Genomic insights into the critically endangered King Island scrubtit.

Small, fragmented or isolated populations are at risk of population decline due to fitness costs associated with inbreeding and genetic drift. The King Island scrubtit Acanthornis magna greeniana is a critically endangered subspecies of the nominate Tasmanian scrubtit A. m. magna, with an estimated population of < 100 individuals persisting in three patches of swamp forest. The Tasmanian scrubtit is widespread in wet forests on mainland Tasmania. We sequenced the scrubtit genome using PacBio HiFi and undertook a population genomic study of the King Island and Tasmanian scrubtits using a double-digest restriction site-associated DNA (ddRAD) dataset of 5,239 SNP loci. The genome was 1.48 Gb long, comprising 1,518 contigs with an N50 of 7.715 Mb. King Island scrubtits formed one of four overall genetic clusters, but separated into three distinct subpopulations when analysed independently of the Tasmanian scrubtit. Pairwise FST values were greater among the King Island scrubtit subpopulations than among most Tasmanian scrubtit subpopulations. Genetic diversity was lower and inbreeding coefficients were higher in the King Island scrubtit than all except one of the Tasmanian scrubtit subpopulations. We observed crown baldness in 8/15 King Island scrubtits, but 0/55 Tasmanian scrubtits. Six loci were significantly associated with baldness, including one within the DOCK11 gene which is linked to early feather development. Contemporary gene flow between King Island scrubtit subpopulations is unlikely, with further field monitoring required to quantify the fitness consequences of its small population size, low genetic diversity and high inbreeding. Evidence-based conservation actions can then be implemented before the taxon goes extinct.

Using conservation genetics to prioritise management options for an endangered songbird.

Genetic data can be highly informative for answering questions relevant to practical conservation efforts, but remain one of the most neglected aspects of species recovery plans. Framing genetic questions with reference to practical and tractable conservation objectives can help bypass this limitation of the application of genetics in conservation. Using a single-nucleotide polymorphism dataset from reduced-representation sequencing (DArTSeq), we conducted a genetic assessment of remnant populations of the endangered forty-spotted pardalote (Pardalotus quadragintus), a songbird endemic to Tasmania, Australia. Our objectives were to inform strategies for the conservation of genetic diversity in the species and estimate effective population sizes and patterns of inter-population movement to identify management units relevant to population conservation and habitat restoration. We show population genetic structure and identify two small populations on mainland Tasmania as 'satellites' of larger Bruny Island populations connected by migration. Our data identify management units for conservation objectives relating to genetic diversity and habitat restoration. Although our results do not indicate the immediate need to genetically manage populations, the small effective population sizes we estimated for some populations indicate that they are vulnerable to genetic drift, highlighting the urgent need to implement habitat restoration to increase population size and to conduct genetic monitoring. We discuss how our genetic assessment can be used to inform management interventions for the forty-spotted pardalote and show that by assessing contemporary genetic aspects, valuable information for conservation planning and decision-making can be produced to guide actions that account for genetic diversity and increase chances of recovery in species of conservation concern.

Mistletoes could moderate drought impacts on birds, but are themselves susceptible to drought-induced dieback.

Mistletoes are hemiparasitic plants and keystone species in many ecosystems globally. Given predicted increases in drought frequency and intensity, mistletoes may be crucial for moderating drought impacts on community structure. Dependent on host vascular flows, mistletoes can succumb to stress when water availability falls, making them susceptible to mortality during drought. We counted mistletoe across greater than 350 000 km2 of southeastern Australia and conducted standardized bird surveys between 2016 and 2021, spanning a major drought event in 2018-2019. We aimed to identify predictors of mistletoe abundance and mortality and determine whether mistletoes might moderate drought impacts on woodland birds. Live mistletoe abundance varied with tree species composition, land use and presence of mistletoebirds. Mistletoe mortality was widespread, consistent with high 2018/2019 summer temperatures, low 2019/2020 summer rainfall and the interaction between summer temperatures and rainfall in 2019/2020. The positive association between surviving mistletoes and woodland birds was greatest in the peak drought breeding seasons of 2018/2019 and 2019/2020, particularly for small residents and insectivores. Paradoxically, mistletoes could moderate drought impacts on birds, but are themselves vulnerable to drought-induced mortality. An improved understanding of the drivers and dynamics of mistletoe mortality is needed to address potential cascading trophic impacts associated with mistletoe die-off.

Loss of vocal culture and fitness costs in a critically endangered songbird.

Cultures in humans and other species are maintained through interactions among conspecifics. Declines in population density could be exacerbated by culture loss, thereby linking culture to conservation. We combined historical recordings, citizen science and breeding data to assess the impact of severe population decline on song culture, song complexity and individual fitness in critically endangered regent honeyeaters (Anthochaera phrygia). Song production in the remaining wild males varied dramatically, with 27% singing songs that differed from the regional cultural norm. Twelve per cent of males, occurring in areas of particularly low population density, completely failed to sing any species-specific songs and instead sang other species' songs. Atypical song production was associated with reduced individual fitness, as males singing atypical songs were less likely to pair or nest than males that sang the regional cultural norm. Songs of captive-bred birds differed from those of all wild birds. The complexity of regent honeyeater songs has also declined over recent decades. We therefore provide rare evidence that a severe decline in population density is associated with the loss of vocal culture in a wild animal, with concomitant fitness costs for remaining individuals. The loss of culture may be a precursor to extinction in declining populations that learn selected behaviours from conspecifics, and therefore provides a useful conservation indicator.

An Empirical and Mechanistic Explanation of Abundance-Occupancy Relationships for a Critically Endangered Nomadic Migrant.

The positive abundance-occupancy relationship (AOR) is a pervasive pattern in macroecology. Similarly, the association between occupancy (or probability of occurrence) and abundance is also usually assumed to be positive and in most cases constant. Examples of AORs for nomadic species with variable distributions are extremely rare. Here we examined temporal and spatial trends in the AOR over 7 years for a critically endangered nomadic migrant that relies on dynamic pulses in food availability to breed. We predicted a negative temporal relationship, where local mean abundances increase when the number of occupied sites decreases, and a positive relationship between local abundances and the probability of occurrence. We also predicted that these patterns are largely attributable to spatiotemporal variation in food abundance. The temporal AOR was significantly negative, and annual food availability was significantly positively correlated with the number of occupied sites but negatively correlated with abundance. Thus, as food availability decreased, local densities of birds increased, and vice versa. The abundance-probability of occurrence relationship was positive and nonlinear but varied between years due to differing degrees of spatial aggregation caused by changing food availability. Importantly, high abundance (or occupancy) did not necessarily equate to high-quality habitat and may be indicative of resource bottlenecks or exposure to other processes affecting vital rates. Our results provide a rare empirical example that highlights the complexity of AORs for species that target aggregated food resources in dynamic environments.

Sex ratio bias and shared paternity reduce individual fitness and population viability in a critically endangered parrot.

Sex-biased mortality can lead to altered adult sex ratios (ASRs), which may in turn lead to harassment and lower fitness of the rarer sex and changes in the mating system. Female critically endangered swift parrots (Lathamus discolor) suffer high predation while nesting due to an introduced mammalian predator, the sugar glider (Petaurus breviceps). High predation on females is causing severe population decline alongside strongly biased adult sex ratios (≥73% male). Our 6-year study showed that 50.5% of critically endangered swift parrot nests had shared paternity although the birds remained socially monogamous. Shared paternity increased significantly with the local rate of predation on breeding females, suggesting that rates of shared paternity increased when the ASR became more biased. Nests that were not predated produced fewer fledglings as the local ASR became more male-biased possibly due to higher interference during nesting from unpaired males. Population viability analyses showed that part of the predicted decline in the swift parrot population is due to reduced reproductive success when paternity is shared. The models predicted that the population would decline by 89.4% over three generations if the birds maintained the lowest observed rate of shared paternity. This compares with predicted population reductions of 92.1-94.9% under higher rates of shared paternity. We conclude that biases in the ASR, in this case caused by sex-specific predation from an introduced predator, can lead to changes in the mating system and negative impacts on both individual fitness and long-term population viability.

The importance of incorporating functional habitats into conservation planning for highly mobile species in dynamic systems.

The distribution of mobile species in dynamic systems can vary greatly over time and space. Estimating their population size and geographic range can be problematic and affect the accuracy of conservation assessments. Scarce data on mobile species and the resources they need can also limit the type of analytical approaches available to derive such estimates. We quantified change in availability and use of key ecological resources required for breeding for a critically endangered nomadic habitat specialist, the Swift Parrot (Lathamus discolor). We compared estimates of occupied habitat derived from dynamic presence-background (i.e., presence-only data) climatic models with estimates derived from dynamic occupancy models that included a direct measure of food availability. We then compared estimates that incorporate fine-resolution spatial data on the availability of key ecological resources (i.e., functional habitats) with more common approaches that focus on broader climatic suitability or vegetation cover (due to the absence of fine-resolution data). The occupancy models produced significantly (P < 0.001) smaller (up to an order of magnitude) and more spatially discrete estimates of the total occupied area than climate-based models. The spatial location and extent of the total area occupied with the occupancy models was highly variable between years (131 and 1498 km2 ). Estimates accounting for the area of functional habitats were significantly smaller (2-58% [SD 16]) than estimates based only on the total area occupied. An increase or decrease in the area of one functional habitat (foraging or nesting) did not necessarily correspond to an increase or decrease in the other. Thus, an increase in the extent of occupied area may not equate to improved habitat quality or function. We argue these patterns are typical for mobile resource specialists but often go unnoticed because of limited data over relevant spatial and temporal scales and lack of spatial data on the availability of key resources. Understanding changes in the relative availability of functional habitats is crucial to informing conservation planning and accurately assessing extinction risk for mobile resource specialists.

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.

Orange-bellied parrots.

Dejan Stojanovic and Robert Heinsohn introduce the Critically Endangered orange-bellied parrot from Australia.

The phenotypic costs of captivity.

The breeding of threatened species in captivity for release is a central tool in conservation biology. Given gloomy predictions for biodiversity trends in the Anthropocene, captive breeding will play an increasingly important role in preventing future extinctions. Relative to the wild, captive environments drastically alter selection pressures on animals. Phenotypic change in captive animals in response to these altered selection pressures can incur fitness costs post-release, jeopardising their potential contribution to population recovery. We explore the ways in which captive environments can hinder the expression of wild phenotypes. We also stress that the phenotypes of captive-bred animals differ from their wild counterparts in multiple ways that remain poorly understood. We propose five new research questions relating to the impact of captive phenotypes on reintroduction biology. With better use of monitoring and experimental reintroductions, a more robust evidence base should help inform adaptive management and minimise the phenotypic costs of captivity, improving the success of animal reintroductions.

The lengths birds will go to avoid incest.

Cooperatively breeding species, in which some individuals help others to rear their offspring, face a high risk of inbreeding because of close relatedness within social groups. Many species circumvent this problem via sex-biased dispersal, in which one sex is more likely to disperse (and to disperse further), while the other stays and helps. In the absence of sex-biased dispersal, more complex dispersal patterns can arise, based on kin recognition. However, this can also present challenges when dispersal distances are short, leading to clusters of relatives on neighbouring territories. In this issue, Nelson-Flower et al. (2012) break important new ground by unravelling adaptive incest-avoidance mechanisms in a cooperatively breeding bird without sex-biased dispersal. They provide an elegant demonstration of finely tuned dispersal distances together with cognitively based methods for knowing whom to avoid as mates.

Visual mimicry of host nestlings by cuckoos.

Coevolution between antagonistic species has produced instances of exquisite mimicry. Among brood-parasitic cuckoos, host defences have driven the evolution of mimetic eggs, but the evolutionary arms race was believed to be constrained from progressing to the chick stage, with cuckoo nestlings generally looking unlike host young. However, recent studies on bronze-cuckoos have confounded theoretical expectations by demonstrating cuckoo nestling rejection by hosts. Coevolutionary theory predicts reciprocal selection for visual mimicry of host young by cuckoos, although this has not been demonstrated previously. Here we show that, in the eyes of hosts, nestlings of three bronze-cuckoo species are striking visual mimics of the young of their morphologically diverse hosts, providing the first evidence that coevolution can select for visual mimicry of hosts in cuckoo chicks. Bronze-cuckoos resemble their own hosts more closely than other host species, but the accuracy of mimicry varies according to the diversity of hosts they exploit.

The absence of sex-biased dispersal in the cooperatively breeding grey-crowned babbler.

1. Cooperatively breeding birds are thought to be especially vulnerable to habitat fragmentation, in part because dispersal is typically restricted for one sex, increasing the likelihood of inbreeding. Knowledge of dispersal is essential to conservation efforts, but is often hampered by our inability to measure its frequency and distance when dispersal is infrequent and difficult to observe. 2. Disrupted dispersal is a purported cause of decline in the Australian grey-crowned babbler (Pomatostomus temporalis). Both sexes of offspring delay dispersal for up to several years to help parents raise subsequent broods, yet little else is known about the dispersal of this cooperatively breeding woodland bird. 3. As both sexes appear to help, but only male helpers boost fledgling production, we hypothesized that males would be the more philopatric sex in this species, and that female grey-crowned babblers would disperse over greater distances. 4. To ensure reliable determination of sex and minimize bias towards detecting short-distance dispersal events, we combined molecular-based sexing and analyses of population genetic structure using polymorphic microsatellite loci with observational data obtained over multiple field seasons. 5. Observations of banded birds showed only infrequent fission of groups or short-distance dispersal (mean=854 m), but no apparent sex-bias in these patterns. 6. There was significant genetic differentiation between social groups, but not between the sexes. Spatial genetic autocorrelation analysis of breeders revealed a random distribution of genotypes across the study area for both sexes. Thus, contrary to expectations, we found no genetic evidence for restricted dispersal or for sex-biased dispersal over the 85-km scale of this study, indicating that effective dispersal occurs over greater distances and more frequently than recoveries of banded birds indicated. 7. We conclude that while constraints on independent breeding encourage high rates of philopatry, incest avoidance nonetheless drives high rates of dispersal by both sexes. In fragmented habitat, the dispersal dynamics of this cooperatively breeding species are unlikely to render them particularly vulnerable to genetic consequences such as inbreeding, but may lead to increased group dissolution.

Shifting latitudinal clines in avian body size correlate with global warming in Australian passerines.

Intraspecific latitudinal clines in the body size of terrestrial vertebrates, where members of the same species are larger at higher latitudes, are widely interpreted as evidence for natural selection and adaptation to local climate. These clines are predicted to shift in response to climate change. We used museum specimens to measure changes in the body size of eight passerine bird species from south-eastern Australia over approximately the last 100 years. Four species showed significant decreases in body size (1.8-3.6% of wing length) and a shift in latitudinal cline over that period, and a meta-analysis demonstrated a consistent trend across all eight species. Southern high-latitude populations now display the body sizes typical of more northern populations pre-1950, equivalent to a 7 degrees shift in latitude. Using ptilochronology, we found no evidence that these morphological changes were a plastic response to changes in nutrition, a likely non-genetic mechanism for the pattern observed. Our results demonstrate a generalized response by eight avian species to some major environmental change over the last 100 years or so, probably global warming.

Genomic impact of severe population decline in a nomadic songbird.

Uncovering the population genetic histories of non-model organisms is increasingly possible through advances in next generation sequencing and DNA sampling of museum specimens. This new information can inform conservation of threatened species, particularly those for which historical and contemporary population data are unavailable or challenging to obtain. The critically endangered, nomadic regent honeyeater Anthochaera phrygia was abundant and widespread throughout south-eastern Australia prior to a rapid population decline and range contraction since the 1970s. A current estimated population of 250-400 individuals is distributed sparsely across 600,000 km2 from northern Victoria to southern Queensland. Using hybridization RAD (hyRAD) techniques, we obtained a SNP dataset from 64 museum specimens (date 1879-1960), 102 'recent' (1989-2012) and 52 'current' (2015-2016) wild birds sampled throughout the historical and contemporary range. We aimed to estimate population genetic structure, genetic diversity and population size of the regent honeyeater prior to its rapid decline. We then assessed the impact of the decline on recent and current population size, structure and genetic diversity. Museum sampling showed population structure in regent honeyeaters was historically low, which remains the case despite a severe fragmentation of the breeding range. Population decline has led to minimal loss of genetic diversity since the 1980's. Capacity to quantify the overall magnitude of both genetic diversity loss and population decline was limited by the poorer quality of genomic data derived from museum specimens. A rapid population decline, coupled with the regent honeyeater's high mobility, means a detectable genomic impact of this decline has not yet manifested. Extinction may occur in this nomadic species before a detectable genomic impact of small population size is realised. We discuss the implications for genetic management of endangered mobile species and enhancing the value of museum specimens in population genomic studies.

Ecology and evolution of the enigmatic eclectus parrot (Eclectus roratus).

Eclectus parrots (Eclectus roratus) exhibit a form of reversed sexual dichromatism (plumage coloration) not found in other birds. The females are a striking vermilion and blue, whereas the males are shiny green. Here, I summarize the major findings of a 10-year research program conducted on a wild population of eclectus parrots on Cape York Peninsula, Australia, aimed primarily at understanding the ecologic and evolutionary forces behind their unique coloration. Unlike most other parrots, eclectus parrots breed polyandrously (where multiple males mate with 1 female) and polygynandrously (where both sexes have multiple sexual partners). Their mating system appears to be driven by a shortage of nest hollows. Females with good nest sites are rare, and this forces males to share females. The red plumage of females acts as a signal of nest hollow ownership, whereas the green of males allows them to be camouflaged while foraging to feed the females and chicks. Eclectus parrots can also control the sex of their offspring, although the reasons for this are not yet clear.

Tool-assisted rhythmic drumming in palm cockatoos shares key elements of human instrumental music.

All human societies have music with a rhythmic "beat," typically produced with percussive instruments such as drums. The set of capacities that allows humans to produce and perceive music appears to be deeply rooted in human biology, but an understanding of its evolutionary origins requires cross-taxa comparisons. We show that drumming by palm cockatoos (Probosciger aterrimus) shares the key rudiments of human instrumental music, including manufacture of a sound tool, performance in a consistent context, regular beat production, repeated components, and individual styles. Over 131 drumming sequences produced by 18 males, the beats occurred at nonrandom, regular intervals, yet individual males differed significantly in the shape parameters describing the distribution of their beat patterns, indicating individual drumming styles. Autocorrelation analyses of the longest drumming sequences further showed that they were highly regular and predictable like human music. These discoveries provide a rare comparative perspective on the evolution of rhythmicity and instrumental music in our own species, and show that a preference for a regular beat can have other origins before being co-opted into group-based music and dance.

Personality predicts the propensity for social learning in a wild primate.

Social learning can play a critical role in the reproduction and survival of social animals. Individual differences in the propensity for social learning are therefore likely to have important fitness consequences. We asked whether personality might underpin such individual variation in a wild population of chacma baboons (Papio ursinus). We used two field experiments in which individuals had the opportunity to learn how to solve a task from an experienced conspecific demonstrator: exploitation of a novel food and a hidden item of known food. We investigated whether the (1) time spent watching a demonstrator and (2) changes in task-solving behaviour after watching a demonstrator were related to personality. We found that both boldness and anxiety influenced individual performance in social learning. Specifically, bolder and more anxious animals were more likely to show a greater improvement in task solving after watching a demonstrator. In addition, there was also evidence that the acquisition of social information was not always correlated with its use. These findings present new insights into the costs and benefits of different personality types, and have important implications for the evolution of social learning.

Animal personality: what are behavioural ecologists measuring?

The discovery that an individual may be constrained, and even behave sub-optimally, because of its personality type has fundamental implications for understanding individual- to group-level processes. Despite recent interest in the study of animal personalities within behavioural ecology, the field is fraught with conceptual and methodological difficulties inherent in any young discipline. We review the current agreement of definitions and methods used in personality studies across taxa and systems, and find that current methods risk misclassifying traits. Fortunately, these problems have been faced before by other similar fields during their infancy, affording important opportunities to learn from past mistakes. We review the tools that were developed to overcome similar methodological problems in psychology. These tools emphasise the importance of attempting to measure animal personality traits using multiple tests and the care that needs to be taken when interpreting correlations between personality traits or their tests. Accordingly, we suggest an integrative theoretical framework that incorporates these tools to facilitate a robust and unified approach in the study of animal personality.

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.