Characterising population structure and diversity of Australian Eimeria

Develop microsatellite markers to distinguish strains of Eimeria acervulina, E. brunetti and E. maxima. Conduct nationwide sampling of chicken faeces to build baseline of Eimeria population genetic diversity for 5 economically important speces (3 species above plus E. tenella and E. necatrix). Conduct focused local screening to assess temporal changes in populations historically sampled.

Extremely Low Microsatellite Diversity but Distinct Population Structure in a Long-Lived Threatened Species, the Australian Lungfish Neoceratodus forsteri (Dipnoi)

The Australian lungfish is a unique living representative of an ancient dipnoan lineage, listed as ‘vulnerable’ to extinction under Australia’s Environment Protection and Biodiversity Conservation Act 1999. Historical accounts indicate this species occurred naturally in two adjacent river systems in Australia, the Burnett and Mary. Current day populations in other rivers are thought to have arisen by translocation from these source populations. Early genetic work detected very little variation and so had limited power to answer questions relevant for management including how genetic variation is partitioned within and among sub-populations. In this study, we use newly developed microsatellite markers to examine samples from the Burnett and Mary Rivers, as well as from two populations thought to be of translocated origin, Brisbane and North Pine. We test whether there is significant genetic structure among and within river drainages; assign putatively translocated populations to potential source populations; and estimate effective population sizes. Eleven polymorphic microsatellite loci genotyped in 218 individuals gave an average within-population heterozygosity of 0.39 which is low relative to other threatened taxa and for freshwater fishes in general. Based on F_ST values (average over loci = 0.11) and STRUCTURE analyses, we identify three distinct populations in the natural range, one in the Burnett and two distinct populations in the Mary. These analyses also support the hypothesis that the Mary River is the likely source of translocated populations in the Brisbane and North Pine rivers, which agrees with historical published records of a translocation event giving rise to these populations. We were unable to obtain bounded estimates of effective population size, as we have too few genotype combinations, although point estimates were low, ranging from 29 - 129. We recommend that, in order to preserve any local adaptation in the three distinct populations that they be managed separately.

Genetic variation within two sympatric spotted gum eucalypts exceeds between taxa variation

Population substructure and hybridization, among other factors, have the potential to cause erroneous associations in linkage disequilibrium (LD) mapping. Two closely related spotted gum eucalypts, Corymbia variegata and C. henryi (Myrtaceae) occur in sympatry in the east coast of Australia and potentially interbreed. They are morphologically similar but are distinguished as separate species based on capsule and foliage size. To determine whether they hybridize in nature and its implications for LD mapping, we investigated the level of molecular divergence between the two species at two sympatric locations separated by 300 kilometres. Very few individuals of intermediate morphology were identified, despite the two species occurring only metres apart. Analysis of genetic structure using 12 microsatellite loci showed that genetic differentiation between populations of the same species at different locations (FST = 0.07 for both species; p = 0.0001) was significantly higher than that observed between species at each location (mean FST = 0.02 and 0.04 for Cherry tree and Bunyaville respectively; p = 0.0001; all Mann-Whitney U-test p ≤ 0.01). No species-specific alleles or significant allele frequency differences were detected within a site, suggesting recurrent local gene flow between the two species. The lack of significant allele frequency differences implies no population stratification along taxonomic lines. This suggested that there is little concern for cryptic hybridization when sampling from sites of sympatry for LD mapping.

Population genetics of the frog-killing fungus Batrachochytrium dendrobatidis

Global amphibian decline by chytridiomycosis is a major environmental disaster that has been attributed to either recent fungal spread or environmental change that promotes disease. Here, we present a population genetic comparison of Batrachochytrium dendrobatidis isolates from an intensively studied region of frog decline, the Sierra Nevada of California. In support of a novel pathogen, we find low diversity, no amphibian-host specificity, little correlation between fungal genotype and geography, local frog extirpation by a single fungal genotype, and evidence of human-assisted fungus migration. In support of endemism, at a local scale, we find some diverse, recombining populations. Therefore neither epidemic spread nor endemism alone explains this particular amphibian decline. Recombination raises the possibility of resistant sporangia and a mechanism for rapid spread as well as persistence that could greatly complicate global control of the pathogen.

Refined Global Analysis of Bemisia tabaci (Hemiptera: Sternorrhyncha: Aleyrodoidea: Aleyrodidae) Mitochondrial Cytochrome Oxidase 1 to Identify Species Level Genetic Boundaries.

Identifying species boundaries within morphologically indistinguishable cryptic species complexes is often contentious. For the whitefly Bemisia tabaci (Gennadius) (Hemiptera: Sternorrhyncha: Aleyrodoidea: Aleyrodidae), the lack of a clear understanding about the genetic limits of the numerous genetic groups and biotypes so far identified has resulted in a lack of consistency in the application of the terms, the approaches use to apply them and in our understanding of what genetic structure within B. tabaci means. Our response has been to use mitochondrial gene cytochrome oxidase one to consider how to clearly and consistently define genetic separation. Using Bayesian phylogenetic analysis and analysis of sequence pairwise divergence we found a considerably higher to number of genetic groups than had been previously determined with two breaks in the distribution, one at 11% and another at 3.5%. At >11% divergence, 11 distinct groups were resolved, whereas at >3.5% divergence 24 groups were identified. Consensus sequences for each of these groups were determined and were shown to be useful in the correct assignment of sequences of unknown origin. The 3.5% divergence bound is consistent with species level separations in other insect taxa and Suggests that B. tabaci is it cryptic species composed of at least 24 distinct species. We further show that the placement of Bemesia atriplex (Froggatt) within the B. tabaci in, group adds further weight to the argument for species level separation within B. tabaci. This new analysis, which constructs consensus sequences and uses these its a standard against which unknown sequences call be compared, provides for the first time it consistent means of identifying the genetic hounds of each species with it high degree of certainty.

Increased reproductive success in older female red kangaroos and the impact of harvesting

Wildlife harvesting has a long history in Australia, including obvious examples of overexploitation. Not surprisingly, there is scepticism that commercial harvesting can be undertaken sustainably. Kangaroo harvesting has been challenged regularly at Administrative Appeals Tribunals and elsewhere over the past three decades. Initially, the concern from conservation groups was sustainability of the harvest. This has been addressed through regular, direct monitoring that now spans > 30 years and a conservative harvest regime with a low risk of overharvest in the face of uncertainty. Opposition to the harvest now continues from animal rights groups whose concerns have shifted from overall harvest sustainability to side effects such as animal welfare, and changes to community structure, genetic composition and population age structure. Many of these concerns are speculative and difficult to address, requiring expensive data. One concern is that older females are the more successful breeders and teach their daughters optimal habitat and diet selection. The lack of older animals in a harvested population may reduce the fitness of the remaining individuals; implying population viability would also be compromised. This argument can be countered by the persistence of populations under harvesting without any obvious impairment to reproduction. Nevertheless, an interesting question is how age influences reproductive output. In this study, data collected from a number of red kangaroo populations across eastern Australia indicate that the breeding success of older females is up to 7-20% higher than that of younger females. This effect is smaller than that of body condition and the environment, which can increase breeding success by up to 30% and 60% respectively. Average age of mature females in a population may be reduced from 9 to 6 years old, resulting in a potential reduction in breeding success of 3-4%. This appears to be offset in harvested populations by improved condition of females from a reduction in kangaroo density. There is an important recommendation for management. The best insurance policy against overharvest and unwanted side effects is not research, which could be never-ending. Rather, it is a harvest strategy that includes safeguards against uncertainty such as harvest reserves, conservative quotas and regular monitoring. Research is still important in fine tuning that strategy and is most usefully incorporated as adaptive management where it can address the key questions on how populations respond to harvesting.

Modeling population growth and site specific control of the invasive Lantana camara L. (Verbenaceae) under differing fire regimes

It is at the population level that an invasion either fails or succeeds. Lantana camara L. (Verbenaceae) is a weed of great significance in Queensland Australia and globally but its whole life-history ecology is poorly known. Here we used 3 years of field data across four land use types (farm, hoop pine plantation and two open eucalyptus forests, including one with a triennial fire regime) to parameterise the weed’s vital rates and develop size-structured matrix models. Lantana camara in its re-colonization phase, as observed in the recently cleared hoop pine plantation, was projected to increase more rapidly (annual growth rate, λ = 3.80) than at the other three sites (λ 1.88–2.71). Elasticity analyses indicated that growth contributed more (64.6 %) to λ than fecundity (18.5 %) or survival (15.5 %), while across size groups, the contribution was of the order: juvenile (19–27 %) ≥ seed (17–28 %) ≥ seedling (16–25 %) > small adult (4–26 %) ≥ medium adult (7–20 %) > large adult (0–20 %). From a control perspective it is difficult to determine a single weak point in the life cycle of lantana that might be exploited to reduce growth below a sustaining rate. The triennial fire regime applied did not alter the population elasticity structure nor resulted in local control of the weed. However, simulations showed that, except for the farm population, periodic burning could work within 4–10 years for control of the weed, but fire frequency should increase to at least once every 2 years. For the farm, site-specific control may be achieved by 15 years if the biennial fire frequency is tempered with increased burning intensity.

Searching for common threads in threadfins: phylogeography of Australian polynemids in space and time

Proper management of marine fisheries requires an understanding of the spatial and temporal dynamics of marine populations, which can be obtained from genetic data. While numerous fisheries species have been surveyed for spatial genetic patterns, temporally sampled genetic data is not available for many species. We present a phylogeographic survey of the king threadfin Polydactylus macrochir across its species range in northern Australia and at a temporal scale of 1 and 10 yr. Spatially, the overall AMOVA fixation index was Omega(st) = 0.306 (F-st' = 0.838), p < 0.0001 and isolation by distance was strong and significant (r(2) = 0.45, p < 0.001). Temporally, genetic patterns were stable at a time scale of 10 yr. However, this did not hold true for samples from the eastern Gulf of Carpentaria, where populations showed a greater degree of temporal instability and lacked spatial genetic structure. Temporal but not spatial genetic structure in the Gulf indicates demographic interdependence but also indicates that fishing pressure may be high in this area. Generally, genetic patterns were similar to another co-distributed threadfin species Eleutheronema tetradactylum, which is ecologically similar. However, the historical demography of both species, evaluated herein, differed, with populations of P. macrochir being much younger. The data are consistent with an acute population bottleneck at the last glacio-eustatic low in sea level and indicate that the king threadfin may be sensitive to habitat disturbances.

Evidence for reproductive philopatry in the bull shark Carcharhinus leucas

Reproductive philopatry in bull sharks Carcharhinus leucas was investigated by comparing mitochondrial (NADH dehydrogenase subunit 4, 797 base pairs and control region genes 837 base pairs) and nuclear (three microsatellite loci) DNA of juveniles sampled from 13 river systems across northern Australia. High mitochondrial and low microsatellite genetic diversity among juveniles sampled from different rivers (mitochondrial fST = 0.0767, P < 0.05; microsatellite FST = -0.0022, P > 0.05) supported female reproductive philopatry. Genetic structure was not further influenced by geographic distance (P > 0.05) or long-shore barriers to movement (P > 0.05). Additionally, results suggest that C. leucas in northern Australia has a long-term effective population size of 11 000-13 000 females and has undergone population bottlenecks and expansions that coincide with the timing of the last ice-ages.

Isolation and characterization of 21 polymorphic microsatellite loci in the iconic Australian lungfish, Neoceratodus forsteri, using the Ion Torrent next-generation sequencing platform

We isolated and characterized 21 microsatellite loci in the vulnerable and iconic Australian lungfish, Neoceratodus forsteri. Loci were screened across eight individuals from the Burnett River and 40 individuals from the Pine River. Genetic diversity was low with between one and six alleles per locus within populations and a maximum expected heterozygosity of 0.774. These loci will now be available to assess effective population sizes and genetic structure in N. forsteri across its natural range in South East Queensland, Australia.

Characterization, development and multiplexing of microsatellite markers in three commercially exploited reef fish and their application for stock identification

Thirty-four microsatellite loci were isolated from three reef fish species; golden snapper Lutjanus johnii, blackspotted croaker Protonibea diacanthus and grass emperor Lethrinus laticaudis using a next generation sequencing approach. Both IonTorrent single reads and Illumina MiSeq paired-end reads were used, with the latter demonstrating a higher quality of reads than the IonTorrent. From the 1–1.5 million raw reads per species, we successfully obtained 10–13 polymorphic loci for each species, which satisfied stringent design criteria. We developed multiplex panels for the amplification of the golden snapper and the blackspotted croaker loci, as well as post-amplification pooling panels for the grass emperor loci. The microsatellites characterized in this work were tested across three locations of northern Australia. The microsatellites we developed can detect population differentiation across northern Australia and may be used for genetic structure studies and stock identification.

Predicting dispersal and recruitment of Miconia calvescens (Melastomataceae) in Australian tropical rainforests

Miconia calvescens (Melastomataceae) is a serious invader in the tropical Pacific, including the Hawaiian and Tahitian Islands, and currently poses a major threat to native biodiversity in the Wet Tropics of Australia. The species is fleshy-fruited, small-seeded and shade tolerant, and thus has the potential to be dispersed widely and recruit in relatively intact rainforest habitats, displacing native species. Understanding and predicting the rate of spread is critical for the design and implementation of effective management actions. We used an individual-based model incorporating a dispersal function derived from dispersal curves for similar berry-fruited native species, and life-history parameters of fecundity and mortality to predict the spatial structure of a Miconia population after a 30 year time period. We compared the modelled population spatial structure to that of an actual infestation in the rainforests of north Queensland. Our goal was to assess how well the model predicts actual dispersion and to identify potential barriers and conduits to seed movement and seedling establishment. The model overpredicts overall population size and the spatial extent of the actual infestation, predicting individuals to occur at a maximum 1,750 m from the source compared with the maximum distance of any detected individual in the actual infestation of 1,191 m. We identify several characteristic features of managed invasive populations that make comparisons between modelled outcomes and actual infestations difficult. Our results suggest that the model’s ability to predict both spatial structure and spread of the population will be improved by incorporating a spatially explicit element, with dispersal and recruitment probabilities that reflect the relative suitability of different parts of the landscape for these processes.

New efforts at biological control of Mikania micrantha H.B.K. (Asteraceae) in Papua New Guinea and Fiji.

New efforts at biological control of Miconia calvescens (Melastomataceae) is a serious invader in the tropical Pacific, including the Hawaiian and Tahitian Islands, and currently poses a major threat to native biodiversity in the Wet Tropics of Australia. The species is fleshy-fruited, small-seeded and shade tolerant, and thus has the potential to be dispersed widely and recruit in relatively intact rainforest habitats, displacing native species. Understanding and predicting the rate of spread is critical for the design and implementation of effective management actions. We used an individual-based model incorporating a dispersal function derived from dispersal curves for similar berry-fruited native species, and life-history parameters of fecundity and mortality to predict the spatial structure of a Miconia population after a 30 year time period. We compared the modelled population spatial structure to that of an actual infestation in the rainforests of north Queensland. Our goal was to assess how well the model predicts actual dispersion and to identify potential barriers and conduits to seed movement and seedling establishment. The model overpredicts overall population size and the spatial extent of the actual infestation, predicting individuals to occur at a maximum 1,750 m from the source compared with the maximum distance of any detected individual in the actual infestation of 1,191 m. We identify several characteristic features of managed invasive populations that make comparisons between modelled outcomes and actual infestations difficult. Our results suggest that the model’s ability to predict both spatial structure and spread of the population will be improved by incorporating a spatially explicit element, with dispersal and recruitment probabilities that reflect the relative suitability of different parts of the landscape for these processes. Mikania micrantha H.B.K. (Asteraceae) in Papua New Guinea and Fiji.

Two sympatric spotted gum species are molecularly homogeneous.

Large fruited spotted gum eucalypt Corymbia henryi occurs sympatrically with small fruited spotted gum Corymbia citriodora subspecies variegata over a large portion of its range on the east coast of Australia. The two taxa are interfertile, have overlapping flowering times and share a common set of insect and vertebrate pollinators. Previous genetic analysis of both taxa from two geographically remote sites suggested that the two were morphotypes rather than genetically distinct species. In this study we further explore this hypothesis of genic species by expanding sampling broadly through their sympatric locations and examine local-scale spatial genetic structure in stands that differ in species and age composition. Delineation of populations at five microsatellite loci, using an individual-based approach and Bayesian modelling, as well as clustering of individuals based on allele frequencies showed the two species to be molecularly homogeneous. Genetic structure aligned largely with geographic areas of origin, and followed an isolation-by-distance model, where proximal populations were generally less differentiated than more distant ones. At the stand level, spotted gums also generally showed little structure consistent with the high levels of gene flow inferred across the species range. Disturbances in the uniformity of structuring were detected, however, and attributed to localised events giving rise to even aged stands, probably due to regeneration from a few individuals following fire.

Scalloped Hammerhead microsatellite genotypes (eight loci) representing five regions on Australia's east coast and one location in central Indonesia.

Biodiversity of sharks in the tropical Indo-Pacific is high, but species-specific information to assist sustainable resource exploitation is scarce. The null hypothesis of population genetic homogeneity was tested for scalloped hammerhead shark (Sphyrna lewini, n=244) and the milkshark (Rhizoprionodon acutus, n=209) from northern and eastern Australia, using nuclear (S. lewini, eight microsatellite loci; R. acutus, six loci) and mitochondrial gene markers (873 base pairs of NADH dehydrogenase subunit 4). We were unable to reject genetic homogeneity for S. lewini, which was as expected based on previous studies of this species. Less expected were similar results for R. acutus, which is more benthic and less vagile than S. lewini. These features are probably driving the genetic break found between Australian and central Indonesian R. acutus (F-statistics; mtDNA, 0.751 to 0.903; microsatellite loci, 0.038 to 0.047). Our results support the spatially-homogeneous management plan for shark species in Queensland, but caution is advised for species yet to be studied.