Ancient genomes reveal over two thousand years of dingo population structure.

Dingoes are culturally and ecologically important free-living canids whose ancestors arrived in Australia over 3,000 B.P., likely transported by seafaring people. However, the early history of dingoes in Australia-including the number of founding populations and their routes of introduction-remains uncertain. This uncertainty arises partly from the complex and poorly understood relationship between modern dingoes and New Guinea singing dogs, and suspicions that post-Colonial hybridization has introduced recent domestic dog ancestry into the genomes of many wild dingo populations. In this study, we analyzed genome-wide data from nine ancient dingo specimens ranging in age from 400 to 2,746 y old, predating the introduction of domestic dogs to Australia by European colonists. We uncovered evidence that the continent-wide population structure observed in modern dingo populations had already emerged several thousand years ago. We also detected excess allele sharing between New Guinea singing dogs and ancient dingoes from coastal New South Wales (NSW) compared to ancient dingoes from southern Australia, irrespective of any post-Colonial hybrid ancestry in the genomes of modern individuals. Our results are consistent with several demographic scenarios, including a scenario where the ancestry of dingoes from the east coast of Australia results from at least two waves of migration from source populations with varying affinities to New Guinea singing dogs. We also contribute to the growing body of evidence that modern dingoes derive little genomic ancestry from post-Colonial hybridization with other domestic dog lineages, instead descending primarily from ancient canids introduced to Sahul thousands of years ago.

Genomic Consequences of Isolation and Inbreeding in an Island Dingo Population.

Dingoes come from an ancient canid lineage that originated in East Asia around 8,000 to 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 (ROHs)-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.

Genomic consequences of isolation and inbreeding in an island dingo population.

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.

Genomic signatures of bottleneck and founder effects in dingoes.

Dingoes arrived in Australia during the mid-Holocene and are the top-order terrestrial predator on the continent. Although dingoes subsequently spread across the continent, the initial founding population(s) could have been small. We investigated this hypothesis by sequencing the whole genomes of three dingoes and also obtaining the genome data from nine additional dingoes and 56 canines, including wolves, village dogs and breed dogs, and examined the signatures of bottlenecks and founder effects. We found that the nucleotide diversity of dingoes was low, 36% less than highly inbred breed dogs and 3.3 times lower than wolves. The number of runs of homozygosity (RoH) segments in dingoes was 1.6-4.7 times higher than in other canines. While examining deleterious mutational load, we observed that dingoes carried elevated ratios of nonsynonymous-to-synonymous diversities, significantly higher numbers of homozygous deleterious Single Nucleotide Variants (SNVs), and increased numbers of loss of function SNVs, compared to breed dogs, village dogs, and wolves. Our findings can be explained by bottlenecks and founder effects during the establishment of dingoes in mainland Australia. These findings highlight the need for conservation-based management of dingoes and the need for wildlife managers to be cognisant of these findings when considering the use of lethal control measures across the landscape.

Mitochondrial Genome Fragmentation Occurred Multiple Times Independently in Bird Lice of the Families Menoponidae and Laemobothriidae.

Mitochondrial (mt) genome fragmentation has been discovered in all five parvorders of parasitic lice (Phthiraptera). To explore whether minichromosomal characters derived from mt genome fragmentation are informative for phylogenetic studies, we sequenced the mt genomes of 17 species of bird lice in Menoponidae and Laemobothriidae (Amblycera). Four species of Menoponidae (Actornithophilus sp. 1 ex [pied oystercatcher], Act. sp. 2 ex [masked lapwing], Austromenopon sp. 2 ex [sooty tern and crested tern], Myr. sp. 1 ex [satin bowerbird]) have fragmented mt genomes, whereas the other 13 species retain the single-chromosome mt genomes. The two Actornithophilus species have five and six mt minichromosomes, respectively. Aus. sp. 2 ex [sooty tern and crested tern] has two mt minichromosomes, in contrast to Aus. sp. 1 ex [sooty shearwater], which has a single mt chromosome. Myr. sp. 1 ex [satin bowerbird] has four mt minichromosomes. When mapped on the phylogeny of Menoponidae and Laemobothriidae, it is evident that mt genome fragmentation has occurred multiple times independently among Menoponidae and Laemobothriidae species. We found derived mt minichromosomal characters shared between Myrsidea species, between Actornithophilus species, and between and among different ischnoceran genera, respectively. We conclude that while mt genome fragmentation as a general feature does not unite all the parasitic lice that have this feature, each independent mt genome fragmentation event does produce minichromosomal characters that can be informative for phylogenetic studies of parasitic lice at different taxonomic levels.

Unexpected Pathogen Diversity Detected in Australian Avifauna Highlights Potential Biosecurity Challenges.

Birds may act as hosts for numerous pathogens, including members of the family Chlamydiaceae, beak and feather disease virus (BFDV), avipoxviruses, Columbid alphaherpesvirus 1 (CoAHV1) and Psittacid alphaherpesvirus 1 (PsAHV1), all of which are a significant biosecurity concern in Australia. While Chlamydiaceae and BFDV have previously been detected in Australian avian taxa, the prevalence and host range of avipoxviruses, CoAHV1 and PsAHV1 in Australian birds remain undetermined. To better understand the occurrence of these pathogens, we screened 486 wild birds (kingfisher, parrot, pigeon and raptor species) presented to two wildlife hospitals between May 2019 and December 2021. Utilising various qPCR assays, we detected PsAHV1 for the first time in wild Australian birds (37/486; 7.61%), in addition to BFDV (163/468; 33.54%), Chlamydiaceae (98/468; 20.16%), avipoxviruses (46/486; 9.47%) and CoAHV1 (43/486; 8.85%). Phylogenetic analysis revealed that BFDV sequences detected from birds in this study cluster within two predominant superclades, infecting both psittacine and non-psittacine species. However, BFDV disease manifestation was only observed in psittacine species. All Avipoxvirus sequences clustered together and were identical to other global reference strains. Similarly, PsAHV1 sequences from this study were detected from a series of novel hosts (apart from psittacine species) and identical to sequences detected from Brazilian psittacine species, raising significant biosecurity concerns, particularly for endangered parrot recovery programs. Overall, these results highlight the high pathogen diversity in wild Australian birds, the ecology of these pathogens in potential natural reservoirs, and the spillover potential of these pathogens into novel host species in which these agents cause disease.

A new candling procedure for thick and opaque eggs and its application to avian conservation management.

The ability to monitor developing avian embryos and their associated vascular system via candling enables the application of important reproductive management techniques. Egg candling facilitates the confirmation of egg viability throughout the incubation process and identification of a precise position on a vein for the safe extraction of blood. Blood samples may then be analysed to retrieve vital health and genetic information to assist in conservation management. However, the thick or opaque egg shell characteristics of some avian species prevents the observation of egg contents using traditional candling methods, thus limiting management options. This paper tests a novel method of preparing thick-shelled or opaque eggs so that traditional egg candling and blood extraction methods may be applied. Eggs from captive emu (Dromaius novaehollandiae, Latham 1790) and southern cassowary (Casuarius casuarius johnsonii, Linnaeus 1758) were obtained, and partial fenestration was performed on two areas of shell either before incubation or at ⅓ of incubation. Hatchability and weight loss were examined as a measure of effect of the fenestration process on the developing embryo. Clear observation of vascular development was successful in 97% of viable fenestrated eggs, without affecting hatchability or weight loss. Blood samples were taken from developing embryos and DNA was successfully extracted for proof of concept of this new technique. The ability to observe vascular development and monitor the developing embryo in thick and opaque eggs will significantly improve both in situ and ex situ population management options such as in ovo sexing in species of concern.

Emerging and well-characterized chlamydial infections detected in a wide range of wild Australian birds.

Birds can act as successful long-distance vectors and reservoirs for numerous zoonotic bacterial, parasitic and viral pathogens, which can be a concern given the interconnectedness of animal, human and environmental health. Examples of such avian pathogens are members of the genus Chlamydia. Presently, there is a lack of research investigating chlamydial infections in Australian wild and captive birds and the subsequent risks to humans and other animals. In our current study, we investigated the prevalence and genetic diversity of chlamydial organisms infecting wild birds from Queensland and the rate of co-infections with beak and feather disease virus (BFDV). We screened 1114 samples collected from 564 different birds from 16 orders admitted to the Australia Zoo Wildlife Hospital from May 2019 to February 2021 for Chlamydia and BFDV. Utilizing species-specific quantitative polymerase chain reaction (qPCR) assays, we revealed an overall Chlamydiaceae prevalence of 29.26% (165/564; 95% confidence interval (CI) 25.65-33.14), including 3.19% (18/564; 95% CI 2.03-4.99%) prevalence of the zoonotic Chlamydia psittaci. Chlamydiaceae co-infection with BFDV was detected in 9.75% (55/564; 95% CI 7.57-12.48%) of the birds. Molecular characterization of the chlamydial 16S rRNA and ompA genes identified C. psittaci, in addition to novel and other genetically diverse Chlamydia species: avian Chlamydia abortus, Ca. Chlamydia ibidis and Chlamydia pneumoniae, all detected for the first time in Australia within a novel avian host range (crows, figbirds, herons, kookaburras, lapwings and shearwaters). This study shows that C. psittaci and other emerging Chlamydia species are prevalent in a wider range of avian hosts than previously anticipated, potentially increasing the risk of spill-over to Australian wildlife, livestock and humans. Going forward, we need to further characterize C. psittaci and other emerging Chlamydia species to determine their exact genetic identity, potential reservoirs, and factors influencing infection spill-over.

Short distance pollen dispersal and low genetic diversity in a subcanopy tropical rainforest tree, Fontainea picrosperma (Euphorbiaceae).

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.

A multidisciplinary approach to inform assisted migration of the restricted rainforest tree, Fontainea rostrata.

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.

The impact of human activities on Australian wildlife.

Increasing human population size and the concomitant expansion of urbanisation significantly impact natural ecosystems and native fauna globally. Successful conservation management relies on precise information on the factors associated with wildlife population decline, which are challenging to acquire from natural populations. Wildlife Rehabilitation Centres (WRC) provide a rich source of this information. However, few researchers have conducted large-scale longitudinal studies, with most focussing on narrow taxonomic ranges, suggesting that WRC-associated data remains an underutilised resource, and may provide a fuller understanding of the anthropogenic threats facing native fauna. We analysed admissions and outcomes data from a WRC in Queensland, Australia Zoo Wildlife Hospital, to determine the major factors driving admissions and morbidity of native animals in a region experiencing rapid and prolonged urban expansion. We studied 31,626 admissions of 83 different species of native birds, reptiles, amphibians, marsupials and eutherian mammals from 2006 to 2017. While marsupial admissions were highest (41.3%), admissions increased over time for all species and exhibited seasonal variation (highest in Spring to Summer), consistent with known breeding seasons. Causes for admission typically associated with human influenced activities were dominant and exhibited the highest mortality rates. Car strikes were the most common reason for admission (34.7%), with dog attacks (9.2%), entanglements (7.2%), and cat attacks (5.3%) also high. Admissions of orphaned young and overt signs of disease were significant at 24.6% and 9.7%, respectively. Mortality rates were highest following dog attacks (72.7%) and car strikes (69.1%) and lowest in orphaned animals (22.1%). Our results show that WRC databases offer rich opportunities for wildlife monitoring and provide quantification of the negative impacts of human activities on ecosystem stability and wildlife health. The imminent need for urgent, proactive conservation management to ameliorate the negative impacts of human activities on wildlife is clearly evident from our results.

In silico detection of polymorphic microsatellites in the endangered Isis tamarind, Alectryon ramiflorus (Sapindaceae).

PREMISE OF THE STUDY: Alectryon ramiflorus (Sapindaceae) is an endangered rainforest tree known from only two populations. In this study, we identified polymorphic microsatellites, in silico, improving the effectiveness and efficiency of microsatellite development of nonmodel species. The development of genetic markers will support future conservation management of the species. METHODS AND RESULTS: We used next-generation sequencing and bioinformatics to detect polymorphic microsatellites, in silico, reducing both the time and cost of marker development. A panel of 15 microsatellites, 12 of which were polymorphic, were subsequently characterized in 64 adult trees representing the entire species range. Mean observed heterozygosity and expected heterozygosity were 0.471 and 0.425, respectively. The polymorphism information content across loci ranged from 0.152 to 0.875. CONCLUSIONS: The microsatellite markers developed in this study will be useful in gaining an understanding of A. ramiflorus' genetic diversity, level of inbreeding, and population structure and for guiding future restoration and management efforts.

Permanent genetic resources added to molecular ecology resources database 1 April 2013-31 May 2013.

This article documents the addition of 234 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Acipenser sinensis, Aleochara bilineata, Aleochara bipustulata, Barbus meridionalis, Colossoma macropomum, Delia radicum, Drosophila nigrosparsa, Fontainea picrosperma, Helianthemum cinereum, Liomys pictus, Megabalanus azoricus, Pelteobagrus vachelli, Pleuragramma antarcticum, Podarcis hispanica type 1A, Sardinella brasiliensis and Sclerotinia homoeocarpa. These loci were cross-tested on the following species: Acipenser dabryanus, Barbus balcanicus, Barbus barbus, Barbus cyclolepis, Drosophila hydei, Drosophila melanogaster, Drosophila obscura, Drosophila subobscura, Fontainea australis, Fontainea fugax, Fontainea oraria, Fontainea rostrata, Fontainea venosa, Podarcis bocagei, Podarcis carbonelli, Podarcis liolepis, Podarcis muralis and Podarcis vaucheri.