Genetic heterogeneity among isolates of Ross River virus from different geographical regions.

The RNase T1 maps of 80 isolates of Ross River virus from different regions of mainland Australia and the Pacific Islands were compared. Four different clusters of isolates with greater than an estimated 5 to 6% diversity at the nucleotide level were found. There was a pattern of differences between eastern and western Australian strains; however, the pattern was disturbed by overlaps and incursants. Pacific Islands isolates belonged to the eastern Australian topotype. Our findings suggest that certain genetic types of Ross River virus predominate in different geographical regions. In contrast, populations of other important Australian arboviruses (Murray Valley encephalitis, Kunjin, and Sindbis viruses) are distributed across the Australian continent as minor variants of one strain. Our data also show that in one region, strains of Ross River virus with identical RNase T1 maps circulate during both years when epidemics occur and years when they do not. This finding suggests that Ross River virus epidemics are not dependent on the introduction or evolution of new strains of the virus. Two strains, belonging to the eastern Australian topotype, were isolated in Western Australia. It is likely that viremic humans or possibly domestic livestock travelling by aircraft were responsible for this movement.     

Radiolaria as a reflection of environmental conditions in the eastern and southern sectors of the Indian Ocean: A new statistical approach

Cluster analysis and species abundance plots of radiolarian abundance counts from core tops from the eastern Indian Ocean between 12° S and 31° S, and the southern Indian Ocean between 31° S and 62.5° S, demonstrate the existence of environmentally-related provinces supporting distinct taxa assemblages. These provinces are closely associated with currents in the eastern sector of the Indian Ocean and with fronts in the southern sector.The radiolarian assemblages correlate strongly with salinity-normalised total alkalinity (NTA) at the sea-surface, with temperature, salinity, and density from the sea-surface to 300 m, and with dissolved oxygen and nitrate and phosphate concentrations from the sea-surface to 100 m. Palaeo-reconstructions of these parameters at the sea-surface have been made for six Last Glacial Maximum (LGM) samples from five eastern Indian Ocean cores. The LGM sea-surface temperature estimates are comparable with those based on planktonic foraminiferal counts of the same samples obtained by other researchers. The reconstructions show that, since the LGM, density increased markedly along the Western Australian coast south of 20° S but changed little further from the Western Australian coast. By contrast, phosphate concentrations were marginally lower than modern values along the Western Australian coast south of 20° S but more than twice modern values in the other LGM samples.The utility of various regression and calibration techniques is discussed. It is concluded that, probably due to the effects of differences in radiolarian habitat, ocean currents, and/or environmental gradients, only one method, weighted averaging — partial least squares, is reliable in a study area of this size and complexity. If other methods are to be used, the study area must be partitioned into at least two separate regions with the major split between the eastern and southern sectors of the Indian Ocean.     

Rotifera from Western Australian wetlands with descriptions of two new species

The rotifer fauna of 100 fresh and saline wetlands of southwest Western Australia is documented. A systematic list of 83 recorded taxa is given, with eleven new records for the continent and two new species (Brachionus pinneenaus n. sp. and Lecane boorali n. sp.) described and figured. Species assemblages are distinct from those of eastern Australia, with predominant taxa halophilous or indicative of ephemeral waters. Evolutionary and biogeographical relationships of the Western Australian rotifers are considered.     

Historical biogeography of Australian Rhamnaceae, tribe Pomaderreae

Aim To discover the pattern of relationships of areas of endemism for Australian genera in the plant family Rhamnaceae tribe Pomaderreae for comparison with other taxa and interpretation of biogeographical history. Location Australian mainland, Tasmania and New Zealand. Methods A molecular phylogeny and geographic distribution of species within four clades of Pomaderreae are used as a basis for recognition of areas of endemism and analysis of area relationships using paralogy‐free subtrees. The taxon phylogeny is the strict consensus tree from a parsimony analysis of 54 taxa, in four clades, and sequence data for the internal transcribed spacer regions of ribosomal DNA (ITS1‐5.8S‐ITS2) and the plastid DNA region trnL‐F. Results The biogeographical analysis identified five subtrees, which, after parsimony analysis, resulted in a minimal tree with 100% consistency and seven resolved nodes. Three sets of area relationships were identified: the areas of Arnhem and Kimberley in tropical north Australia are related based on the phylogeny of taxa within Cryptandra; the moister South‐west of Western Australia, its sister area the coastal Geraldton Sandplains, the semi‐arid Interzone region and arid Western Desert are related, based on taxa within Cryptandra, Spyridium, Trymalium and Pomaderris; and the eastern regions of Queensland, McPherson‐Macleay, south‐eastern New South Wales (NSW), Victoria, southern Australia, Tasmania and New Zealand are related based on Cryptandra, Pomaderris and Spyridium. Tasmania and NSW are related based entirely on Cryptandra, but the position of New Zealand relative to the other south‐eastern Australian regions is unresolved. Main conclusions The method of paralogy‐free subtrees identified a general pattern of geographic area relationships based on Australian Pomaderreae. The widespread distribution of clades, the high level of endemicity and the age of fossils for the family, suggest that the Pomaderreae are an old group among the Australian flora. Their biogeographical history may date to the early Palaeogene with subsequent changes through to the Pleistocene.     

Biogeographical structure and affinities of the marine demersal ichthyofauna of Australia

Aim To investigate the biogeographical structure and affinities of the Australian marine demersal ichthyofauna at the scale of provinces and bathomes for the purposes of regional marine planning. Location Australia. Methods Patterns of distribution in the Australian fish fauna, at both intra‐regional and global scales, were examined using a science‐based, management framework dividing Australia’s marine biodiversity into 16 province‐level biogeographical units. Occurrences of 3734 species in eight depth‐stratified bathomes (from the coast to the mid‐continental slope) within each province were analysed to determine the structure and local affinities of their assemblages and their association with faunas of nearby regions and oceans basins. Results Strong geographic and depth‐related structure was evident. Fish assemblages in each province, and in each bathome of each province, were distinct, with the shelf‐break bathome more similar to the adjacent continental shelf bathome than to the upper slope bathome. Data based only on endemic species performed well as a surrogate of the entire dataset, yielding comparable patterns of similarity between provinces and bathomes. Tropical and temperate elements were better discriminated than elements of the Pacific and Indian oceans, with the central western province more similar to the tropical provinces (including those in the east), and the eastern province closer to southern temperate provinces. The fauna shares the closest regional affinities with those of the adjacent south‐west Pacific, western Pacific Rim, and elements of wide‐ranging Indo‐Pacific components. Elements unique to the Pacific and Indian oceans are poorly represented. Main conclusions The complex nature of Australia’s marine ichthyofauna is confirmed. A hierarchy of provinces and bathomes, used to ensure that Australia’s developing marine reserve network is both representative and comprehensive, is equally robust when based on all known Australian fish species or on only those species endemic to this continent. Latitude and depth are more important than oceanic influences on the composition of this fauna at these scales.     

Broad‐scale patterns in smoke‐responsive germination from the south‐eastern Australian flora

Questions

Fire is a crucial component of many ecosystems. Plants whose seeds germinate in response to smoke may benefit from resource availability in the post‐fire environment. Smoke can influence germination timing and success, as well as seedling vigour, resulting in burgeoning research interest in smoke‐responsive germination. Research in this field has largely focused on four key ‘Mediterranean‐type’ fire‐prone ecosystems: the Mediterranean Basin, South African fynbos, Californian chaparral and Western Australia. There are far fewer studies from south‐eastern Australia, a fire‐prone but not “Mediterranean‐type” region. How does smoke‐responsive germination in this region vary according to ecological, phylogenetic, and methodological variables?

Location

South‐eastern Australia.

Methods

We investigated patterns of smoke‐promoted germination in south‐eastern Australian plants across habitat types, growth forms, fire response strategies, phylogeny, taxonomic levels and smoke application methods. We compiled and interrogated data comprising 303 entries on germination responses to smoke in 233 south‐eastern Australian plant species, from 33 different sources.

Results

Smoke‐responsive germination occurs at a lower rate (~41% of tested species) in south‐eastern Australian flora than it does in fynbos and Western Australian floras, and there is clear patterning within these data. Obligate‐seeding species were more likely to respond, Leguminosae and Rubiaceae were less likely to respond (although we question the generality of these results), while Poaceae were more likely to respond to smoke. Finally, studies using aerosol smoke and studies conducted in situ were most likely to find smoke‐promoted germination.

Conclusions

Obligate seeders and Poaceae may be selected for in habitats with higher fire frequencies, consistent with literature suggesting that short inter‐fire intervals favour grasslands over forests. These findings may be particular to south‐eastern Australia, or more widely applicable; more broad‐scale comparative research will reveal the answer. By synthesizing the south‐eastern Australian smoke germination literature we broaden our understanding beyond the better‐studied Mediterranean‐type floras.

     

Botryocladius gen.n.: a new transantarctic genus of orthocladiine midge (Diptera: Chironomidae)

A new genus of orthocladiine Chironomidae, Botryocladius (type species B. grapeth sp.n. from eastern Australia) is described and illustrated in all life history stages. All thirteen included species are described as new, six from eastern Australia (B. grapeth, B. brindabella, B. mdfrc, B. collessi, B. tasmania, B. australoalpinus), two from Western Australia (B. bibulmun and B. freemani), one from ephemeral streams in Australia (B. petrophilus) and four from Patagonian Argentina and Chile (B. edwardsi, B. glacialis, B. mapuche and B. tronador). All Australian species are known from at least pupal exuviae, most from adult males and several from larvae. In contrast, only B. edwardsi amongst Neotropical species is known from the adult male; all others are described from pupal exuviae. The immature stages are lotic in Australian permanent and temporary streams and Patagonian glacial streams and rivers, and lentic in Neotropical glacial-fed and Australian subalpine lakes. Botryocladius appears to belong with a grouping centred on two formally undescribed taxa from Australia. The genus evidently demonstrates a vicariant distribution with at least two sister-group relationships between South American and Australian taxa, providing a minimum dating for the clade of 38 Ma., with apparent absence from New Zealand indicating a maximum date of 80 Ma.     

Isolation and genetic diversity of endangered grey nurse shark (Carcharias taurus) populations

Anthropogenic impacts are believed to be the primary threats to the eastern Australian population of grey nurse sharks (Carcharias taurus), which is listed as critically endangered, and the most threatened population globally. Analyses of 235 polymorphic amplified fragment length polymorphisms (AFLP) loci and 700 base pairs of mitochondrial DNA control region provide the first account of genetic variation and geographical partitioning (east and west coasts of Australia, South Africa) in C. taurus. Assignment tests, analysis of relatedness and Fst values all indicate that the Australian populations are isolated from South Africa, with negligible migration between the east and west Australian coasts. There are significant differences in levels of genetic variation among regions. Australian C. taurus, particularly the eastern population, has significantly less AFLP variation than the other sampling localities. Further, the eastern Australian sharks possess only a single mitochondrial haplotype, also suggesting a small number of founding individuals. Therefore, historical, rather than anthropogenic processes most likely account for their depauperate genetic variation. These findings have implications for the viability of the eastern Australian population of grey nurse sharks.     

Population genetics of commercial and feral honey bees in Western Australia

Due to the introduction of exotic honey bee (Apis mellifera L.) diseases in the eastern states, the borders of the state of Western Australia were closed to the import of bees for breeding and other purposes > 25 yr ago. To provide genetically improved stock for the industry, a closed population breeding program was established that now provides stock for the majority of Western Australian beekeepers. Given concerns that inbreeding may have resulted from the closed population breeding structure, we assessed the genetic diversity within and between the breeding lines by using microsatellite and mitochondrial markers. We found that the breeding population still maintains considerable genetic diversity, despite 25 yr of selective breeding. We also investigated the genetic distance of the closed population breeding program to that of beekeepers outside of the program, and the feral Western Australian honey bee population. The feral population is genetically distinct from the closed population, but not from the genetic stock maintained by beekeepers outside of the program. The honey bees of Western Australia show three mitotypes, originating from two subspecies: Apis mellifera ligustica (mitotypes C1 and M7b) and Apis mellifera iberica (mitotype M6). Only mitotypes C1 and M6 are present in the commercial populations. The feral population contains all three mitotypes.     

Genetic population structure of grey mackerel Scomberomorus semifasciatus in northern Australia

This study used mtDNA sequence and microsatellite markers to elucidate the population structure of Scomberomorus semifasciatus collected from 12 widespread sampling locations in Australia. Samples (n = 544) were genotyped with nine microsatellite loci, and 353 were sequenced for the control (384 bp) and ATPase (800 bp) mtDNA gene regions. Combined interpretation of microsatellite and mtDNA data identified four genetic stocks of S. semifasciatus: Western Australia, north-west coast of the Northern Territory, Gulf of Carpentaria and the eastern coast of Queensland. Connectivity among stocks across northern Australia from the Northern Territory to the eastern coast of Queensland was high (mean F(ST) = 0·003 for the microsatellite data and Φ(ST) = 0·033 and 0·009 for control region and ATPase, respectively) leading to some uncertainty about stock boundaries. In contrast, there was a clear genetic break between the stock in Western Australia compared to the rest of northern Australia (mean F(ST) = 0·132 for the microsatellite data and Φ(ST) = 0·135 and 0·188 for control region and ATPase, respectively). This indicates a restriction to gene flow possibly associated with suboptimal habitat along the Kimberley coast (north Western Australia). The appropriate scale of management for this species corresponds to the jurisdictions of the three Australian states, except that authorities in Queensland and Northern Territory should co-ordinate the management of the Gulf of Carpentaria stock.     

Production of the rotifer Brachionus plicatilis for aquaculture in Kuwait

Macrophytes, plankton samples, salinity and depth data were collected from wetlands in October 1981. Species diversity and distributions are recorded and relationships drawn between macrophytes and plankton occurrence. An examination of the data of Geddes et al. (1981) enables comparisons of species composition in a similar range of Western Australian lakes in 1978 at a different stage in the seasonal cycle. Comparison with the biota of salt lakes in Australia's eastern states and elsewhere lead to biogeographical speculations for the macrophytes and for some of the planktonic species.     

Chromosome numbers of Western Australian species ofVillarsia (Menyanthaceae)

Chromosome numbers are reported for eight of the nine Western AustralianVillarsia species.Villarsia albiflora, V. calthifolia, V. capitata, V. congestiflora, V. lasiosperma, V. latifolia, andV. violifolia are diploid with n=9. Five populations ofV. parnassiifolia are diploid and three are tetraploid (n=18). The morphological, ecological, and breeding-system diversity of the Western Australian species is largely not associated with the tetraploidy or hexaploidy that characterizes otherVillarsia species in eastern Australia and South Africa. The majority of Western AustralianVillarsia species are restricted to the high rainfall zone of southwestern Western Australia, where favorable climatic and edaphic conditions may have existed since mid-late Tertiary times.     

Eastern Australian Pleurobranchomorpha (Gastropoda, Opisthobranchia)

Collections of pleurobranchomorph gastropods made in 1968 are described, and compared with material in the British Museum (Natural History) and with live Mediterranean specimens examined in the Naples Aquarium. All the eastern Australian species obtained are illustrated by line diagrams. Three species new for Australia are described, one is transferred to another known species, and six others are re-described. A list of the 12 species (with synonyms) reliably reported for eastern Australian waters concludes the paper, together with a key for their identification.     

Diversity patterns of eucalypt canopy arthropods in eastern and western Australia

1. As part of a larger study on canopy arthropods and birds, a 1‐year chemical knockdown study was carried out in one Western Australian forest, where jarrah Eucalyptus marginata and marri E. (Corymbia) calophylla were sampled, and one eastern Australian (New South Wales) forest, where narrow‐leaved ironbark E. crebra and grey box E. moluccana were sampled. 2. Ten trees of each species were sampled during each of the four seasons and the arthropods were sorted to morphospecies level. This paper documents the foliage‐associated component of arboreal arthropod communities and compares arthropod species richness within orders and families, between tree species, and between the two forest types. 3. Hymenoptera, Coleoptera, Diptera, and Araneae were the richest in species. Nine hundred and seventy‐six species in 173 families were found in the eastern Australian forest, while 687 species in 176 families were found in the western Australian forest. Only 53% of families were common to both forests, but almost half the families recorded were represented by fewer than five species. Species overlap between tree species in each region was 40–53%. 4. Analysis using nonparametric bootstrapping procedures showed that sampling of foliage was comprehensive and that only 4–9% more species would be expected with more intensive sampling of the canopy. Absolute richness, as well as differences between tree species and regions, therefore appear to be real and not the result of sampling errors. As a consequence, arthropod species richness in Australian eucalypt forests is shown to be substantially greater than previous estimates.     

Allopatric speciation in the nematode parasites of frogs in southern Western Australia

The nematodes parasitic in frogs in southern Western Australia are closely related to those found in South Australian hosts, with two cosmocercoid species common to both regions and at least two of the three Western Australian species of Parathelandros forming pairs with species in South Australia.
The host distribution of the Western Australian species of Parathelandros suggests a host specificity, at generic level, with one species restricted to the genus Hyla, one largely restricted to the genus Helioporus and one, more widespread, in the genera Neobatrachus, Helioporus and Limnodynastes.
Studies of the hosts have demonstrated that the four species of Helioporus in which P. carinae is known to occur do not represent a local radiation but are the result of at least three host invasions from the eastern side of the Nullarbor Plain. Because of this it is argued that the speciation of the parasites was independent of that of the hosts, was allopatric and probably involved intra-host competition.
The importance of using the divisions of their environment recognized by the parasites, rather than those recognized by their hosts, in studies of host: parasite relationships is stressed. As a consequence it is argued that although the theoretical basis of using parasites as indicators of host relationships is weakened their practical value remains unimpaired. Attention is drawn to the danger of circularity in the use of parasites in establishing host relationships.     

Historical processes and contemporary ocean currents drive genetic structure in the seagrass Thalassia hemprichii in the Indo‐Australian Archipelago

Understanding spatial patterns of gene flow and genetic structure is essential for the conservation of marine ecosystems. Contemporary ocean currents and historical isolation due to Pleistocene sea level fluctuations have been predicted to influence the genetic structure in marine populations. In the Indo‐Australian Archipelago (IAA), the world's hotspot of marine biodiversity, seagrasses are a vital component but population genetic information is very limited. Here, we reconstructed the phylogeography of the seagrass Thalassia hemprichii in the IAA based on single nucleotide polymorphisms (SNPs) and then characterized the genetic structure based on a panel of 16 microsatellite markers. We further examined the relative importance of historical isolation and contemporary ocean currents in driving the patterns of genetic structure. Results from SNPs revealed three population groups: eastern Indonesia, western Indonesia (Sunda Shelf) and Indian Ocean; while the microsatellites supported five population groups (eastern Indonesia, Sunda Shelf, Lesser Sunda, Western Australia and Indian Ocean). Both SNPs and microsatellites showed asymmetrical gene flow among population groups with a trend of southwestward migration from eastern Indonesia. Genetic diversity was generally higher in eastern Indonesia and decreased southwestward. The pattern of genetic structure and connectivity is attributed partly to the Pleistocene sea level fluctuations modified to a smaller level by contemporary ocean currents.     

Variation in foliar nutrients in Eucalyptus trees in eastern and Western Australia

Abstract Levels of nitrogen, phosphorus and potassium were measured for the foliage of two co-dominant eucalypts at each of two sites, one in eastern Australia and the other in Western Australia. In eastern Australia, foliage was sampled in the canopy and subcanopy for narrow-leaved ironbark Eucalyptus crebra and grey box E. mollucana and in Western Australia, for jarrah E. marginata and marri E. calophylla. The Western Australian trees were also sampled for ‘young’ and ‘old’ leaves. Both eucalypts in eastern Australia had greater nitrogen and phosphorus levels, but lower potassium, than E. marginata or E. calophylla. Eucalyptus calophylla foliage had greater levels of all three nutrients than E. marginata foliage as did E. crebra relative to E. mollucana. At both sites, foliar nutrient levels were greater in the canopy than subcanopy foliage, and, at least in Western Australia, the younger leaves had greater nutrient levels than the older leaves. The observed differences in foliar nutrient levels are consistent with observed trends in the abundance and diversity of foliage arthropods and the use of the trees as foraging substrates by birds.     

A phylogeographic analysis of southern and eastern populations of the Australian magpie: evidence for selection in maintenance of the distribution of two plumage morphs

The Australian magpie ( Gymnorhina tibicen ) is polymorphic for back colour with three distinct morphs recognized: the black-backed form (BB) which occurs in northern and north-eastern Australia; the white-backed form (WB) which occurs in south-eastern Australia and Tasmania and the Western form which occurs in the far south-west corner of the continent. Male and female WBs and BBs are both monomorphic for back colour while Westerns are sexually dimorphic, with males white-backed and females black-backed. In the south-east the WB and BB distributions overlap with individuals of intermediate phenotype interspersed with pure WB and BB phenotypes. This study used mtDNA control-region sequences to test the predictions of two alternative hypotheses to explain the distribution of WB and BB populations in eastern Australia and Tasmania. Our data support the hypothesis that the variation has evolved in situ, as no population genetic structuring was evident in eastern Australia related to back colour and Tasmanian WBs were no more closely related to mainland WBs than to mainland BBs (primary contact hypothesis). Back colour patterns may be maintained by different forms of natural selection favouring BB genes in the north-east and WB genes in the south-east.     

Paroster peelensis sp. nov.: a new stygobitic water beetle from alluvial gravels in northern New South Wales (Coleoptera: Dytiscidae)

Abstract  A second stygobitic carnivorous water beetle is reported from eastern Australia. Unlike the recently discovered Carabhydrus stephanieae (Watts et al .) from the same general region, the new species is from the inland draining Peel River, part of the Murray-Darling basin. Its morphology and mitochondrial DNA sequences, place it in the Hydroporine genus Paroster Sharp. Phylogenetic analysis shows that the new species is more closely related to the Western Australian species of Paroster than to the geographical less distant Paroster species of the Northern Territory.     

Domestication bottlenecks limit genetic diversity and constrain adaptation in narrow-leafed lupin (Lupinus angustifolius L.)

In contrast to most widespread broad-acre crops, the narrow-leafed lupin (Lupinus angustifolius L.) was domesticated very recently, in breeding programmes isolated in both space and time. Whereas domestication was initiated in Central Europe in the early twentieth century, the crop was subsequently industrialized in Australia, which now dominates world production. To investigate the ramifications of these bottlenecks, the genetic diversity of wild (n = 1,248) and domesticated populations (n = 95) was characterized using diversity arrays technology, and adaptation studied using G × E trials (n = 31) comprising all Australian cultivars released from 1967 to 2004 (n = 23). Principal coordinates analysis demonstrates extremely limited genetic diversity in European and Australian breeding material compared to wild stocks. AMMI analysis indicates that G × E interaction is a minor, albeit significant effect, dominated by strong responses to local, Western Australian (WA) optima. Over time Australian cultivars have become increasingly responsive to warm, intermediate rainfall environments in the northern WA grainbelt, but much less so to cool vegetative phase eastern environments, which have considerably more yield potential. G × E interaction is well explained by phenology, and its interaction with seasonal climate, as a result of varying vernalization responses. Yield differences are minimized when vegetative phase temperatures fully satisfy the vernalization requirement (typical of eastern Australia), and maximized when they do not (typical of WA). In breeding for WA optima, the vernalization response has been eliminated and there has been strong selection for terminal drought avoidance through early phenology, which limits yield potential in longer season eastern environments. Conversely, vernalization-responsive cultivars are more yield-responsive in the east, where low temperatures moderately extend the vegetative phase. The confounding of phenology and vernalization response limits adaptation in narrow-leafed lupin, isolates breeding programmes, and should be eliminated by widening the flowering time range in a vernalization-unresponsive background. Concomitantly, breeding strategies that will widen the genetic base of the breeding pool in an ongoing manner should be initiated.