Impact of invasive cane toads on Australian birds

The cane toad (Bufo marinus), a large, toxic, American anuran, was introduced to Australia in 1935. Populations of many of Australia's reptiles (snakes, varanid lizards, crocodiles) and carnivorous mammals (dasyurid marsupials) have declined because these predators are killed by the toad's powerful toxins. In contrast to these well-studied species, little is known about the cane toads impacts on Australian birds. We reviewed published and unpublished data on behavioral interactions between Australian avian predators and cane toads and collated distributional and dietary information to identify avian taxa potentially at risk from cane toad invasion. Cane toads are sympatric with 172 frog-eating bird species in Australia, and an additional 8 bird species overlap with the predicted future range of the toad. Although many bird species thus are potentially at risk, behavioral observations suggest the risk level is generally low. Despite occasional reports of Australian birds being killed when they ingest cane toads, most birds either ignore toads or survive the predation event. The apparently higher tolerance of Australian birds to toad toxins, compared with Australian reptiles and marsupials, may reflect genetic exchange between Australian birds and Asian populations that encounter other bufonid species regularly and hence have evolved the capacity to recognize or tolerate this toxic prey. 

Biogeographic models of gene flow in two waterfowl of the Australo-Papuan tropics

There are many large, easy-to-observe anseriform birds (ducks, geese, and swans) in northern Australia and New Guinea and they often gather in large numbers. Yet, the structure of their populations and their regional movements are poorly understood. Lack of understanding of population structure limits our capacity to understand source-sink dynamics relevant to their conservation or assess risks associated with avian-borne pathogens, in particular, avian influenza for which waterfowl are the main reservoir species. We set out to assess present-day genetic connectivity between populations of two widely distributed waterfowl in the Australo-Papuan tropics, magpie goose Anseranas semipalmata (Latham, 1798) and wandering whistling-duck Dendrocygna arcuata (Horsfield, 1824). Microsatellite data were obtained from 237 magpie geese and 64 wandering whistling-duck. Samples were collected across northern Australia, and at one site each in New Guinea and Timor Leste. In the wandering whistling-duck, genetic diversity was significantly apportioned by region and sampling location. For this species, the best model of population structure was New Guinea as the source population for all other populations. One remarkable result for this species was genetic separation of two flocks sampled contemporaneously on Cape York Peninsula only a few kilometers apart. In contrast, evidence for population structure was much weaker in the magpie goose, and Cape York as the source population provided the best fit to the observed structure. The fine scale genetic structure observed in wandering whistling-duck and magpie goose is consistent with earlier suggestions that the west-coast of Cape York Peninsula is a flyway for Australo-Papuan anseriforms between Australia and New Guinea across Torres Strait.

Little evidence that condition, stress indicators, sex ratio, or homozygosity are related to landscape or habitat attributes in declining woodland birds

Habitat loss, fragmentation and degradation are drivers of major declines in biodiversity and species extinctions. The actual causes of species population declines following habitat change are more difficult to discern and there is typically high covariation among the measures used to infer the causes of decline. The causes of decline may act directly on individual fitness and survival, or through disruption of population processes. We examined the relationships among configuration, extent and status of native vegetation and three commonly used indicators of individual body condition and chronic stress (haemoglobin level, haematocrit, residual body mass condition index) in 13 species of woodland-dependent birds in south-eastern Australia. We also examined two measures of changes to population processes (sex ratio and individual homozygosity) in ten species and alleic richness in five species. We found little support for relationships between site or landscape characteristics and individual or population response variables, notwithstanding that our simulations showed we had sufficient power to detect relatively small effects. We discuss possible causes of the absence of detectable habitat effects in this system and the implications for the usefulness of individual body condition and easily measured haematological indices as indicators of the response of avian populations to habitat change. © 2012 The Authors.

Transcriptome analysis of pigeon milk production - role of cornification and triglyceride synthesis genes

BACKGROUND : The pigeon crop is specially adapted to produce milk that is fed to newly hatched young. The process of pigeon milk production begins when the germinal cell layer of the crop rapidly proliferates in response to prolactin, which results in a mass of epithelial cells that are sloughed from the crop and regurgitated to the young. We proposed that the evolution of pigeon milk built upon the ability of avian keratinocytes to accumulate intracellular neutral lipids during the cornification of the epidermis. However, this cornification process in the pigeon crop has not been characterised. RESULTS: We identified the epidermal differentiation complex in the draft pigeon genome scaffold and found that, like the chicken, it contained beta-keratin genes. These beta-keratin genes can be classified, based on sequence similarity, into several clusters including feather, scale and claw keratins. The cornified cells of the pigeon crop express several cornification-associated genes including cornulin, S100-A9 and A16-like, transglutaminase 6-like and the pigeon 'lactating' crop-specific annexin cp35. Beta-keratins play an important role in 'lactating' crop, with several claw and scale keratins up-regulated. Additionally, transglutaminase 5 and differential splice variants of transglutaminase 4 are up-regulated along with S100-A10. CONCLUSIONS: This study of global gene expression in the crop has expanded our knowledge of pigeon milk production, in particular, the mechanism of cornification and lipid production. It is a highly specialised process that utilises the normal keratinocyte cellular processes to produce a targeted nutrient solution for the young at a very high turnover.

Predator behaviour and predation risk in the heterogeneous Arctic environment

1. Habitat heterogeneity and predator behaviour can strongly affect predator–prey interactions but these factors are rarely considered simultaneously, especially when systems encompass multiple predators and prey.

2. In the Arctic, greater snow geese Anser caerulescens atlanticus L. nest in two structurally different habitats: wetlands that form intricate networks of water channels, and mesic tundra where such obstacles are absent. In this heterogeneous environment, goose eggs are exposed to two types of predators: the arctic fox Vulpes lagopus L. and a diversity of avian predators. We hypothesized that, contrary to birds, the hunting ability of foxes would be impaired by the structurally complex wetland habitat, resulting in a lower predation risk for goose eggs.

3. In addition, lemmings, the main prey of foxes, show strong population cycles. We thus further examined how their fluctuations influenced the interaction between habitat heterogeneity and fox predation on goose eggs.

4. An experimental approach with artificial nests suggested that foxes were faster than avian predators to find unattended goose nests in mesic tundra whereas the reverse was true in wetlands. Foxes spent 3·5 times more time between consecutive attacks on real goose nests in wetlands than in mesic tundra. Their attacks on goose nests were also half as successful in wetlands than in mesic tundra whereas no difference was found for avian predators.

5. Nesting success in wetlands (65%) was higher than in mesic tundra (56%) but the difference between habitats increased during lemming crashes (15%) compared to other phases of the cycle (5%). Nests located at the edge of wetland patches were also less successful than central ones, suggesting a gradient in accessibility of goose nests in wetlands for foxes.

6. Our study shows that the structural complexity of wetlands decreases predation risk from foxes but not avian predators in arctic-nesting birds. Our results also demonstrate that cyclic lemming populations indirectly alter the spatial distribution of productive nests due to a complex interaction between habitat structure, prey-switching and foraging success of foxes.

Common ravens raid arctic fox food caches

Cache recovery is critical for evolution of hoarding behaviour, because the energy invested in caching may be lost if consumers other than the hoarders benefit from the cached food. By raiding food caches, animals may exploit the caching habits of others, that should respond by actively defending their caches. The arctic fox (Alopex lagopus) is the main predator of lemmings and goose eggs in the Canadian High Arctic and stores much of its prey in the ground. Common ravens (Corvus corax) are not as successful as foxes in taking eggs from goose nests. This generalist avian predator regularly uses innovation and opportunism to survive in many environments. Here, we provide the first report that ravens can successfully raid food cached by foxes, and that foxes may defend their caches from ravens.

New and improved molecular sexing methods for museum bird specimens

We present two new avian molecular sexing techniques for nonpasserine and passerine birds (Neognathae), which are more suitable for use with museum specimens than earlier methods. The technique for nonpasserines is based on a new primer (M5) which, in combination with the existing P8 primer, targets a smaller amplicon in the CHD1 sex-linked gene than previously. Primers targeting ATP5A1, an avian sex-linked gene not previously used for sex identification, were developed for passerines. Comprehensive testing across species demonstrated that both primer pairs sex a range of different species within their respective taxonomic groups. Rigorous evaluation of each method within species showed that these permitted sexing of specimens dating from the 1850s. For corn bunting museum specimens, the ATP5A1 method sexed 98% of 63 samples (1857–1966). The M5/P8 CHD1 method was similarly successful, sexing 90% of 384 moorhen specimens from six different museum collections (1855–2001). In contrast, the original P2/P8 CHD1 sexing method only identified the sex of less than half of 111 museum moorhen samples. In addition to dried skin samples, these methods may be useful for other types of material that yield degraded or damaged DNA, and are hence potential new sexing tools for avian conservation genetics, population management and wildlife forensics.

Molecular determination of sex-ratio in Yellowhammer Emberiza citrinella offspring

Theory predicts skewed offspring sex-ratios in a range of situations in which the economics of producing the two sexes differ. Offspring sex-ratio skews in birds are relatively scarcely observed compared to other taxa. This could be because avian molecular sexing techniques, which allow young birds to be sexed, have only recently become available. Alternatively, birds may be largely constrained from adaptively manipulating the sex-ratio of their offspring. We used a recently-developed molecular sexing technique for birds to sex 420 Yellowhammer Emberiza citrinella offspring from 168 clutches found in Oxfordshire. Clutch sex-ratio of the population did not depart from the expected binomial distribution, and there was no variation in clutch sex-ratio with laying date, breeding attempt, or a variety of habitat variables which were predicted to differentially affect the survival and future reproductive success of offspring of the two sexes. There was no difference in size or growth rate of the sexes and nestling mortality was not sex-biased. Hence, although we can identify possible advantages of manipulating the sex-ratio in this species, it seems not to be used as a breeding strategy. Given the lack of consistent evidence for skewed avian offspring sex-ratios, more experimental work is required to determine whether, and how, birds may adaptively manipulate their offspring sex-ratio.

Silencing host genes using RNAi to impact virus growth in vitro

Using short interfering RNAs to silence individual human host genes we were able to demonstrate that alpha coatamer protein (COPA) is important for the replication of highly pathogenic Avian Influenza A/chicken/Vietnam/008/2004 H5N1 in vitro and may therefore hold potential as a target for novel antiviral therapeutics.

From little things, big things grow: trends and fads in 110 years of Australian ornithology

Publishing histories can reveal changes in ornithological effort, focus or direction through time. This study presents a bibliometric content analysis of Emu (1901–2011) which revealed 115 trends (long-term changes in publication over time) and 18 fads (temporary increases in publication activity) from the classification of 9,039 articles using 128 codes organised into eight categories (author gender, author affiliation, article type, subject, main focus, main method, geographical scale and geographical location). Across 110 years, private authorship declined, while publications involving universities and multiple institutions increased; from 1960, female authorship increased. Over time, question-driven studies and incidental observations increased and decreased in frequency, respectively. Single species and ‘taxonomic group’ subjects increased while studies of birds at specific places decreased. The focus of articles shifted from species distribution and activities of the host organisation to breeding, foraging and other biological/ecological topics. Site- and Australian-continental-scales slightly decreased over time; non-Australian studies increased from the 1970s. A wide variety of fads occurred (e.g. articles on bird distribution, 1942–1951, and using museum specimens, 1906–1913) though the occurrence of fads decreased over time. Changes over time are correlated with technological, theoretical, social and institutional changes, and suggest ornithological priorities, like those of other scientific disciplines, are temporally labile

Activity patterns of insectivorous bats and birds in northern Scandinavia (69° N), during continuous midsummer daylight

Previous studies suggest that many species of insectivorous bats are nocturnal, despite the relatively low availability of their insect prey at night, because of the risk of predation by diurnal predatory birds. We hypothesised that if this was the case bats living above the arctic circle would alter their feeding behaviour during midsummer because there would no longer be any benefit to restricting their activity to the period when their prey are least abundant. Alternatively, if bats were more influenced by competition from aerial insectivorous birds they would continue to feed at ‘night’ to avoid such competition. In northern Norway (69° N), during continuous midsummer daylight, insectivorous sand martins (Riparia riparia) concentrated their aerial feeding activity when aerial insects were most abundant. The birds stopped feeding between 23:00 and 07:00 when aerial insects were least abundant. In contrast, northern bats (Eptesicus nilssonii), fed mostly between 22:00 and 02:00, coinciding with the lowest aerial insect availability, and with the period when light levels were lowest (ca 1000 lux). Bat activity patterns were closest to those predicted by the avian competition hypothesis. The low densities of both sand martins and Northern bats in the study area, however, were less consistent with this hypothesis. Possibly populations of both species were higher historically and the observed patterns reflected historical competition. Bat activity was most closely correlated to ambient light levels. This raised two alternative explanations that we could not eliminate. Perhaps there was differential predation risk, between the brightest and darkest parts of the day, because the visual capacities of falcons are strongly dependent on luminance. Alternatively the bats may have been entrained to emerge at given light levels by their behaviour at other times of year.

Use of nest-boxes by the Zebra Finch (Taeniopygia guttata): implications for reproductive success and research

Nest-boxes have been used widely and for many decades in Europe and North America to increase avian reproductive success in species management and conservation programs and to increase the amenability and efficiency with which a species can be studied. Here we describe the establishment of a breeding population of Zebra Finches using nest-boxes in semi-arid, far-western New South Wales, over three breeding seasons (2005–07). The nest-boxes were used readily by Zebra Finches, with a total of 572 breeding attempts recorded in this study. After the introduction of nest-boxes, nearly all breeding attempts were made in these artificial cavities. Zebra Finches breeding in natural nests are prone to high levels of nest predation (>60% in previous studies), but such predation was almost completely eliminated with nest-boxes, with <2% of nests being depredated. Not surprisingly, the reproductive success of pairs breeding in nest-boxes (58% of nests successfully fledged at least one young) was significantly higher than in the natural nests monitored at the same sites in a previous year, and by comparison with previous studies of the same species in other localities across Australia. Our study of the Zebra Finch, a laboratory model used throughout the world, shows the effectiveness of artificial nest-boxes at decreasing levels of predation in the wild and increasing the capacity for research.

Nest visit synchrony is high and correlates with reproductive success in the wild Zebra finch Taeniopygia guttata

Nest visit synchrony, whereby adults coordinate their visits to the nest, has been documented in several species of cooperative breeders. Visit synchrony may reduce nest predation rate or sibling competition, or instead follow from synchronisation of other behaviours, such as foraging. However, nest visit synchrony has rarely been considered in species with bi-parental care, even though it could conceivably bring similar fitness benefits to that seen in cooperative breeders. In addition, in species with bi-parental care, we might expect nest visit synchrony to reflect the quality of the pair or the overall coordination of breeding activity between partners. Here, we tested whether nest visit synchrony occurs in a classic avian model for the study of bi-parental care, the zebra finch Taeniopygia guttata. We found that in the wild, both zebra finch parents visited the nest very infrequently during nestling provisioning, with only one visit per hour, and that nest visits were highly synchronised with parents visiting the nest together on 78% of the visits. In addition, we found that nest visit synchrony was correlated with hatching rate, brood size at hatching and the number of offspring in the nest a few days prior to fledging. Our results suggest that, while more work is required to understand the benefits of nest visit synchrony in this species, considering behavioural synchrony and cooperation between mated partners may offer new insight into the study of parental investment, including in species with bi-parental care.

Conspecific attraction and nest site selection in a nomadic species, the zebra finch

Conspecific nesting density affects many aspects of breeding biology, as well as habitat selection decisions. However, the large variations in breeding density observed in many species are yet to be fully explained. Here, we investigated the settlement patterns in a colonial species with variable breeding density and where resource distribution could be manipulated. The zebra finch, Taeniopygia guttata, is a classic avian model in evolutionary biology but we know surprisingly very little about nest site selection strategies and nesting densities in this species, and in fact, in nomadic species in general. Yet, important determinants of habitat selection strategies, including temporal predictability and breeding synchrony, are likely to be different in nomadic species than in the non-nomadic species studied to date. Here, we manipulated the distribution of nesting sites (by providing nest boxes) and food patches (feeders) to test four non-exclusive habitat selection hypotheses that could lead to nest aggregation: 1) attraction to resources, 2) attraction to breeding conspecifics, and 3) attraction to successful conspecifics and 4) use of private information (i.e. own reproductive success on a site). We found that wild zebra finches used conspecific presence and possibly reproductive success, to make decisions over where to locate their nests, but did not aggregate around water or food within the study areas. Moreover, there was a high degree of inter-individual variation in nesting density preference. We discuss the significance of our results for habitat selection strategy in nomadic species and with respect to the differential selection pressures that individuals breeding at different densities may experience.

Visualising single molecules of HIV-1 and miRNA nucleic acids

Background
The scarcity of certain nucleic acid species and the small size of target sequences such as miRNA, impose a significant barrier to subcellular visualization and present a major challenge to cell biologists. Here, we offer a generic and highly sensitive visualization approach (oligo fluorescent in situ hybridization, O-FISH) that can be used to detect such nucleic acids using a single-oligonucleotide probe of 19–26 nucleotides in length.

Results
We used O-FISH to visualize miR146a in human and avian cells. Furthermore, we reveal the sensitivity of O-FISH detection by using a HIV-1 model system to show that as little as 1–2 copies of nucleic acids can be detected in a single cell. We were able to discern newly synthesized viral cDNA and, moreover, observed that certain HIV RNA sequences are only transiently available for O-FISH detection.

Conclusions
Taken together, these results suggest that the O-FISH method can potentially be used for in situ probing of, as few as, 1–2 copies of nucleic acid and, additionally, to visualize small RNA such as miRNA. We further propose that the O-FISH method could be extended to understand viral function by probing newly transcribed viral intermediates; and discern the localisation of nucleic acids of interest. Additionally, interrogating the conformation and structure of a particular nucleic acid in situ might also be possible, based on the accessibility of a target sequence.