McDonald, Brenda J. (2005) Population genetics of dugongs around Australia : implications of gene flow and migration. PhD thesis, James Cook University.

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Abstract

Dugongs (Dugong dugon) live in tropical inshore areas around Northern Australia and throughout the Indo-West Pacific. These marine mammals are obligate seagrass feeders and are thus largely restricted in distribution to areas of seagrass habitat. The turbid environment and the lack of a dorsal fin for individual identification makes it impractical to study these animals using standard observational methods. Consequently very little is known about dugong population structure and migration patterns. From satellite tracking of individuals and aerial surveys it appears that dugongs, like many other marine mammals, can move long distances, but the timing and length of movements vary individually. If dugongs move and mate in their new locality, there will be substantial gene flow across large spatial scales and very little population differentiation around the tropical Australian coast. However, if dugongs maintain a home range and are philopatric (i.e. any long distance movements are for food or other reasons not including mating), then there would be very limited gene flow and substantial structuring among populations. In order to ascertain which pattern of population structure is present in the dugong, I used a variety of molecular techniques to assess dugong population genetic structure around the North Australian coast. A comparison of the two published mitochondrial genomes of dugongs showed that most variation was contained within the control region. I subsequently characterised the entire control region of eight individual dugongs (four available from previous studies and four sequenced in this study) and identified the amount of variation among them. I also made a comparison of the mitochondrial control region of dugongs with available sequences of their closest relatives, the paenungulates (Proboscidea, Hyracoidea, and other members of the Sirenia), in order to assess whether the control region was capable of producing reasonable phylogenies and its usefulness as a marker for phylogeographic and population studies on the dugong. The 5’ domain of the control region was identified as the most appropriate section of this locus for use in the phylogeographic analysis. This domain demonstrates high diversity in the dugong. Phylogeographic analysis of the 492 bp alignment of 115 dugongs, identified two divergent Australian mitochondrial lineages. I hypothesise that the Australian lineages diverged historically during periods of low sea level that would have reduced habitat availability and produced geological barriers such as the Torres Strait land bridge between Northern Australia and Papua New Guinea. One lineage is restricted geographically to the coast of Queensland and into the Northern Territory, while the other is more widespread occurring from Shark Bay in Western Australia to Moreton Bay in Queensland (i.e. across the entire Australian range). The widespread lineage is poorly represented in Southeastern Queensland. Given the availability of continuous habitat with higher sea level for the past 7000 years and the high mobility of dugongs, I expected that more complete geographic mixing of lineages would have occurred. Mitochondrial DNA sequences of dugongs from Asia are distinct from those of Australian dugongs. These results suggest long-term isolation between dugong lineages and subsequent partial geographic mixing of dugong matrilines. Nuclear DNA microsatellite loci isolated from the Florida manatee were tested for use as population genetic markers the dugong. These loci displayed considerable allelic diversity in the dugong, significantly greater than observed in the Florida manatee. For example, 27 alleles were identified in the dugong at locus TmaA04, while only one allele was identified in the Florida manatee at the same locus. These microsatellite markers reveal a high level of gene flow among dugongs in Australia and a significant level of isolation-by-distance across Australia. Comparison of the results from mtDNA and nDNA indicate that members of the two distinct mitochondrial lineages within Australia interbreed in areas where they overlap geographically. The contrasting patterns of structure presented by the mtDNA and nDNA suggest male-biased gene flow in the dugong. This pattern has not yet been identified from ecological studies, but is consistent with common dispersal patterns in mammals. The major findings of this study are the detection of ‘healthy’ levels of genetic diversity of Australian dugongs, a suggestion of male-biased gene flow, and a demonstration of significant gene flow around Australia. This high level of gene flow makes the allocation of management units difficult. These results indicate the importance of a co-ordinated management strategy at a spatial scale of thousands of kilometres. Dugongs within Australia cannot be managed at a bay level due to the connectivity between bays observed in this study. Co-operation between management agencies at local, state, national and international spatial scales is required in order to conserve this vulnerable species.

Item ID:	1327
Item Type:	Thesis (PhD)
Keywords:	dugongs, Dugong dugon, population structure, population genetics, gene flow, phylogeography, north Australia, mitochondrial genome, control region, nuclear DNA, microsatellites, management implications
Date Deposited:	28 Sep 2007
FoR Codes:	06 BIOLOGICAL SCIENCES > 0604 Genetics > 060409 Molecular Evolution @ 0% 06 BIOLOGICAL SCIENCES > 0604 Genetics > 060411 Population, Ecological and Evolutionary Genetics @ 0% 06 BIOLOGICAL SCIENCES > 0603 Evolutionary Biology > 060302 Biogeography and Phylogeography @ 0%
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