Single copy nuclear DNA markers characterized for comparative phylogeography in Australian wet tropics rainforest skinks

In order to investigate population history and demography in skinks endemic to the wet tropics of Australia, multiple nuclear DNA markers were sought. The utility of 72 primers (including 63 published intron-spanning 'CATS' primers) was tested.. Seven loci were characterized and shown to be single copy by single-strand conformation polymorphism analysis. Primers to five nuclear loci were developed, four with utility in skinks and three with utility in frogs. These observations extend the available information on intron-spanning primers for amphibians and reptiles.

Phylogeography of the scarab beetle Antitrogus parvulus Britton (Coleoptera : Scarabaeidae) in south-eastern Queensland, Australia

This study surveys the population genetic structure of Childers canegrub, Antitrogus parvulus, to elucidate its population dynamics and gene flow. Antitrogus parvulus is a pest of sugarcane in the Bundaberg region and this knowledge can be used to optimise integrated pest management practices. Here, base-pair differences in the cytochrome oxidase II gene (COII) were used to characterise haplotypic diversity, infer levels of gene flow, and phylogenetic relationships of alleles and their phylogeographical structure. There were 28 unique haplotypes among the 70 sequenced individuals from the seven locations. All three variance components (among regions, among populations, within populations) are highly significant, with highest genetic diversity among regions and lowest among populations within regions. A positive correlation between migration rates and geographical distance and significant phylogeographical structure between four main geographical regions. The main implication of these findings for pest management is that if a grower can eliminate an existing infestation within a field, then reinvasion will be slow and further outbreaks within that field are unlikely to occur. The low dispersal ability of females also means that any resistance to insecticides that develops is likely to remain localised, but will rapidly become dominant within the affected population.

Divergent environments and population bottlenecks fail to generate premating isolation in Drosophila pseudoobscura

While the feasibility of bottleneck-induced speciation is in doubt, population bottlenecks may still affect the speciation process by interacting with divergent selection. To explore this possibility, I conducted a laboratory speciation experiment using Drosophila pseudoobscura involving 78 replicate populations assigned in a two-way factorial design to both bottleneck (present vs. absent) and environment (ancestral vs. novel) treatments. Populations independently evolved under these treatments and were then tested for assortative mating and male mating success against their common ancestor. Bottlenecks alone did not generate any premating isolation, despite an experimental design that was conducive to bottleneck-induced speciation. Premating isolation also did not evolve in the novel environment treatment, neither in the presence nor absence of bottlenecks. However, male mating success was significantly reduced in the novel environment treatment, both as a plastic response to this environment and as a result of environment-dependent inbreeding effects in the bottlenecked populations. Reduced mating success of derived males will hamper speciation by enhancing the mating success of immigrant, ancestral males. Novel environments are generally thought to promote ecological speciation by generating divergent natural selection. In the current experiment, however, the novel environment did not cause the evolution of any premating isolation and it reduced the likelihood of speciation through its effects on male mating success.

Regional and population-scale influences on genetic diversity partitioning within costa rican populations of the pioneer tree Vochysia ferruginea mart.

The neotropical pioneer species Vochysia ferruginea is locally important for timber and is being increasingly exploited. The sustainable utilisation of this species would benefit from an understanding of the level and partitioning of genetic diversity within remnant and secondary regrowth populations. We used data from total genome (amplified fragment length polymorphism, AFLP) and chloroplast genome markers to assay diversity levels within seven Costa Rican populations. Significant chloroplast differentiation between Atlantic and Pacific watersheds was observed, suggesting divergent historical origins for these populations. Contemporary gene flow, though extensive, is geographically constrained and a clear pattern of isolation by distance was detectable when an inter-population distance representing gene flow around the central Costa Rican mountain range was used. Overall population differentiation was low (F-ST = 0.15) and within-population diversity high, though variable (H-s=0.16-0.32), which fits with the overall pattern of population genetic structure expected for a widespread, outcrossed tropical tree. However genetic diversity was significantly lower and differentiation higher for recently colonised and disturbed populations compared to that at more established sites. Such a pattern seems indicative of a pioneer species undergoing repeated cycles of colonisation and succession.

Significant patterns of population genetic structure and limited gene flow in a threatened macropodid marsupial despite continuous habitat in southeast Queensland, Australia

Many endangered species worldwide are found in remnant populations, often within fragmented landscapes. However, when possible, an understanding of the natural extent of population structure and dispersal behaviour of threatened species would assist in their conservation and management. The brush-tailed rock-wallaby (Petrogale penicillata), a once abundant and widespread rock-wallaby species across southeastern Australia, has become nearly extinct across much of the southern part of its range. However, the northern part of the species' range still sustains many small colonies closely distributed across suitable habitat, providing a rare opportunity to investigate the natural population dynamics of a listed threatened species. We used 12 microsatellite markers to investigate genetic diversity, population structure and gene flow among brush-tailed rock-wallaby colonies within and among two valley regions with continuous habitat in southeast Queensland. We documented high and signifcant levels of population genetic structure between rock-wallaby colonies embedded in continuous escarpment habitat and forest. We found a strong and significant pattern of isolation-by-distance among colonies indicating restricted gene flow over a small geographic scale (< 10 km) and conclude that gene flow is more likely limited by intrinsic factors rather than environmental factors. In addition, we provide evidence that genetic diversity was significantly lower in colonies located in a more isolated valley region compared to colonies located in a valley region surrounded by continuous habitat. These findings shed light on the processes that have resulted in the endangered status of rock-wallaby species in Australia and they have strong implications for the conservation and management of both the remaining 'connected' brush-tailed rock-wallaby colonies in the northern parts of the species' range and the remnant endangered populations in the south.

Genetic diversity and population structure of Tasmanian devils, the largest marsupial carnivore

Genetic diversity and population structure were investigated across the core range of Tasmanian devils (Sarcophilus laniarius; Dasyuridae), a wide-ranging marsupial carnivore restricted to the island of Tasmania. Heterozygosity (0.386-0.467) and allelic diversity (2.7-3.3) were low in all subpopulations and allelic size ranges were small and almost continuous, consistent with a founder effect. Island effects and repeated periods of low population density may also have contributed to the low variation. Within continuous habitat, gene flow appears extensive up to 50 km (high assignment rates to source or close neighbour populations; nonsignificant values of pairwise F-ST), in agreement with movement data. At larger scales (150-250 km), gene flow is reduced (significant pairwise F-ST) but there is no evidence for isolation by distance. The most substantial genetic structuring was observed for comparisons spanning unsuitable habitat, implying limited dispersal of devils between the well-connected, eastern populations and a smaller northwestern population. The genetic distinctiveness of the northwestern population was reflected in all analyses: unique alleles; multivariate analyses of gene frequency (multidimensional scaling, minimum spanning tree, nearest neighbour); high self-assignment (95%); two distinct populations for Tasmania were detected in isolation by distance and in Bayesian model-based clustering analyses. Marsupial carnivores appear to have stronger population subdivisions than their placental counterparts.

An investigation into effects of long-distance seed dispersal on organelle population genetic structure and colonization rate: a model analysis

A simulation-based modelling approach is used to examine the effects of stratified seed dispersal (representing the distribution of the majority of dispersal around the maternal parent and also rare long-distance dispersal) on the genetic structure of maternally inherited genomes and the colonization rate of expanding plant populations. The model is parameterized to approximate postglacial oak colonization in the UK, but is relevant to plant populations that exhibit stratified seed dispersal. The modelling approach considers the colonization of individual plants over a large area (three 500 km x 10 km rolled transects are used to approximate a 500 km x 300 km area). Our approach shows how the interaction of plant population dynamics with stratified dispersal can result in a spatially patchy haplotype structure. We show that while both colonization speeds and the resulting genetic structure are influenced by the characteristics of the dispersal kernel, they are robust to changes in the periodicity of long-distance events, provided the average number of long-distance dispersal events remains constant. We also consider the effects of additional physical and environmental mechanisms on plant colonization. Results show significant changes in genetic structure when the initial colonization of different haplotypes is staggered over time and when a barrier to colonization is introduced. Environmental influences on survivorship and fecundity affect both the genetic structure and the speed of colonization. The importance of these mechanisms in relation to the postglacial spread and genetic structure of oak in the UK is discussed.

Population structure of the peridomestic mosquito Ochlerotatus notoscriptus in Australia

Ochlerotatus notoscriptus (Skuse) (Diptera: Culicidae) is the predominant peridomestic mosquito in Australia where it is the primary vector of dog heartworm, Dirofilaria immitis (Leidy), and a potentially important vector of arboviruses (Barmah Forest, Ross River) with geographical variation of vector competence. Although widespread, Oc. notoscriptus has low dispersal ability, so it may have isolated subpopulations. The identification of gene flow barriers may assist in understanding arbovirus epidemiology and disease risk, and for developing control strategies for this species. We investigated the population structure of Oc. notoscriptus from 17 sites around Australia, using up to 31 putative allozyme loci, 11 of which were polymorphic. We investigated the effect of larval environment and adult morphology on genetic variation. At least five subpopulations were found, four in New South Wales (NSW) and one unique to Darwin. Perth samples appear to be a product of recent colonization from the Australian east coast. For NSW sites, a Mantel test revealed an isolation by distance effect and spatial autocorrelation analysis revealed an area of effective gene flow of 67 km, which is high given the limited dispersal ability of this species. No consistent difference was observed between 'urban' and 'sylvan' habitats, which suggests frequent movement between these sites. However, a finer-scaled habitat study at Darwin revealed small but significant allele frequency differences, including for Gpi. No fixed allozyme differences were detected for sex, size, integument colour or the colour of species-diagnostic pale scales on the scutum. The domestic habit of Oc. notoscriptus and assisted dispersal have helped to homogenize this species geographically but population structure is still detectable on several levels associated with geographical variation of vector competence.

A multilocus perspective on refugial isolation and divergence in rainforest skinks (Carlia)

To explore the evolutionary consequences of climate-induced fluctuations in distribution of rainforest habitat we contrasted demographic histories of divergence among three lineages of Australian rainforest endemic skinks. The red-throated rainbow skink, Carlia rubrigularis, consists of morphologically indistinguishable northern and southern mitochondrial DNA (mtDNA) lineages that are partially reproductively isolated at their parapatric boundary. The third lineage (C. rhomboidalis) inhabits rainforests just to the south of C. rubrigularis, has blue, rather than red-throated males, and for mtDNA is more closely related to southern C. rubrigularis than is northern C. rubrigularis. Multigene coalescent analyses supported more recent divergence between morphologically distinct lineages than between morphologically conservative lineages. There was effectively no migration and therefore stronger isolation between southern C. rubrigularis and C. rhomboidalis, and low unidirectional migration between morphologically conservative lineages of C. rubrigularis. We found little or no evidence for strong differences in effective population size, and hence different contributions of genetic drift in the demographic history of the three lineages. Overall the results suggest contrasting responses to long-term fluctuations in rainforest habitats, leading to varying opportunities for speciation.

Genetic population structure and call variation in a passerine bird, the satin bowerbird, Ptilonorhynchus violaceus

Geographic variation in vocalizations is widespread in passerine birds, but its origins and maintenance remain unclear. One hypothesis to explain this variation is that it is associated with geographic isolation among populations and therefore should follow a vicariant pattern similar to that typically found in neutral genetic markers. Alternatively, if environmental selection strongly influences vocalizations, then genetic divergence and vocal divergence may be disassociated. This study compared genetic divergence derived from 11 microsatellite markers with a metric of phenotypic divergence derived from male bower advertisement calls. Data were obtained from 16 populations throughout the entire distribution of the satin bowerbird, an Australian wet-forest-restricted passerine. There was no relationship between call divergence and genetic divergence, similar to most other studies on birds with learned vocalizations. Genetic divergence followed a vicariant model of evolution, with the differentiation of isolated populations and isolation-by-distance among continuous populations. Previous work on Ptilonorhynchus violaceus has shown that advertisement call structure is strongly influenced by the acoustic environment of different habitats. Divergence in vocalizations among genetically related populations in different habitats indicates that satin bowerbirds match their vocalizations to the environment in which they live, despite the homogenizing influence of gene flow. In combination with convergence of vocalizations among genetically divergent populations occurring in the same habitat, this shows the overriding importance that habitat-related selection can have on the establishment and maintenance of variation in vocalizations.