A molecular and population genetics study of the Bluff Oyster (Ostrea chilensis)

• Main Author: Thomas, Leighton James
• Other Authors: Gardner, Jonathan, Ritchie, Peter
• Format: Doctoral or Postdoctoral Thesis
• Language: English
• Published: Victoria University of Wellington 2015
• Subjects: Population genetics; Oysters; New Zealand; Antarctic; The Bluff; Antarc*
• Online Access: http://researcharchive.vuw.ac.nz/handle/10063/4263

New Zealand has a long history of isolation and has evolved a unique biota. Spanning from a sub-tropical climate in the North to a sub-Antarctic climate in the far south New Zealand provides an interesting opportunity to study the processes that lead to evolution. This thesis attempts to study the evolution of Ostrea chilensis at a population genetics and molecular level. Chapter Two: Microsatellite DNA loci represent an ideal marker for population genetics studies due to high levels of length polymorphism between individuals. Genomic sequencing technologies offer the potential to quickly identify thousands of loci, from which PCR primers can be developed and screened for polymorphisms. I aimed to develop PCR primers to amplify length polymorphic microsatellite loci and to use the genomic data set to elucidate patterns and processes of microsatellite evolution. DNA was extracted from a single Ostrea chilensis individual and used for a 1/8 plate sequencing run on a Roche 454. The subsequent quality checked DNA database was annotated for microsatellite loci. 6,208 dinucleotide, 7,326 trinucleotide repeats, 2,414 tetranucleotide, 33 hexanucleotide and 356 pentanucleotides were annotated on the partial genome. Four microsatellite loci were successfully amplified and genotyped. The loci have a low number of alleles compared to other bivalve studies and two have significant departures from HWE (Fst = 0.126 and -0.348). There were a number of highly significant BLAST hits (< 1xE⁻²⁰) with repetitive Oyster DNA sequences obtained from GenBank. Due to difficulties the microsatellite loci were abandoned as markers for later population genetic analysis. This work, however, provides the ground work for further developments of PCR primers for polymorphic microsatellite DNA and provides some observations of molecular evolution of repetitive DNA, which will lead to a greater understanding of these sequences. Chapter Three: This chapter forms the first population genetic study of Ostrea chilensis using New Zealand and Chilean ...