G. Barry Baker

Mutability Dynamics of an Emergent Single Stranded DNA Virus in a Naïve Host

Quasispecies variants and recombination were studied longitudinally in an emergent outbreak of beak and feather disease virus (BFDV) infection in the orange-bellied parrot (Neophema chrysogaster). Detailed health monitoring and the small population size (<300 individuals) of this critically endangered bird provided an opportunity to longitudinally track viral replication and mutation events occurring in a circular, single-stranded DNA virus over a period of four years within a novel bottleneck population. Optimized PCR was used with different combinations of primers, primer walking, direct amplicon sequencing and sequencing of cloned amplicons to analyze BFDV genome variants. Analysis of complete viral genomes (n = 16) and Rep gene sequences (n = 35) revealed that the outbreak was associated with mutations in functionally important regions of the normally conserved Rep gene and immunogenic capsid (Cap) gene with a high evolutionary rate (3.41×10−3 subs/site/year) approaching that for RNA viruses; simultaneously we observed significant evidence of recombination hotspots between two distinct progenitor genotypes within orange-bellied parrots indicating early cross-transmission of BFDV in the population. Multiple quasispecies variants were also demonstrated with at least 13 genotypic variants identified in four different individual birds, with one containing up to seven genetic variants. Preferential PCR amplification of variants was also detected. Our findings suggest that the high degree of genetic variation within the BFDV species as a whole is reflected in evolutionary dynamics within individually infected birds as quasispecies variation, particularly when BFDV jumps from one host species to another.

Molecular provenance analysis for shy and white-capped albatrosses killed by fisheries interactions in Australia, New Zealand, and South Africa

Shy and white-capped albatrosses, Thalassarche cauta and T. steadi, respectively, are phenotypically similar and are known to suffer fisheries-related bycatch mortality across their foraging range. Assessments of the extent or scale of impact of bycatch mortality on these species have previously been precluded by difficulties identifying bycatch carcasses to species level. In this study, a fast and simple molecular test based on a single nucleotide polymorphism in mtDNA of shy and white-capped albatrosses was used to determine the species composition of fisheries bycatch carcasses recovered from Australian, New Zealand, and South African waters. The only area where bycatch mortality of both species co-occurred was in Tasmanian waters; in all other zones the bycatch was exclusively comprised of white-capped albatrosses. Genotypic provenance assignment tests of shy albatrosses, a species with significant genetic structure between island colonies, correctly assigned 72% to their island of origin. These data are the first to provide insight into the relative vulnerability of shy and white-capped albatrosses to bycatch mortality across their foraging range, and to establish the vast differences in the at-sea distributions of these two species.

Longline Fisheries and Foraging Distribution of Flesh-Footed Shearwaters in Eastern Australia

Abstract Incidental seabird mortality associated with bycatch during longline commercial fishing is a conservation concern. An initial step to estimating likelihood of seabird bycatch and conceiving conservation strategies is determining amount of overlap between foraging birds and commercial fishing effort, identifying oceanographic features associated with foraging birds, and quantifying dive characteristics. We tracked 24 adult flesh-footed shearwaters (Puffinus carneipes) breeding on Lord Howe Island located east of Australia during incubation and early and late chick-rearing periods from 6 January to 17 April 2005. At-sea foraging distribution of flesh-footed shearwaters was primarily confined within the jurisdictional Australian Fishing Zone. Foraging was strongly associated with sea-surface temperature >24° C. Spatial and temporal overlap of longline fishing with foraging shearwaters varied throughout the breeding season, but was greatest (63% overlap) during early chick-rearing. Mean maximum distance reached from the breeding colony during a foraging event was 804 km (SD = 280) from Lord Howe Island. Foraging behavior was strongly diurnal, with 91% of dives occurring during daylight, and most dives (77%) were <5 m. Given that longline fishing and flesh-footed shearwaters overlap substantially, the Australian Fisheries Management Authority should consider implementing additional regulations to further reduce bycatch. Conservation strategies such as setting longlines at nights may reduce flesh-footed shearwater bycatch.

Daytime incubation temperatures in nests of the Nankeen Kestrel, Falco cenchroides

Abstract Telemetric eggs were used to monitor daytime incubation temperatures at Nankeen Kestrel, Falco cenchroides, nests on the outskirts of Canberra, Australia. During monitoring, only the females incubated. Once the second-last egg in the clutch was laid incubation began in earnest and temperatures averaged about 37°C. Incubation temperature was not constant; rather, it varied according to the day of incubation and showed marked variation over the course of the day and between individuals. On average, temperatures increased about 0.6°C per day until five days after the first egg was laid. After this, average temperature began to level off but continued to increase throughout incubation, at a rate of about 0.2°C per day. Mean temperature was positively correlated with chick condition at banding; we suggest that this was because better-fed females have little need to hunt and can thus maintain higher mean temperatures. At successful nests the eggs were incubated for about 73% of observation time, less than for kestrels’ colder-climate congeners and suggesting that for kestrels in warmer climates such as in Australia the costs of incubation may be comparatively low.

Quantifying extinction risk and forecasting the number of impending Australian bird and mammal extinctions

A critical step towards reducing the incidence of extinction is to identify and rank the species at highest risk, while implementing protective measures to reduce the risk of extinction to such species. Existing global processes provide a graded categorisation of extinction risk. Here we seek to extend and complement those processes to focus more narrowly on the likelihood of extinction of the most imperilled Australian birds and mammals. We considered an extension of existing IUCN and NatureServe criteria, and used expert elicitation to rank the extinction risk to the most imperilled species, assuming current management. On the basis of these assessments, and using two additional approaches, we estimated the number of extinctions likely to occur in the next 20 years. The estimates of extinction risk derived from our tighter IUCN categorisations, NatureServe assessments and expert elicitation were poorly correlated, with little agreement among methods for which species were most in danger-highlighting the importance of integrating multiple approaches when considering extinction risk. Mapped distributions of the 20 most imperilled birds reveal that most are endemic to islands or occur in southern Australia. The 20 most imperilled mammals occur mostly in northern and central Australia. While there were some differences in the forecasted number of extinctions in the next 20 years among methods, all three approaches predict further species loss. Overall, we estimate that another seven Australian mammals and 10 Australian birds will be extinct by 2038 unless management improves.

No evidence of cryptic bycatch causing New Zealand sea lion population decline

In PNAS, Meyer et al. (1) analyze whether exclusion devices in trawl nets contributed to New Zealand sea lion (NZSL; Phocarctos hookeri ) population decline at the Auckland Islands. We refute the primary conclusion from their correlative assessment: that annual pup production changes (as a measure of population size) were primarily driven by cryptic bycatch of adults in sub-Antarctic trawl fisheries. We also contest their interpretation that sea lion exclusion devices (SLEDs), used throughout the Auckland Islands squid trawl fishery since 2004, “…can obscure rather than alleviate fishery impacts on marine megafauna” (1). Meyer et al. (1) compare annual pup estimates with factors that could impact NZSL populations, reporting that when the fisheries interaction rate (IR; NZSL interactions per trawl) was high in one year, … [↵][1]1To whom correspondence should be addressed. Email: sheryl.hamilton{at}utas.edu.au. [1]: #xref-corresp-1-1

Breeding success, mate-fidelity and nest-site fidelity in Red-tailed Tropicbirds (Phaethon rubricauda) on Christmas Island, Indian Ocean

Abstract Disruption of pair-bonds and switching nest-site are associated with breeding failure in many seabirds. Both strategies can prevent repetition of poor performance with a low-quality mate or at a poor-quality nesting site. In the Red-tailed Tropicbird (Phaethon rubricauda), the relationship between mate-fidelity, nest-site fidelity and reproductive performance is poorly understood. We therefore examined this relationship in Red-tailed Tropicbirds, using data collected on Christmas Island in the Indian Ocean from 1984 to 1986, corresponding to three successive breeding seasons. Birds showed strong between-season mate-fidelity, despite previous breeding failure, and subsequent breeding success in birds faithful to their mate was significantly higher than in pairs that bred together for the first time, indicating that mate-fidelity may outweigh the costs of disruption of pair-bonds. Although switching of nest-site was more likely to occur after previous breeding failure, it did not increase subsequent breeding success, indicating that nest-site switching may not be advantageous in Red-tailed Tropicbirds on Christmas Island. Although effects of age, dispersal rates to inaccessible parts of the island and adult survival were not examined in this study, our results provide a valuable basis for the evaluation of population dynamics of Red-tailed Tropicbirds on Christmas Island.