Linda Neaves

Conservation (or safe) havens are protected areas where barriers (e.g., fences) separate biodiversity from threatening processes and are being increasingly used to support conservation. Differences between selection pressures inside and outside havens can be anticipated; however, understanding of the evolutionary consequences of these differences is limited, and many changes may be going unnoticed. This hampers assessments of the extent to which haven populations will continue to represent natural populations and wild-type traits and their potential as a source of robust individuals suitable for restoration projects outside havens. Although many haven populations are essentially wild, they have similarities to ex situ conservation populations and even domestic and cultivated species that can shed light on potential changes in selection pressures and their consequences. By assessing how features of havens can alter selection pressures, one can begin to make predictions about the likelihood of genetic change and develop monitoring strategies to further inform risks that phenotypic changes in protected populations will be maladaptive outside havens. Havens could also provide opportunities as outdoor laboratories to improve understanding of selection and evolutionary processes. Research, combined with effective monitoring and adaptive management in havens, is essential to ensure the continued effectiveness of havens as a conservation tool and their ability to supply robust individuals for future in situ conservation.

Invasive predators present a major threat to the conservation of native species. For birds, this often comes in the form of increased nest predation. Conservation managers have used numerous interventions to reduce this risk. However, their effectiveness varies depending on the specific technique used and the predators targeted. In this study, we tested the effectiveness of nest site modifications used to protect endangered Norfolk Island Green Parrot Cyanoramphus cookii nests from introduced mammalian predators. We compared the breeding outcomes and nest site characteristics of a sample of natural, unprotected nests with those of predator-proofed nests, and examined contemporary phenology and breeding parameters. We observed moderate, but variable, breeding seasonality, and significantly fewer nesting attempts in recent years. Nests had a median clutch size of five (range = 1–10) and a median brood size of three (range = 1–7). Nest success was 74.8% (157/210) for predator-proofed nesting attempts, and 40% (4/10) for unprotected nesting attempts. Predator-proofing had a small but significant effect on daily survival rate (estimated at 0.995 for predator-proofed nests and 0.972 for unprotected nests), but did not significantly affect the number of birds fledged. We observed nest predation by both Black Rats and feral Cats at unprotected nests. Unprotected nest sites had significantly shorter chambers than predator-proofed nest sites, suggesting that while predator-proofing significantly increases nest success for Green Parrots, preferred nest site characteristics have not been preserved through modifications. These findings highlight the importance of assessing the effectiveness of management actions regularly to inform evidence-based decision-making and adaptive management.

Interspecific competition is often assumed in ecosystems where co-occurring species have similar resource requirements. The potential for competition can be investigated by measuring the dietary overlap of putative competitor species. The degree of potential competition between generalist species has often received less research attention than competition between specialist species. We examined dietary overlap between two naturally co-occurring dietary generalist species: the common brushtail possum Trichosurus vulpecula and the bush rat Rattus fuscipes. To gauge the potential for competition, we conducted a diet analysis using DNA extracted from faecal samples to identify the range of food items consumed by both species within a shared ecosystem and quantify their dietary overlap. We used DNA metabarcoding on faecal samples to extract plant, fungal, and invertebrate DNA, identifying diet items and quantifying dietary range and overlap. The species' diets were similar, with a Pianka's overlap index score of 0.84 indicating high dietary similarity. Bush rats had a large dietary range, consisting of many plant and fungal species and some invertebrates, with almost no within-species variation. Possums had a more restricted dietary range, consisting primarily of plants. We suggest that the larger dietary range of the bush rat helps buffer it from the impacts of competition from possums by providing access to more food types. We conclude that, despite the high ostensible overlap in the foods consumed by dietary generalist species, fine-scale partitioning of food resources may be a key mechanism to alleviate competition and permit co-existence.

Trophic rewilding aims to restore lost ecological functions and diversity by focusing on top-down regulation through predator reintroductions. Genetic-based diet studies can provide valuable insights into trophic interactions, and the wider impacts of reintroductions and rewilding. We investigated the diet of a reintroduced mesopredator (eastern quoll, Dasyurus viverrinus) using metabarcoding of faeces. We analysed both vertebrate (12S rRNA) and invertebrate (CO1) prey species. Unexpectedly, we found mammals dominated eastern quoll diet (55 % relative read abundance and 73 % frequency of occurrence), likely due to persistent drought conditions and a lack of competing ground-dwelling predators. Invertebrate prey was present in at least one third of all samples across all seasons, underscoring their continued importance as a food source. While trophic rewilding focusses on returning ecological function, complexities and unexpected outcomes can arise in novel environments, challenging our assumptions regarding niche and trophic interactions. DNA metabarcoding proved efficient in diet analyses, supporting its use in long-term rewilding studies to understand trophic interactions over time.

In theory, emancipation from parental care is expected to favor promiscuous mating systems. However, in avian brood parasites, monogamy is surprisingly widespread, and it has been proposed that this may be favored by factors such as low population density and territoriality. Correspondingly, our previous research revealed that brood parasitic Horsfield's bronze-cuckoos (Chalcites basalis), which occur at low population densities and defend territories, are monogamous. Here, we contrast this study with the mating system of the congeneric little bronze-cuckoo (C. minutillus), an obligate brood parasite that exploits more concentrated hosts and is, therefore, likely to occur at higher population densities. We use single nucleotide polymorphisms to characterize the reproductive patterns of unsampled adults by inferring sibling relationships among 30 offspring. We show that (1) little bronze-cuckoos occurred at high densities, (2) polygamy was the most common mating pattern found in this study in both sexes, and (3) where multiple cuckoo eggs are laid in the same nest, they were unrelated. These results indicate that females do not defend exclusive territories, and males do not defend multiple females (polygyny). Instead, little bronze-cuckoos appear to have a non-territorial, promiscuous mating system. Our results are consistent with theoretical predictions that polygamy is more likely to evolve in species that are emancipated from parental care, where there are plenty of available mates, and where home ranges are not defended.
Monogamy is predicted to occur when both sexes care for young, defend a territory, and have limited access to new mates. Little bronze-cuckoos show none of these traits and mate promiscuously. Using molecular genetic analyses, we show that little bronze-cuckoos, which are brood parasites and are therefore free of parental care, occur at high densities, are non-territorial, and, consistent with theoretical predictions, they exhibit a promiscuous mating system.

Genetic diversity and population structure can have important implications for the management of threatened species. This is particularly true for small, isolated populations that have experienced significant declines or population bottlenecks. The Norfolk Island green parrot
Cyanoramphus cookii
is an endangered species at risk of inbreeding and loss of genetic diversity due to its restricted range and the population bottlenecks experienced in recent decades. To assess the severity of inbreeding and loss of genetic diversity in the population we analyzed single nucleotide polymorphisms (SNPs) for 157 unique genetic samples collected from nestlings and randomly captured adult birds between 2015 and 2022. We also assessed the population for genetic structure, calculated sex ratios, and looked for evidence of past population bottlenecks. Our analysis revealed that 17.83% of individuals sampled were highly inbred (
F
 > 0.125), although expected heterozygosity (
H
E
) did not significantly differ from observed heterozygosity (
H
O
) and the average inbreeding coefficient was low. The estimated effective population size (
N
e
) was 43.8 and we found no evidence of genetic structure. Demographic simulations provided support for scenarios including multiple population bottlenecks, when compared to those with a single population bottleneck or no past bottlenecks. We discuss the implications of our findings for the future management of the species including any potential attempt to establish an insurance population via translocation. Our study highlights the importance of considering population genetics when determining appropriate management actions for threatened species and the need to assess non-model species on an individual basis.

Genetic diversity is the foundation of biodiversity, and preserving it is therefore fundamental to conservation practice. However, global conservation efforts face significant challenges integrating genetic and genomic approaches into applied management and policy. As collaborative partnerships are increasingly recognized as key components of successful conservation efforts, we explore their role and relevance in the Australian context, by engaging with key entities from across the conservation sector, including academia, botanic gardens, herbaria, seed banks, governmental/non-governmental organisations, private industry, museums, Traditional Owners, Indigenous rangers, and zoos and aquaria. By combining perspectives from these entities with comprehensive literature review, we identified five guiding principles for conservation genetic and genomic research and explored the different elements of, and approaches to, collaboration. Our reflections suggest that there is a substantial overlap in research interests across the Australian conservation sector, and our findings show that collaboration is increasing. We discuss approaches to building collaborative partnerships, the reciprocal benefits of collaborating, and some remaining challenges associated with data generation, data collection, and cross-cultural considerations. We emphasise the need for long-term national resourcing for sample and data storage and consistency in collecting, generating and reporting genetic data. While informed by the Australian experience, our goal is to support researchers and practitioners to foster meaningful collaborations that achieve measurable management outcomes in conservation genetics and genomics, both in Australia and globally.

Genetic management is a critical component of threatened species conservation. Understanding spatial patterns of genetic diversity is essential for evaluating the resilience of fragmented populations to accelerating anthropogenic threats. Nowhere is this more relevant than on the Australian continent, which is experiencing an ongoing loss of biodiversity that exceeds any other developed nation. Using a proprietary genome complexity reduction-based method (DArTSeq), we generated a data set of 3239 high quality Single Nucleotide Polymorphisms (SNPs) to investigate spatial patterns and indices of genetic diversity in the koala (Phascolarctos cinereus), a highly specialised folivorous marsupial that is experiencing rapid and widespread population declines across much of its former range. Our findings demonstrate that current management divisions across the state of New South Wales (NSW) do not fully represent the distribution of genetic diversity among extant koala populations, and that care must be taken to ensure that translocation paradigms based on these frameworks do not inadvertently restrict gene flow between populations and regions that were historically interconnected. We also recommend that koala populations should be prioritised for conservation action based on the scale and severity of the threatening processes that they are currently faced with, rather than placing too much emphasis on their perceived value (e.g., as reservoirs of potentially adaptive alleles), as our data indicate that existing genetic variation in koalas is primarily partitioned among individual animals. As such, the extirpation of koalas from any part of their range represents a potentially critical reduction of genetic diversity for this iconic Australian species.

Conservation genetics and genomics examines the role of evolutionary and genetic processes in the persistence of organisms, and its research is intended to inform biodiversity management. To characterize the fields within the discipline and map their trends over time and across the globe, we used text analysis to synthesize the peer-reviewed literature (n = 36,159). We then searched for reference to this literature in government documents to determine the frequency with which research was referenced. We found dramatic shifts in research topics associated with the advent of next generation sequencing, including the emergence of environmental DNA analyses. However, we also found a lag in the uptake of these methods, leaving markers such as microsatellites still widely used. Most research was undertaken in higher-income countries, while research involving lower-income countries was typically conducted though collaboration with higher-income countries. Although the number of peer-reviewed publications in the field has increased rapidly, the number referenced in biodiversity management documents has not, instead plateauing at ~10 % of publications since 2010. This suggests a growing disconnect between genomic research and its application. Similar topics attracted both academic citations and mentions in “on-the-ground” documentation, although some of the topics with increasing prevalence in research, such as genomic technologies, appeared less frequently in practice. Promoting co-design and long-term collaboration, rather than post hoc translation of research to application, could provide a more direct pathway for integration between research and governments by ensuring that the research is embraced by, and relevant to, stakeholders and on the ground conservation actions.
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The eastern or Tasmanian bettong (Bettongia gaimardi) is one of four extant bettong species and is listed as ‘Near Threatened’ by the IUCN. We sequenced short read data on the 10x system to generate a reference genome 3.46Gb in size and contig N50 of 87.36Kb and scaffold N50 of 2.93Mb. Additionally, we used GeMoMa to provide and accompanying annotation for the reference genome. The generation of a reference genome for the eastern bettong provides a vital resource for the conservation of the species.