Evolutionary biology of Gondwanan non-biting midges (Diptera: Chironomidae)

The potential restriction to effective dispersal and gene flow caused by habitat fragmentation can apply to multiple levels of evolutionary scale; from the fragmentation of ancient supercontinents driving diversification and speciation on disjunct landmasses, to the isolation of proximate populations as a result of their inability to cross intervening unsuitable habitat. Investigating the role of habitat fragmentation in driving diversity within and among taxa can thus include inferences of phylogenetic relationships among taxa, assessments of intraspecific phylogeographic structure and analyses of gene flow among neighbouring populations. The proposed Gondwanan clade within the chironomid (non-biting midge) subfamily Orthocladiinae (Diptera: Chironomidae) represents a model system for investigating the role that population fragmentation and isolation has played at different evolutionary scales. A pilot study by Krosch et al (2009) indentified several highly divergent lineages restricted to ancient rainforest refugia and limited gene flow among proximate sites within a refuge for one member of this clade, Echinocladius martini Cranston. This study provided a framework for investigating the evolutionary history of this taxon and its relatives more thoroughly. Populations of E. martini were sampled in the Paluma bioregion of northeast Queensland to investigate patterns of fine-scale within- and among-stream dispersal and gene flow within a refuge more rigorously. Data was incorporated from Krosch et al (2009) and additional sites were sampled up- and downstream of the original sites. Analyses of genetic structure revealed strong natal site fidelity and high genetic structure among geographically proximate streams. Little evidence was found for regular headwater exchange among upstream sites, but there was distinct evidence for rare adult flight among sites on separate stream reaches. Overall, however, the distribution of shared haplotypes implied that both larval and adult dispersal was largely limited to the natal stream channel. Patterns of regional phylogeographic structure were examined in two related austral orthoclad taxa – Naonella forsythi Boothroyd from New Zealand and Ferringtonia patagonica Sæther and Andersen from southern South America – to provide a comparison with patterns revealed in their close relative E. martini. Both taxa inhabit tectonically active areas of the southern hemisphere that have also experienced several glaciation events throughout the Plio-Pleistocene that are thought to have affected population structure dramatically in many taxa. Four highly divergent lineages estimated to have diverged since the late Miocene were revealed in each taxon, mirroring patterns in E. martini; however, there was no evidence for local geographical endemism, implying substantial range expansion post-diversification. The differences in pattern evident among the three related taxa were suggested to have been influenced by variation in the responses of closed forest habitat to climatic fluctuations during interglacial periods across the three landmasses. Phylogeographic structure in E. martini was resolved at a continental scale by expanding upon the sampling design of Krosch et al (2009) to encompass populations in southeast Queensland, New South Wales and Victoria. Patterns of phylogeographic structure were consistent with expectations and several previously unrecognised lineages were revealed from central- and southern Australia that were geographically endemic to closed forest refugia. Estimated divergence times were congruent with the timing of Plio-Pleistocene rainforest contractions across the east coast of Australia. This suggested that dispersal and gene flow of E. martini among isolated refugia was highly restricted and that this taxon was susceptible to the impacts of habitat change. Broader phylogenetic relationships among taxa considered to be members of this Gondwanan orthoclad group were resolved in order to test expected patterns of evolutionary affinities across the austral continents. The inferred phylogeny and estimated divergence times did not accord with expected patterns based on the geological sequence of break-up of the Gondwanan supercontinent and implied instead several transoceanic dispersal events post-vicariance. Difficulties in appropriate taxonomic sampling and accurate calibration of molecular phylogenies notwithstanding, the sampling regime implemented in the current study has been the most intensive yet performed for austral members of the Orthocladiinae and unsurprisingly has revealed both novel taxa and phylogenetic relationships within and among described genera. Several novel associations between life stages are made here for both described and previously unknown taxa. Investigating evolutionary relationships within and among members of this clade of proposed Gondwanan orthoclad taxa has demonstrated that a complex interaction between historical population fragmentation and dispersal at several levels of evolutionary scale has been important in driving diversification in this group. While interruptions to migration, colonisation and gene flow driven by population fragmentation have clearly contributed to the development and maintenance of much of the diversity present in this group, long-distance dispersal has also played a role in influencing diversification of continental biotas and facilitating gene flow among disjunct populations.

Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer

Background Phylogeographic reconstruction of some bacterial populations is hindered by low diversity coupled with high levels of lateral gene transfer. A comparison of recombination levels and diversity at seven housekeeping genes for eleven bacterial species, most of which are commonly cited as having high levels of lateral gene transfer shows that the relative contributions of homologous recombination versus mutation for Burkholderia pseudomallei is over two times higher than for Streptococcus pneumoniae and is thus the highest value yet reported in bacteria. Despite the potential for homologous recombination to increase diversity, B. pseudomallei exhibits a relative lack of diversity at these loci. In these situations, whole genome genotyping of orthologous shared single nucleotide polymorphism loci, discovered using next generation sequencing technologies, can provide very large data sets capable of estimating core phylogenetic relationships. We compared and searched 43 whole genome sequences of B. pseudomallei and its closest relatives for single nucleotide polymorphisms in orthologous shared regions to use in phylogenetic reconstruction. Results Bayesian phylogenetic analyses of >14,000 single nucleotide polymorphisms yielded completely resolved trees for these 43 strains with high levels of statistical support. These results enable a better understanding of a separate analysis of population differentiation among >1,700 B. pseudomallei isolates as defined by sequence data from seven housekeeping genes. We analyzed this larger data set for population structure and allele sharing that can be attributed to lateral gene transfer. Our results suggest that despite an almost panmictic population, we can detect two distinct populations of B. pseudomallei that conform to biogeographic patterns found in many plant and animal species. That is, separation along Wallace's Line, a biogeographic boundary between Southeast Asia and Australia. Conclusion We describe an Australian origin for B. pseudomallei, characterized by a single introduction event into Southeast Asia during a recent glacial period, and variable levels of lateral gene transfer within populations. These patterns provide insights into mechanisms of genetic diversification in B. pseudomallei and its closest relatives, and provide a framework for integrating the traditionally separate fields of population genetics and phylogenetics for other bacterial species with high levels of lateral gene transfer.

A new geological model of Cenozoic New Zealand suggests a complex phylogeographic history for New Zealand terrestrial taxa

The new model of North Island Cenozoic palaeogeography developed by Kamp et al. has a range of important implications for the evolution of New Zealand terrestrial taxa over the past 30 Ma. Key aspects include the prolonged isolation of the biota on the North Island landmass from the larger and more diverse greater South Island, and the founding of North Island taxa from the potentially unusual ecosystem of a small island around Northland. The prolonged period of isolation is expected to have generated deep phylogenetic splits within taxa present on both islands, and an important current aim should be to identify such signals in surviving endemics to start building a picture of the historical phylogeography, and inferred ecology of both islands through the Cenozoic. Given the potential differences in founding terrestrial species and climatic conditions, it seems likely that the ecology may have been very diferent between the North and South Islands. New genetic data from the 10 or so species of extinct moa suggest that the radiation of moa was much more recent than previously suggested, and reveals a complex pattern that is inferred to result from the interplay of the Cenozoic biogeography, marine barriers, and glacial cycles.

Taxonomy and palaeoecology of Quaternary faunas from caves in eastern tropical Queensland : a record of broad-scale environmental change

Analysis of fossils from cave deposits at Mount Etna (eastern-central Queensland) has established that a species-rich rainforest palaeoenvironment existed in that area during the middle Pleistocene. This unexpected finding has implications for several fields (e.g., biogeography/phylogeography of rainforest-adapted taxa, and the impact of climate change on rainforest communities), but it was unknown whether the Mount Etna sites represented a small refugial patch of rainforest or was more widespread. In this study numerous bone deposits in caves in north-east Queensland are analysed to reconstruct the environmental history of the area during the late Quaternary. Study sites are in the Chillagoe/Mitchell Palmer and Broken River/Christmas Creek areas. The cave fossil records in these study areas are compared with dated (middle Pleistocene-Holocene) cave sites in the Mount Etna area. Substantial taxonomic work on the Mount Etna faunas (particularly dasyurid marsupials and murine rodents) is also presented as a prerequisite for meaningful comparison with the study sites further north. Middle Pleistocene sites at Mount Etna contain species indicative of a rainforest palaeoenvironment. Small mammal assemblages in the Mount Etna rainforest sites (>500-280 ka) are unexpectedly diverse and composed almost entirely of new species. Included in the rainforest assemblages are lineages with no extant representatives in rainforest (e.g., Leggadina), one genus previously known only from New Guinea (Abeomelomys), and forms that appear to bridge gaps between related but morphologically-divergent extant taxa ('B-rat' and 'Pseudomys C'). Curiously, some taxa (e.g., Melomys spp.) are notable for their absence from the Mount Etna rainforest sites. After 280 ka the rainforest faunas are replaced by species adapted to open, dry habitats. At that time the extinct ‘rainforest’ dasyurids and rodents are replaced by species that are either extant or recently extant. By the late Pleistocene all ‘rainforest’ and several ‘dry’ taxa are locally or completely extinct, and the small mammal fauna resembles that found in the area today. The faunal/environmental changes recorded in the Mount Etna sites were interpreted by previous workers as the result of shifts in climate during the Pleistocene. Many samples from caves in the Chillagoe/Mitchell-Palmer and Broken River/Christmas Creek areas are held in the Queensland Museum’s collection. These, supplemented with additional samples collected in the field as well as samples supplied by other workers, were systematically and palaeoecologically analysed for the first time. Palaeoecological interpretation of the faunal assemblages in the sites suggests that they encompass a similar array of palaeoenvironments as the Mount Etna sites. ‘Rainforest’ sites at the Broken River are here interpreted as being of similar age to those at Mount Etna, suggesting the possibility of extensive rainforest coverage in eastern tropical Queensland during part of the Pleistocene. Likewise, faunas suggesting open, dry palaeoenvironments are found at Chillagoe, the Broken River and Mount Etna, and may be of similar age. The 'dry' faunal assemblage at Mount Etna (Elephant hole Cave) dates to 205-170 ka. Dating of one of the Chillagoe sites (QML1067) produced a maximum age for the deposit of approximately 200 ka, and the site is interpreted as being close to that age, supporting the interpretation of roughly contemporaneous deposition at Mount Etna and Chillagoe. Finally, study sites interpreted as being of late Pleistocene-Holocene age show faunal similarities to sites of that age near Mount Etna. This study has several important implications for the biogeography and phylogeography of murine rodents, and represents a major advance in the study of the Australian murine fossil record. Likewise the survey of the northern study areas is the first systematic analysis of multiple sites in those areas, and is thus a major contribution to knowledge of tropical Australian faunas during the Quaternary. This analysis suggests that climatic changes during the Pleistocene affected a large area of eastern tropical Queensland in similar ways. Further fieldwork and dating is required to properly analyse the geographical extent and timing of faunal change in eastern tropical Queensland.

Cryptic diversity and evolutionary relationships among Australian closed-forest Melomys (Rodentia: Muridae) and related Australo-Papuan mosaic-tailed rats

This thesis investigates patterns of evolution in a group of native Australo-Papuan rodents. Past climatic change and associated sea level fluctuations, and fragmentation of wet forests in eastern Australia has facilitated rapid radiation, diversification and speciation in this group. This study adds to our understanding of the evolution of Australia’s rainforest fauna and describes the evolutionary relationships of a new genus of Australian rodent.

Time and space in biogeography : response to Parenti & Ebach (2013)

A recent Guest Editorial by Parenti & Ebach (2013, Journal of Biogeography, 40, 813–820) disagrees with the methods or interpretations in two of our recent papers. In addition, the authors open a debate on biogeographical concepts, and present an alternative philosophy for biogeographical research in the context of their recently described biogeographical subregion called ‘Pandora’. We disagree with their approach and conclusions, and comment on several issues related to our differing conceptual approaches for biogeographical research; namely, our use of molecular phylogenetic analyses, including time estimates; and Parenti & Ebach's reliance on taxon/general area cladograms. Finally, we re-examine their ‘tests’ supporting the existence of ‘Pandora’.

Impacts of climatic factors on evolution of molecular diversity and the natural distribution of wild stocks of the giant freshwater prawn (Macrobrachium rosenbergii)

Natural distributions of most freshwater taxa are restricted geographically, a pattern that reflects dispersal limitation. Macrobrachium rosenbergii is unusual because it occurs naturally in rivers from near Pakistan in the west, across India and Bangladesh to the Malay Peninsula, and across the Sunda Shelf and Indonesian archipelago to western Java. Individuals cannot tolerate full marine conditions, so dispersal between river drainage basins must occur at limited geographical scales when ecological or climatic factors are favorable. We examined molecular diversity in wild populations of M. rosenbergii across its complete natural range to document patterns of diversity and to relate them to factors that have driven evolution of diversity in this species. We found 3 clades in the mitochondrial deoxyribonucleic acid (mtDNA) data set that corresponded geographically with eastern, central, and western sets of haplotypes that last shared a common ancestor 1 × 106 y ago. The eastern clade was closest to the common ancestor of all 3 clades and to the common ancestor with its congener, Macrobrachium spinipes, distributed east of Huxley's Line. Macrobrachium rosenbergii could have evolved in the western Indonesian archipelago and spread westward during the early to mid-Pleistocene to India and Sri Lanka. Additional groups identified in the nuclear DNA data set in the central and western clades probably indicate secondary contact via dispersal between regions and modern introductions that have mixed nuclear and mtDNA genes. Pleistocene sea-level fluctuations can explain dispersal across the Indonesian archipelago and parts of mainland southeastern Asia via changing river drainage connections in shallow seas on wide continental shelves. At the western end of the modern distribution where continental shelves are smaller, intermittent freshwater plumes from large rivers probably permitted larval dispersal across inshore areas of lowered salinity.

Pleistocene climate fluctuations influence phylogeographical patterns in Melomys cervinipes across the mesic forests of eastern Australia

Aim Our aim was to clarify the lineage-level relationships for Melomys cervinipes and its close relatives and investigate whether the patterns of divergence observed for these wet-forest-restricted mammals may be associated with recognized biogeographical barriers. Location Mesic closed forest along the east coast of Australia, from north Queensland to mid-eastern New South Wales. Methods To enable rigorous phylogenetic reconstruction, divergence-date estimation and phylogeographical inference, we analysed DNA sequence and microsatellite data from 307 specimens across the complete distribution of M. cervinipes (45 localities). Results Three divergent genetic lineages were found within M. cervinipes, corresponding to geographically delineated northern, central and southern clades. Additionally, a fourth lineage, comprising M. rubicola and M. capensis, was identified and was most closely related to the northern M. cervinipes lineage. Secondary contact of the northern and central lineages was identified at one locality to the north of the Burdekin Gap. Main conclusions Contemporary processes of repeated habitat fragmentation and contraction, local extinction events and subsequent re-expansion across both small and large areas, coupled with the historical influence of the Brisbane Valley Barrier, the St Lawrence Gap and the Burdekin Gap, have contributed to the present phylogeographical structure within M. cervinipes. Our study highlights the need to sample close to the periphery of putative biogeographical barriers or risk missing vital phylogeographical information that may significantly alter the interpretation of biogeographical hypotheses.

Comparison of intraspecific genetic structure among related chironomids (Diptera) from New Zealand and Patagonia : disparity between potential and realized dispersal

Population genetic studies of freshwater invertebrate taxa in New Zealand and South America are currently few despite the geologically and climatically dynamic histories of these regions. The focus of our study was a comparison of the influence on realized dispersal of 2 closely related nonbiting midges (Chironomidae) of population fragmentation on these separated austral land masses. We used a 734-base pair (bp) fragment of cytochrome c oxidase subunit I (COI) to investigate intraspecific genetic structure in Naonella forsythi Boothroyd in New Zealand and Ferringtonia patagonica Edwards in Patagonia. We proposed hypotheses about their potential dispersal and, hence, expected patterns of genetic structure in these 2 species based on published patterns for the closely related Australian taxon Echinocladius martini Cranston. Genetic structure revealed for both N. forsythi and F. patagonica was characterized by several highly divergent (2.0–10.5%) lineages of late Miocene–Pliocene age within each taxon that were not geographically localized. Many were distributed widely. This pattern differed greatly from population structure in E. martini, which was typified by much greater endemicity of divergent genetic lineages. Nevertheless, diversification of lineages in all 3 taxa appeared to be temporally congruent with the onset of late Miocene glaciations in the southern hemisphere that may have driven fragmentation of suitable habitat, promoting isolation of populations and divergence in allopatry. We argue that differences in realized dispersal post-isolation may be the result of differing availability of suitable habitat in interglacial periods.

Conservation genetics of the water mouse, Xeromys myoides Thomas, 1889

The water mouse, Xeromys myoides, is currently recognised as a vulnerable species in Australia, inhabiting a small number of distinct and isolated coastal regions of Queensland and the Northern Territory. An examination of the evolutionary history and contemporary influences shaping the genetic structure of this species is required to make informed conservation management decisions. Here, we report the first analysis undertaken on the phylogeography and population genetics of the water mouse across its mainland Australian distribution. Genetic diversity was assessed at two mitochondrial DNA (Cytochrome b, 1000 bp; D-loop, 400 bp) and eight microsatellite DNA loci. Very low genetic diversity was found, indicating that water mice underwent a recent expansion throughout their Australian range and constitute a single evolutionarily significant unit. Microsatellite analyses revealed that the highest genetic diversity was found in the Mackay region of central Queensland; population substructure was also identified, suggesting that local populations may be isolated in this region. Conversely, genetic diversity in the Coomera region of south-east Queensland was very low and the population in this region has experienced a significant genetic bottleneck. These results have significant implications for future management, particularly in terms of augmenting populations through translocations or reintroducing water mice in areas where they have gone extinct.

High connectivity in rastrelliger kanagurta: Influence of historical signatures and migratory behaviour inferred from mtDNA Cytochrome b

Phylogeographic patterns and population structure of the pelagic Indian mackerel, Rastrelliger kanagurta were examined in 23 populations collected from the Indonesian-Malaysian Archipelago (IMA) and the West Indian Ocean (WIO). Despite the vast expanse of the IMA and neighbouring seas, no evidence for geographical structure was evident. An indication that R. kanagurta populations across this region are essentially panmictic. This study also revealed that historical isolation was insufficient for R. kanagurta to attain migration drift equilibrium. Two distinct subpopulations were detected between the WIO and the IMA (and adjacent populations); interpopulation genetic variation was high. A plausible explanation for the genetic differentiation observed between the IMA and WIO regions suggest historical isolation as a result of fluctuations in sea levels during the late Pleistocene. This occurrence resulted in the evolution of a phylogeographic break for this species to the north of the Andaman Sea.