Robert Lamont

Dingoes come from an ancient canid lineage that originated in East Asia around 8000-11,000 years BP. As Australia's largest terrestrial predator, dingoes play an important ecological role. A small, protected population exists on a world heritage listed offshore island, K'gari (formerly Fraser Island). Concern regarding the persistence of dingoes on K'gari has risen due to their low genetic diversity and elevated inbreeding levels. However, whole-genome sequence data is lacking from this population. Here, we include five new whole-genome sequences of K'gari dingoes. We analyze a total of 18 whole genome sequences of dingoes sampled from mainland Australia and K'gari to assess the genomic consequences of their demographic histories. Long (>1 Mb) runs of homozygosity (ROH)-indicators of inbreeding-are elevated in all sampled dingoes. However, K'gari dingoes showed significantly higher levels of very long ROH (>5 Mb), providing genomic evidence for small population size, isolation, inbreeding, and a strong founder effect. Our results suggest that, despite current levels of inbreeding, the K'gari population is purging strongly deleterious mutations, which, in the absence of further reductions in population size, may facilitate the persistence of small populations despite low genetic diversity and isolation. However, there may be little to no purging of mildly deleterious alleles, which may have important long-term consequences, and should be considered by conservation and management programs.Dingoes come from an ancient canid lineage that originated in East Asia around 8000-11,000 years BP. As Australia's largest terrestrial predator, dingoes play an important ecological role. A small, protected population exists on a world heritage listed offshore island, K'gari (formerly Fraser Island). Concern regarding the persistence of dingoes on K'gari has risen due to their low genetic diversity and elevated inbreeding levels. However, whole-genome sequence data is lacking from this population. Here, we include five new whole-genome sequences of K'gari dingoes. We analyze a total of 18 whole genome sequences of dingoes sampled from mainland Australia and K'gari to assess the genomic consequences of their demographic histories. Long (>1 Mb) runs of homozygosity (ROH)-indicators of inbreeding-are elevated in all sampled dingoes. However, K'gari dingoes showed significantly higher levels of very long ROH (>5 Mb), providing genomic evidence for small population size, isolation, inbreeding, and a strong founder effect. Our results suggest that, despite current levels of inbreeding, the K'gari population is purging strongly deleterious mutations, which, in the absence of further reductions in population size, may facilitate the persistence of small populations despite low genetic diversity and isolation. However, there may be little to no purging of mildly deleterious alleles, which may have important long-term consequences, and should be considered by conservation and management programs.

The increased severity and frequency of wildfires are a growing threat to biodiversity globally posing a complex challenge for the management of protected areas. K'gari, a World Heritage-listed sand barrier island located off the coast of Australia, was extensively burnt in wildfires in 2019 and 2020. Banksia aemula low open woodland (BALOW) is a fire-adapted ecosystem, and Banksia aemula is the dominant vegetation type on the island. This research explored interactions between vertebrate fauna and flora species richness and structure after fires in the BALOW habitat. We employed camera trapping and vegetation surveys to estimate species richness and habitat structure. We detected 28 fauna and 56 plant species, including two vulnerable species. Fauna species richness differed between sites; the site with the most intense, extensive, and recent fire had the lowest fauna species richness and mammal species richness. In contrast, the site with lower intensity and more frequent historical fires had the highest fauna diversity. The long unburnt site had higher overall tree diversity and reduced shrub diversity. This research further highlights the need for evidence-based fire management in protected areas and the risk that large-scale and/or high-intensity fires may pose to biodiversity even within fire-adapted ecosystems.

Dingoes come from an ancient canid lineage that originated in East Asia around 8000-11,000 years BP. As Australia's largest terrestrial predator, dingoes play an important ecological role. A small, protected population exists on a world heritage listed offshore island, K'gari (formerly Fraser Island). Concern regarding the persistence of dingoes on K'gari has risen due to their low genetic diversity and elevated inbreeding levels. However, whole-genome sequencing data is lacking from this population. Here, we include five new whole-genome sequences of K'gari dingoes. We analyze a total of 18 whole genome sequences of dingoes sampled from mainland Australia and K'gari to assess the genomic consequences of their demographic histories. Long (>1 Mb) runs of homozygosity (ROH) - indicators of inbreeding - are elevated in all sampled dingoes. However, K'gari dingoes showed significantly higher levels of very long ROH (>5 Mb), providing genomic evidence for small population size, isolation, inbreeding, and a strong founder effect. Our results suggest that, despite current levels of inbreeding, the K'gari population is purging strongly deleterious mutations, which, in the absence of further reductions in population size, may facilitate the persistence of small populations despite low genetic diversity and isolation. However, there may be little to no purging of mildly deleterious alleles, which may have important long-term consequences, and should be considered by conservation and management programs.

Fontainea is a plant genus with nine recognised species that occur across the tropical and subtropical rainforests of Australia, Papua New Guinea, New Caledonia, and Vanuatu. One of these species is cultivated commercially as the source of a cancer therapeutic, and several other species are under threat of extinction. Despite this, the phylogenetic relationships of the genus have not been explored. Our study assessed the phylogeny of seven Fontainea taxa from the Australian and Pacific Island complex using chloroplast DNA sequence data and reduced-representation genome sequencing. Maximum-likelihood and consensus network trees were used to infer the topology of phylogenetic relationships between species, which highlighted three distinct lineages and a number of sister species. Our results indicated that the geographically disjunct species Fontainea venosa and F. pancheri formed a sister group at the earliest position of divergence for the genus. The data also revealed that the vulnerable Fontainea australis and the critically endangered F. oraria form a sister subclade with evidence of some shared plastid genotypes. Generally, our phylogenetic reconstruction supports the modern taxonomical nomenclature. However, we suggest further accessions across several species may support improved genetic distinctions between the sister groups of Fontainea within the genus.

The dingo population on world heritage-listed K’gari-Fraser Island (K’gari) is amongst the most wellknown in Australia. However, an absence of population genetic data limits capacity for informed conservation management. We used 9 microsatellite loci to compare the levels of genetic diversity and genetic structure of 175 K’gari dingo tissue samples with 264 samples from adjacent mainland regions. Our results demonstrated that the K’gari population has signifcantly lower genetic diversity than mainland dingoes (AR, HE, PAR; p < 0.05) with a fourfold reduction in efective population size (Ne= 25.7 vs 103.8). There is also strong evidence of genetic diferentiation between the island and mainland populations. These results are in accordance with genetic theory for small, isolated, island populations, and most likely the result of low initial diversity and founder efects such as bottlenecks leading to decreased diversity and drift. As the frst study to incorporate a large sample set of K’gari dingoes, this provides invaluable baseline data for future research, which should incorporate genetic and demographic monitoring to ensure long-term persistence. Given that human-associated activities will continue to result in dingo mortality, it is critical that genetic factors are considered in conservation management decisions to avoid deleterious consequences for this iconic dingo population.

Brachychiton sp. Ormeau (L.H. Bird AQ435851), commonly known as the Ormeau bottle tree, is listed as Critically Endangered under the Environment Protection and Biodiversity Conservation Act 1999. Undescribed and extremely rare, it is known only from several sites within a very small geographic range near Ormeau in southeast Queensland. Using microsatellite markers developed for this study, we found Brachychiton sp. Ormeau to be genetically distinct from several closely related species, confirming unique specific status. We also assessed levels of genetic variation found within B. sp. Ormeau subpopulations to provide recommendations for recovery projects. The species exhibited low levels of variation (H e = 0.065); however, no evidence of inbreeding (F = –0.290). We infer that the species' current restricted range and low genetic diversity is due to a combination of the effects of well documented climate shifts across the Plio-Pleistocene, exacerbated by extensive rates of relatively recent and ongoing human-mediated habitat loss. Our results suggest that, to enhance the long-term viability of B. sp. Ormeau, the most effective recovery strategies include the protection and restoration of the existing remnant habitat, as well as enhancement of local subpopulations and existing isolated plants, with additional plants to increase the genetic diversity.

Habitat modification and destruction are known to be responsible for declines in avian taxa. Specialist species such as the vulnerable Glossy Black-cockatoo (Calyptorhynchus lathami ssp. lathami) are particularly at risk due to the limited number of Casuarina and Allocasuarina species on which they feed, which is compounded by their propensity for selecting only specific individual feed trees within patches. This study aims to address the lack of understanding surrounding Glossy Black-cockatoo feeding ecology in southeast Queensland, Australia, by examining determinants of tree selection for Allocasuarina littoralis and A. torulosa. We conducted surveys to identify feed and non-feed trees of both Allocasuarina species, and differences between the physical and chemical characteristics of trees, cones, and seeds were investigated. We found that larger trees were preferentially foraged, with nutritional profitability as the primary factor governing tree selection. Feed tree cones had higher seed number and seed mass, with seeds containing higher levels of fatty acids and nutrients than non-feed tree cones. We conclude that further research should aim to delineate the factors contributing to these differences, alongside determining appropriate management strategies to support viable feeding habitat, which is most likely comprised of mixed age patches, capable of maintaining mature trees offering sufficient nutrient reward.

Gene flow via pollen movement affects genetic variation in plant populations and is an important consideration in plant domestication. Fontainea picrosperma is a subcanopy rainforest tree that is of commercial interest because it is the source of tigilanol tiglate, a natural product used for the treatment of solid tumors. We identify patterns of pollen-mediated gene flow within natural populations of F. picrosperma and estimate genetic parameters and genetic structure between adult and juvenile groups using microsatellite markers. Our results show pollination events occur over much shorter distances than reported for tropical canopy species. At least 63% of seeds are sired by male trees located within 30 m of the mother. On average, 27% of the local male population contributed to successful reproduction of F. picrosperma with most fathers siring a single seed, however, the contributions to reproduction were uneven. Larger male trees with more flowers had greater reproductive success than those with less flowers (P < 0.05). There were comparatively low levels of genetic variation across the species (HE = 0.405 for adult trees and 0.379 for juveniles) and we found no loss of genetic diversity between adult and juvenile trees. Short distance pollen flow and low genetic diversity is theoretically a prelude to genetic impoverishment, however F. picrosperma has persisted through multiple significant climatic oscillations. Nevertheless, the remaining low genetic diversity is of concern for domestication programs which require maximal genetic diversity to facilitate efficient selective breeding and genetic improvement of this commercially significant species.

The striped legless lizard, Delma impar, is a specialist grassland species restricted to south-eastern Australia. Anthropogenic influences have seen the destruction of much of its habitat and the species is threatened with extinction. Known populations of D. impar in Canberra (Australia) have recently been cleared for urban development. In 2015, Bush Heritage Australia translocated 41 individuals from these populations to Scottsdale Reserve. In this study, we completed the first population genetics analysis of D. impar in Canberra, providing a baseline for assessment of the genetic success of the translocation to Scottsdale Reserve. We analysed 154 D. impar individuals from six populations in Canberra, assessing levels of genetic diversity and differentiation within and between populations, using eight highly polymorphic microsatellite loci. High levels of genetic diversity and negligible levels of genetic differentiation were observed. Measures of allelic diversity were lower in the translocated population compared to the Canberra populations and Bayesian analysis revealed a disproportionate representation of two genetic clusters identified by STRUCTURE between the Scottsdale Reserve and Canberra populations, indicating that the initial genetic capture failed to 'capture' recommended levels of genetic diversity to support an ongoing population. If the species successfully establishes itself at Scottsdale Reserve, the data suggests that the population should be augmented with individuals from other sites in Canberra, with the aim of increasing genetic diversity to recommended levels (i.e. > 95% genetic variation). This will maximise resilience, adaptability and long-term survival potential of the Scottsdale Reserve population of striped legless lizards from a genetic context.

Assisted migration can aid in the conservation of narrowly endemic species affected by habitat loss, fragmentation and climate change. Here, we employ a multidisciplinary approach by examining the population genetic structure of a threatened, dioecious rainforest tree of the subtropical notophyll vine forests of eastern Australia, Fontainea rostrata, and its potential requirements for population enhancement and translocation to withstand the effects of anthropogenic fragmentation and climate change. We used microsatellite markers to gain an understanding of the way genetic diversity is partitioned within and among the nine extant populations of F. rostrata identified in this study. We combined the results with species distribution modelling to identify populations vulnerable to possible future range shifts based on climate change projections. We found regional differences between the species' main distribution in the south and a disjunct northern population cluster (FRT = 0.074, FSR = 0.088, FST = 0.155), in mean allelic richness (AR = 2.77 vs 2.33, p & 0.05), expected heterozygosity (HE = 0.376 vs 0.328), and inbreeding (F = 0.116 vs 0.219). Species distribution models predicted that while southern populations of F. rostrata are likely to persist for the next 50 years under the RCP6.0 climate change scenario, with potential for a small-scale expansion to the south-east, the more highly inbred and less genetically diverse northern populations will come under increasing pressure to expand southwards as habitat suitability declines. Given the species' genetic structure and with the aim to enhance genetic diversity and maximise the likelihood of reproductive success, we recommend that plant reintroductions to supplement existing populations should be prioritised over translocation of the species to new sites. However, future conservation efforts should be directed at translocation to establish new sites to increase population connectivity, focussing particularly on habitat areas identified as persisting under conditions of climate change.