Population genetics of the black scar oyster, Crassostrea iredalei : repercussion of anthropogenic interference

Abstract

Mitochondrial cytochrome oxidase subunit I (COI) gene was utilized to assess the population genetics of the commercially important black scar oyster, Crassostrea iredalei among 11 populations throughout the west and east coasts Peninsular Malaysia and Sabah (Malaysian Borneo). Overall, populations of C. iredalei demonstrated low nucleotide diversity π (0.000-0.004) and low-to-high haplotype diversity h (0.000-0.795) levels. Genetic structuring was detected between the Peninsular Malaysia and Sabah populations as revealed by the FST analysis. However, the COI gene analyses showed minimal and non-significant (p > 0.05) population differentiation within the east and west coasts Peninsular Malaysia and Sabah regions. This was attributed to both high larval dispersal along the east and west coasts and human-driven spat translocation between the two coastlines due to C. iredalei cultivation practices. Phylogeographic relationships inferences were also conducted to further support these hypotheses. The neutrality and mismatch distribution analyses suggested that C. iredalei had experienced a/several bottleneck event(s), followed by population expansion. The molecular information obtained from this study could be incorporated in a pragmatic aquaculture management strategy of wild broodstock and the hatchery lines of C. iredalei in Malaysia.

Population genetics ofCerastoderma edulein Ria Formosa (southern Portugal): the challenge of understanding an intraspecific hotspot of genetic diversity

“…It is also important to stress that although the work of Krakau et al (2012) was carried out in several localities at a large spatial scale showing high values of genetic diversity in the northern populations, comparisons among different lagoons and several localities inside each lagoon were not included; the authors did not consider the analysis of microgeographic genetic variation in C. edule, assuming genetic homogeneity inside each sampled coastal bay, estuary or lagoon Sequences of a particular fragment of the mitochondrial COI have been employed in a number of studies to investigate genetic structuring and demographic history in populations of marine bivalve species, in which the observed values of haplotype diversity (h) and nucleotide diversity (p) were lower than those recorded for C. edule in the present study. For example, lower diversity values were recorded in other bivalve species: Amusium pleuronectes with h ¼ 0.237, p ¼ 0.0006 (Mahidol et al, 2007), Ruditapes decussatus at h ¼ 0.486 and p ¼ 0.011 (Gharbi et al, 2010), Scrobicularia plana with h ¼ 0.52, p ¼ 0.0016 (Santos et al, 2012), Donax serra with h ¼ 0.30, p ¼ 0.001 (Bezuidenhout et al, 2014), Crassostrea iredalei with h ¼ 0.565, p ¼ 0.0018 (Zainal Abidin et al, 2014) and Gemma gemma with values of h ¼ 0.314, p ¼ 0.0012 (Zhang et al, 2014). In our study of C. edule, estimates of haplotype and nucleotide diversity were higher than those recorded in these studies using marine samples.…”

Mitochondrial and nuclear genetic analyses of the tropical black-lip rock oyster (Saccostrea echinata) reveals population subdivision and informs sustainable aquaculture development

“…Few studies have employed genetic data to assist in investigating the distribution of tropical oyster species within the Indo-Pacific region. The tropical rock oyster, C. iredalei , has been confirmed to occur throughout Malaysia, based on mitochondrial COI analyses [24]. Similar research has also been conducted with the tropical black-lip pearl oyster, Pinctada margaritifera, which confirmed broad Indo-Pacific distribution, based on SNP analyses [14].…”

“…For example, analyses of mitochondrial and SNP data revealed many subpopulations of Crassostrea virginica throughout the Gulf of Mexico, despite its potential for high gene flow [23]. Similar results of population differentiation in a species with high dispersal capabilities, have been reported for Crassostrea iredalei throughout Malaysia [24] and Ostrea edulis along the European coast [25]. Therefore, without detailed population genetic analyses, predictions cannot be made regarding the extent of population genetic structure of oyster species.…”

“…Analyses of all locations together resulted in negative mean Tajima’s D and Fu’s F s that were significant (Table 2). Negative Tajima’s D indicates an excess of low frequency polymorphisms and negative Fu’s F s indicates an excess of alleles expected from recent directional selection or population growth [24, 31]. Phylogenetic analysis with ostreid COI sequences placed all S. echinata samples obtained in this study within ‘Lineage J’ as nominated by Sekino and Yamashita [32] (Additional file 2).…”

“…Larvae may conceivably travel hundreds of kilometres before settlement, which leads to the hypothesis that wild populations possess low levels of genetic structure [30]. However, studies on related oyster species have reported both panmictic [19, 30] and highly divergent [23, 24] population structures. To achieve the genetic conservation of oyster stocks in the face of developing aquaculture efforts, a sound knowledge of population genetic structure is essential.…”