Population genomics of wild and laboratory zebrafish (Danio rerio)

Understanding a wider range of genotype–phenotype associations can be achieved through ecological and evolutionary studies of traditional laboratory models. Here, we conducted the first large‐scale geographic analysis of genetic variation within and among wild zebrafish (Danio rerio) populations occurring in Nepal, India, and Bangladesh, and we genetically compared wild populations to several commonly used lab strains. We examined genetic variation at 1832 polymorphic EST‐based single nucleotide polymorphisms (SNPs) and the cytb mitochondrial gene in 13 wild populations and three lab strains. Natural populations were subdivided into three major mitochondrial DNA clades with an average among‐clade sequence divergence of 5.8%. SNPs revealed five major evolutionarily and genetically distinct groups with an overall F_ST of 0.170 (95% CI 0.105–0.254). These genetic groups corresponded to discrete geographic regions and appear to reflect isolation in refugia during past climate cycles. We detected 71 significantly divergent outlier loci (3.4%) and nine loci (0.5%) with significantly low F_ST values. Valleys of reduced heterozygosity, consistent with selective sweeps, surrounded six of the 71 outliers (8.5%). The lab strains formed two additional groups that were genetically distinct from all wild populations. An additional subset of outlier loci was consistent with domestication selection within lab strains. Substantial genetic variation that exists in zebrafish as a whole is missing from lab strains that we analysed. A combination of laboratory and field studies that incorporates genetic variation from divergent wild populations along with the wealth of molecular information available for this model organism provides an opportunity to advance our understanding of genetic influences on phenotypic variation for a vertebrate species.     

The outcome of the invasion of Florida lakes by Daphnia lumholtzi

1. We examined 7–12 years of monthly to quarterly historical data from 15 lakes in FL, U.S.A. to determine the extent and outcome of invasion by the alien cladoceran Daphnia lumholtzi Sars. 2. The alien species was found in 10 of the 15 lakes, including Florida’s three largest lakes: Okeechobee, George and Apopka. All the surveyed lakes had resident populations of the smaller native species Daphnia ambigua Scourfield. 3. In most of the lakes, D. ambigua occurred seven to ninefold more often in plankton samples than D. lumholtzi, and at 10‐ to 100‐fold higher maximal densities. One exception was a small lake in central Florida (Lake Jesup), where D. lumholtzi attained high densities on several occasions in the 10 years of sampling. 4. In Lake Okeechobee, where data were of sufficient quality and quantity to perform statistical analyses, the results of canonical correlation analysis indicated that high densities of D. lumholtzi were correlated with lower concentrations of suspended solids, high algal biomass and higher temperature, whereas the opposite conditions were correlated with high densities of D. ambigua. 5. Based on the majority of data, D. lumholtzi has successfully invaded many lakes in Florida, yet it has not become a substantive component of the zooplankton. Additional research is needed to determine whether resources, fish predation or some other factor is responsible for this outcome of invasion.     

Projecting climate change impacts on species distributions in megadiverse South African Cape and Southwest Australian Floristic Regions: Opportunities and challenges

Increasing evidence shows that anthropogenic climate change is affecting biodiversity. Reducing or stabilizing greenhouse gas emissions may slow global warming, but past emissions will continue to contribute to further unavoidable warming for more than a century. With obvious signs of difficulties in achieving effective mitigation worldwide in the short term at least, sound scientific predictions of future impacts on biodiversity will be required to guide conservation planning and adaptation. This is especially true in Mediterranean type ecosystems that are projected to be among the most significantly affected by anthropogenic climate change, and show the highest levels of confidence in rainfall projections. Multiple methods are available for projecting the consequences of climate change on the main unit of interest – the species – with each method having strengths and weaknesses. Species distribution models (SDMs) are increasingly applied for forecasting climate change impacts on species geographic ranges. Aggregation of models for different species allows inferences of impacts on biodiversity, though excluding the effects of species interactions. The modelling approach is based on several further assumptions and projections and should be treated cautiously. In the absence of comparable approaches that address large numbers of species, SDMs remain valuable in estimating the vulnerability of species. In this review we discuss the application of SDMs in predicting the impacts of climate change on biodiversity with special reference to the species‐rich South West Australian Floristic Region and South African Cape Floristic Region. We discuss the advantages and challenges in applying SDMs in biodiverse regions with high levels of endemicity, and how a similar biogeographical history in both regions may assist us in understanding their vulnerability to climate change. We suggest how the process of predicting the impacts of climate change on biodiversity with SDMs can be improved and emphasize the role of field monitoring and experiments in validating the predictions of SDMs.     

Extensive intraspecific genetic diversity of a freshwater crayfish in a biodiversity hotspot

1. The freshwater crayfish Cherax dispar (Decapoda: Parastacidae) inhabits coastal regions and islands of South East Queensland, Australia. We hypothesised that populations of C. dispar on different islands would be more genetically divergent from each other than populations from different drainages within the same island or on the mainland. 2. Phylogenetic and phylogeographic analyses were conducted on two mitochondrial genes (cytochrome oxidase subunit I & 16S ribosomal DNA) and one nuclear gene (Internal Transcribed Spacer region 2). Phylogeographic patterns were compared with those for other freshwater organisms in the area. 3. Deep genetic divergences were found within C. dispar, including four highly divergent (up to 20%) clades. The geographic distribution of each of the clades revealed strong latitudinal structuring along the coast rather than structuring among the islands. The high genetic divergence observed among the C. dispar clades was estimated to have pre‐dated island formation and may represent ancient river drainage patterns. 4. A restricted distribution was observed for the most divergent clade, which was discovered only on two of the sand islands (North Stradbroke Island and Moreton Island). Furthermore, strong phylogeographic structuring was observed within this clade on North Stradbroke Island, where no haplotypes were shared between samples from opposite sides of the island. This low connectivity within the island supports the idea that C. dispar rarely disperse terrestrially (i.e. across watersheds).     

Elevated atmospheric carbon dioxide and ozone alter soybean diseases at SoyFACE

Human driven changes in the Earth's atmospheric composition are likely to alter plant disease in the future. We evaluated the effects of elevated carbon dioxide (CO₂) and ozone (O₃) on three economically important soybean diseases (downy mildew, Septoria brown spot and sudden death syndrome‐SDS) under natural field conditions at the soybean free air concentration enrichment (SoyFACE) facility. Disease incidence and/or severity were quantified from 2005 to 2007 using visual surveys and digital image analysis, and changes were related to microclimatic variability and to structural and chemical changes in soybean host plants. Changes in atmospheric composition altered disease expression, but responses of the three pathosystems varied considerably. Elevated CO₂ alone or in combination with O₃ significantly reduced downy mildew disease severity (measured as area under the disease progress curve‐AUDPC) by 39–66% across the 3 years of the study. In contrast, elevated CO₂ alone or in combination with O₃ significantly increased brown spot severity in all 3 years, but the increase was small in magnitude. When brown spot severity was assessed in relation to differences in canopy height induced by the atmospheric treatments, disease severity increased under combined elevated CO₂ and O₃ treatment in only one of the 3 years. The atmospheric treatments had no effect on the incidence of SDS or brown spot throughout the study. Higher precipitation during the 2006 growing season was associated with increased AUDPC severity across all treatments by 2.7 and 1.4 times for downy mildew and brown spot, respectively, compared with drought conditions in 2005. In the 2 years with similar precipitation, the higher daily temperatures in the late spring of 2007 were associated with increased severity of downy mildew and brown spot. Elevated CO₂ and O₃ induced changes in the soybean canopy density and leaf age likely contributed to the disease expression modifications.     

Wood density predicts plant damage and vegetative recovery rates caused by cyclone disturbance in tropical rainforest tree species of North Queensland,Australia

Abstract The ability to withstand disturbance (resistance) and the ability to recover biomass following disturbance (resilience) were investigated in Australian wet tropical rainforest tree species. These two attributes are expected to be negatively correlated, because investment of biomass in structural support (conferring resistance) results in trees exhibiting high wood densities and slow growth rates, and vice versa. We examined species’ responses to disturbance caused by a severe tropical cyclone to test this hypothesized trade‐off. We assessed cyclone damage in six species in three Mabi rainforest fragments on the Atherton Tablelands. Species differed in the proportion of individuals within four damage categories (minor damage, severe branch damage, snapped, uprooted). Resistance was positively related to wood density. We found a positive correlation between the proportion of trees experiencing minor damage only and wood density, supporting the hypothesized association between resistance and mechanical strength. Among the subset of trees in which stems snapped, rates of resprouting differed between species and were highest in low wood density species and lowest in species with highest wood density. Resilience, characterized as the ability to recover biomass following disturbance and estimated as growth rate standardized for stem diameter at breast height (g day^?1 · mm^?1), was negatively related to wood density. Thus, species with low wood densities were more likely to suffer stem and branch damage owing to cyclonic winds, but also demonstrated highest resprouting and fastest responses in terms of redeveloping biomass in the 8 months following disturbance. This suggests that a species’ position along the resistance–resilience spectrum can be predicted by mean wood density, which may allow managers to predict species’ responses to future cyclones. Our findings also provide mechanistic evidence for the ‘direct regeneration’ model of post‐cyclone succession, where response is characterized by resprouting and species composition is unchanged.     

Preference induction and the benefits of floral resources for a facultative florivore

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Ants remove virtually all western myall (Acacia papyrocarpa Benth.) seeds at Middleback,South Australia

Abstract Ants can have a profound effect on the numbers of seeds present in the seed-bank. We investigated the removal of seeds of an important arid zone tree species, the western myall (Acacia papyrocarpa Benth.). The species has seed characteristics typical of other Acacia species: a hard seed-coat and a small, white aril or elaiosome; the latter is reported to be attractive to ants. An experiment was conducted to see how rapidly and completely the seeds would be removed under various caging treatments. Observations were also made to discover the major seed removers and the fate of the seeds. Seed removal was rapid (< 12h) and was almost entirely by ants, and while our observations were not conclusive, we speculate that much of the seed supply is effectively destroyed by seed harvester ants which thus act as true granivores, not seed dispersers. Whether this matters for western myall in the long term is problematic because the species is so long-lived; rare but successful recruitment events may well be sufficient for its long-term survival.