Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity^1,2,3,4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference⁵, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families—including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species.

Radio-tracking tagged wildlife remains a critical research technique for understanding the movements, behaviours and survival of many species. However, traditional hand-held tracking techniques on the ground are labour intensive and time consuming. Therefore, researchers are increasingly seeking new technologies to address these challenges, including drone radio-tracking receivers. Following the implementation of drone radio-tracking techniques for five different threatened species projects within different habitat and landscape types, we identified the need to quantify the relative spatial extent of surveys using both drone and hand-held techniques for each project. This was undertaken using viewshed analyses. These analyses demonstrated that survey coverage with drone-based radio-tracking was substantially greater than that of hand-held radio-tracking for all species and landscapes examined. Within mountainous landscapes, drone radio-tracking covered up to four times the area of hand-held tracking, whereas in flat to undulating landscapes, drone surveys covered up to 11.3 times the area that could be surveyed using hand-held techniques from the same locations on the ground. The viewshed analyses were also found to be a valuable visualisation tool for identifying areas for targeted surveys to reduce the risk of ‘losing’ tagged animals, which has traditionally been one of the biggest radio-tracking challenges.

Context: Feral cat predation has had a significant impact on native Australian fauna in the past 200 years. In the early 2000s, population monitoring of the western ground parrot showed a dramatic decline from the pre-2000 range, with one of three meta-populations declining to very low levels and a second becoming locally extinct. We review 8 years of integrated introduced predator control, which trialled the incorporation of the feral cat bait Eradicat® into existing fox baiting programs. Aims: To test the efficacy of integrating feral cat control into an existing introduced predator control program in an adaptive management framework conducted in response to the decline of native species. The objective was to protect the remaining western ground parrot populations and other threatened fauna on the south coast of Western Australia. Methods: A landscape-scale feral cat and fox baiting program was delivered across south coast reserves that were occupied by western ground parrots in the early 2000s. Up to 500 000 ha of national parks and natures reserves were baited per annum. Monitoring was established to evaluate both the efficacy of landscape-scale baiting in management of feral cat populations, and the response of several native fauna species, including the western ground parrot, to an integrated introduced predator control program. Key results: On average, 28% of radio-collared feral cats died from Eradicat® baiting each year, over a 5-year period. The results varied from 0% to 62% between years. Changes in site occupancy by feral cats, as measured by detection on camera traps, was also variable, with significant declines detected after baiting in some years and sites. Trends in populations of native fauna, including the western ground parrot and chuditch, showed positive responses to integrated control of foxes and cats. Implications: Landscape-scale baiting of feral cats in ecosystems on the south coast of Western Australia had varying success when measured by direct knockdown of cats and site occupancy as determined by camera trapping; however, native species appeared to respond favourably to integrated predator control. For the protection of native species, we recommend ongoing baiting for both foxes and feral cats, complemented by post-bait trapping of feral cats. We advocate monitoring baiting efficacy in a well designed adaptive management framework to deliver long-term recovery of threatened species that have been impacted by cats.

Translocation programmes are increasingly being informed by genetic data to monitor and enhance conservation outcomes for both natural and established populations. These data provide a window into contemporary patterns of genetic diversity, structure and relatedness that can guide managers in how to best source animals for their translocation programmes. The inclusion of historical samples, where possible, strengthens monitoring by allowing assessment of changes in genetic diversity over time and by providing a benchmark for future improvements in diversity via management practices. Here, we used reduced representation sequencing (ddRADseq) data to report on the current genetic health of three remnant and seven translocated boodie (Bettongia lesueur) populations, now extinct on the Australian mainland. In addition, we used exon capture data from seven historical mainland specimens and a subset of contemporary samples to compare pre‐decline and current diversity. Both data sets showed the significant impact of population founder source (whether multiple or single) on the genetic diversity of translocated populations. Populations founded by animals from multiple sources showed significantly higher genetic diversity than the natural remnant and single‐source translocation populations, and we show that by mixing the most divergent populations, exon capture heterozygosity was restored to levels close to that observed in pre‐decline mainland samples. Relatedness estimates were surprisingly low across all contemporary populations and there was limited evidence of inbreeding. Our results show that a strategy of genetic mixing has led to successful conservation outcomes for the species in terms of increasing genetic diversity and provides strong rationale for mixing as a management strategy.

The feral cat has been implicated in the decline and extinction of many species worldwide and a range of strategies have been devised for its control. A five-year control program using the aerial broadcast of toxic Eradicat^® baits was undertaken at Fortescue Marsh in the Pilbara region of north-western Australia, for the protection of biodiversity in this important wetland area. This program has been shown to have had a significant detrimental effect on cats in this landscape, but the long-term impact is difficult to ascertain. We assessed population genetics across three cohorts of feral cats sampled as part of the control program. We also compared cat populations in natural habitats and around human infrastructure. A key challenge in any study of wild animal populations is small sample sizes and feral cats are particularly difficult to capture and sample. The results of this study superficially appear to suggest promising trends but were limited by sample size and many were not statistically significant. We find that the use of genetic techniques to monitor the impact of invasive species control programs is potentially useful, but ensuring adequate sample sizes over a long enough time-frame will be critical to the success of such studies.

In mammal reintroductions, effective post-release monitoring often relies on the use of radio-transmitters. Collars are a popular attachment technique but are not necessarily appropriate for all taxa. However, other attachment methods may result in substantially reduced monitoring durations. We assessed several transmitter types for the Shark Bay bandicoot (Perameles bougainville), aiming to optimise animal welfare and attachment duration. Collars (fitted under general anaesthetic) were considered the optimal method and 12 bandicoots were collared and monitored as part of a reintroduction program. We found that our collars permitted monitoring for up to seven weeks, while causing minimal harm to the animals.