Lathamus Research Articles

A reference genome, mitochondrial genome and associated transcriptomes for the critically endangered swift parrot (Lathamus discolor)

Abstract* The swift parrot (Lathamus discolor) is a Critically Endangered migratory parrot that breeds in Tasmania and winters on the Australian mainland. Here we provide a reference genome assembly for the swift parrot. We sequence PacBio HiFi reads to create a high-quality reference assembly and identify a complete mitochondrial sequence. We also generate a reference transcriptome from five organs to inform genome annotation. The genome was 1.24 Gb in length and consisted of 847 contigs with a contig N50 of 18.97 Gb and L50 of 20 contigs. This study provides an annotated reference assembly and transcriptomic resources for the swift parrot to assist in future conservation genomic research.

A reference genome, mitochondrial genome and associated transcriptomes for the critically endangered swift parrot (Lathamus discolor)

Abstract* The swift parrot (Lathamus discolor) is a Critically Endangered migratory parrot that breeds in Tasmania and winters on the Australian mainland. Here we provide a reference genome assembly for the swift parrot. We sequence PacBio HiFi reads to create a high-quality reference assembly and identify a complete mitochondrial sequence. We also generate a reference transcriptome from five organs to inform genome annotation. The genome was 1.24 Gb in length and consisted of 847 contigs with a contig N50 of 18.97 Gb and L50 of 20 contigs. This study provides an annotated reference assembly and transcriptomic resources for the swift parrot to assist in future conservation genomic research.

Influence of molecular marker type on estimating effective population size and other genetic parameters in a critically endangered parrot.

Genetics is a fast-moving field, and for conservation practitioners or ecologists, it can be bewildering. The choice of marker used in studies is fundamental; in the literature, preference has recently shifted from microsatellites to single nucleotide polymorphism (SNP) loci. Understanding how marker type affects estimates of population genetic parameters is important in the context of conservation, especially because the accuracy of estimates has a bearing on the actions taken to protect threatened species. We compare parameter estimates between seven microsatellites, 3761 SNP loci, and a random subset of 100 SNPs for the exact same 324 individual swift parrots, Lathamus discolor, and also use 457 additional samples from subsequent years to compare SNP estimates. Both marker types estimated a lower H O than H E. We show that microsatellites and SNPs mainly indicate a lack of spatial genetic structure, except when a priori collection locations were used on the SNP data in a discriminant analysis of principal components (DAPC). The 100-SNP subset gave comparable results to when the full dataset was used. Estimates of effective population size (N e) were comparable between markers when the same individuals were considered, but SNPs had narrower confidence intervals. This is reassuring because conservation assessments that rely on population genetic estimates based on a few microsatellites are unlikely to be nullified by the general shift toward SNPs in the literature. However, estimates between markers and datasets varied considerably when only adult samples were considered; hence, including samples of all age groups is recommended to be used when available. The estimated N e was higher for the full SNP dataset (2010-2019) than the smaller comparison data (2010-2015), which might be a better reflection of the species status. The lower precision of microsatellites may not necessarily be a barrier for most conservation applications; however, SNPs will improve confidence limits, which may be useful for practitioners.

An ecological risk assessment for the impacts of offshore wind farms on birds in Australia

AbstractAn ecological risk assessment, based on life‐history and behavioural attributes of 273 bird taxa, was used to identify which of those taxa are at high risk from negative interactions with offshore wind farms in Australia. The marine area of Australia was divided by state/territory boundaries perpendicular to the coast into eight regions, with Western Australia further divided into north and south, and a Bass Strait region bounded by the Victoria coast and the north coast of Tasmania. These regions were subdivided into coastal, inshore and offshore sub‐regions and a risk summary for all bird taxa occurring in each of these sub‐regions produced. In coastal and inshore sub‐regions of Bass Strait, South Australia and Tasmania, the species with the highest risk scores were Orange‐bellied Parrot Neophema chrysogaster, Furneaux White‐fronted Tern Sterna striata incerta, Swift Parrot Lathamus discolor, Shy Albatross Thalassarche cauta, Far Eastern Curlew Numenius madagascariensis and Anadyr Bar‐tailed Godwit Limosa lapponica anadyrensis. In offshore sub‐regions in southern Australia, the highest risk species were all albatrosses, comprising Northern Royal Diomedea sanfordi, Eastern Antipodean D. antipodensis antipodensis, Gibson's D. antipodensis gibsoni, Wandering D. exulans, Amsterdam D. amsterdamensis and Grey‐headed Albatross T. chrysostoma. Compared to onshore installations, there are logistical challenges to quantifying the potential and realized impacts of offshore wind farms that require different approaches to data collection and analyses. The extensive development of offshore wind farms in the Northern Hemisphere provides examples of best and emerging approaches to quantify and mitigate negative impacts of offshore wind farms that can be applied in an Australian context. Despite differences in the species involved, the same approaches to identifying high‐risk species and to the monitoring and mitigation of negative impacts should be applied in a coordinated, regional‐scale approach to the development of offshore wind farms in Australia.

Long‐term ecological data confirm and refine conservation assessment of critically endangered swift parrots

AbstractConservation assessments of threatened species are often limited by scarce data and parameter uncertainty. Predictive models, designed to incorporate this uncertainty, may be the only tool available to inform conservation assessments for data‐deficient species, but they are used surprisingly rarely for this purpose. The swift parrotLathamus discoloris the only critically endangered bird to be listed in Australia based on population viability analysis (PVA). We aimed to evaluate the accuracy of the 2015 conservation assessment, which used sparse information, by incorporating new detailed and long‐term data. First, we updated a range of life history parameter estimates, and then we repeated the same PVA as per the original conservation assessment. This process confirmed our earlier finding that swift parrot nests were more likely to survive in places with high mature forest cover. We identify that high forest landscape integrity and abundant hollow‐bearing trees best predict nest daily survival rates. Based on the updated PVA, we predict a 92.3% population decline over three generations (11 years). This supported the predictions of the original conservation assessment, and the main benefit of the additional data was improved confidence in projections (the magnitude and direction of the population decline were similar between the original and updated PVAs). Our results demonstrate that meaningful trends can be inferred for species with imperfect information about their life history. Using predictive models like PVAs can help managers identify which life history parameters impact most on demographic trends. This information can guide targeted data collection so that ‘draft’ models can be later updated to improve certainty around population predictions.

Can an introduced predator select for adaptive sex allocation?

Most species produce equal numbers of sons and daughters, and sex differences in survival after parental care do not usually affect this pattern. Temporary overproduction of the scarcer sex can be adaptive when generations overlap, the sexes differ in life-history expectations, and parents can anticipate future mating opportunities. However, an alternative strategy of maximizing the competitiveness of the more abundant sex in these circumstances remains unexplored. We develop theory showing how mothers can maximize reproductive value when future mate competition will be high by producing more sons in the advantageous early hatching positions within their broods. Our model for optimal birth order was supported by long-term data of offspring sex in a parrot facing catastrophic female mortality caused by introduced predators. Swift parrots (Lathamus discolor) suffer high female mortality due to introduced sugar gliders (Petaurus breviceps) creating fluctuating male-biased adult sex ratios. Offspring hatched early within broods fledged in better condition, and in support of our model were more likely to be male in years with higher adult female mortality. We found a highly significant rank-order correlation between observed and predicted birth sex ratios. Our study shows the potential for mothers to maximize reproductive value via strategic biases in offspring sex depending on the advantages conferred by birth order and the predictability of future mate competition. Our long-term data support the predictions and appear to suggest that sex allocation strategies may evolve surprisingly quickly when anthropogenic pressures on populations are severe.

Parental care does not compensate for the effects of bad years on reproductive success of a vagile bird

AbstractLife history theory predicts that long‐lived animals trade off the costs of reproduction against individual survival. If the costs of reproduction are too high, animals should prioritize their own survival. During bad times, mobile animals may be able to compensate for local food shortages by travelling further to provision their offspring. But, whether inherent mobility alleviates individual fitness costs of this parental strategy is not known. We studied parental investment and breeding success of long‐lived, nomadic, migratory swift parrots Lathamus discolor over two successive years at the same site where food abundance went from locally low to high. We hypothesize that in a bad year, swift parrots should adjust their parental strategy by foregoing breeding altogether, producing smaller clutches/broods or reducing provisioning investment. Fewer swift parrots bred locally when food was scarce. In the bad year, clutch and brood sizes were smaller and nestlings were >20 g lighter (approximately 28% of mean body mass) than in the good year. Compared with the good year, fathers spent longer foraging, less time at the nest and travelled further during provisioning trips in the bad year. Although limited to only 2 years, our results suggest that mobile species may attempt to mitigate the effects of a bad year on their reproductive success by rearing fewer offspring and investing more in provisioning behaviour, but this strategy may not necessarily compensate for environmental conditions.

Making a difference for the Swift Parrot and other declining woodland birds

Making a difference for the Swift Parrot and other declining woodland birds

Do nest boxes breed the target species or its competitors? A case study of a critically endangered bird

Nest boxes are widely used for habitat restoration. Unfortunately, competitors of the target species may exploit nest boxes, creating perverse outcomes. Avoiding habitats preferred by nontarget species, while favoring those of the target species, requires an adaptive management approach if limited information about species preferences is available when deploying boxes. Using nest boxes intended for Swift Parrots Lathamus discolor, we identify factors associated with nontarget species occupancy (Common Starling Sturnus vulgaris and Tree Martin Petrochelidon nigricans) in newly deployed boxes in 2016, and then again after 3 years had elapsed in 2019. Box occupancy by different species depended on the interaction between distance of individual boxes to the forest edge and year. Although the target species exploited similar numbers of nest boxes in both years, competitors were the main beneficiaries of established boxes. A subordinate native nest competitor increased box occupancy likelihood at greater distances from forest edges in both years, but the relationship was stronger in 2019. Introduced Common Starlings S. vulgaris were most likely to occupy boxes close to forest edges, but the magnitude of this relationship was much greater for established than newly deployed boxes. We suggest that permanent box deployments for Swift Parrots may produce perverse outcomes by increasing nesting habitat for Common Starlings. We suggest that for species that only use cavities for part of their life cycle, managers should limit access to boxes outside of critical times to reduce the likelihood that pest populations can exploit restoration efforts and create new problems.

Evaluation of lethal control of introduced sugar gliders as a tool to relieve bird nest predation

Lethal control of invasive mammalian predators can be controversial and is rarely a ‘silver bullet’ for conservation problems. Evaluating the efficacy of lethal control is important for demonstrating the benefits to threatened species are real and detecting unexpected perverse outcomes. We implemented a pilot study to evaluate if lethal control of introduced sugar gliders Petaurus breviceps can reduce the rate of nest predation on Tasmanian hollow nesting birds including swift parrots (Lathamus discolor). Using a before-after-control-impact design, we implemented a lethal control treatment whereby we attempted to remove sugar gliders from three treatment sites. In each time period across sites we monitored quail eggs in nest boxes to record predation, and used cameras to detect sugar gliders. We caught nine sugar gliders over three treatment sites. The model best supported by the data indicated an effect of site×time period on both egg survival and the rate of glider detection on cameras. There was no support for an effect of treatment on our data. We also recorded predation of a real swift parrot nest by sugar gliders at a treatment site where we recorded no predation of quail eggs. Our pilot study shows that at small scales, intensive lethal control of gliders yields low capture rates and no discernible effect on the metrics we measured. We conclude that alternative approaches to controlling the impact of sugar gliders, such as habitat protection, are critical in this study system before lethal control is widely implemented as a management tool.

Comparison of three techniques for genetic estimation of effective population size in a critically endangered parrot

AbstractUnderstanding the current population size of small, spatially aggregating populations of species is essential for their conservation. Reliable estimates of the effective population size (Ne) can be used to provide an early warning for conservation managers of the risks to genetic viability of small populations. Critically endangered, migratory swift parrots Lathamus discolor exist in a single panmictic population in Australia. In their Tasmanian breeding range, they are at severe risk of predation by introduced sugar gliders, exacerbated by deforestation. We used three genetic approaches to estimate Ne using DNA samples genotyped by microsatellite markers and existing life‐history data of swift parrots. Based on all samples, we revealed small contemporary Ne estimates across methods (range: 44–140), supporting the need to urgently address threatening processes. Using the 0.5 Ne/N ratio calculated from demographic data suggests that the minimum potential contemporary population size is below 300 individual swift parrots. This is considerably lower than the published estimates derived from expert elicitation, and accords with modeled estimates of extinction risk in this species. Our study has important implications for other threatened species with unknown population sizes and demonstrates that by utilizing available genetic data, reasonable estimates of Ne can be derived.

Swift declines predicted following mating system changes driven by an introduced predator.

In Focus: Heinsohn, R., Olah, G., Webb, M., Peakall, R., & Stojanovic, D. (2019). Sex ratio bias and shared paternity reduce individual fitness and population viability in a critically endangered parrot. Journal of Animal Ecology, 88, 502-510. While the effects of variation in the sex ratio of offspring have been thoroughly explored over the last century, the sex ratio of adults has received far less attention. A paper by Heinsohn and colleagues in this issue shows that changes in the adult sex ratio can have striking effects on mating systems, reproductive success and population viability. These impacts are all the more dramatic because they occur in a critically endangered species, the swift parrot, Lathamus discolor, of Tasmania. This species suffers heavy predation from the introduced sugar glider, Petaurus breviceps, which kills nesting females and their clutches, resulting in strongly male-biased adult sex ratios. The authors combined demographic and genetic data to show that, at sites with heavier predation, the remaining females were more likely to mate with multiple males. This shift in the mating system also led to lower overall nesting success, with fewer chicks fledged per nest at sites with higher levels of mixed paternity. Population viability models based on these data predicted steep population declines, with models using the highest observed rates of mixed paternity showing the sharpest declines. These results demonstrate that changes in the adult sex ratio can have far-reaching impacts, including on the fitness of populations themselves.

Documenting demise? Sixteen years observing the Swift Parrot Lathamus discolor in suburban Hobart, Tasmania

The Swift Parrot Lathamus discolor is listed as Critically Endangered because modelling suggests that its population is declining by > 80% within three generations (12-18 years) as a result of just one of many factors impacting the species: predation by introduced Sugar Gliders Petaurus breviceps. Unfortunately, verification of this prediction through monitoring of the entire population across its breeding range is difficult because of the amount of observer effort required to count all individuals within the often dense canopies of Eucalyptus trees, where it forages predominantly from flowers. This study entails 16 years of opportunistic observations at a single location within this species’ breeding range. Regression models indicated that over 16 breeding seasons the mean size of the largest flock per month declined by ∼90%, and grand mean size of all flocks per month by ∼70%. This was not the result of decreasing local flowering intensity in the Swift Parrot’s favoured food plants, as adjusting the two measures of abundance for local inter-annual variation in flowering had little effect on the rates of decline. This concordance between observations at the local scale and modelling of the entire population supports the findings of the modelling, suggesting that urgent action is required to prevent extinction of this species.

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.

Robotic ecology: Tracking small dynamic animals with an autonomous aerial vehicle.

Understanding animal movements that underpin ecosystem processes is fundamental to ecology. Recent advances in animal tags have increased the ability to remotely locate larger species; however, this technology is not suitable for up to 70% of the world's bird and mammal species. The most widespread technique for tracking small animals is to manually locate low-power radio transmitters from the ground with handheld equipment. Despite this labor-intensive technique being used for decades, efforts to reduce or automate this process have had limited success. Here, we present an approach for tracking small radio-tagged animals by using an autonomous and lightweight aerial robot. We present experimental results where we used the robot to locate critically endangered swift parrots (Lathamus discolor) within their winter range. The system combines a miniaturized sensor with newly developed estimation algorithms to yield unambiguous bearing- and range-based measurements with associated measures of uncertainty. We incorporated these measurements into Bayesian data fusion and information-based planning algorithms to control the position of the robot as it collected data. We report estimated positions that lie within about 50 meters of the true positions of the birds on average, which are sufficiently accurate for recapture or observation. Further, in comparison with experienced human trackers from locations where the signal was detectable, the robot produced a correct estimate as fast or faster than the human. These results provide validation of robotic systems for wildlife radio telemetry and suggest a way for widespread use as human-assistive or autonomous devices.

Pre‐emptive action as a measure for conserving nomadic species

ABSTRACTNomadic species are globally threatened by anthropogenic habitat change, but management options to address their decline are limited. Their unpredictable settlement patterns pose major challenges for conservation because identifying where to implement action is difficult. We address this challenge by pre‐empting settlement patterns in a nomadic species using data from a long‐term study of the critically endangered, cavity‐nesting swift parrot (Lathamus discolor) and by taking action at the sites identified. We detected flower bud growth (the primary settlement cue) and deployed artificial nests at 3 predicted breeding sites before the birds arrived. At the broad breeding‐range scale, swift parrots settled wherever bud abundance was highest, including the study area. Within the study area, artificial nest occupancy was greatest at the site with abundant historical natural nesting sites. At the local scale, we found significant effects of study site and distance to forest edges on nest box occupancy by swift parrots. Despite significant differences in thermal properties between artificial and natural nests, we found no differences in clutch size, brood size, or body condition of swift parrots in each. Monitoring settlement patterns and future food availability of nomadic wildlife can empower conservation managers to make predictions about breeding and target ecologically relevant times and locations when deploying conservation resources. Our study is an example of how conservation challenges posed by nomadic species can be overcome, and demonstrates that with effective monitoring, practical action can be targeted to address acute conservation needs and augment habitat availability. © 2018 The Wildlife Society.

Managing mature forest features: The production, accuracy and ecological relevance of a landscape‐scale map

SummaryMature trees and forests contain structural features such as tree hollows, large coarse woody debris and large spreading crowns that provide critical habitat for a wide range of species. These features can take hundreds of years to develop and require careful management to ensure their continued availability. Managing these features requires spatial mapping layers to facilitate landscape‐scale management. This paper outlines how a map of mature forest habitat was developed for Tasmania, Australia. The map was produced using spatial data on vegetation type, mature crown density and senescence, a global layer of forest loss data derived from satellite imagery, a database on timber harvest plans and a spatial layer on the extent of fire. The relationship between mapped mature habitat availability (high, medium, low or negligible) and tree hollow availability in wet forest areas was explored, complementing a similar published study in dry forests. The number of large trees likely to have hollows significantly increased with mapped mature habitat availability, although there was considerable variation and overlap between map categories. Data from a fauna locality database and two radio‐tracking studies showed that three of the vertebrate hollow‐using species examined (Swift Parrot, Common Brushtail Possum and the Tasmanian Long‐eared Bat) and nest records of a species reliant on large tree crowns (the Wedge‐tailed Eagle) were all more likely to occur in areas of higher mapped mature habitat availability. It is concluded that this map reflects the relative availability of tree hollows, is ecologically meaningful and will be useful when managing mature forest habitat at large spatial scales, but the variable accuracy of the map at fine scales needs to be taken into account.

Policy failure and conservation paralysis for the critically endangered swift parrot

The critically endangered swift parrot (Lathamus discolor) is among the best studied Australian threatened species. Despite extensive outreach to the public and policy makers, conservation management has not kept pace with advances in knowledge and scientific evidence. Here we summarise policy and management failings that allow swift parrot breeding habitat in Tasmanian forests to continue to be logged. This practice continues in spite of extensive evidence demonstrating that the cessation of logging of swift parrot breeding habitat in Tasmania is urgently required to secure the species.

Occupancy patterns of the introduced, predatory sugar glider in Tasmanian forests

AbstractIntroduced mammals pose serious threats to native island fauna, and understanding their distribution is fundamental to evaluating their conservation impact. Introduced sugar gliders (Petaurus breviceps) are the main predator of critically endangered swift parrots (Lathamus discolor) on mainland Tasmania. We surveyed sugar glider occurrence over ~800 km2 in an important swift parrot breeding area, the Southern Forests. During 4–5 visits per site, we used call broadcast of predatory owls to elicit sugar glider alarm calls and surveyed 100 sites during February/March 2016. Naïve occupancy by sugar gliders was high (0.79), as was detectability (0.52 ± 0.03 SE), resulting in a cumulative detection probability of effectively 1. Occupancy modelling indicated a positive effect of the proportion of mature forest cover on occupancy. The best model, based on AIC scores, included the proportion of mature forest cover within a 500 m radius with constant detectability. Our study revealed surprisingly high rates of occupancy of available forest habitat throughout the heavily logged study area, such that even when mature forest cover was <10%, sugar glider occupancy was >0.5; where forest cover approached 100% (i.e. in the best quality breeding habitat for swift parrots), occupancy by sugar gliders approached 1. Our results reveal that sugar gliders are widespread across the study area which may be indicative of occupancy rates elsewhere in the breeding range of the critically endangered swift parrot. As a result, the risk of predation by sugar gliders for small birds may be widespread across logged Tasmanian forests. Additional work to identify whether population densities of sugar gliders vary with forest cover (and whether this may impact predation likelihood) is critical to understanding the conservation consequences of deforestation in the breeding range of the swift parrot.

Genetic evidence confirms severe extinction risk for critically endangered swift parrots: implications for conservation management

AbstractMobile species pose major challenges for conservation because of their unpredictable, large scale movements in response to fluctuating resources. If locations with critical resources overlap with threats, large proportions of a mobile population may be exposed to threats. Critically endangered and nomadic swift parrots Lathamus discolor nest wherever food is most abundant in their breeding range, but concern exists that nest predation from an introduced predator may severely affect their population. Although swift parrots nest on predator‐free offshore islands, population viability analysis indicates that is land nesting alone may be insufficient to offset extinction risk from high mainland predation rates assuming that the species is a single panmictic population. We test the assumption that swift parrots act as a single conservation unit. We undertook a population genetic analysis using seven microsatellite loci and samples obtained over 6 years from across the breeding range of swift parrots. We found no evidence of departure from Hardy–Weinberg expectations across the species and both Analysis of Molecular Variance and Bayesian Structure analyses failed to detect any evidence for genetic differentiation across the samples both spatially and temporally. These results, supported by simulations, indicate panmixia and a lack of population genetic structure in swift parrots. Unlike a sedentary or site philopatric species, the majority of the swift parrot population may be at risk of exposure to predation when unpredictable resources draw individuals away from islands. These findings support a key assumption of population viability models that predict an extreme reduction in population size for swift parrots, and address a major gap in knowledge of the species’ ecology. Our study has implications both for the development of effective conservation management strategies and for the longer‐term evolution of avoidance of predator‐infested habitat in swift parrots.