Population genetics, phylogeography and the effects of aquaculture on genetic diversity of the silver-lipped pearl oyster, Pinctada maxima (Jameson)

Lind, Curtis E. (2009) Population genetics, phylogeography and the effects of aquaculture on genetic diversity of the silver-lipped pearl oyster, Pinctada maxima (Jameson). PhD thesis, James Cook University.

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The silver/gold-lipped pearl oyster, Pinctada maxima (Jameson 1901), is one of the most important pearl producing species throughout Southeast Asia and northern Australia. The commercial production of high value "South Sea" pearls is based on the culture of P. maxima, and stands to benefit substantially from the implementation of long-term selective breeding programs. Industry-wide interest towards genetic improvement of P. maxima is rapidly growing, however, several fundamental issues must be addressed before selection commences. To achieve sustained response to selective breeding, it is essential that adequate genetic diversity is present within the population; yet currently there is little known about how the culture process affects diversity in P. maxima. This thesis addresses key issues concerning the capture and maintenance of genetic diversity in cultured P. maxima populations, as well as identifying and understanding patterns of genetic structure and diversity distribution throughout its natural range.

As the source of broodstock to create base populations for selective breeding, it is important to understand the genetic properties of wild P. maxima populations. Analysis of microsatellite and mitochondrial DNA (mtDNA) variation in wild P. maxima populations throughout its natural distribution revealed a gradient in genetic diversity across its range, with decreasing levels of variation seen in peripheral populations when compared to those situated more centrally (i.e. central Indonesia). Significant genetic structuring and differentiation was also observed amongst populations, and is attributed to historic and contemporary biogeographic influences. Comparisons between wild and cultured P. maxima populations indicate a high level of genetic erosion has occurred in hatchery-propagated populations, with effective populations sizes (Nₑ) as low as 3.5 and reductions in microsatellite variation as high as 44% occurring as early as two generations beyond wild progenitors. The practice of mass spawning was identified as a major factor in the reduction of diversity, although diversity was not necessarily maintained when a more controlled spawning approach was utilised. Subsequent investigation using DNA parentage analyses revealed highly variable broodstock contributions have played a significant role towards an increase in genetic relatedness and low Nₑ in cultured P. maxima and is likely to be exaggerated by variable survival rates amongst different pearl oyster families. Upon further investigation and experimentation, it was determined that highly variable family survival will affect Nₑ in communally reared P. maxima and the practice of equalising family sizes in order to reduce family size variance (and maximise Nₑ) may only become consistently beneficial once further progress is made towards understanding and then reducing variation in family survival rates. Culture practices related to variation in growth, such as size grading, culling and mass-selection were assessed for the ability to contribute to diversity losses. It was cautioned that broodstock selection for subsequent generations was potentially far more influential on diversity maintenance than culling or grading.

Outcomes of this thesis have provided a substantial advancement in the understanding of factors influencing genetic diversity in wild and cultured P. maxima populations. Population structuring and differentiation found in wild P. maxima provides grounds for further investigation into possible hybrid vigour or outbreeding depression when crossbreeding different stocks, and whether population genetic differences translate into phenotypic variation in commercially significant traits that could be exploited by selective breeding. This thesis also highlights important culture practices that must be improved (or avoided) in order to capture and retain genetic diversity and reduce inbreeding within closed populations, which will increase the likelihood of sustained response to selection programs. It is recommended that to ensure the maintenance of genetic variation and long-term sustainability of future P. maxima selection programs, culturists should employ the use of molecular tools for parentage assignment of candidate broodstock to avoid mating related individuals, or implement structured breeding designs intended to conserve genetic variability whilst maximising genetic response to selection.

Item ID: 29608
Item Type: Thesis (PhD)
Keywords: pearl oyster; Pinctada maxima; selective breeding; genetic properties; culture practices
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Publications arising from this thesis are available from the Related URLs field. The publications are:

Chapter 2. Lind, Curtis E., Evans, Brad S., Elphinstone, Martin S., Taylor, Joseph J.U., and Jerry, Dean R. (2012) Phylogeography of a pearl oyster (Pinctada maxima) across the Indo-Australian Archipelago: evidence of strong regional structure and population expansions but no phylogenetic breaks. Biological Journal of the Linnean Society, 107 (3). pp. 632-646.

Chapter 3. Lind, Curtis E., Evans, Brad S., Taylor, Joseph J.U., and Jerry, Dean R. (2007) Population genetics of a marine bivalve, Pinctada maxima, throughout the Indo-Australian Archipelago shows differentiation and decreased diversity at range limits. Molecular Ecology, 16 (24). pp. 5193-5203.

Chapter 4. Lind, Curtis E., Evans, Brad S., Knauer, Jens, Taylor, Joseph J.U., and Jerry, Dean R. (2009) Decreased genetic diversity and a reduced effective population size in cultured silver-lipped pearl oysters (Pinctada maxima). Aquaculture, 286 (1-2). pp. 12-19.

Chapter 5. Lind, Curtis E., Evans, Brad S., Taylor, Joseph J.U., and Jerry, Dean R. (2010) The consequences of differential family survival rates and equalizing maternal contributions on the effective population size (Ne) of cultured silver-lipped pearl oysters, Pinctada maxima. Aquaculture Research, 41 (8). pp. 1229-1242.

Date Deposited: 15 Oct 2013 05:44
FoR Codes: 06 BIOLOGICAL SCIENCES > 0604 Genetics > 060411 Population, Ecological and Evolutionary Genetics @ 50%
07 AGRICULTURAL AND VETERINARY SCIENCES > 0704 Fisheries Sciences > 070401 Aquaculture @ 50%
SEO Codes: 83 ANIMAL PRODUCTION AND ANIMAL PRIMARY PRODUCTS > 8301 Fisheries - Aquaculture > 830104 Aquaculture Oysters @ 50%
97 EXPANDING KNOWLEDGE > 970106 Expanding Knowledge in the Biological Sciences @ 50%
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