Bay, Line Kolind (2005) The population genetic structure of coral reef fishes on the Great Barrier Reef. PhD thesis, James Cook University.

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Abstract

The population genetic structure of species may be determined by complex interactions among many ecological, evolutionary and genetic processes. I investigated the population genetic structure of coral reef fishes on the Great Barrier Reef (GBR), Australia to better understand how these various processes may interact in a natural system. I firstly examined the spatial genetic structure of a low dispersal species to determine if its genetic structure varied among spatial scales and among regions located in the centre and on the periphery of its distributional range. I then examined the population genetic structure of species with different dispersal potentials and among species sampled at central and peripheral locations in their species range. Using mtDNA control region sequences and three microsatellite loci, I examined the spatial genetic structure of a direct developing coral reef fish, Acanthochromis polyacanthus, with comparatively low dispersal rates. The spatial genetic structure of this species was scale-dependent with evidence of isolation-by-distance among regions, but not within regions. Very strong genetic structure was detected among reefs within regions consistent with a metapopulation model. Pairwise genetic distances increased from offshore and older populations, to inshore and younger ones, supporting a metapopulation propagule-pool model of colonisation. Genetic diversities, mismatch, and coalescence analyses all identified large variation in the demographic history of this species among populations and regions. Evidence of genetic bottlenecks was detected by mismatch analysis in the majority of populations sampled, but in most populations these bottlenecks appeared to be older since genetic diversities and coalescence based population growth estimates did not indicate recent genetic bottlenecks. In contrast, three populations displayed low genetic diversities and large population growth rates indicating a more recent genetic bottleneck. Reductions in genetic diversities of local populations resulted in overall lower genetic diversity and a higher regional expansion rate in the southern region located towards the distributional margin of this species. In all, these results suggest that A. polyacanthus exists as a metapopulation within regions on the GBR and that metapopulation dynamics may differ among regions located in the centre and on the periphery of this species. The pelagic larval duration (PLD) can both affect and record the ecology and evolution of coral reef fishes and emerging evidence suggests that this trait displays considerable intraspecific variation. Here I present new estimates of PLD for ten species of Pomacentridae and two species of Gobiidae, and coupled with previously published estimates, examine spatial and temporal variation of PLDs within and among these species. In eight of the twelve species examined here, within-population mean PLDs differed between sampling times, locations within regions, and among regions. In contrast, the range of these same PLD estimates overlapped at all spatial and temporal scales examined in eleven of the twelve species, but not between regions in one species (Amphiprion melanopus). Therefore, despite tight error estimates typically associated with estimates of PLD taken from a particular population at a particular time in some taxa, the overlapping ranges in PLD reported here indicate that the length of the pelagic larval phase is a much more plastic trait than previously appreciated. Pelagic larval duration (PLD) is a commonly used proxy for dispersal potential in coral reef fishes. Here I examine the relationship between PLD, genetic structure and genetic variability in coral reef fishes from one family (Pomacentridae) that differ in mean larval duration by more than a month. Genetic structure was estimated in eight species using a mitochondrial molecular marker (control region) and in a sub-set of five species using nuclear molecular markers (ISSRs). Estimates of genetic differentiation were similar among species with pelagic larvae, but differed between molecular markers. The mtDNA indicated no structure while the ISSR indicated some structure between the sampling locations. I detected a relationship between PLD and genetic structure using both markers. These relationships, however, were caused by a single species, Acanthochromis polyacanthus, which differs from all the other species examined here in lacking a larval phase. With this species excluded, there was no relationship between PLD and genetic structure using either marker. Genetic diversities were generally high in all species and did not differ significantly among species and locations. Nucleotide diversity and total heterozygosity were negatively related to maximum PLD, but again, these relationships were caused by A. polyacanthus and disappeared when this species was excluded from these analyses. These genetic patterns are consistent with moderate gene flow among well-connected locations and indicate that at this phylogenetic level (i.e., within family) the duration of the pelagic larval phase is not the primary factor affecting patterns of genetic differentiation. Using mtDNA (control region) and nuclear (ISSR) markers, I investigated the population genetic structure of three congeneric species pairs of pomacentrid coral reef fishes (Pomacentridae) in the context of species’ borders theory. This theory predicts that population located on the periphery of the species’ range should be smaller and more fragmented and hence, display stronger genetic structure and lower genetic diversities compared to more centrally located populations. Each species pair consisted of one species sampled at two central locations within its geographic range, and another species sampled at the same locations but which constituted one location toward the centre of its range and another close to its edge. Contrary to expectations from theory, I did not find the predicted border effects in the population genetic structure of the species examined. Gene flow estimates did not differ among central and peripheral species. Genetic diversities were not lower in peripheral populations compared to central populations or in species sampled towards the periphery compared to those sampled in the centre of their ranges. Indeed, genetic diversities were much greater in the peripheral species compared to their central counterparts. The distribution of genetic variation indicated that secondary contact among differentiated lineages may, in part, be responsible for the high genetic diversity in these peripheral species. Elevated mutation rates mediated by environmental stress on the species’ margin may have contributed further genetic variability in these species.

Item ID:	14
Item Type:	Thesis (PhD)
Keywords:	Genetics, Coral, Reef fish, Great Barrier Reef
Date Deposited:	20 Jun 2007
FoR Codes:	06 BIOLOGICAL SCIENCES > 0608 Zoology @ 50% 06 BIOLOGICAL SCIENCES > 0604 Genetics > 060411 Population, Ecological and Evolutionary Genetics @ 50%
SEO Codes:	96 ENVIRONMENT > 9608 Flora, Fauna and Biodiversity > 960808 Marine Flora, Fauna and Biodiversity @ 100%
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