School of BioSciences - Research Publications

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    Climate contributes to the evolution of pesticide resistance
    Maino, JL ; Umina, PA ; Hoffmann, AA (WILEY, 2018-02-01)
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    Environmental variation partitioned into separate heritable components
    Orsted, M ; Rohde, PD ; Hoffmann, AA ; Sorensen, P ; Kristensen, TN (WILEY, 2018-01-01)
    Trait variation is normally separated into genetic and environmental components, yet genetic factors also control the expression of environmental variation, encompassing plasticity across environmental gradients and within-environment responses. We defined four components of environmental variation: plasticity across environments, variability in plasticity, variation within environments, and differences in within-environment variation across environments. We assessed these components for cold tolerance across five rearing temperatures using the Drosophila melanogaster Genetic Reference Panel (DGRP). The four components were found to be heritable, and genetically correlated to different extents. By whole genome single marker regression, we detected multiple candidate genes controlling the four components and showed limited overlap in genes affecting them. Using the binary UAS-GAL4 system, we functionally validated the effects of a subset of candidate genes affecting each of the four components of environmental variation and also confirmed the genetic and phenotypic correlations obtained from the DGRP in distinct genetic backgrounds. We delineate selection targets associated with environmental variation and the constraints acting upon them, providing a framework for evolutionary and applied studies on environmental sensitivity. Based on our results we suggest that the traditional quantitative genetic view of environmental variation and genotype-by-environment interactions needs revisiting.
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    Spatial patterns of genetic diversity among Australian alpine flora communities revealed by comparative phylogenomics
    Bell, N ; Griffin, PC ; Hoffmann, AA ; Miller, AD (WILEY, 2018-01-01)
    AIM: The alpine region of mainland Australia is one of the world's 187 biodiversity hotspots. Genetic analyses of Australian alpine fauna indicate high levels of endemism on fine spatial scales, unlike Northern Hemisphere alpine systems where shallow genetic differentiation is typically observed among populations. These discrepancies have been attributed to differences in elevation and influence from glacial activity, and point to a unique phylogeographic history affecting Australian alpine biodiversity. To test generality of these findings across Australian alpine biota, we assessed patterns of genetic structure across plant species. LOCATION: The Australian Alps, Victoria, eastern Australia. METHODS: We used an economical pooled genotypingâ byâ sequencing (GBS) approach to examine patterns of genetic diversity among seven widespread species including shrubs and forbs from 16 mountain summits in the Australian Alpine National Park. Patterns of genetic structure among summit populations for each species were inferred from an average of 2,778 independent SNP loci using Bayesian phylogenomic inference and clustering approaches. RESULTS: SNP results were consistent across species in identifying deep evolutionary splits among summit communities from the Northern and Central Victorian Alpine regions. These patterns of genetic structure are also consistent with those previously reported for invertebrate and mammal taxa. However, local genetic structure was less pronounced in the plants, supporting the notion that population connectivity tends to be higher in plant species. MAIN CONCLUSION: There is deep lineage diversification between the North and Central Victorian Alpine regions, reflecting a high level of endemism. These findings differ from those reported for alpine biodiversity from New South Wales and much of the Northern Hemisphere, and support the notion that genetic diversity is typically greatest in areas least affected by historical ice sheet formation. We discuss the implications of our findings in the context of conservation planning, and highlight the benefits of this rapid and costâ effective genome scan approach for characterizing evolutionary processes at multispecies and landscape scales.
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    Evidence of genomic adaptation to climate in Eucalyptus microcarpa: Implications for adaptive potential to projected climate change
    Jordan, R ; Hoffmann, AA ; Dillon, SK ; Prober, SM (WILEY, 2017-11-01)
    Understanding whether populations can adapt in situ or whether interventions are required is of key importance for biodiversity management under climate change. Landscape genomics is becoming an increasingly important and powerful tool for rapid assessments of climate adaptation, especially in long-lived species such as trees. We investigated climate adaptation in Eucalyptus microcarpa using the DArTseq genomic approach. A combination of FST outlier and environmental association analyses were performed using >4200 genomewide single nucleotide polymorphisms (SNPs) from 26 populations spanning climate gradients in southeastern Australia. Eighty-one SNPs were identified as putatively adaptive, based on significance in FST outlier tests and significant associations with one or more climate variables related to temperature (70/81), aridity (37/81) or precipitation (35/81). Adaptive SNPs were located on all 11 chromosomes, with no particular region associated with individual climate variables. Climate adaptation appeared to be characterized by subtle shifts in allele frequencies, with no consistent fixed differences identified. Based on these associations, we predict adaptation under projected changes in climate will include a suite of shifts in allele frequencies. Whether this can occur sufficiently rapidly through natural selection within populations, or would benefit from assisted gene migration, requires further evaluation. In some populations, the absence or predicted increases to near fixation of particular adaptive alleles hint at potential limits to adaptive capacity. Together, these results reinforce the importance of standing genetic variation at the geographic level for maintaining species' evolutionary potential.
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    Testing the niche-breadth-range-size hypothesis: habitat specialization vs. performance in Australian alpine daisies
    Hirst, MJ ; Griffin, PC ; Sexton, JP ; Hoffmann, AA (WILEY, 2017-10-01)
    Relatively common species within a clade are expected to perform well across a wider range of conditions than their rarer relatives, yet experimental tests of this "niche-breadth-range-size" hypothesis remain surprisingly scarce. Rarity may arise due to trade-offs between specialization and performance across a wide range of environments. Here we use common garden and reciprocal transplant experiments to test the niche-breadth-range-size hypothesis, focusing on four common and three rare endemic alpine daisies (Brachyscome spp.) from the Australian Alps. We used three experimental contexts: (1) alpine reciprocal seedling experiment, a test of seedling survival and growth in three alpine habitat types differing in environmental quality and species diversity; (2) warm environment common garden, a test of whether common daisy species have higher growth rates and phenotypic plasticity, assessed in a common garden in a warmer climate and run simultaneously with experiment 1; and (3) alpine reciprocal seed experiment, a test of seed germination capacity and viability in the same three alpine habitat types as in experiment 1. In the alpine reciprocal seedling experiment, survival of all species was highest in the open heathland habitat where overall plant diversity is high, suggesting a general, positive response to a relatively productive, low-stress environment. We found only partial support for higher survival of rare species in their habitats of origin. In the warm environment common garden, three common daisies exhibited greater growth and biomass than two rare species, but the other rare species performed as well as the common species. In the alpine reciprocal seed experiment, common daisies exhibited higher germination across most habitats, but rare species maintained a higher proportion of viable seed in all conditions, suggesting different life history strategies. These results indicate that some but not all rare, alpine endemics exhibit stress tolerance at the cost of reduced growth rates in low-stress environments compared to common species. Finally, these findings suggest the seed stage is important in the persistence of rare species, and they provide only weak support at the seedling stage for the niche-breadth-range-size hypothesis.
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    Measuring the effects of reduced snow cover on Australia's alpine arthropods
    Slatyer, RA ; Nash, MA ; Hoffmann, AA (WILEY, 2017-11-01)
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    Does increased heat resistance result in higher susceptibility to predation? A test using Drosophila melanogaster selection and hardening
    Hangartner, S ; Dworkin, I ; Denieu, M ; Hoffmann, AA (Wiley, 2017-06-01)
    Heat resistance of ectotherms can be increased both by plasticity and evolution, but these effects may have trade‐offs resulting from biotic interactions. Here, we test for predation costs in Drosophila melanogaster populations with altered heat resistance produced by adult hardening and directional selection for increased heat resistance. In addition, we also tested for genetic trade‐offs by testing heat resistance in lines that have evolved under increased predation risk. We show that while 35/37 °C hardening increases heat resistance as expected, it does not increase predation risk from jumping spiders or mantids; in fact, there was an indication that survival may have increased under predation following a triple 37 °C compared to a single 35 °C hardening treatment. Flies that survived a 39 °C selection cycle showed lower survival under predation, suggesting a predation cost of exposure to a more severe heat stress. There was, however, no correlated response to selection because survival did not differ between control and selected lines after selection was relaxed for one or two generations. In addition, lines selected for increased predation risk did not differ in heat resistance. Our findings suggest independent evolutionary responses to predation and heat as measured in laboratory assays, and no costs of heat hardening on susceptibility to predation.
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    Detecting invertebrate species in archived collections using next-generation sequencing
    Carew, ME ; Metzeling, L ; St Clair, R ; Hoffmann, AA (WILEY, 2017-09-01)
    Invertebrate biodiversity measured at mostly family level is widely used in biological monitoring programmes to assess anthropogenic impacts on ecosystems. However, next-generation sequencing (NGS) could allow development of new more sensitive biomonitoring tools by allowing rapid species identification. This could be accelerated if archived invertebrate collections and environmental information from past programmes are used to understand species distributions and their environmental responses. In this study, we take archived macroinvertebrate samples from two sites collected on multiple occasions and test whether NGS can successfully detect species. Samples had been stored in 70% ethanol at room temperature for up to 12 years. Three amplicons ranging from 197 to 274 bps within the DNA barcode region were amplified from samples and compared to DNA barcoding libraries to identify species. We were able to amplify partial DNA barcodes from most samples, and species were often detected with multiple amplicons. However, some singletons and taxa poorly covered by DNA barcoding were missed. This suggests additional DNA barcodes will be required to fill 'gaps' in current DNA barcode libraries for aquatic macroinvertebrates and/or that it may not be possible to detect all taxa in a sample. Furthermore, older samples often detected fewer taxa and were less reliable for amplification, suggesting NGS is best used on samples within 8 years of collection. Nevertheless, many common taxa with existing DNA barcodes were reliably identified with NGS and were often present at sites across multiple years, showing the potential of NGS for detecting common and abundant species in archived material.
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    Detecting copper toxicity in sediments: from the subindividual level to the population level
    Jeppe, KJ ; Yang, J ; Long, SM ; Carew, ME ; Zhang, X ; Pettigrove, V ; Hoffmann, AA ; Piggott, J (WILEY, 2017-10-01)
    Sediments accumulate chemicals that can be toxic to biota and often contribute to aquatic ecosystem decline. Measuring mortality in laboratoryâ bred organisms is a common way to assess sediment toxicity. However, mortalityâ based responses of resilient laboratory organisms may not reflect indigenous macroinvertebrate responses, which can be relatively more sensitive to sediment toxicants. A possible solution is to also measure responses at the subindividual level. Several organism responses to sediment copper toxicity were assessed in a fieldâ based microcosm. Responses of laboratoryâ bred chironomids and snails deployed in microcosms were compared at subindividual (metabolomic and gene expression), individual (survival and dry weight) and population (reproduction) levels, and contrasted to the abundance of colonizing macroinvertebrates in the microcosms. Colonizing macroinvertebrate abundance showed a range of sensitivities based on EC50 (effect dose 50% change). Chironomidae made up 94·5% of the microcosm macroinvertebrates, with Paratanytarsus the most sensitive genus (EC50: 89 mg kg⠻¹ copper) and Procladius the least sensitive (EC50: 681 mg kg⠻¹). Survival of laboratoryâ bred organisms was the least sensitive response, comparable to decreased abundance of the least sensitive macroinvertebrate. Juvenile production in the snail, Potamopyrgus antipodarum, was the most sensitive populationâ level response (EC50: 121 mg kg⠻¹), in contrast the snail Physella acuta was relatively more tolerant (EC50: 298 mg kg⠻¹). Changes in subindividual responses (gene expression and metabolite abundance) in laboratoryâ bred chironomid, Chironomus tepperi, were evident at 60 mg kg⠻¹. These changes likely reflect the direct effects of copper exposure and represent metalâ specific responses. Synthesis and applications. We showed that copper toxicity in sediments could be readily detected through changes in gene expression and metabolites in laboratoryâ bred chironomids exposed in fieldâ based microcosms. These responses were more sensitive than mortality, and detected copper levels that caused microcosm chironomid populations to decline. These novel approaches will provide managers with new tools to better assess sediment toxicity.