Dao, Hoc Tan (2016) Recruitment and genetic population genetics of spiny lobsters, Panulirus ornatus and P. homarus in the south-east Asian archipelago. PhD thesis, James Cook University.

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Abstract

Spiny lobsters are one of the world's most valuable seafood with high market value and where demand far exceeds supply. Accordingly, tropical spiny lobsters are a very valuable resource for most Southeast Asian countries, although populations of spiny lobsters in the region are currently subject to severe fishing pressure, primarily through the harvest of pueruli for aquaculture grow-out, which is considered a serious threat to the long-term sustainability of stocks. In 2004, a workshop was held at the Institute of Oceanography, Nha Trang, Vietnam, to discuss what was known about the ecology and exploitation of tropical spiny lobsters. This workshop identified several knowledge gaps that, at the time, were affecting the development of sustainable management policy for tropical spiny lobsters, including lack of information on genetic stock structure, where sink or source populations for recruiting larvae were located, and the comparative value of seed as stock recruits. With these knowledge gaps in mind, the overarching aim of the current thesis was designed to gain an increased understanding of recruitment patterns in two commercially important spiny lobsters, Panulirus ornatus and P. homarus, along with how populations of these two species were genetically structured across a wide range of their distribution. Particular focus was centered on Vietnamese stocks which were observed to exhibit large variations in recruitment prior to 2004.

Chapter 2 first examined patterns in recruitment of the spiny lobster species Panulirus ornatus and P. homarus. Here long-term data that had been collected over six fishing seasons (2005 to 2011) on the abundance of juvenile seed (pueruli) caught by fishers along the central coast of Vietnam was coalesced.Recruitment data indicated large fluctuations in the monthly and annual pueruli catch of the two species of Panulirus, especially for P. ornatus. There was a similar pattern of spatial and temporal variation of total monthly catch in both species during the study period, with catch peaks occurring from November to the following February. The increase of total seed catch of P. ornatus was found to be highly correlated with that of southward wind stress(Exponential trendline; R² = 0.885, p-value < 0.05), suggesting that recruitment of P. ornatus could be predicted for the following season in Vietnam using wind stress as an indicator. This information would be useful to fishery managers, as it will allow them to predict the next season's likely scale of recruitment and the number of wild pueruli that could be sustainably harvested as aquaculture seed.

To understand if spiny lobster recruits throughout the Indo-West Pacific originate from local stocks, or from a common widespread source, Chapters 3, 4 and 5 applied a population genetic approach to determine stock structure of P.ornatus and P. homarus. Genetic resources (mtDNA control region and nuclear microsatellite markers) were firstly developed in Chapter 3 and subsequently used to reveal the genetic structure of both species. Genetic analyses forP. ornatus (Chapter 4) showed no evidence for genetic differentiation among populations over thebroad and oceanographically complex region spanning Australia, Papua New Guinea, Indonesia and Vietnam (mtDNA control region sequences Φ(ST) = -0.008; microsatellite loci F(ST)= 0.003). A lack of evidence for regional or localized mtDNA haplotype clusters, or geographic clusters of microsatellite genotypes, reveals a pattern of high gene flow leading to panmixia in P. ornatus throughout the Indo-West Pacific. Based on biological and oceanographic data, a dispersal pathway of this species was developed to explain the genetic findings. Simulations incorporating known P. ornatus spawning areas, larval pelagic duration, and oceanographic data show that genetic homogeneity of P. ornatus can be explained by the oceanography-driven dispersal of the pelagic lobster larvae, which occurs from known spawning grounds in Papua New Guinea, the Philippines and, possibly, Indonesia. Results suggest the existence of a single panmictic population of P. ornatus in the Indo-West Pacific for conservation and fisheries management.

In terms of P. homarus, the mtDNA control region analyses (Chapter 5) revealed moderate levels of genetic structure among populations(Φ(ST) = 5.31%; P < 0.05), whilst analyses atsix microsatellites detected significant genetic divergence between populations from Masirah, Oman, and several Southeast Asian Archipelago populations (Φ(ST) = 7.5% - 19.8%). Low levels of genetic structure were also observed within the Southeast Asian Archipelago. Bayesian individual assignment analysis based on microsatellites showed that lobsters from Masirah, Oman were more homogeneous to a single genetic cluster, which was not revealed by the mtDNA, suggesting the possibility of a one-way migration pattern by females. The findings of the present study suggest regional genetic structuring of P. homarus across the Indo-West Pacific, and consequently the assignment of different genetic stocks, or management units, for this lobster species.

Finally, the strength of microsatellite markers as a useful resource for parentage assignment in simulated P. ornatus breeding programs was examined (Chapter 6). Results indicated that a marker suite of the five loci with the highest PIC could be used to correctly assign parentage with high confidence.

Overall, the work in this thesis has significantly advanced our knowledge on recruitment patterns and processes, along with genetic population structure, of two of the most important and heavily exploited tropical spiny lobsters in the Indo-Pacific. Data provided by this thesis will have application in the formulation of new management policies for these species, leading to more sustainable harvest of wild pueruli for fisheries and aquaculture purposes.

Item ID:	48783
Item Type:	Thesis (PhD)
Keywords:	454 sequencing, breeding, crustacea, genetics, microsatellite, mitrochondrial DNA, Panulirus, south-east Asia, spiny lobster
Related URLs:	https://researchonline.jcu.edu.au/23150/ https://researchonline.jcu.edu.au/42445/
Additional Information:	Publications arising from this thesis are available from the Related URLs field. The publications are: Chapter 3: Dao, Hoc Tan, Todd, Erica V., and Jerry, Dean R. (2013) Characterization of polymorphic microsatellite loci for the spiny lobster Panulirus spp. and their utility to be applied to other Panulirus lobsters. Conservation Genetics Resources, 5 (1). pp. 43-46. Chapter 4: Dao, Hoc Tan, Smith-Keune, Carolyn, Wolanski, Eric, Jones, Clive M., and Jerry, Dean R. (2015) Oceanographic currents and local ecological knowledge indicate, and genetics does not refute, a contemporary pattern of larval dispersal for the ornate spiny lobster, Panulirus ornatus in the south-east Asian archipelago. PLoS ONE, 10 (5). pp. 1-19.
Date Deposited:	25 Apr 2017 21:45
FoR Codes:	07 AGRICULTURAL AND VETERINARY SCIENCES > 0704 Fisheries Sciences > 070401 Aquaculture @ 70% 06 BIOLOGICAL SCIENCES > 0604 Genetics > 060499 Genetics not elsewhere classified @ 20% 06 BIOLOGICAL SCIENCES > 0606 Physiology > 060699 Physiology not elsewhere classified @ 10%
SEO Codes:	83 ANIMAL PRODUCTION AND ANIMAL PRIMARY PRODUCTS > 8301 Fisheries - Aquaculture > 830106 Aquaculture Rock Lobster @ 100%
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