ORCID Profile
0000-0001-7984-8159
Current Organisations
New South Wales Department of Primary Industries
,
University of Tasmania
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Publisher: MDPI AG
Date: 12-10-2019
Abstract: In an era of unprecedented global change, exploring patterns of gene expression among wild populations across their geographic range is crucial for characterizing adaptive potential. RNA-sequencing studies have successfully characterized gene expression differences among populations experiencing ergent environmental conditions in a wide variety of taxa. However, few of these studies have identified transcriptomic signatures to multivariate, environmental stimuli among populations in their natural environments. Herein, we aim to identify environmental and sex-driven patterns of gene expression in the Tasmanian devil (Sarcophilus harrisii), a critically endangered species that occupies a heterogeneous environment. We performed RNA-sequencing on ear tissue biopsies from adult male and female devils from three populations at the extremes of their geographic range. There were no transcriptome-wide patterns of differential gene expression that would be suggestive of significant, environmentally-driven transcriptomic responses. The general lack of transcriptome-wide variation in gene expression levels across the devil’s geographic range is consistent with previous studies that documented low levels of genetic variation in the species. However, genes previously implicated in local adaptation to abiotic environment in devils were enriched for differentially expressed genes. Additionally, three modules of co-expressed genes were significantly associated with either population of origin or sex.
Publisher: Cold Spring Harbor Laboratory
Date: 27-05-2022
DOI: 10.1101/2022.05.27.493404
Abstract: Tasmanian devils have spawned two transmissible cancer lineages, named devil facial tumour 1 (DFT1) and devil facial tumour 2 (DFT2). We investigated the genetic ersity and evolution of these clones by analysing 78 DFT1 and 41 DFT2 genomes relative to a newly assembled chromosome-level reference. Time-resolved phylogenetic trees reveal that DFT1 first emerged in 1986 (1982-1989), and DFT2 in 2011 (2009-2012). Subclone analysis documents transmission of heterogeneous cell populations. DFT2 has faster mutation rates than DFT1 across all variant classes, including substitutions, indels, rearrangements, transposable element insertions and copy number alterations, and we identify a hypermutated DFT1 lineage with defective DNA mismatch repair. Several loci show plausible evidence of positive selection in DFT1 or DFT2, including loss of chromosome Y and inactivation of MGA , but none are common to both cancers. This study illuminates the parallel long-term evolution of two transmissible cancers inhabiting a common niche in Tasmanian devils.
Publisher: CSIRO Publishing
Date: 09-12-2022
DOI: 10.1071/WR22117
Publisher: Wiley
Date: 24-03-2022
DOI: 10.1002/JWMG.22207
Abstract: Deer (Cervidae) are key components of many ecosystems and estimating deer abundance or density is important to understanding these roles. Many field methods have been used to estimate deer abundance and density, but the factors determining where, when, and why a method was used, and its usefulness, have not been investigated. We systematically reviewed journal articles published during 2004–2018 to evaluate spatio‐temporal trends in study objectives, methodologies, and deer abundance and density estimates, and determine how they varied with biophysical and anthropogenic attributes. We also reviewed the precision and bias of deer abundance estimation methods. We found 3,870 deer abundance and density estimates. Most estimates (58%) were for white‐tailed deer ( Odocoileus virginianus ), red deer ( Cervus elaphus ), and roe deer ( Capreolus capreolus ). The 6 key methods used to estimate abundance and density were pedestrian sign (track or fecal) counts, pedestrian direct counts, vehicular direct counts, aerial direct counts, motion‐sensitive cameras, and harvest data. There were regional differences in the use of these methods, but a general pattern was a temporal shift from using harvest data, pedestrian direct counts, and aerial direct counts to using pedestrian sign counts and motion‐sensitive cameras. Only 32% of estimates were accompanied by a measure of precision. The most precise estimates were from vehicular spotlight counts and from capture–recapture analysis of images from motion‐sensitive cameras. For aerial direct counts, capture–recapture methods provided the most precise estimates. Bias was robustly assessed in only 16 studies. Most abundance estimates were negatively biased, but capture–recapture methods were the least biased. The usefulness of deer abundance and density estimates would be substantially improved by 1) reporting key methodological details, 2) robustly assessing bias, 3) reporting the precision of estimates, 4) using methods that increase and estimate detection probability, and 5) staying up to date on new methods. The automation of image analysis using machine learning should increase the accuracy and precision of abundance estimates from direct aerial counts (visible and thermal infrared, including from unmanned aerial vehicles [drones]) and motion‐sensitive cameras, and substantially reduce the time and cost burdens of manual image analysis.
Publisher: CSIRO Publishing
Date: 10-07-2023
DOI: 10.1071/WR22128
Publisher: CSIRO Publishing
Date: 06-07-2023
DOI: 10.1071/WR22129
Publisher: Wiley
Date: 29-08-2023
Abstract: Invasive deer have undesirable impacts on native ecosystems. Culling is commonly used to reduce those impacts, but is expensive and sometimes controversial. It is therefore important to robustly assess how culling reduces the impacts of invasive deer. We conducted a Before‐After Control‐Impact (BACI) experiment to determine how culling affects the impacts of invasive sambar deer Cervus unicolor in an endangered alpine peatland ecosystem in south‐eastern Australia. We established two blocks, each with four 4300‐ha experimental units, in which two units were randomly assigned to a treatment of deer culling and the other two were non‐treatment areas. Sambar deer relative abundance (faecal pellet count) and three impacts (ground degradation, pugging intensity and water turbidity) in three peatland features (peatlands, natural pools and sambar deer wallows) were surveyed before and after culling was implemented. We used four metrics to quantify the culling intensity in each treatment unit: treatment versus non‐treatment, number of deer culled on each unit, deer culled within a 500‐m buffer of impact monitoring sites and local probability of use by the cullers (1‐ha grid). The effects of culling on deer abundance and impacts were estimated using Bayesian generalised linear mixed models. Our analysis revealed that the effect of culling differed between the two experimental blocks. In one block, culling reduced deer abundance and three impacts. In the other block, culling did not reduce deer abundance but reduced three impacts and increased two impacts. The effects of culling were generally stronger when culling was estimated using finer‐scale (500‐m) than coarser‐scale (experimental unit) culling metrics. Synthesis and applications . Our study provides experimental evidence that culling invasive sambar deer reduces some of their undesirable impacts on endangered peatlands. That not all impacts were reduced by culling suggests that some effects of invasive species are slow to recover or require higher culling intensities to be reversed.
Publisher: CSIRO Publishing
Date: 26-05-2022
DOI: 10.1071/WR21147
Abstract: Context Of the six species of non-native deer present in Australia, the sambar deer is the largest and has been identified as a major threat to high-elevation peatlands in south-eastern Australia. However, little is known about sambar deer activity in high-elevation peatlands. Aims The aims of this study were to quantify sambar deer activity (including wallowing) seasonally and daily in response to biotic and abiotic variables, and how activity was impacted by ground-based shooting. Methods To estimate sambar deer activity, camera traps were continuously deployed for 4 years in two ~4300-ha areas in Alpine National Park, Victoria, south-eastern Australia. One area was subject to management operations using ground-based shooting to target deer and the other was not. Monthly activity of sambar deer was modelled using biotic (woody vegetation cover), abiotic (snow depth, aspect, slope, distance to water, road and peatland) and management (treatment versus non-treatment) covariates. Additional camera traps were deployed to monitor sambar deer activity at wallows. Key results Sambar deer activity decreased when snow depth increased (between July and September), and was highest in easterly and northerly aspects with dense woody vegetation close to high-elevation peatlands and roads. During our 4-year study, sambar deer activity decreased in the treatment area but increased in the non-treatment area. Sambar deer exhibited a crepuscular diel cycle, with greatest activity around sunset. Only male sambar deer were observed to wallow, with most wallowing occurring in the afternoon during October–June. Conclusions Sambar deer utilised high-elevation peatlands during October–June. Daily activity was crepuscular and was greatest in dense tree cover close to roads. Ground-based shooting reduced sambar deer activity in and around high-elevation peatlands. Implications Control operations targeting sambar deer at high elevations in south-eastern Australia should be conducted during October–June. Outside this period sambar deer appear to use lower-elevation habitats. The effectiveness of ground-based shooting could be improved by focusing this control action around sunset (when sambar deer are most active) and in places with dense vegetation close to roads and high-elevation peatlands.
Publisher: MDPI AG
Date: 31-10-2021
DOI: 10.3390/ANI11113125
Abstract: Movements that extend beyond the usual space use of an animal have been documented in a range of species and are particularly prevalent in arid areas. We present long-distance movement data on five feral cats (Felis catus) GPS/VHF-collared during two different research projects in arid and semi-arid Australia. We compare these movements with data from other feral cat studies. Over a study period of three months in the Ikara-Flinders Ranges National Park, 4 out of 19 collared cats moved to sites that were 31, 41, 53 and 86 km away. Three of the cats were males, one female their weight was between 2.1 and 4.1 kg. Two of the cats returned to the area of capture after three and six weeks. During the other study at Arid Recovery, one collared male cat (2.5 kg) was relocated after two years at a distance of 369 km from the area of collar deployment to the relocation area. The movements occurred following three years of record low rainfall. Our results build on the knowledge base of long-distance movements of feral cats reported at arid study sites and support the assertion that landscape-scale cat control programs in arid and semi-arid areas need to be of a sufficiently large scale to avoid rapid reinvasion and to effectively reduce cat density. Locally, cat control strategies need to be adjusted to improve coverage of areas highly used by cats to increase the efficiency of control operations.
Publisher: Oxford University Press (OUP)
Date: 18-10-2023
Publisher: MDPI AG
Date: 23-10-2020
Abstract: The impact of emerging infectious diseases is increasingly recognised as a major threat to wildlife. Wild populations of the endangered Tasmanian devil, Sarcophilus harrisii, are experiencing devastating losses from a novel transmissible cancer, devil facial tumour disease (DFTD) however, despite the rapid decline of this species, there is currently no information on the presence of haemoprotozoan parasites. In the present study, 95 Tasmanian devil blood s les were collected from four populations in Tasmania, Australia, which underwent molecular screening to detect four major groups of haemoprotozoa: (i) trypanosomes, (ii) piroplasms, (iii) Hepatozoon, and (iv) haemosporidia. Sequence results revealed Trypanosoma infections in 32/95 in iduals. Trypanosoma copemani was identified in 10 Tasmanian devils from three sites and a second Trypanosoma sp. was identified in 22 in iduals that were grouped within the poorly described T. cyclops clade. A single blood s le was positive for Babesia sp., which most closely matched Babesia lohae. No other blood protozoan parasite DNA was detected. This study provides the first insight into haemoprotozoa from the Tasmanian devil and the first identification of Trypanosoma and Babesia in this carnivorous marsupial.
Publisher: CSIRO Publishing
Date: 12-12-2022
DOI: 10.1071/WR22030
Publisher: Public Library of Science (PLoS)
Date: 17-01-2023
DOI: 10.1371/JOURNAL.PONE.0280011
Abstract: Although the home range and habitat selection of animal species is among the fundamental pieces of biological information collected by research projects during recent decades, published information on the snow leopard ( Panthera uncia ) home range is limited. The Altai Mountains of central Asia contain some of the largest and most important remaining conservation landscapes for snow leopards globally, but there is a limited understanding of the species’ ecology in this region. First, we used the data from 5 snow leopards equipped with GPS collars at four study sites in the Altai Mountains of Mongolia to broadly characterize patterns of home range use between 2013 and 2019. The data was used to calculate home range size from a 10 month period using three different estimators: minimum convex polygons (MCP), kernel density distributions (KDE), and local convex hulls (LoCoH). Second, ten data sets from 8 in idual snow leopards were combined to cover all 12 months of a year and to generate a general additive mixed model of seasonal home range use and seasonal resource use. We found 1) large variation in home ranges between sites during the monitoring period ranging minimally between 26.1 and 395.3km 2 (MCP) 2) Local convex hull home ranges were smaller compared to home ranges based on minimum convex polygons and kernels and yielded more biologically appropriate home range estimates 3) monthly home ranges of males were larger than females 4) female monthly home ranges decreased in summer, while male monthly range use remained stable throughout the year and, 5) while both sexes shared similar habitat preference in winter (steep south-western slopes at high elevation), our data suggest different habitat preferences between sexes in summer. Knowledge of the space use of threatened species is crucial for their conservation, and this is especially true for apex predators who often provide benefits for an entire ecosystem. Our study provides a preliminary understanding of the spatial ecology of this important species in an area of critical conservation concern.
Publisher: American Association for the Advancement of Science (AAAS)
Date: 21-04-2023
Abstract: Tasmanian devils have spawned two transmissible cancer lineages, named devil facial tumor 1 (DFT1) and devil facial tumor 2 (DFT2). We investigated the genetic ersity and evolution of these clones by analyzing 78 DFT1 and 41 DFT2 genomes relative to a newly assembled, chromosome-level reference. Time-resolved phylogenetic trees reveal that DFT1 first emerged in 1986 (1982 to 1989) and DFT2 in 2011 (2009 to 2012). Subclone analysis documents transmission of heterogeneous cell populations. DFT2 has faster mutation rates than DFT1 across all variant classes, including substitutions, indels, rearrangements, transposable element insertions, and copy number alterations, and we identify a hypermutated DFT1 lineage with defective DNA mismatch repair. Several loci show plausible evidence of positive selection in DFT1 or DFT2, including loss of chromosome Y and inactivation of MGA , but none are common to both cancers. This study reveals the parallel long-term evolution of two transmissible cancers inhabiting a common niche in Tasmanian devils.
Publisher: Wiley
Date: 06-2021
DOI: 10.1002/ECE3.7636
Abstract: Devil facial tumor disease (DFTD) is a transmissible cancer affecting Tasmanian devils Sarcophilus harrisii . The disease has caused severe population declines and is associated with demographic and behavioral changes, including earlier breeding, younger age structures, and reduced dispersal and social interactions. Devils are generally solitary, but social encounters are commonplace when feeding upon large carcasses. DFTD tumors can disfigure the jaw and mouth and so diseased in iduals might alter their diets to enable ingestion of alternative foods, to avoid conspecific interactions, or to reduce competition. Using stable isotope analysis (δ 13 C and δ 15 N) of whiskers, we tested whether DFTD progression, measured as tumor volume, affected the isotope ratios and isotopic niches of 94 infected Tasmanian devils from six sites in Tasmania, comprising four eucalypt plantations, an area of smallholdings and a national park. Then, using tissue from 10 devils s led before and after detection of tumors and 8 devils where no tumors were detected, we examined whether mean and standard deviation of δ 13 C and δ 15 N of the same in iduals changed between healthy and diseased states. δ 13 C and δ 15 N values were generally not related to tumor volume in infected devils, though at one site, Freycinet National Park, δ 15 N values increased significantly as tumor volume increased. Infection with DFTD was not associated with significant changes in the mean or standard deviation of δ 13 C and δ 15 N values in in idual devils s led before and after detection of tumors. Our analysis suggests that devils tend to maintain their isotopic niche in the face of DFTD infection and progression, except where ecological conditions facilitate a shift in diets and feeding behaviors, demonstrating that ecological context, alongside disease severity, can modulate the behavioral responses of Tasmanian devils to DFTD.
Publisher: American Association for the Advancement of Science (AAAS)
Date: 11-12-2020
Abstract: The emergence of a devastating transmissible facial cancer among Tasmanian devils over the past few decades has caused substantial concern for their future because these animals are already threatened by a regional distribution and other stressors. Little is known about the overall history and trajectory of this disease. Patton et al. used an epidemiological phylodynamic approach to reveal the pattern of disease emergence and spread. They found that low Tasmanian devil densities appear to be contributing to slower disease growth and spread, which is good news for Tasmanian devil persistence and suggests that care should be taken when considering options for increasing devil populations. Science , this issue p. eabb9772
Publisher: Oxford University Press (OUP)
Date: 08-03-2022
Abstract: Globally, many wild deer populations are actively studied or managed for conservation, hunting, or damage mitigation purposes. These studies require reliable estimates of population state parameters, such as density or abundance, with a level of precision that is fit for purpose. Such estimates can be difficult to attain for many populations that occur in situations that are poorly suited to common survey methods. We evaluated the utility of combining camera trap survey data, in which a small proportion of the s le is in idually recognizable using natural markings, with spatial mark–resight (SMR) models to estimate deer density in a variety of situations. We surveyed 13 deer populations comprising four deer species (Cervus unicolor, C. timorensis, C. elaphus, Dama dama) at nine widely separated sites, and used Bayesian SMR models to estimate population densities and abundances. Twelve surveys provided sufficient data for analysis and seven produced density estimates with coefficients of variation (CVs) ≤ 0.25. Estimated densities ranged from 0.3 to 24.6 deer km−2. Camera trap surveys and SMR models provided a powerful and flexible approach for estimating deer densities in populations in which many detections were not in idually identifiable, and they should provide useful density estimates under a wide range of conditions that are not amenable to more widely used methods. In the absence of specific local information on deer detectability and movement patterns, we recommend that at least 30 cameras be spaced at 500–1,000 m and set for 90 days. This approach could also be applied to large mammals other than deer.
Location: Australia
Location: France
Location: Switzerland
No related grants have been discovered for Sebastien Comte.