van der Meer, Martin H. (2013) Coming, going, gone?: Population connectivity and extinction risk in restricted range coral reef fishes on isolated islands. PhD thesis, James Cook University.

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Abstract

In the terrestrial environment the highest rates of extinction have been in endemic species on isolated islands. In recent years, threats to coral reefs on isolated islands have increased causing both local and global extinctions. Effective management that maintains restricted range species must be based on identified important source and/or sink populations. This requires knowledge of abundance, distribution, habitat specialization, patterns and levels of population connectivity and levels of genetic diversity within and among inhabited locations for all species of interest. Here I evaluate the genetic risk of extinction in six species of coral reef fishes with different distribution range sizes (widespread, restricted, endemic), found in Australian coastal waters or on remote offshore islands. Population structure, connectivity and levels of genetic diversity were obtained and compared over spatial- and time- scales using mtDNA and species specific msatDNA (generated explicitly for this study). The six species examined were the Great Barrier Reef anemonefish (Amphiprion akindynos), McCulloch's anemonefish (A. mccullochi), Three-striped butterflyfish (Chaetodon tricinctus), large Doubleheader wrasse (Coris bulbifrons), Black cod (Epinephelus daemelii) and Galapagos shark (Carcharhinus galapagensis).

Chapter 1 defines endemic species; discusses what the biggest threats faced by endemic species are; defines the IUCN criteria for assessing extinction risk; establishes how genetic traits - especially population connectivity and genetic diversity - over different time scales (using both mt- and msatDNA) are vital to adequately evaluate realised dispersal.

Chapter 2 outlines general Material and Methods, provides species descriptions and general laboratory techniques and analyses used in each chapter; whilst species specific Material and Methods details are retained in individual thesis chapters.

Chapter 3 discovers historical hybridization between two sister species of anemonefish, the widespread Great Barrier Reef anemonefish (Amphiprion akindynos) and the endemic McCulloch's anemonefish (A. mccullochi), informed by a diverse range of mtDNA and msatDNA data analyses.

Chapter 4 reveals patterns and levels of population connectivity and genetic diversity in the endemic McCulloch's anemonefish (A. mccullochi), informed by a diverse range of mtDNA and msat DNA data analyses.

Chapter 5 reveals patterns and levels of population connectivity and genetic diversity in the endemic three-striped butterflyfish (Chaetodon tricinctus) using similar approaches to those used in the previous chapters.

Chapter 6 reveals patterns and levels of population connectivity and genetic diversity in the endemic doubleheader wrasse (Coris bulbifrons) using similar approaches to those used in the previous chapters.

Chapter 7 does three things. Firstly, it combines data from previous chapters with data published on black cod (Epinephelus daemelii) and Galapagos shark (Carcharhinus galapagensis) populations structure to determine whether patterns and levels of population connectivity and levels of genetic diversity of the diverse assemblage of fish species from five different families (Pomacentridae, Chaetodontidae, Labridae, Epinephelinae, Carcharhinidae) (Chapters 3 – 6, A1 – 3), within the restricted distribution range of the Lord Howe Island and Norfolk Island rises are the same or not. Secondly, it assesses the local or global genetic extinction risk of each examined species in an IUCN framework by ranking relevant traits in an extinction risk matrix to generate a relative genetic extinction risk for each species. Finally, this chapter establishes if a single or multiple spatial management strategies are required to protect the unique biodiversity at the isolated South-west Pacific Ocean islands they inhabit (Chapter 7).

Appendix A1 describes a suite of new msatDNA markers that I developed for McCulloch's anemonefish (A. mccullochi) population genetic studies.

Appendix A2 describes a suite of new msatDNA markers that I developed for three-striped butterflyfish (Chaetodon tricinctus) population genetic studies.

Appendix A3 describes a suite of new msatDNA markers that I developed for doubleheader wrasse (Coris bulbifrons) population genetic studies.

Both anemonefishes and the wrasse were more susceptible to extinction than the other three species, due to their relatively low levels of historic and demographic gene flow. All species had high genetic diversity, suggesting high levels of adaptive capacity and thus some resilience to environmental change. However, the high levels of self-replenishment (and consequently low levels of recent migration) are a cause for concern on one hand, as it suggests that most locations are largely self-sustaining. Although isolated reefs/islands are less prone to major disturbances than coastal reefs, when they do occur, their remoteness may increase the risk of extinction faced by endemic species, as a viable population may not exist following a disturbance (especially if populations have high self-replenishment). On the other hand, high levels of self-replenishment are crucial for the persistence of populations on demographic time scales. The similar levels of population connectivity and high self-replenishment shown across this taxonomically wide range of species that vary in ecological and life history traits, suggests that environment shapes genetic traits in species at this study system. This is encouraging as a single management plan for the design of effective marine reserves in the region may be feasible. This management strategy involving a network of MPAs that protects part of each location in the geographic range of endemics is likely to be effective at conserving the unique biodiversity of endemism hotspots. However, computer models incorporating ecology, life history, population connectivity, oceanography and different environmental change scenarios are needed to further our understanding of extinction risk at these remote islands, now and in the future.

Item ID:	40691
Item Type:	Thesis (PhD)
Keywords:	amphiprion; Australia; carcharhinus; chaetodon; chaetodontidae; coral reef fishes; coral reefs; ecological specialist; Elizabeth-Middleton Reef; endemic hotspot; endemic species; endemism; epinephelus; evolutionary; extinction risk; extinction; genetic diversity; genetics; Great Barrier Reef; isolated islands; Lord Howe Island; marine dispersal; marine protected areas; msatDNA; mtDNA; Norfolk Island; overfishing; peripheral isolation; population connectivity; population viability; populations; self-replenishment; wrasses
Related URLs:	http://researchonline.jcu.edu.au/24581/ http://researchonline.jcu.edu.au/24731/ http://researchonline.jcu.edu.au/28515/ http://researchonline.jcu.edu.au/37648/
Copyright Information:	Copyright © 2013 Martin H. van der Meer
Additional Information:	Publications arising from this thesis are available from the Related URLs field. The publications are: Chapter 3: van der Meer, M.H., Jones, G.P., Hobbs, J.-P.A., and Van Herwerden, L. (2012) Historic hybridization and introgression between two iconic Australian anemonefish and contemporary patterns of population connectivity. Ecology and Evolution, 2 (7). pp. 1592-1604. Chapter 4: van der Meer, Martin, Hobbs, Jean-Paul, Jones, Geoffrey, and Van Herwerden, Lynne (2012) Genetic Connectivity among and self-replenishment within island populations of a restricted range subtropical reef fish. PLoS ONE, 7 (11). pp. 1-11. Chapter 5: van der Meer, Martin H., Horne, John B., Gardner, Michael G., Hobbs, Jean-Paul A., Pratchett, Morgan, and van Herwerden, Lynne (2013) Limited contemporary gene flow and high self-replenishment drives peripheral isolation in an endemic coral reef fish. Ecology and Evolution, 3 (6). pp. 1653-1666. Chapter 6: van der Meer, M.H., Berumen, M.L., Hobbs, J.-P.A., and van Herwerden, L. (2015) Population connectivity and the effectiveness of marine protected areas to protect vulnerable, exploited and endemic coral reef fishes at an endemic hotspot. Coral Reefs, 34 (2). pp. 393-402.
Date Deposited:	01 Oct 2015 04:00
FoR Codes:	06 BIOLOGICAL SCIENCES > 0604 Genetics > 060411 Population, Ecological and Evolutionary Genetics @ 33% 06 BIOLOGICAL SCIENCES > 0603 Evolutionary Biology > 060311 Speciation and Extinction @ 34% 06 BIOLOGICAL SCIENCES > 0603 Evolutionary Biology > 060302 Biogeography and Phylogeography @ 33%
SEO Codes:	96 ENVIRONMENT > 9613 Remnant Vegetation and Protected Conservation Areas > 961303 Protected Conservation Areas in Marine Environments @ 100%
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