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An genomic appraisal of the stock structure of South African sardines

This study examines the stock structure of South African sardines using genomic analysis, focusing on two species: Callichirus kraussii and Upogebia africana. The research explores the genetic subdivisions, neutral markers, and correlations with sea-surface temperature. The potential for transcriptome sequencing is also discussed.

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An genomic appraisal of the stock structure of South African sardines

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  1. An genomic appraisal of the stock structure of South African sardines terra-nova.co.za Peter Teske, Carl van der Lingen, Tiru Golla, Jonathan Sandoval-Castillo, Luciano Beheregaray

  2. Callichirus kraussii (sandprawn) Upogebia africana (mudprawn) Teske et al. (2011) S Afr J Sci 107:1-11

  3. http://www.surg.co.za/ Psammogobius knysnaensis A single lineage (with some mtDNA structure) Drost et al. (2016) Marine Biodiversity

  4. ddRAD-seq Next-generation sequencing • Variable sites (SNPs) • mtDNA COI: 28 • nuDNA S72: 7 • ddRAD-seq: 23 368 • Raw data processed using STACKS 1.19 • Quality screnning with dDocent 1.0 • Identify selectively neutral markers with BAYESCAN 2.0 • Correlation between genotypes and sea-surface temperature with gINland • Discriminate Function Analysis in ADEGENET • Genetic subdivisions in fastSTRUCTURE

  5. DAPC scatterplot: Selectively neutral loci DAPC scatterplot: 107 loci under thermal selection STRUCTURE barplot: loci under thermal selection

  6. Sardines • 143 samples processed • (west: 39, south: 56, east: 49) • 9252 SNPs shared by all individuals • Mantel test on selectively neutral data: • r = 1.0, P = 0.025 • DAPC analyses: K = 1 (only one lineage) gINLAnd: 37 loci under thermal selection

  7. gINLAnd grouping: Tried to group according to temperature trends

  8. DAPC scatterplot: Loci under thermal selection DAPC compoplot: Loci under thermal selection

  9. What next? Increase samples sizes? Sequence transcriptome? RNA extracted from the livers of 16 sardines; results available in ~1 month

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