Determining evolutionary origin and phylogenetic relationships of mallard-like ducks of Oceania, greater Indonesia, and the Philippines with ddRAD-seq data

AIM

We aim to determine the evolutionary origins and population genetics of mallard-like ducks of Oceania, greater Indonesia, and the Philippines.

LOCATION

Oceania, greater Indonesia, and the Philippines.

TAXON

Mallard (Anas platyrhynchos), Pacific black duck (A. superciliosa spp.), and Philippine duck (A. luzonica) METHODS: Thousands of nuclear ddRAD-seq loci and the mitochondrial DNA control region were assayed across individuals representative of each species' range. We assessed population structure and phylogenetic relationships, as well as estimated demographic histories to reconstruct the biogeographical history of each species.

RESULTS

Philippine and Pacific black ducks represent unique genetic lineages that diverged from the mallard 1-2 million years ago. We find no support for the Philippine duck representing a hybrid species as once posited; however, their low levels of genetic diversity requires further attention. We find a lack of substructure among Philippine ducks. However, we found pronounced differentiation between subspecies of Pacific black ducks, especially between A. s. superciliosa from New Zealand and A. s. rogersi from Australia, Papua New Guinea, and Timor-Leste, Indonesia. Anas superciliosa pelewensis gave mixed results; individuals from the Solomon Islands were differentiated from the other subspecies, but those from the island of Aunu'u, American Samoa, were genetically more similar to A. s. rogersi than A. s. pelewensis samples from the Solomon Islands. Finally, we find limited evidence of interspecific gene flow at evolutionary scales, and mallard introgression among contemporary samples.

MAIN CONCLUSIONS

Mallard-like ducks radiated across Oceania, greater Indonesia, and the Philippines within the last 2 million years. Only the Pacific black duck showed unique sub-structuring that largely followed known sub-species ranges, except for A. s. pelewensis. We posit that the high interrelatedness among Solomon Island samples suggests that their genetic distinctiveness may simply be the result of high levels of genetic drift. In contrast, we conclude that mainland Australian Pacific black ducks were the most likely source for the recent colonization of American Samoa. As a result, our findings suggest that either the A. s. pelewensis subspecies designations and/or its geographical range may require re-evaluation. Continued re-evaluation of evolutionary and taxonomic relationships is necessary when attempting to reconstruct and understand biogeographical histories, with important implications towards any attempts to implement conservation strategies.

The utility of coded very high frequency telemetry for monitoring reintroduced mammal populations

Very high frequency (VHF) radio tracking technology deployed on terrestrial vertebrates has been well utilized in ecology without much evolution since the 1960s. With the advent of multi-species rewilding projects, and the new field of reintroduction biology, there has been an increase in requirements for telemetry systems to monitor survival and mortality for many animals simultaneously. Common, pulsed VHF can only monitor one individual on each radio frequency, and the number of individuals monitored is constrained by the amount of time spent on each frequency to facilitate a detection and the number of receivers. Coded VHF largely removes these constraints by using a digital code that can simultaneously monitor up to 512 individuals on a single frequency. Incorporated into an autonomous monitoring system, the coded VHF system also greatly reduces time in the field to confirm the status of individuals. Here we demonstrate the utility of coded VHF technologies applied to monitoring a reintroduced population of brush-tailed bettong (Bettongia penicillata) on the Southern Yorke Peninsula in southern Australia. A system of autonomous monitoring towers was able to monitor 28 different individuals simultaneously without having to change frequency on any of the towers. During a single 24-h period, one individual was recorded 24,078 times. Key benefits of the high detection rate and autonomous recording are, a timely response to mortalities or a predation event, the detection of nocturnal, cryptic, or burrowing species whenever they are active, and the reduced need for personnel to be in the field.

Strong host phylogenetic and ecological effects on host competency for avian influenza in Australian wild birds

Host susceptibility to parasites is mediated by intrinsic and external factors such as genetics, ecology, age and season. While waterfowl are considered central to the reservoir community for low pathogenic avian influenza A viruses (LPAIV), the role of host phylogeny has received limited formal attention. Herein, we analysed 12 339 oropharyngeal and cloacal swabs and 10 826 serum samples collected over 11 years from wild birds in Australia. As well as describing age and species-level differences in prevalence and seroprevalence, we reveal that host phylogeny is a key driver in host range. Seasonality effects appear less pronounced than in the Northern Hemisphere, while annual variations are potentially linked to El Niño-Southern Oscillation. Our study provides a uniquely detailed insight into the evolutionary ecology of LPAIV in its avian reservoir community, defining distinctive processes on the continent of Australia and expanding our understanding of LPAIV globally.

Evaluating expert-based habitat suitability information of terrestrial mammals with GPS-tracking data

AIM

Macroecological studies that require habitat suitability data for many species often derive this information from expert opinion. However, expert-based information is inherently subjective and thus prone to errors. The increasing availability of GPS tracking data offers opportunities to evaluate and supplement expert-based information with detailed empirical evidence. Here, we compared expert-based habitat suitability information from the International Union for Conservation of Nature (IUCN) with habitat suitability information derived from GPS-tracking data of 1,498 individuals from 49 mammal species.

LOCATION

Worldwide.

TIME PERIOD

1998-2021.

MAJOR TAXA STUDIED

Forty-nine terrestrial mammal species.

METHODS

Using GPS data, we estimated two measures of habitat suitability for each individual animal: proportional habitat use (proportion of GPS locations within a habitat type), and selection ratio (habitat use relative to its availability). For each individual we then evaluated whether the GPS-based habitat suitability measures were in agreement with the IUCN data. To that end, we calculated the probability that the ranking of empirical habitat suitability measures was in agreement with IUCN's classification into suitable, marginal and unsuitable habitat types.

RESULTS

IUCN habitat suitability data were in accordance with the GPS data (> 95% probability of agreement) for 33 out of 49 species based on proportional habitat use estimates and for 25 out of 49 species based on selection ratios. In addition, 37 and 34 species had a > 50% probability of agreement based on proportional habitat use and selection ratios, respectively.

MAIN CONCLUSIONS

We show how GPS-tracking data can be used to evaluate IUCN habitat suitability data. Our findings indicate that for the majority of species included in this study, it is appropriate to use IUCN habitat suitability data in macroecological studies. Furthermore, we show that GPS-tracking data can be used to identify and prioritize species and habitat types for re-evaluation of IUCN habitat suitability data.

Spring foraging movements of an urban population of grey-headed flying foxes (Pteropus poliocephalus)

Flying foxes provide ecologically and economically important ecosystem services but extensive clearing and modification of habitat and drought combined with the planting of commercial and non-commercial trees across various landscapes, has meant flying foxes in Australia are increasingly seeking foraging resources in new areas. In 2011, grey-headed flying foxes formed a camp in Adelaide, South Australia, outside their previously recorded range. We used global positioning system telemetry to study the movements and foraging behaviour of this species in Adelaide in spring (September to November) 2015. High-frequency location data were used to determine the foraging range and the most frequently visited foraging sites used by each bat which were ground-truthed to identify forage plants. A total of 7239 valid locations were collected over 170 nights from four collars. Despite being a highly mobile species, the mean core foraging range estimate was only 7.30 km2 (range 3.3–11.2 km2). Maximum foraging distance from the camp in the Botanic Park was 9.5 km but most foraging occurred within a 4-km radius. The most common foraging sites occurred within the residential area of Adelaide and included introduced forage plant species, Lemon-scented gum (Corymbia citriodora) and Port Jackson fig (Ficus rubiginosa). Other observed movement activities included dipping behaviour on inland and marine waters and travel across flight paths around Adelaide airport. Our findings suggest that urban habitats in Adelaide provide sufficient foraging resources for grey-headed flying foxes to use these areas exclusively, at least in spring. This creates substantial opportunities for bats to interact with humans and their infrastructure.

Serologic Evidence of Exposure to Highly Pathogenic Avian Influenza H5 Viruses in Migratory Shorebirds, Australia

Highly pathogenic avian influenza (HPAI) H5Nx viruses of the goose/Guangdong/96 lineage continue to cause outbreaks in poultry and wild birds globally. Shorebirds, known reservoirs of avian influenza viruses, migrate from Siberia to Australia along the East-Asian-Australasian Flyway. We examined whether migrating shorebirds spending nonbreeding seasons in Australia were exposed to HPAI H5 viruses. We compared those findings with those for a resident duck species. We screened >1,500 blood samples for nucleoprotein antibodies and tested positive samples for specific antibodies against 7 HPAI H5 virus antigens and 2 low pathogenicity avian influenza H5 virus antigens. We demonstrated the presence of hemagglutinin inhibitory antibodies against HPAI H5 virus clade 2.3.4.4 in the red-necked stint (Calidris ruficolis). We did not find hemagglutinin inhibitory antibodies in resident Pacific black ducks (Anas superciliosa). Our study highlights the potential role of long-distance migratory shorebirds in intercontinental spread of HPAI H5 viruses.

Avian influenza in Australia: a summary of 5 years of wild bird surveillance

BACKGROUND

Avian influenza viruses (AIVs) are found worldwide in numerous bird species, causing significant disease in gallinaceous poultry and occasionally other species. Surveillance of wild bird reservoirs provides an opportunity to add to the understanding of the epidemiology of AIVs.

METHODS

This study examined key findings from the National Avian Influenza Wild Bird Surveillance Program over a 5-year period (July 2007-June 2012), the main source of information on AIVs circulating in Australia.

RESULTS

The overall proportion of birds that tested positive for influenza A via PCR was 1.9 ± 0.1%, with evidence of widespread exposure of Australian wild birds to most low pathogenic avian influenza (LPAI) subtypes (H1-13, H16). LPAI H5 subtypes were found to be dominant and widespread during this 5-year period.

CONCLUSION

Given Australia's isolation, both geographically and ecologically, it is important for Australia not to assume that the epidemiology of AIV from other geographic regions applies here. Despite all previous highly pathogenic avian influenza outbreaks in Australian poultry being attributed to H7 subtypes, widespread detection of H5 subtypes in wild birds may represent an ongoing risk to the Australian poultry industry.

Movement patterns of southern bell frogs (Litoria raniformis) in response to flooding

Within the semiarid regions of New South Wales, Australia, the endangered southern bell frog (Litoria raniformis) occupies a landscape that is characterised by unpredictable rainfall and periodic flooding. Limited knowledge of the movement and habitat-occupancy patterns of this species in response to flood events has hampered conservation efforts. We used radio-tracking to assess changes in movement patterns and habitat occupancy of L. raniformis (n = 40) over three different periods (November, January and April/May) that coincided with the flooding, full capacity and subsequent drying of waterbodies within an irrigation landscape. We assessed (1) the use of permanent and ephemeral habitats in response to flooding and drying and (2) distances moved, turning angles and dispersion of frogs during wetland flooding, full capacity and drying. Individuals remained in permanent waterbodies in November but had abandoned these areas in favour of flooded ephemeral waterbodies by January. As the ephemeral waterbodies dried, radio-tracked individuals moved back into permanent waterbodies. The movement patterns of radio-tracked individuals were significantly different in the three radio-tracking periods, but did not differ significantly between sexes. Individuals moved significantly greater distances over 24 h, in straighter lines and movements were more dispersed while they occupied ephemeral waterbodies during January than when they occupied permanent waterbodies during November and April/May. Local weather conditions did not influence movement patterns when all three tracking periods were modelled together using a single linear stepwise regression. The dynamic distribution of habitat patches over space and time, combined with changing patterns of resource utilisation and movement of L. raniformis, highlights the importance of incorporating both permanent and ephemeral habitat patches into conservation plans. Reductions in flood frequency and extent of ephemeral wetlands due to modified flooding regimes have the capacity to limit dispersal of this species, even when permanent waterbodies remain unchanged.