Few genetic differences between Victorian and Western Australian blue penguins,Eudyptula minor

Abstract

Blue penguins, Eudyptula minor, breeding on Penguin Island, Western Australia are considerably larger than other blue penguins in Australia. If genetic isolation is the cause, it may have implications for the conservation status of some blue penguin populations. We compared the sequences of two mitochondrial gene regions (cytochrome‐b and the control region) from Western Australian blue penguins with other populations of blue penguins from Australia and New Zealand. We found few differences between sequences from Western Australia, Phillip Island, Victoria and Otago, New Zealand, although all three differed considerably from other New Zealand blue penguins. Sequences for the control region from the Western Australian blue penguins and 30 more birds breeding at various Australasian sites provided further support for two major clades within Eudyptula; an Australian clade (including Otago) and a New Zealand clade.     

Invasion history of Lycium ferocissimum in Australia: The impact of admixture on genetic diversity and differentiation

Aim

We investigated the invasion history of Lycium ferocissimum, a spine-covered shrub native to South Africa that was introduced to Australia in the mid-1800s, and has since developed into a damaging invasive plant of undisturbed landscapes and pastures. In addition to identifying the provenance of the Australian plants, we tested for evidence of admixture, and contrasted genetic diversity and structuring across the native and introduced ranges.

Location

Samples were collected across South Africa (24 localities) and Australia (26 localities).

Methods

We used genotyping-by-sequencing (3117 SNPs across 381 individuals) to assess population genetic structuring in L. ferocissimum across Australia and South Africa. Coalescent analyses were used to explicitly test contrasting invasion scenarios.

Results

Clear geographic genetic structuring was detected across South Africa, with distinct clusters in the Eastern and Western Cape provinces. The L. ferocissimum plants in Australia form their own genetic cluster, with a similar level of genetic diversity as plants in South Africa. Coalescent analyses demonstrated that the lineage in Australia was formed by admixture between Eastern Cape and Western Cape plants, with most of the genetic material from the Australian lineage originating from the Western Cape. Our analyses suggest that L. ferocissimum plants were originally introduced to South Australia, though it is unclear whether admixture occurred before or after its introduction to Australia. We detected little evidence of geographic genetic structure across Australia, although many of the populations were genetically distinct from one another.

Main Conclusions

Our results illustrate how admixture can result in genetically diverse and distinct invasive populations. The complex invasion history of L. ferocissimum in Australia poses particular challenges for biological control. We suggest potential biological control agents should be screened against admixed plants (in addition to plants from the Eastern and Western Cape) to test whether they provide effective control of the genetically distinct invasive lineage.     

Gene flow of the canker pathogen Botryosphaeria australis between Eucalyptus globulus plantations and native eucalypt forests in Western Australia

Abstract The eucalypt plantation industry in Western Australia provides a unique opportunity to study the movement of pathogens between closely related host taxa. Eucalyptus globulus, a native to Tasmania and south‐eastern Australia, is the predominant species in Western Australian plantations, often being planted adjacent to native forest containing Eucalyptus marginata and Eucalyptus diversicolor. Since the commencement of the plantation industry 20 years ago, several fungal species, previously known only to eastern Australia or overseas, have been reported on E. globulus in Western Australia. Botryosphaeria australis is a newly described species, recently found causing cankers on Acacia spp. in eastern Australia. However, during a routine survey, B. australis was found to be the predominant species associated with E. globulus plantations and native Eucalyptus spp. in Western Australia. In this study, six short simple repeat markers were used to evaluate genetic diversity and gene flow between collections of B. australis from native eucalypt forest and E. globulus plantations at two locations in south‐western Australia. In both cases, there was no restriction to gene flow between the plantations and the adjacent native forest. Botryosphaeria australis has now been isolated from a wide range of hosts across south‐western Australia and was not isolated from E. globulus in Tasmania or South Australia. This extensive distribution and host range suggests B. australis is native to Western Australia. This study demonstrates the ability of a pathogen to move between plantation and forests.     

Morphological and molecular genetic characterization of Cryptoperidiniopsis brodyi (Dinophyceae) from Australia-wide isolates

Cryptoperidiniopsis brodyi is a common heterotrophic dinoflagellate known to often co-occur with Pfiesteria species in eastern U.S. estuaries. In this study, C. brodyi from Australia and Pfiesteria piscicida from ballast water from Indonesia were characterized by morphological and genetic analyses. Two P. piscicida strains originating from ballast water samples showed little genetic differences compared to P. piscicida from other countries and their morphology was identical. This finding indicates a potential inflow of P. piscicida into Australian estuaries via ballast water. Nine cultures of C. brodyi were established from Tasmania, South Australia and Western Australia. All C. brodyi cultures exhibited identical thecal plate patterns and could not be discriminated from other non-Australian strains. In contrast, two distinct genotypes could be identified by rDNA sequence analyses which were distinct from the U.S. genotype of C. brodyi. A previous survey using PCR-based methods reported a wide distribution of Pfiesteria shumwayae in Australia. However, the present study demonstrated that SSU rDNA-based P. shumwayae-specific primers produce false-positive PCR reactions with Australian C. brodyi. These results suggest that genetic variants of C. brodyi are widely distributed in Australia and Australian genotypes of C. brodyi had previously been misidentified as P. shumwayae. This finding also indicates that previous Australian distribution studies of P. shumwayae using SSU rDNA-based primers are potentially erroneous and need to be revisited.     

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.     

Induction of sexual forms in the rose aphid Macrosiphum rosae

The rose aphid, Macrosiphum rosae (L.), was tested for its ability to produce sexual forms on rose leaves, after induction by environmental conditions in the field and in the laboratory. Clones were collected in Tübingen, Federal Republic of Germany, and in south-eastern New South Wales, Australia. The German clones all produced sexual forms, while the response of the Australian clones was weak. There appeared to be a bias in the sex ratio towards females: This is discussed in developmental terms. The environmental and genetic factors influencing the response are considered.     

GENETIC VARIATION AMONG STRAINS OF THE TOXIC DINOFLAGELLATE GYMNODINIUM CATENATUM (DINOPHYCEAE)

The toxic dinoflagellate Gymnodinium catenatum Graham has formed recurrent toxic blooms in southeastern Tasmanian waters since its discovery in the area in 1986. Current evidence suggests that this species might have been introduced to Tasmania prior to 1973, possibly in cargo vessel ballast water carried from populations in Japan or Spain, followed by recent dispersal to mainland Australia. To examine this hypothesis, cultured strains from G. catenatum populations in Australia, Spain, Portugal, and Japan were examined using allozymes and randomly amplified polymorphic DNA (RAPD). Allozyme screening detected very limited polymorphism and was not useful for population comparisons; however, Australian, Spanish, Portuguese, and Japanese strains showed considerable RAPD diversity, and all strains examined represented unique genotypes. Multidimensional scaling analysis (MDS) of RAPD genetic distances between strains showed clear separation of strains into three nonoverlapping regional clusters: Australia, Japan, and Spain/Portugal. Analysis of genetic distances between strains from the three regional populations indicated that Australian strains were almost equally related to both the Spanish/Portuguese population and the Japanese population. Analysis of molecular variance (AMOVA) found that genetic variation was partitioned mainly within populations (87%) compared to the variation between the regions (8%) and between populations within regions (5%). The potential source population for Tasmania’s introduced G. catenatum remains equivocal; however, strains from the recently discovered mainland Australian population (Port Lincoln, South Australia, 1996) clustered with Tasmanian strains, supporting the notion of a secondary relocation of Tasmanian G. catenatum populations to the mainland via a shipping vector. Geographic and temporal clustering of strains was evident among the Tasmanian strains, indicating that genetic exchange between neighboring estuaries is limited and that Tasmanian G. catenatum blooms are composed of localized, estuary-bound subpopulations.     

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.     

Genetic diversity and structure of the globally invasive tree, <Emphasis Type="Italic">Paraserianthes lophantha</Emphasis> subspecies <Emphasis Type="Italic">lophantha</Emphasis>, suggest an introduction history characterised by varying propagule pressure

An emerging insight in invasion biology is that intra-specific genetic variation, human usage, and introduction histories interact to shape genetic diversity and its distribution in populations of invasive species. We explore these aspects for the tree species Paraserianthes lophantha subsp. lophantha, a close relative of Australian wattles (genus Acacia). This species is native to Western Australia and is invasive in a number of regions globally. Using microsatellite genotype and DNA sequencing data, we show that native Western Australian populations of P. lophantha subsp. lophantha are geographically structured and are more diverse than introduced populations in Australia (New South Wales, South Australia, and Victoria), the Hawaiian Islands, Portugal, and South Africa. Introduced populations varied greatly in the amount of genetic diversity contained within them, from being low (e.g. Portugal) to high (e.g. Maui, Hawaiian Islands). Irrespective of provenance (native or introduced), all populations appeared to be highly inbred (F _IS ranging from 0.55 to 0.8), probably due to selfing. Although introduced populations generally had lower genetic diversity than native populations, Bayesian clustering of microsatellites and phylogenetic diversity indicated that introduced populations comprise a diverse array of genotypes, most of which were also identified in Western Australia. The dissimilarity in the distribution and number of genotypes in introduced regions suggests that non-native populations originated from different native sources and that introduction events differed in propagule pressure.     

New Genera and Species of ‘Giant’ Ostracods (Crustacea: Cyprididae) from Australia

Two new genera of giant ostracods Lacrimicypris n. gen. and Repandocypris n. gen. from Australia are described and eight new species:L. kumbar n. sp., R. austinensis n. sp., R. gleneagles n. sp., Mytilocypris coolcalalaya n. sp., Australocypris bennetti n. sp., A. beaumonti n. sp., A. mongerensis n. sp. and Caboncypris kondininensis n. sp. The number of known Australian genera and species of giant ostracods are now 6 and 21, respectively. Keys to genera and species are provided: all species can be distinguished using the hemipenis and male first leg. The usefulness of the bursa copulatrix as a species-level taxonomic character is highlighted. Most of the species described in this paper occur in salt lakes and existing ecological information on Western Australian species, as well as the distributions of all species, are summarized. Western Australia has a particularly rich halobiont fauna but current explanations relating richness of the halobiont fauna to the widespread occurrence of salt lakes appear incomplete. Australocypris bennetti is unusual in that it is frequently found at pH < 4. Its morphology differs slightly in acidic and alkaline waters.     

Tetranucleotide microsatellites in the gecko Oedura reticulata isolated from an enriched library

Ten tetranucleotide microsatellite loci were isolated from an enriched library for the gecko Oedura reticulata. The species is endemic to the southwest of Western Australia, known to be a habitat specialist, and exposed to severe habitat fragmentation in the Western Australian wheatbelt. These highly polymorphic markers (two to 25 alleles) will facilitate the population genetic analyses of this species. In particular, they will enable estimates of gene flow between remnant populations — a critical element in assessing extinction dynamics in fragmented populations.     

Genetic variability,local selection and demographic history: genomic evidence of evolving towards allopatric speciation in Asian seabass

Genomewide analysis of genetic divergence is critically important in understanding the genetic processes of allopatric speciation. We sequenced RAD tags of 131 Asian seabass individuals of six populations from South‐East Asia and Australia/Papua New Guinea. Using 32 433 SNPs, we examined the genetic diversity and patterns of population differentiation across all the populations. We found significant evidence of genetic heterogeneity between South‐East Asian and Australian/Papua New Guinean populations. The Australian/Papua New Guinean populations showed a rather lower level of genetic diversity. F_ST and principal components analysis revealed striking divergence between South‐East Asian and Australian/Papua New Guinean populations. Interestingly, no evidence of contemporary gene flow was observed. The demographic history was further tested based on the folded joint site frequency spectrum. The scenario of ancient migration with historical population size changes was suggested to be the best fit model to explain the genetic divergence of Asian seabass between South‐East Asia and Australia/Papua New Guinea. This scenario also revealed that Australian/Papua New Guinean populations were founded by ancestors from South‐East Asia during mid‐Pleistocene and were completely isolated from the ancestral population after the last glacial retreat. We also detected footprints of local selection, which might be related to differential ecological adaptation. The ancient gene flow was examined and deemed likely insufficient to counteract the genetic differentiation caused by genetic drift. The observed genomic pattern of divergence conflicted with the ‘genomic islands’ scenario. Altogether, Asian seabass have likely been evolving towards allopatric speciation since the split from the ancestral population during mid‐Pleistocene.     

Spatial subdivision among assemblages of Spanish mackerel, Scomberomorus commerson (Pisces: Scombridae) across northern Australia: implications for fisheries management

Aim This study investigated the use of stable δ¹³C and δ¹⁸O isotopes in the sagittal otolith carbonate of narrow‐barred Spanish mackerel, Scomberomorus commerson, as indicators of population structure across Australia. Location Samples were collected from 25 locations extending from the lower west coast of Western Australia (30°), across northern Australian waters, and to the east coast of Australia (18°) covering a coastline length of approximately 9500 km, including samples from Indonesia. Methods The stable δ¹³C and δ¹⁸O isotopes in the sagittal otolith carbonate of S. commerson were analysed using standard mass spectrometric techniques. The isotope ratios across northern Australian subregions were subjected to an agglomerative hierarchical cluster analysis to define subregions. Isotope ratios within each of the subregions were compared to assess population structure across Australia. Results Cluster analysis separated samples into four subregions: central Western Australia, north Western Australia, northern Australia and the Gulf of Carpentaria and eastern Australia. Isotope signatures for fish from a number of sampling sites from across Australia and Indonesia were significantly different, indicating population separation. No significant differences were found in otolith isotope ratios between sampling times (no temporal variation). Main conclusions Significant differences in the isotopic signatures of S. commerson demonstrate that there is unlikely to be any substantial movement of fish among these spatially discrete adult assemblages. The lack of temporal variation among otolith isotope ratios indicates that S. commerson populations do not undergo longshore spatial shifts in distribution during their life history. The temporal persistence of spatially explicit stable isotopic signatures indicates that, at these spatial scales, the population units sampled comprise functionally distinct management units or separate ‘stocks’ for many of the purposes of fisheries management. The spatial subdivision evident among populations of S. commerson across northern and western Australia indicates that it may be advantageous to consider S. commerson population dynamics and fisheries management from a metapopulation perspective (at least at the regional level).     

Review of the Australian hagfishes with description of two new species of Eptatretus (Myxinidae)

This paper revises and updates taxonomic and distributional information about hagfishes (Myxinidae) from Australia. It covers five species of the genus Eptatretus: Eptatretus cirrhatus known from eastern Australia and also distributed around New Zealand, Eptatretus longipinnis endemic to South Australia, Eptatretus strahani originally described from the Philippines and reported here as a new record from Western Australia and two new species described herein as Eptatretus alastairi and Eptatretus gomoni, both from Western Australia. Eptatretus alastairi is distinguished from all congeners by the unique combination of the following characters: six pairs of gill pouches; three‐cusp multicusps on the anterior and posterior rows of cusps; anterior unicusps 9–12; posterior unicusps 8–11; total cusps 48–56; prebranchial pores 13–16; branchial pores 5–6; trunk pores 50–55; tail pores 11–13; total pores 83–88; two bilaterally symmetrical nasal‐sinus papillae in the dorsal surface of the nasal sinus. Eptatretus gomoni is distinguished from all congeners by the unique combination of the following characters: eight pairs of gill pouches; three‐cusp multicusps on the anterior and two‐cusp multicusps on the posterior row of cusps; anterior unicusps 10–11; posterior unicusps 9–10; total cusps 50; prebranchial pores 12–13; branchial pores 7–8; trunk pores 57–58; tail pores 14–15; total pores 91–93; no nasal‐sinus papillae. An identification key for the Australian species of Eptatretus is also provided.     

Optimising predictive modelling of Ross River virus using meteorological variables

BackgroundStatistical models are regularly used in the forecasting and surveillance of infectious diseases to guide public health. Variable selection assists in determining factors associated with disease transmission, however, often overlooked in this process is the evaluation and suitability of the statistical model used in forecasting disease transmission and outbreaks. Here we aim to evaluate several modelling methods to optimise predictive modelling of Ross River virus (RRV) disease notifications and outbreaks in epidemiological important regions of Victoria and Western Australia.Methodology/Principal findingsWe developed several statistical methods using meteorological and RRV surveillance data from July 2000 until June 2018 in Victoria and from July 1991 until June 2018 in Western Australia. Models were developed for 11 Local Government Areas (LGAs) in Victoria and seven LGAs in Western Australia. We found generalised additive models and generalised boosted regression models, and generalised additive models and negative binomial models to be the best fit models when predicting RRV outbreaks and notifications, respectively. No association was found with a model’s ability to predict RRV notifications in LGAs with greater RRV activity, or for outbreak predictions to have a higher accuracy in LGAs with greater RRV notifications. Moreover, we assessed the use of factor analysis to generate independent variables used in predictive modelling. In the majority of LGAs, this method did not result in better model predictive performance.Conclusions/SignificanceWe demonstrate that models which are developed and used for predicting disease notifications may not be suitable for predicting disease outbreaks, or vice versa. Furthermore, poor predictive performance in modelling disease transmissions may be the result of inappropriate model selection methods. Our findings provide approaches and methods to facilitate the selection of the best fit statistical model for predicting mosquito-borne disease notifications and outbreaks used for disease surveillance.     

Contextualized niche shifts upon independent invasions by the dung beetle <Emphasis Type="Italic">Onthophagus taurus</Emphasis>

The historical contingencies of biological invasions may have important consequences for final invasion outcomes. Here, we characterize the variations in the realized niche during the invasions of the bull-headed dung beetle Onthophagus taurus (Coleoptera: Scarabaeidae) from its native Mediterranean range following accidental (Eastern North America) as well as deliberate (Western North America, Western Australia, and Eastern Australia) releases into novel, exotic ranges approximately 50 years ago. Specifically, we examined whether the climatic responses of exotic O. taurus have diverged from those characterizing their native range, and if so, to what degree and in what dimensions. We found that when compared to the native range, all exotic populations exhibited similar overlap proportions regardless of invasion history. However, more detailed analysis of climatic niche features showed that all three deliberately established populations were characterized by overall similar climatic niche features, whereas the accidentally-established Eastern North American populations have undergone significant changes in their climatic niche. Specifically, when analog climates were considered on the background of each pairwise range comparison, accidentally-established Eastern North American populations showed a different climatic niche expansion than their deliberately introduced Australian or Western North American counterparts, in particular towards colder and more humid climates. We discuss our results in the context of the widely divergent introduction histories of O. taurus in Australia and North America, and highlight the possible roles of contrasting propagule sizes, disparate genetic profiles and variances, adaptive processes and invadable landscapes in shaping invasion outcomes in the different exotic ranges.     

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.

     

Regional genetic differentiation in Western Australian sandalwood (<Emphasis Type="Italic">Santalum spicatum</Emphasis>) as revealed by nuclear RFLP analysis

Western Australian sandalwood, Santalum spicatum, is widespread in the semi-arid and arid regions of Western Australia, and there is some morphological variation suggestive of two ecotypes. The level and structuring of genetic diversity within the species was investigated using anonymous nuclear RFLP loci. Santalum spicatum showed moderate levels of genetic diversity compared to other Australian tree species. The northern populations in the arid region showed greater levels of diversity and less population differentiation than the southern populations in the semi-arid region due to differences in the distribution of rare alleles. Equilibrium between drift and gene flow in the northern populations indicated that they have been established for a long period of time with stable conditions conducive to gene flow. In contrast, the southern populations showed a relationship between drift and gene flow indicative of a pattern of fragmentation and isolation where drift has greater effect than gene flow. The different patterns of diversity suggest that the ecotypes in the two regions have been subject to differences in the relative influences of drift and gene flow during their evolutionary history.Communicated by D.B. Neale