Linda Neaves

Australian National University | ANU · Fenner School of Environment & Society

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 succe...

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 biodiv...

Small, fragmented or isolated populations are at risk of population decline due to fitness costs associated with inbreeding and genetic drift. The King Island scrubtit Acanthornis magna greeniana is a critically endangered subspecies of the nominate Tasmanian scrubtit A. m. magna, with an estimated population of < 100 individuals persisting in thre...

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 Horsf...

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 lo...

Molecular tools are increasingly applied for assessing and monitoring biodiversity and informing conservation action. While recent developments in genetic and genomic methods provide greater sensitivity in analysis and the capacity to address new questions, they are not equally available to all practitioners: There is considerable bias across insti...

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 biodiv...

Small, fragmented or isolated populations are at risk of population decline due to fitness costs associated with inbreeding and genetic drift. The King Island scrubtit Acanthornis magna greeniana is a critically endangered endemic subspecies of the nominate Tasmanian scrubtit A. m. magna, with an estimated population of <100 individuals persisting...

Small, fragmented or isolated populations are at risk of population decline due to fitness costs associated with inbreeding and genetic drift. The King Island scrubtit Acanthornis magna greeniana is a critically endangered endemic subspecies of the nominate Tasmanian scrubtit A. m. magna, with an estimated population of <100 individuals persisting...

Premise of the study: Paubrasilia echinata (Lam.) Gagnon, H. C. Lima & G. P. Lewis ("Pau Brasil") is the national tree of Brazil, an endangered species endemic to the Brazilian Atlantic Forest. The wide distribution, spanning over 2000 km, matches extensive plasticity in leaf morphology. Three morphotypes are commonly identified based on leaf size...

Translocations are an important conservation tool that enable the restoration of species and their ecological functions. They are particularly important during the current environmental crisis. We used a combination of text‐analysis tools to track the history and evolution of the peer‐reviewed scientific literature on animal translocation science....

Conservation translocation - the movement of species for conservation benefit - includes reintroducing species into the wild, reinforcing dwindling populations, helping species shift ranges in the face of environmental change, and moving species to enhance ecosystem function. Conservation translocation can lead to clear conservation benefits and ca...

Paubrasilia echinata (Lam.) Gagnon, H. C. Lima & G. P. Lewis (“Pau Brasil”) is the national tree of Brazil and an endangered species endemic to the Brazilian Atlantic Forest. The extensive range of distribution, spanning over 2000 km distance, is matched by extensive plasticity in leaf morphology. Three morphotypes are commonly identified based on...

Reintroduction biology is a key tool for mitigating the catastrophic reduction in species’ ranges, caused by humans over the last 500 years. To assess where reintroduction biology scientific research is targeted, we used text-analysis methods to extract taxonomic and geographic mentions from animal reintroduction-focused articles published between...

Invasive predators are responsible for declines in many animal species across the globe. To redress these declines, conservationists have undertaken substantial work to remove invasive predators or mitigate their effects. Yet, the challenges associated with removal of invasive predators mean that most successful conservation programs have been rest...

Climatic and evolutionary processes are inextricably linked to conservation. Avoiding extinction in rapidly changing environments often depends upon a species’ capacity to adapt in the face of extreme selective pressures. Here, we employed exon capture and high‐throughput next‐generation sequencing to investigate the mechanisms underlying populatio...

Incorporating genetic data into conservation programmes improves management outcomes, but the impact of different sample grouping methods on genetic diversity analyses is poorly understood. To this end, the multi‐source reintroduction of the eastern bettong Bettongia gaimardi was used as a long‐term case study to investigate how sampling regimes ma...

Population genetic assessment is crucial for the conservation and management of threatened species. Xanthocyparis vietnamensis is an endangered species that is currently restricted to karst mountains in southwestern China and Vietnam. This rare conifer was first recorded in 2002 from northern Vietnam and then in 2013 from Guangxi, China, yet nothin...

Some animals fashion tools or constructions out of plant materials to aid foraging, reproduction, self-maintenance, or protection. Their choice of raw materials can affect the structure and properties of the resulting artifacts, with considerable fitness consequences. Documenting animals' material preferences is challenging, however, as manufacture...

Robins in the family Petroicidae are characteristic of the woodland bird community that is threatened in Australia as a result of habitat loss and fragmentation. Flame Robin (Petroica phoenicea) populations declined by 56% between 1980 and 2000, with habitat loss likely being the primary cause. Given that Flame Robins primarily breed at high elevat...

Bass Strait is an important biogeographic barrier for Australian mammals, often resulting in significant genetic differentiation between populations on the mainland and Tasmania for species with a trans-Bassian distribution. King and Flinders Islands, in Bass Strait, are the largest remnants of the land bridge that once linked Tasmania with mainlan...

As there is no agreed national list of species of socio-economic and/or cultural value for Scotland, a set of criteria for selecting species has been developed. These include: • Species prioritised for conservation value • Species identified as being culturally important • Species providing important ecosystem services • Game species • Species coll...

Aichi Target 13 (T13) focuses on the conservation of genetic diversity. • Major challenges in implementing T13 are that the type of genetic diversity to conserve is not clearly defined, and that key issues in genetic conservation vary across different sectors (e.g., forestry vs agriculture vs other species of socio-economic importance). • In Scotla...

Little genetic research has been undertaken on mammals across the vast expanse of the arid biome in Australia, despite continuing species decline and need for conservation management. Here, we evaluate the contemporary and historical genetic connectivity of the yellow-footed rock-wallaby, Petrogale xanthopus xanthopus, a threatened macropodid which...

The rapid and extensive loss of biodiversity globally has resulted in an increased urgency to capture and conserve the diversity which is present, including genetic diversity within species. However, for many species there is currently no detailed genetic data available to inform the collection and use of material held in ex situ collections and th...

The unique geography and climate of the Qinghai-Tibet plateau (QTP) have impacted the formation of species in this area, with a large number of relatively young endemic species associated with the uplift of the QTP and Quaternary climatic changes. In our study, we used two chloroplast DNA fragments and seven nuclear genes to investigate the populat...

Background: Processed seafood products are not readily identifiable based on physical characteristics, which leaves the industry vulnerable to high levels of product mislabelling (globally estimated at 5-30% mislabelled). This is both a food safety issue and a consumer protection issue as cheaper species could be substituted for more expensive spe...

The rufous hare-wallaby (Lagorchestes hirsutus) is now extinct in the wild on mainland Australia, but survives in captivity. However, endemic populations persist on Bernier and Dorre Islands, Western Australia. This study aimed to compare the genetic diversity and differentiation amongst three remaining rufous hare-wallaby populations using mitocho...

Black-flanked rock-wallabies (Petrogale lateralis lateralis) were thought to be locally extinct in Kalbarri National Park, Western Australia, until 2015 when a pair were photographed in the Murchison River gorge. Subsequent searches failed to locate any other populations and, in combination with previous surveys, suggest that these animals were the...

Historically, reports of insectivory in family Pteropodidae have largely been anecdotal and thought to be an incidental corollary of flying-foxes feeding on plant products. More recent direct observations of flying-foxes catching and consuming insects, as well as advances in techniques that increase our ability to detect dietary items, suggest that...

A fundamental challenge in resolving evolutionary relationships across the Tree of Life is to account for heterogeneity in the evolutionary signal across loci. Studies of marsupial mammals have demonstrated that this heterogeneity can be substantial, leaving considerable uncertainty in the evolutionary timescale and relationships within the group....

The koala, the only extant species of the marsupial family Phascolarctidae, is classified as 'vulnerable' due to habitat loss and widespread disease. We sequenced the koala genome, producing a complete and contiguous marsupial reference genome, including centromeres. We reveal that the koala's ability to detoxify eucalypt foliage may be due to expa...

Pteropus (flying-foxes) are a speciose group of non-echolocating large bats, with five extant Australian species and 24 additional species distributed amongst the Pacific Islands. In 2015, an injured flying-fox with unusual facial markings was found in Sydney, Australia, following severe and widespread storms. Based on an initial assessment, the in...

Genes, primers and PCR cycling conditions used in this study. (DOCX)

Samples and gene regions sequenced (with GenBank accession numbers) from the Australian Museum, Sydney, Australia. (XLSX)

Bayesian tree based on 497 bp of mitochondrial DNA control region. Support for clades are shown, with posterior probabilities shown above, and maximum likelihood values below branches. Branches with dashed lines were not recovered in the ML trees. See Table 2 and S2 and S3 Tables for locations. (EPS)

Bayesian tree based on 1085 bp of Recombination activating gene 1 (RAG1). Support for clades are shown, with posterior probabilities shown above, and maximum likelihood values below branches. Branches with dashed lines were not recovered in the ML trees. See Table 2 and S2 and S3 Tables for locations. (EPS)

Bayesian tree showing the relationship between the unknown Pteropus sample and sequences obtained from GenBank for 287 bp of cytochrome b. Support for clades are shown, with posterior probabilities shown above, and maximum likelihood values below branches. Branches with dashed lines were not recovered in the ML trees. See S3 Table for locations. (T...

Sequences obtained from GenBank and used in analysis presented in this study. (XLSX)

Bayesian tree based on 657 bp of cytochrome c oxidase subunit 1. Support for clades are shown, with posterior probabilities shown above, and maximum likelihood values below branches. Branches with dashed lines were not recovered in the ML trees. See Table 2 and S2 and S3 Tables for locations. (EPS)

The brush-tailed rock-wallaby (Petrogale penicillata) is now extinct west of the Great Dividing Range, apart from remnant populations in the Warrumbungles and at Mt Kaputar. Previous genetic analysis has identified deep genetic subdivisions within P. penicillata, but samples from Mt Kaputar were not included. Mitochondrial DNA sequences obtained fr...

The Yellow Chat Epthianura crocea is comprised of three disjunct subspecies. Subspecies E. c. macgregori (Capricorn Yellow Chat) is listed as Critically Endangered under the EPBC Act and has a distribution that also appears to be disjunct, with a limited geographic area of less than 7,000 ha. Some populations are threatened by rapid industrial deve...

This study examines genetic relationships among and within the South American species of Oreobolus that span the temperate and tropical Andes hotspots and represent a good case study to investigate diversification in the Páramo. A total of 197 individuals covering the distributional range of most of these species were sequenced for the nuclear ribo...

Only a green world, rich in plants, can sustain us and the millions of other species with which we share this planet. But, in an era of global change, nature is on the retreat. Like the communities they form, many plant species are becoming rarer, threatened even to the point of extinction. The worldwide community of almost three thousand botanic g...

The tammar wallaby (Notamacropus eugenii) is one of the most intensively studied of all macropodids and was the first Australasian marsupial to have its genome sequenced. However, comparatively little is known about genetic diversity and differentiation amongst the morphologically distinct allopatric populations of tammar wallabies found in Western...

Allele frequencies for 16 autosomal microsatellite loci in ten tammar wallaby (Notamacropus eugenii) populations. KI = Kangaroo Island; KwI = Kawau Island, New Zealand; Tut = Tutanning; Per = Perup; GI = Garden Island; EWI = East Wallabi Island; WWI = West Wallabi Island; NI = North Island; MI = Middle Island; NTP = North Twin Peak Island. (DOCX)

Microsatellite genotypes at 16 autosomal loci in ten tammar wallaby (Notamacropus eugenii) populations. (XLSX)

Allelic combinations of the 32 Y haplotypes identified in nine tammar wallaby (Notamacropus eugenii) populations. KI = Kangaroo Island; KwI = Kawau Island, New Zealand; Tut = Tutanning; Per = Perup; GI = Garden Island; EWI = East Wallabi Island; WWI = West Wallabi Island; NI = North Island; MI = Middle Island. (DOCX)

Structure output showing a) maximum L(K) at K = 7 and b) maximum ΔK at K = 8 (b). (DOCX)

Animals exhibit a range of dispersal strategies that impact on the organisation of individuals and can be influenced by both the environment and population demography. We examined the fine-scale spatial genetic structure and patterns of relatedness in 139 adult eastern grey kangaroos (Macropus giganteus) to test predictions of male-biased dispersal...

Intraspecific variation is a major component of biodiversity, yet it has received relatively little attention from governmental and non-governmental organizations, especially with regard to conservation plans and the management of wild species. This omission is ill-advised because phenotypic and genetic variation within and among populations can ha...

The Australian continent exhibits complex biogeographic patterns but studies of the impacts of Pleistocene climatic oscillation on the mesic environments of the Southern Hemisphere are limited. The koala (Phascolarctos cinereus), one of Australia's most iconic species, was historically widely distributed throughout much of eastern Australia but cur...

BEAST input files. (ZIP)

Sample information. (XLSX)

Habitat loss and fragmentation are key threats to local koala (Phascolarctos cinereus) populations. Broad-scale management is suboptimal for koalas because distribution models are not easily generalised across regions. Therefore, it is imperative that data relevant to local management bodies are available. Genetic data provides important informatio...

Threatened species often have small and isolated populations where mating among relatives can result in inbreeding depression increasing extinction risk. Effective management is hampered by a lack of syntheses summarising the magnitude of, and variation in inbreeding depression. Here we describe the nature and scope of the literature examining phen...

[The Code was produced by Scottish Natural Heritage and the Royal Botanic Garden Edinburgh on behalf of the National Species Reintroduction Forum. It was written by Peter Hollingsworth, Martin Gaywood, Sarah Dalrymple, Sally Blyth, Stephen Redpath, Linda Neaves. The formal citation is: National Species Reintroduction Forum 2014. The Scottish Code f...

Planting of native trees for habitat restoration is a widespread practice, but the consequences for the retention and transmission of genetic diversity in planted and natural populations are unclear. Using Inga vera subsp. affinis as a model species, we genotyped five natural and five planted populations in the Atlantic forest of northeastern Brazi...

Plant Reintroduction in a Changing Climate: Promises and Perils. Edited by MaschinskiJ. & HaskinsK. E.. Washington, DC: Island Press. 2012. 432 pp. ISBN 978 1 59726 831 8. £32. - Volume 70 Issue 1 - Linda Neaves

There are several aspects of biology in which the contribution of males and females is unequal. In these instances the examination of Y chromosome markers may be used to elucidate male specific attributes. Here, male dispersal patterns and genetic structuring were examined using four Y-microsatellite loci in 186 male western grey kangaroos (Macropu...

Aim Climatic fluctuations during the Pleistocene have shaped the population structure of many extant taxa. However, few studies have examined widespread species inhabiting the Australian continent, where periods of increased aridity characterized the Pleistocene. Here we investigate the phylogeography and population history of a widespread and vagi...