler site<br>6A: Algoa Bay adult site<br>6L:
 Algoa Bay larval site<br>7A: Cape Padrone adult site<br>7L:
 Cape Padrone larval site<br>8A: Cannon Rocks adult site<br>8R:
 Cannon Rocks recruit site<br>8S: Cannon Rocks settler
 site<br>8L: Cannon Rocks larval site<br>9A: Kenton-on-Sea
 adult site<br>9R: Kenton-on-Sea recruit site<br>9S:
 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