Gel‐free species identification using melt‐curve analysis

DNA‐based identification of organisms is an important tool in biosecurity, ecological monitoring and wildlife forensics. Current methods usually involve post‐polymerase chain reaction (PCR) manipulations (e.g. restriction digest, gel electrophoresis), which add to the expense and time required for processing samples, and may introduce error. We developed a method of species identification that uses species‐specific primers and melt‐curve analysis, and avoids post‐PCR manipulation of samples. The method was highly accurate when trialled on DNA from six large carnivore species from Tasmania, Australia. Because of its flexibility and cost‐effectiveness, this method should find wide use in many areas of applied biological science.     

Coral Adaptation and Acclimatization: A Most Ingenious Paradox

SYNOPSIS. Reef corals and the communities they form evidentlypossess effective mechanisms of adaptation and acclimation thathave ensured their survival and recurrence over geologic time.Current reef degradation suggests that these mechanisms arebeing taxed beyond their limits; understanding of the problemis hampered by serious inadequacies in our understanding ofphysiological stress responses, the range and implications ofreproductive strategies, and the mechanisms of calcificationand algal symbiosis. Reef community and population responsesto environmental change appear substantially different on differenttime scales, and a combination of short-term perspectives anddefinitional confusion complicates interpretation and predictionof reef responses. Calcium carbonate saturation state is nowrecognized as a potentially important control of reef calcification,which means that rising atmospheric CO₂ represents a directthreat to reef ecosystems on a global scale.     

Cavity selection for roosting,and roosting ecology of forest-dwelling Australian Owlet-nightjars (Aegotheles cristatus)

Abstract We compared a variety of attributes of tree cavities used for roosting by radio-tagged Australian Owlet-nightjars Aegotheles cristatus with randomly chosen prospective cavities to test which features are important for the species. Owlet-nightjars preferentially roosted in tree cavities closer to the ground, in trees with a significantly greater number of cavities and significantly closer to another tree with a cavity than expected by chance. There was also a significant interaction between cavity height and number of cavities in the tree. Tree size, decay stage and tree species were not statistically important cues used for making site choices. The requirements for Owlet-nightjars differ from those of most other Australian birds that use tree holes and also from most insectivorous bats. Telemetry data indicate that Owlet-nightjars move ～300 m between roost sites every 9 days on average. Individual birds used 2-6 different cavities during the 1–4-month period over which they were followed. The reasons for the relatively low levels of site fidelity are unknown.     

Genetic control of predator avoidance behaviour in Daphnia

1. The vertical migration behaviour in electrophoretically distinguishable clones of Daphnia magna Straus was investigated. 2. Clones differed significantly in their tendency to stay near the surface of the tank during the light phase of the daily light/dark cycle, indicating that vertical migration has a genetic component. 3. There was a significant difference in behaviour between juvenile and adult Daphnia: overall the juveniles stayed closer to the water surface than the adults, but the characteristic pattern of clonal differences persisted in the juveniles. 4. When an adult population of each clone was exposed to a fish predator in an experimental tank, the position a clone maintained in the tank at the start of the day had a direct effect on its survival. Clones remaining near to the surface of the water suffered greatest predarion.     

Predicting impacts of climate-induced range expansion: an experimental framework and a test involving key grazers on temperate rocky shores

Climate change has strong potential to modify the structure and functioning of ecosystems, but experimental field studies into its effects are rare. On rocky shores, grazing limpets strongly affect ecosystem structure and their distribution in NW Europe is changing in response to climate change. Three limpet species co-occur in SW Britain ( Patella vulgata, Patella ulyssiponensis and Patella depressa ) on open rock and in pools. Shores in Ireland are similar, but currently lack P. depressa . It is anticipated that P. depressa will expand its range into Ireland as the climate warms, but we currently lack an empirical basis to predict the consequences of this change. Recent studies show that increasing abundance of P. depressa on British shores has been accompanied by a decline of P. vulgata suggesting interspecific competition. In this study, a new experimental framework was used to examine the potential for P. depressa to affect P. vulgata on Irish shores. P. vulgata was experimentally transplanted into enclosures on open rock and in pools in both Ireland and Britain. In pools, treatments also included transplanted P. ulyssiponensis to mimic natural assemblages. Growth and mortality of P. vulgata were measured over 6 months with no differences between Ireland and Britain. In Britain, P. vulgata caged in pools with transplanted P. depressa and P. ulyssiponensis showed reduced growth, compared with when caged in pools with P. ulyssiponensis alone. There was no effect of P. depressa on the growth rate of P. vulgata on open rock. Results indicate that if the range of P. depressa extends into Ireland, it would reduce the growth of P. vulgata where it co-occurs with P. ulyssiponensis in pools. The framework used here provides a field-based approach that could be used to examine the impacts of climate-induced range expansions on the structure and functioning of other ecosystems.     

Landscape genetic structure of coastal tailed frogs (Ascaphus truei) in protected vs. managed forests

Habitat loss and fragmentation are the leading causes of species’ declines and extinctions. A key component of studying population response to habitat alteration is to understand how fragmentation affects population connectivity in disturbed landscapes. We used landscape genetic analyses to determine how habitat fragmentation due to timber harvest affects genetic population connectivity of the coastal tailed frog (Ascaphus truei), a forest-dwelling, stream-breeding amphibian. We compared rates of gene flow across old-growth (Olympic National Park) and logged landscapes (Olympic National Forest) and used spatial autoregression to estimate the effect of landscape variables on genetic structure. We detected higher overall genetic connectivity across the managed forest, although this was likely a historical signature of continuous forest before timber harvest began. Gene flow also occurred terrestrially, as connectivity was high across unconnected river basins. Autoregressive models demonstrated that closed forest and low solar radiation were correlated with increased gene flow. In addition, there was evidence for a temporal lag in the correlation of decreased gene flow with harvest, suggesting that the full genetic impact may not appear for several generations. Furthermore, we detected genetic evidence of population bottlenecks across the Olympic National Forest, including at sites that were within old-growth forest but surrounded by harvested patches. Collectively, this research suggests that absence of forest (whether due to natural or anthropogenic changes) is a key restrictor of genetic connectivity and that intact forested patches in the surrounding environment are necessary for continued gene flow and population connectivity.     

Queen condition,mating frequency,queen loss,and levels of worker reproduction in the hornets Vespa affinis and V. simillima

Abstract 1. Mature queens of the hornet Vespa affinis are unusual in that they lose all their body hair and wings. This has been used as evidence for matricide in hornets. Factors favouring matricide such as low paternity and long annual lifecycle are present in most hornets. 2. We determined paternity in V. affinis and compared queen condition, levels of queen loss, and worker reproduction in 163 V. affinis and 63 V. simillima colonies. These two species have very similar lifecycles and colony sizes, but different paternities (1.3 vs 2.4). Furthermore, in queen‐right V. affinis colonies small proportions (4%) of reproductive workers were present, whereas in queen‐right V. simillima colonies no reproductive workers were detected. 3. Despite these differences, queen damage in both species was influenced predominantly by her age and in V. affinis was not influenced by presence of reproductive workers. 4. The number of queen‐less V. simillima (9/63 = 14%) and V. affinis (28/163 = 17%) colonies were also not significantly different (P = 0.8). Therefore, queen damage and proportions of queen‐less colonies were not linked making it a poor indicator of matricide. 5. It is proposed that graded control of sexual and worker production in wasps and hornets prevents a situation where kin‐selected matricide is ever favoured.     

Long-term patterns of mass loss during the decomposition of leaf and fine root litter: an intersite comparison

Decomposition is a critical process in global carbon cycling. During decomposition, leaf and fine root litter may undergo a later, relatively slow phase; past long-term experiments indicate this phase occurs, but whether it is a general phenomenon has not been examined. Data from Long-term Intersite Decomposition Experiment Team, representing 27 sites and nine litter types (for a total of 234 cases) was used to test the frequency of this later, slow phase of decomposition. Litter mass remaining after up to 10 years of decomposition was fit to models that included (dual exponential and asymptotic) or excluded (single exponential) a slow phase. The resultant regression equations were evaluated for goodness of fit as well as biological realism. Regression analysis indicated that while the dual exponential and asymptotic models statistically and biologically fit more of the litter type–site combinations than the single exponential model, the latter was biologically reasonable for 27–65% of the cases depending on the test used. This implies that a slow phase is common, but not universal. Moreover, estimates of the decomposition rate of the slowly decomposing component averaged 0.139–0.221 year⁻¹ (depending on method), higher than generally observed for mineral soil organic matter, but one-third of the faster phase of litter decomposition. Thus, this material may be slower than the earlier phases of litter decomposition, but not as slow as mineral soil organic matter. Comparison of the long-term integrated decomposition rate (which included all phases of decomposition) to that for the first year of decomposition indicated the former was on average 75% that of the latter, consistent with the presence of a slow phase of decomposition. These results indicate that the global store of litter estimated using short-term decomposition rates would be underestimated by at least one-third.