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.

Designing a large-scale track-based monitoring program to detect changes in species distributions in arid Australia.

Monitoring trends in animal populations in arid regions is challenging due to remoteness and low population densities. However, detecting species' tracks or signs is an effective survey technique for monitoring population trends across large spatial and temporal scales. In this study, we developed a simulation framework to evaluate the performance of alternative track-based monitoring designs at detecting change in species distributions in arid Australia. We collated presence-absence records from 550 2-ha track-based plots for 11 vertebrates over 13 years and fitted ensemble species distribution models to predict occupancy in 2018. We simulated plausible changes in species' distributions over the next 15 years and, with estimates of detectability, simulated monitoring to evaluate the statistical power of three alternative monitoring scenarios: (1) where surveys were restricted to existing 2-ha plots, (2) where surveys were optimized to target all species equally, and (3) where surveys were optimized to target two species of conservation concern. Across all monitoring designs and scenarios, we found that power was higher when detecting increasing occupancy trends compared to decreasing trends owing to the relatively low levels of initial occupancy. Our results suggest that surveying 200 of the existing plots annually (with a small subset resurveyed twice within a year) will have at least an 80% chance of detecting 30% declines in occupancy for four of the five invasive species modeled and one of the six native species. This increased to 10 of the 11 species assuming larger (50%) declines. When plots were positioned to target all species equally, power improved slightly for most compared to the existing survey network. When plots were positioned to target two species of conservation concern (crest-tailed mulgara and dusky hopping mouse), power to detect 30% declines increased by 29% and 31% for these species, respectively, at the cost of reduced power for the remaining species. The effect of varying survey frequency depended on its trade-off with the number of sites sampled and requires further consideration. Nonetheless, our research suggests that track-based surveying is an effective and logistically feasible approach to monitoring broad-scale occupancy trends in desert species with both widespread and restricted distributions.

Visitation of artificial watering points by the red fox (Vulpes vulpes) in semiarid Australia.

The introduced red fox (Vulpes vulpes) now occupies most of the Australian continent outside the tropics, including arid and semiarid ecosystems. Information on the water requirements of foxes is scant, but free water is not thought to be required if adequate moisture-containing food is available. The frequency and duration of visits by foxes fitted with GPS collars to known artificial watering points in semiarid Australia were recorded for 22 individual foxes across four austral seasons between October 2015 and November 2017, providing >93,000 location fixes. We modeled home range and the distance traveled by range-resident foxes beyond their home range to reach known water sources. We used recurse analysis to determine the frequency of visitation and step-selection functions to model the speed and directionality of movement inside and outside the home range. Our study demonstrates that some foxes in this semiarid environment utilize free-standing water. The findings suggest that artificial watering points can be used as a focal point for conducting strategic fox control in arid and semiarid environments. Additionally, strategies that restrict access to water by foxes may reduce their duration of occupancy and/or long-term abundance in parts of the landscape, thus providing benefits for conservation and agriculture.

Accelerometer informed time-energy budgets reveal the importance of temperature to the activity of a wild, arid zone canid.

BACKGROUND: Globally, arid regions are expanding and becoming hotter and drier with climate change. For medium and large bodied endotherms in the arid zone, the necessity to dissipate heat drives a range of adaptations, from behaviour to anatomy and physiology. Understanding how apex predators negotiate these landscapes and how they balance their energy is important as it may have broad impacts on ecosystem function. METHODS: We used tri-axial accelerometry (ACC) and GPS data collected from free-ranging dingoes in central Australia to investigate their activity-specific energetics, and activity patterns through time and space. We classified dingo activity into stationary, walking, and running behaviours, and estimated daily energy expenditure via activity-specific time-energy budgets developed using energy expenditure data derived from the literature. We tested whether dingoes behaviourally thermoregulate by modelling ODBA as a function of ambient temperature during the day and night. We used traditional distance measurements (GPS) as well as fine-scale activity (ODBA) data to assess their daily movement patterns. RESULTS: We retrieved ACC and GPS data from seven dingoes. Their mass-specific daily energy expenditure was significantly lower in summer (288 kJ kg- 1 day- 1) than winter (495 kJ kg- 1 day- 1; p = 0.03). Overall, dingoes were much less active during summer where 91% of their day was spent stationary in contrast to just 46% during winter. There was a sharp decrease in ODBA with increasing ambient temperature during the day (R2 = 0.59), whereas ODBA increased with increasing Ta at night (R2 = 0.39). Distance and ODBA were positively correlated (R = 0.65) and produced similar crepuscular patterns of activity. CONCLUSION: Our results indicate that ambient temperature may drive the behaviour of dingoes. Seasonal differences of daily energy expenditure in free-ranging eutherian mammals have been found in several species, though this was the first time it has been observed in a wild canid. We conclude that the negative relationship between dingo activity (ODBA) and ambient temperature during the day implies that high heat gain from solar radiation may be a factor limiting diurnal dingo activity in an arid environment.

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.

Toward reliable population density estimates of partially marked populations using spatially explicit mark-resight methods.

Camera traps are used increasingly to estimate population density for elusive and difficult to observe species. A standard practice for mammalian surveys is to place cameras on roads, trails, and paths to maximize detections and/or increase efficiency in the field. However, for many species it is unclear whether track-based camera surveys provide reliable estimates of population density.Understanding how the spatial arrangement of camera traps affects population density estimates is of key interest to contemporary conservationists and managers given the rapid increase in camera-based wildlife surveys.We evaluated the effect of camera-trap placement, using several survey designs, on density estimates of a widespread mesopredator, the red fox Vulpes vulpes, over a two-year period in a semi-arid conservation reserve in south-eastern Australia. Further, we used the certainty in the identity and whereabouts of individuals (via GPS collars) to assess how resighting rates of marked foxes affect density estimates using maximum likelihood spatially explicit mark-resight methods.Fox detection rates were much higher at cameras placed on tracks compared with off-track cameras, yet in the majority of sessions, camera placement had relatively little effect on point estimates of density. However, for each survey design, the precision of density estimates varied considerably across sessions, influenced heavily by the absolute number of marked foxes detected, the number of times marked foxes was resighted, and the number of detection events of unmarked foxes.Our research demonstrates that the precision of population density estimates using spatially explicit mark-resight models is sensitive to resighting rates of identifiable individuals. Nonetheless, camera surveys based either on- or off-track can provide reliable estimates of population density using spatially explicit mark-resight models. This underscores the importance of incorporating information on the spatial behavior of the subject species when planning camera-trap surveys.

Proximate cues to phases of movement in a highly dispersive waterfowl, Anas superciliosa.

BACKGROUND: Waterfowl can exploit distant ephemeral wetlands in arid environments and provide valuable insights into the response of birds to rapid environmental change, and behavioural flexibility of avian movements. Currently much of our understanding of behavioural flexibility of avian movement comes from studies of migration in seasonally predictable biomes in the northern hemisphere. We used GPS transmitters to track 20 Pacific black duck (Anas superciliosa) in arid central Australia. We exploited La Niña conditions that brought extensive flooding, so allowing a rare opportunity to investigate how weather and other environmental factors predict initiation of long distance movement toward freshly flooded habitats. We employed behavioural change point analysis to identify three phases of movement: sedentary, exploratory and long distance oriented movement. We then used random forest models to determine the ability of meteorological and remote sensed landscape variables to predict initiation of these phases. RESULTS: We found that initiation of exploratory movement phases is influenced by fluctuations in local weather conditions and accumulated rainfall in the landscape. Initiation of long distance movement phases was found to be highly individualistic with minor influence from local weather conditions. CONCLUSIONS: Our study reveals how individuals utilise local conditions to respond to changes in resource distribution at broad scales. Our findings suggest that individual movement decisions of dispersive birds are informed by the integration of multiple weather cues operating at different temporal and spatial scales.

Exploiting the richest patch has a fitness pay-off for the migratory swift parrot.

1. Unlike philopatric migrants, the ecology of nomadic migrants is less well understood. This life-history strategy reflects responses to spatiotemporal variation in resource availability and the need to find resource rich patches to initiate breeding. The fitness consequences of movements between regions of patchily distributed resources can provide insight into ecology of all migrants and their responses to global change. 2. We link broad-scale data on spatiotemporal fluctuation in food availability to data on settlement patterns and fitness outcomes for a nomadic migrant, the endangered swift parrot Lathamus discolor. We test several predictions to determine whether facultative movements are adaptive for individual swift parrots in an environment where resources are patchily distributed over time and space. 3. Variation in the availability of swift parrot food resources across our study period was dramatic. As a consequence, swift parrots moved to breed wherever food was most abundant and did not resettle nesting regions in successive years when food availability declined. By moving, swift parrots exploited a variable food resource and reproduced successfully. 4. Exploiting the richest patches allowed swift parrots to maintain stable fitness outcomes between discrete breeding events at different locations. Unlike sedentary species that often produce few or lower quality offspring when food is scarce, nomadic migration buffered swift parrots against extreme environmental variation. 5. We provide the first detailed evidence that facultative movements and nomadic migration are adaptive for individuals in unpredictable environments. Our data support the widely held assumption that nomadic migration allows animals to escape resource limitation.

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.

A simple parametric method for reducing sample sizes in gut passage time trials.

Seed dispersal is now regularly analyzed using spatially explicit models, relying in part on frugivore gut passage times to produce model outputs. In determining species-specific gut passage times, there is a trade-off in sample size between minimizing collection effort and maintaining statistical reliability. Here we demonstrate that a two-parameter lognormal parametric distribution reliably fits empirical gut passage time distributions and is easily parameterized using relatively small data sets of approximately 30 defecations. We suggest this approach as a statistically reliable substitute for larger empirical gut passage data sets in seed dispersal modeling, and also as a way of using published gut passage data sets to parameterize new models.

Animal movement in dynamic landscapes: interaction between behavioural strategies and resource distributions.

Most ecological and evolutionary processes are thought to critically depend on dispersal and individual movement but there is little empirical information on the movement strategies used by animals to find resources. In particular, it is unclear whether behavioural variation exists at all scales, or whether behavioural decisions are primarily made at small spatial scales and thus broad-scale patterns of movement simply reflect underlying resource distributions. We evaluated animal movement responses to variable resource distributions using the grey teal (Anas gracilis) in agricultural and desert landscapes in Australia as a model system. Birds in the two landscapes differed in the fractal dimension of their movement paths, with teal in the desert landscape moving less tortuously overall than their counterparts in the agricultural landscape. However, the most striking result was the high levels of individual variability in movement strategies, with different animals exhibiting different responses to the same resources. Teal in the agricultural basin moved with both high and low tortuosity, while teal in the desert basin primarily moved using low levels of tortuosity. These results call into question the idea that broad-scale movement patterns simply reflect underlying resource distributions, and suggest that movement responses in some animals may be behaviourally complex regardless of the spatial scale over which movement occurs.