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School of Marine Studies

SMS




Fish and Fisheries Biology and Conservation

Research subline: Evolutionary genomics of marine fisheries and aquaculture resources

The subline in integrative conservation and evolutionary genomics of marine renewable resources pursues a research program based on the basic conceptual foundations of evolutionary biology and whose primary objective is to generate knowledge that will stimulate long-term economic viability and social value of marine organisms in three complementary areas: conservation of biodiversity, fisheries and mariculture. This research program aims to build a bridge between fundamental interdisciplinary research and applied research. The second objective is to increase the training of highly qualified personnel in the priority research areas that are evolutionary genomics, bioinformatics and conservation biology. A third objective is to increase the visibility of university research and to inform the public about its importance for the management and conservation of marine renewable resources.

The original character of this research program lies in its integrative vision that is reflected in the topics covered. Although, issues related to conservation of biodiversity, fisheries and mariculture are generally regarded as distinct and having little connection between them, our work is based on the premise that these three sectors face a common problem caused by the erosion of genetic diversity. The solution to this problem involves the elucidation of the evolutionary processes that shape genetic diversity, as well as acquiring a better understanding of the impact of environmental changes induced by human activities on the dynamics of these processes. The research program incorporates the innovative nature of state-of-the-art technology such as Next Generation Sequencing (NGS), analysis of gene expression and high-throughput genotyping to elucidate the processes that can lead to the adaptation of species to their environment and to understand the impact of human activities (climate change, overexploitation, domestication, introduction of alien species, restocking, pollution) on the genetic integrity of marine natural populations.

Conceptual framework of the research program

Understanding how the interactions "genome-environment" modulate the organisation of genetic diversity within and between populations is a major challenge of modern biology1. The importance of this knowledge comes from the paradigm of local adaptation, that is, the fragmentation of the gene pool of a species is translated into a geographical and ecological structure of populations exposed to different selective regimes, resulting in co-adapted gene complexes2. Maintenance of the genetic integrity of populations is also essential in a modern perspective of conservation to preserve the processes that generate biodiversity and the sustainable use of wild and mariculture populations3. The acquisition of knowledge about the nature of adaptive genetic differences between populations can enhance the decision-making process in conservation by identifying priority populations to protect or to use for restocking4. In addition, this information is the basis for a rational definition of management units5 that provide a spatially explicit framework necessary for any management plan6. It is therefore important to elucidate the evolutionary processes that shape the genetic diversity, to understand the impact of environmental changes induced by human activities on the dynamics of these processes and the potential of populations to adapt to these changes.

Despite the importance of understanding the processes responsible for the maintenance of adaptive genetic diversity, until recently, few studies have been done in this direction1, most have used a small number of genetic markers without apparent adaptive value. Evolutionary and conservation biology are currently experiencing a phenomenal technological and analytical burst due to the NGS revolution7,8, just as they did with the discovery of PCR 25 years ago 9. However, its potential benefits for the conservation and management of wild taxa are still underexploited 10. An important innovation that led to this “NGS-revolution” is the possibility to study neutral and adaptive genetic diversity at a genomic scale in non-model species and at a cost that is nowadays a fraction of what used to be very recently 7. For example, several methods collectively known as "reduced-representation-libraries" (RRL) such RAD-seq, DArT Seq or genotyping by sequencing (GBS), allow low-cost analysis of thousands of markers distributed throughout the genome without any prior development7,11. With these approaches, it is possible to substantially increase the accuracy of estimated genetic parameters essential to management and conservation, to rigorously quantify the level of intra-population genetic diversity and the adaptive genetic differentiation between populations12. The approach GBS also allows to construct genetic maps of high resolution in non-model species13, thus increasing the potential for identification of quantitative trait loci (or QTL) used to improve breeding programs in mariculture14,15. Continuously decreasing sequencing costs also allows undertaking studies of populations based on re-sequencing of the entire genome of several individuals16.

Research projects

Evolutionary ecogenomics and conservation of scalloped hammerhead sharks in the WCPO: implications for the assessment of Non-Detrimental Findings under CITES regulations

Summary: Three sharks die every second worldwide either because of their fins, as bycatch of tuna and other fishing industries, or through the destruction of their natural habitats and thus are among the most vulnerable fishes in the world. The Scalloped Hammerhead Shark (SHS) (Sphyrna lewini) is among the most globally threatened shark species and has recently being included in the Appendix II of CITES. Establishing a sound scientific program to acquire additional data to determine Non-Detrimental Findings (NDFs) for hammerhead sharks in the region and to establish a network of regional collaboration to assess the hammerhead stocks is a priority identified in the last Regional Workshop on the Implementation of CITES Appendix II Shark Listings. The primary goal of this research program is to test the general hypothesis that the SHS populations follow a metapopulation dynamics model with clearly differentiated management and evolutionary significant units focusing in their adaptive divergence and connectivity. To this end, we will conduct a thorough characterization of the genetic diversity and structure of SHS nursing areas in Viti Levu and Vanua Levu, determine the minimal number of adult females that use each nursing area, the number of pups that survive at different length/age classes, the number of cohorts that are present in the nursing areas throughout the year and determine the spatial distribution of different cohorts within each river. Furthermore, we will determine the adaptive and neutral population genetic structure throughout the western and central Pacific Ocean (WCPO), test for the existence of a mixed stock structure from the sharks captured by the fishing industry and estimate the effective population sizes of the management and/or evolutionary significant units identified.

Integrative assessment of the population genetics and the fisheries and tourist-related economic benefits of bull sharks in Fiji.

Summary: The bull shark is a circumglobally distributed highly-migratory and large coastal shark species. It occurs in Fiji coastal areas and its genetic diversity suggests that it might represent a distinct subspecies. Bull sharks in Fijian waters are regularly caught in the artisanal fisheries and in the large scale longline fishery as target species and/or as bycatch and constitute an important tourist attraction through the shark diving industry whose estimated annual economic benefits exceeds USD 40 million. If indeed the genetic differentiation and possible geographic isolation of Fijian bull sharks is demonstrated, it will make this population especially vulnerable to local extinction through overfishing jeopardising not only the health of the ecosystem for their role as apex predators, but the livelihoods of fishermen and those who earn a living from the shark dive industry. This study seeks to investigate these issues by addressing four objectives. 1) Test the general hypothesis that the bull shark populations follow a metapopulation dynamics model with clearly differentiated management and evolutionary significant units focusing on their adaptive divergence and connectivity. In locally adapted populations of bull sharks, individuals would display similar migration or habitat uses, resulting from a common spatial learning among individuals and with distinctive genetics signature of local adaptation imprinted in the early years of their life cycle supporting a metapopulation dynamics model throughout its geographic range. 2) Assess the current rate of mortality as target and bycatch on the artisanal and subsistence fisheries operating in the Fiji Islands to evaluate the temporal (annual) dynamic of the captures with respect to size and sex. 3) Explore the extent of income and employment loss of fishermen (both regulated and unregulated) due to the potential ban on fishing for coastal sharks.4) Compare the relative benefits of fishing with those of the shark diving industry and to forecast the growth potential of the latter sector.

Meta-population dynamics, population genomics and determination of management units of tuna species in the WCPO.

Tunas are among the most demanded and valued wild caught fishes of the world, accounting for up to 8% of total fish and shellfish products in the international seafood markets and thus, most species are either fully exploited (37.5%) or overexploited (33.5%) worldwide17. In the Western and Central Pacific Ocean (WCPO), four species account for most of the tuna fishery: albacore (Thunnus alalunga), bigeye (T. obesus), yellowfin (T. albacares) and skipjack (Katsuwonus pelamis), and represent 2.6 million tons of the total tuna industry; that is 60.5% of the 4.3 million tons of the 14 tuna species exploited worldwide17. One of the most common problems in fisheries is the definition of management units. The number of genetically distinct populations in tuna species that have been identified using different molecular markers hitherto exceeds the number of stocks managed by Regional Fisheries Management Organisations, suggesting an urgent need to re-evaluate fishery management policies in these tunas18. The primary aim of this project is to conduct population genomics of the most commercially important four tuna species in the WCPO to fill important gaps in the current knowledge of tuna meta-population dynamics and focuses on the structure of stocks, their adaptive divergence and the genetic connectivity between these biological and management units. Testing the same hypothesis, namely “tuna populations follow a metapopulation dynamics model with clearly differentiated management and evolutionary significant units focusing on their adaptive divergence and connectivity”, on species with different life history strategies and under different fishing pressure is highly recommended, as it allows to identify general processes in nature responsible for the maintenance and distribution of the neutral and adaptive genetic diversity. To do so we will characterise the neutral and adaptive genetic diversity and structure of skipjack, yellowfin, bigeye and albacore tuna stocks throughout the WCPO by obtaining at least 10,000 single nucleotide polymorphisms (SNP) in each species through a genotyping by sequencing of reduced representation library protocol such as DArTseq which provide a significant advantage via an intelligent selection of genome fraction corresponding predominantly to active genes.

 

 

Master thesis:

Krystelle Lavaki (s11023755@usp.ac.fj): Assessing the variability in life history parameters of two important coral reef fish species in Fiji

Ronnick Spenly Shedrack (s11062153@usp.ac.fj): Milkfish, Chanos chanos (Forsskal, 1775), fry seasonality in Vanuatu: their availability and abundance in the coastal shoreline of Efate Island

 

PhD Thesis:

Behavioural, biological and environmental mechanisms that may underlie chaotic genetic patchiness in three tuna species

PhD Candidate: Giulia Anderson (giuanders(at)gmail.com)

Summary: Tunas support a lucrative and high-volume industry, but stocks of numerous species are already maximally or over-exploited. Tunas are traditionally assumed to be a single breeding population within an ocean basin because of their highly mobility, but an increasing body of genetic evidence suggests that this is inaccurate. If tunas are not managed at biologically relevant scales, there is potential to unknowingly over-exploit subpopulations to the point of local extirpation. This scale also changes between tuna species. An ongoing genomic study which is using Next Generation Sequencing (NGS) technology has described fine-scale structuring in populations of four principle market tuna species (albacore, bigeye, skipjack, and yellowfin) that varies independent of distance between populations, and changes over time. This form of structure is called chaotic genetic patchiness, and suggests that biological, behavioural and environmental factors drive a complex set of interactions among subpopulations. In order to assure that these species are sustainably managed, the mechanisms that produce chaotic genetic patchiness much be identified, as they may be linked to stronger population patterning than is reflected in measurements of general genomic differentiation between populations. Candidate mechanisms include collective dispersal of larvae, kin recognition and preference during schooling, and the influence of the dynamic oceanic environment on larvae dispersal and adult movements and migrations. Depending on the extent to which these different mechanisms are present in each tuna species, the implications for management will differ. For example, if collective dispersal is confirmed as a significant mechanism, then fishing out large portions of schools via purse seine net could extract entire families that carry rare alleles, which would disproportionately impact population genetic diversity. The distribution of catch between schools and fishing gear types would require review. Alternatively, if the oceanic environment proves a dominant mechanism in predicting the movement of larvae, recruits, or even adults, then population assessment protocols must be revised to describe populations based on their oceanographic, rather than geographic, locations. It is the intention of the proposed study to examine potential drivers of chaotic genetic patchiness in albacore, skipjack and yellowfin tuna, in order to provide either specific management recommendations or provide direction for future investigations into alternative mechanisms. It is the ultimate goal of the investigation to promote sustainable management of tuna stocks in the Western and Central Pacific Ocean.

Population genomics of Bigeye tuna: a tool to curb Illegal, Unregulated and Underreported (IUU) fishing in the Pacific Ocean.

PhD Candidate: Janice Natasha (janice.natasha(at)usp.ac.fj)

Summary: The West and Central Pacific Ocean (WCPO) are home to the largest and most valuable tuna fishery in the world. WCPO tuna fishery ranges from small-scale, artisanal operations in the coastal waters of Pacific states, to large-scale, industrial purse-seine, pole-line and longline operations in the exclusive economic zones of Pacific states and in international waters. Out of the four key tuna stocks of WCPO, Bigeye tuna has a higher proportion (19%) of illegal, unreported and unregulated (IUU) fishing. This volume is mainly driven by illegal transhipping and re-supply at sea. Pacific Island Countries (PICs) lose a considerable amount of foreign earnings through IUU fishing. The lack of traceability and enforcement of regulation coupled with already dwindling Bigeye tuna stocks is a serious concern for WCPO tuna fishery. There is an urgent need to address these issues to curb IUU fishing and also effectively manage the remaining Bigeye tuna stocks. Existing fisheries legislation and Regional Fisheries Management Organisations (RMFOs) often refer to fish stocks or geographic regions as relevant units for law enforcement and this warrants the need for methods identifying the population of origin of landed fish. The proposed study aims to fill the gaps in the current knowledge of tuna meta-population dynamics and focusses on the structure of stocks, their adaptive divergence and the genetic connectivity between evolutionary significant and management units. This study will use single-nucleotide polymorphism (SNP) markers and next generation sequencing (NGS) to study the population genetic structure of Bigeye tuna by determining the spatial and temporal distribution of the neutral and adaptive genetic diversity of the species in the WCPO. The outputs will be used to develop a high-throughput genotyping method for accurate population assignment of Bigeye Tuna to its population of origin and thus allowing geographical traceability to improve compliance with fishing regulation. Inclusion of genetic identification of geographic origin in certification schemes or in random testing as catches are landed around the world should help deter unlawful practices, such illegal transhipping and re-supply at sea, and enhance product traceability, authenticity, consumer confidence and also should boost sustainable exploitation of remaining Bigeye tuna populations across its global range.

Integrative assessment of the population genetics, fisheries and tourist-related economic benefits of bull sharks in Fiji.

PhD Candidate: Kerstin Glaus (kerstin_glaus(at)outlook.com)

The bull shark is a circumglobally distributed highly-migratory and large coastal shark species. Despite the species’ worldwide distribution, microsatellite analyses revealed that the bull sharks in Fijian waters show a distinctive genetic differentiation and thus may be locally adapted. In locally adapted populations, individuals would display similar migration or habitat uses, resulting from a common spatial learning among individuals and with distinctive genetics signature of local adaptation imprinted in the early years of their life cycle supporting a metapopulation dynamics model throughout its geographic range. If indeed the genetic differentiation and possible geographic isolation of Fijian bull sharks is demonstrated, it will make this population especially vulnerable to local extinction through overfishing and habitat loss, since depletion cannot be compensated through dispersal. Especially in Fiji, bull sharks are an important tourist attraction through the shark diving industry which accounts for annual economic benefits exceeding USD $40 million. Besides fishing pressure exerted by large-scale longline fisheries, bull sharks are also caught by Fijian artisanal fishermen both as target species and/or as bycatch. Hence, local habitat and species management is needed, to prevent jeopardising not only the health of the ecosystem for the bull sharks role as apex predators, but the livelihoods of fishermen and those who earn a living from the shark dive industry. The main objective of this study is to test the general hypothesis that the bull shark populations follow a metapopulation dynamics model with clearly differentiated management and evolutionary significant units. Specific aims are to: (1) determine the adaptive and neutral population genetic structure throughout the WCPO; (2) detect if there is evidence of a mixed stock structure from the sharks captured by the fishing industry; (3) estimate the effective population size of the management and/or evolutionary significant units identified(4) assess the current rate of mortality as target and bycatch on the artisanal and subsistence fisheries operating in the Fiji Islands; (5) elaborate community-based management

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2 Kawecki, T. J. & Ebert, D. Conceptual issues in local adaptation. Ecology Letters 7, 1225-1241, doi:10.1111/j.1461-0248.2004.00684.x (2004).

3 Bowen, B. W. & Roman, J. Gaia's handmaidens: the Orlog model for conservation biology. Conservation Biology 19, 1037-1043, doi:10.1111/j.1523-1739.2005.00100.x (2005).

4 Funk, W. C., McKay, J. K., A., H. P. & W., A. F. Harnessing genomics for delineating conservation units Trends in Ecology and Evolution 27, 8 (2012).

5 Waples, R. S. & Gaggiotti, O. What is a population? An empirical evaluation of some genetic methods for identifying the number of gene pools and their degree of connectivity. Molecular Ecology 15, 1419–1439 (2006).

6 Conover, D. O., Clarke, L. M., Munch, S. B. & Wagner, G. N. Spatial and temporal scales of adaptive divergence in marine fishes and the implications for conservation. Journal of Fish Biology 69, 21-47, doi:10.1111/j.1095-8649.2006.01274.x (2006).

7 Hohenlohe, P. A., Catchen, J. & Cresko, W. A. Population genomic analysis of model and nonmodel organisms using sequenced RAD tags. Methods in molecular biology (Clifton, N.J.) 888, 235-260 (2012).

8 Margulies, M. et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437, 376-380, doi:10.1038/nature03959 (2005).

9 Saiki, R. K. et al. Primer-directed enzymatic amplification of DNA with a thermostable DNA-polymerase. Science 239, 487-491, doi:10.1126/science.2448875 (1988).

10 Angeloni, F., Wagemaker, N., Vergeer, P. & Ouborg, J. Genomic toolboxes for conservation biologists. Evolutionary Applications 5, 130-143, doi:10.1111/j.1752-4571.2011.00217.x (2012).

11 Davey, J. W. et al. Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nature Reviews Genetics 12, 499-510, doi:10.1038/nrg3012 (2011).

12 Hohenlohe, P. A., Bassham, S., Currey, M. & Cresko, W. A. Extensive linkage disequilibrium and parallel adaptive divergence across threespine stickleback genomes. Philosophical Transactions of the Royal Society B: Biological Sciences 367, 395-408, doi:10.1098/rstb.2011.0245 (2012).

13 Amores, A., Catchen, J., Ferrara, A., Fontenot, Q. & Postlethwait, J. H. Genome Evolution and Meiotic Maps by Massively Parallel DNA Sequencing: Spotted Gar, an Outgroup for the Teleost Genome Duplication. Genetics 188, 799-U779, doi:10.1534/genetics.111.127324/-/DC1 (2011).

14 Sauvage, C., Vagner, M., Derome, N., Audet, C. & Bernatchez, L. Coding Gene Single Nucleotide Polymorphism Mapping and Quantitative Trait Loci Detection for Physiological Reproductive Traits in Brook Charr, Salvelinus fontinalis. G3-Genes Genomes Genetics 2, 379-392, doi:10.1534/g3.111.001867 (2012).

15 Sauvage, C., Vagner, M., Derome, N., Audet, C. & Bernatchez, L. Coding Gene SNP Mapping Reveals QTL Linked to Growth and Stress Response in Brook Charr (Salvelinus fontinalis). G3-Genes Genomes Genetics 2, 707-720, doi:10.1534/g3.112.001990 (2012).

16 Jones, F. C. et al. A Genome-wide SNP Genotyping Array Reveals Patterns of Global and Repeated Species-Pair Divergence in Sticklebacks. Current Biology 22, 83-90, doi:10.1016/j.cub.2011.11.045 (2012).

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18 Kumar, G. & Kocour, M. Population Genetic Structure of Tunas Inferred from Molecular Markers: A Review. Rev. Fish. Sci. Aquac.. 23, 72-89, doi:10.1080/23308249.2015.1024826 (2015).


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