Genetic analysis reveals spatial structure in an expanding introduced rusa deer population

Context. Rusa deer (Cervus timorensis), originally introduced in the 1860s, are still spreading in eastern Australia. The expanding peri-urban rusa deer population in the Illawarra region of New South Wales, Australia is having undesirable impacts on human and ecological communities, but the spatial structure of this population has not been investigated. Genetic information on invasive species is potentially useful in identifying management units to mitigate undesirable impacts. Aims. The aim of this study was to investigate population structure, characterise dispersal, and determine if natural and human-made landscape features affected gene flow in rusa deer invading the Illawarra region of New South Wales. Methods. We used reduced representation sequencing (DArT-Seq) to analyse single nucleotide polymorphisms distributed throughout the genomic DNA of rusa deer culled during a management program. We used admixture and Principal Component Analyses to investigate population structure with respect to natural and human-made landscape features, and we investigated whether our genetic data supported the presence of sex-biased dispersal. Key results. Genetic diversity was highest in the north, near the original introduction site. A railway line demarcated restricted gene flow. Surprisingly, the Illawarra escarpment, a prominent landscape feature, did not restrict gene flow. There was no evidence of sex-biased dispersal and seven individuals were identified as genetic outliers. Conclusions. The genetic structure of the Illawarra rusa deer population is consistent with individuals spreading south from their introduction site in Royal National Park. The population is not panmictic, and a landscape feature associated with urbanisation was associated with increased spatial genetic structure. Outliers could indicate hybridisation or secondary incursion events. Implications. Rusa deer can be expected to continue invading southwards in the Illawarra region, but landscape features associated with urbanisation might reduce dispersal across the landscape. The genetic structuring of the population identified three potential management units on which to prioritise ground shooting operations

Estimating deer density and abundance using spatial mark–resight models with camera trap data

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 sample is individually 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 individually 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

Human habitat modification, not apex scavenger decline, drives isotopic niche variation in a carnivore community

Top carnivores can influence the structure of ecological communities, primarily through competition and predation; however, communities are also influenced by bottom-up forces such as anthropogenic habitat disturbance. Top carnivore declines will likely alter competitive dynamics within and amongst sympatric carnivore species. Increasing intraspecific competition is generally predicted to drive niche expansion and/or individual specialisation, while interspecific competition tends to constrain niches. Using stable isotope analysis of whiskers, we studied the effects of Tasmanian devil Sarcophilus harrisii declines upon the population- and individual-level isotopic niches of Tasmanian devils and sympatric spotted-tailed quolls Dasyurus maculatus subsp. maculatus. We investigated whether time since the onset of devil decline (a proxy for severity of decline) and landscape characteristics affected the isotopic niche breadth and overlap of devil and quoll populations. We quantified individual isotopic niche breadth for a subset of Tasmanian devils and spotted-tailed quolls and assessed whether between-site population niche variation was driven by individual-level specialisation. Tasmanian devils and spotted-tailed quolls demonstrated smaller population-level isotopic niche breadths with increasing human-modified habitat, while time since the onset of devil decline had no effect on population-level niche breadth or interspecific niche overlap. Individual isotopic niche breadths of Tasmanian devils and spotted-tailed quolls were narrower in human-modified landscapes, likely driving population isotopic niche contraction, however, the degree of individuals’ specialisation relative to one another remained constant. Our results suggest that across varied landscapes, mammalian carnivore niches can be more sensitive to the bottom-up forces of anthropogenic habitat disturbance than to the top-down effects of top carnivore decline

Evolution and lineage dynamics of a transmissible cancer in Tasmanian devils.

Devil facial tumour 1 (DFT1) is a transmissible cancer clone endangering the Tasmanian devil. The expansion of DFT1 across Tasmania has been documented, but little is known of its evolutionary history. We analysed genomes of 648 DFT1 tumours collected throughout the disease range between 2003 and 2018. DFT1 diverged early into five clades, three spreading widely and two failing to persist. One clade has replaced others at several sites, and rates of DFT1 co-infection are high. DFT1 gradually accumulates copy number variants (CNVs) and its telomere lengths are short but constant. Recurrent CNVs reveal genes under positive selection, sites of genome instability and repeated loss of a small derived chromosome. Cultured DFT1 cell lines have increased CNV frequency and undergo highly reproducible convergent evolution. Overall, DFT1 is a remarkably stable lineage whose genome illustrates how cancer cells adapt to diverse environments and persist in a parasitic niche.This work was supported by grants from Wellcome (102942/Z/13/A), the National Science Foundation (DEB-1316549), the University of Tasmania Foundation (Eric Guiler Tasmanian Devil Research Grants), the Australian Research Council (DE 170101116) and a Philip Leverhulme Prize from the Leverhulme Trust. YMK was supported by a Herchel Smith Postgraduate Fellowship

Evolution and lineage dynamics of a transmissible cancer in Tasmanian devils

Devil facial tumour 1 (DFT1) is a transmissible cancer clone endangering the Tasmanian devil. The expansion of DFT1 across Tasmania has been documented, but little is known of its evolutionary history. We analysed genomes of 648 DFT1 tumours collected throughout the disease range between 2003 and 2018. DFT1 diverged early into five clades, three spreading widely and two failing to persist. One clade has replaced others at several sites, and rates of DFT1 coinfection are high. DFT1 gradually accumulates copy number variants (CNVs), and its telomere lengths are short but constant. Recurrent CNVs reveal genes under positive selection, sites of genome instability, and repeated loss of a small derived chromosome. Cultured DFT1 cell lines have increased CNV frequency and undergo highly reproducible convergent evolution. Overall, DFT1 is a remarkably stable lineage whose genome illustrates how cancer cells adapt to diverse environments and persist in a parasitic niche

Seasonal variation in the foraging activity of desert argali (Ovis ammon) in Mongolia

Debate remains whether energy maximizing or time minimizing strategies best explain foraging in ungulates. It has also been hypothesized that the capacity of an animal to dissipate body heat regulates animal activity. We investigated these hypotheses while measuring the daily activity of desert argali (Ovis ammon: Linnaeus,1758) for 12 months and relating the activity pattern to environmental seasonality. We found significant seasonal cycles in argali activity, with the greatest proportion of daytime in winter spent foraging, the greatest proportion of daytime in summer spent bedding. Consistent with an energy maximizing strategy, argali reduced all behaviors during the winter in favor of foraging, compensating for the increased energy demands of winter at a time of low forage quality. Consistent with a time minimization strategy, argali in summer significantly reduced foraging and spent more time bedding in shaded areas to avoid hyperthermia due to high ambient temperatures. Both optimal foraging and heat dissipation can be used to explain the observed foraging pattern. Foraging behavior in argali is best described by the extent to which the animals schedule their activities to meet their physiological demands, the way these demands are affected by environmental variables, and the time that is available to accomplish them.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

Villes connectées : détection du risque biologique

International audienceLa sécurité dans les villes est un enjeu majeur dans les pays européens. Le projet IMPETUS vise à développer une plateforme numérique pour améliorer la gestion des évènements.Parmi les outils disponibles, il apparait des manques pour la sécurisation. Un outil pour détecter une attaque biologique est proposé. Il fonctionne en continu et analyse de manière régulière la concentration en bactéries dans l’air. Il permet d’alerter lorsqu’une concentration mesurée présente une valeur supérieure à un seuil. Suite à cette alerte, une phase d’identification de l’organisme sera entreprise. Les campagnes d’essais réalisées dans 3 villes ont permis de montrer une différence entre le contenu microbien de l’air dans des salles vides, des salles avec des activités classiques et des salles avec une simulation d’attaque biologique

Villes connectées : détection du risque biologique

International audienceLa sécurité dans les villes est un enjeu majeur dans les pays européens. Le projet IMPETUS vise à développer une plateforme numérique pour améliorer la gestion des évènements.Parmi les outils disponibles, il apparait des manques pour la sécurisation. Un outil pour détecter une attaque biologique est proposé. Il fonctionne en continu et analyse de manière régulière la concentration en bactéries dans l’air. Il permet d’alerter lorsqu’une concentration mesurée présente une valeur supérieure à un seuil. Suite à cette alerte, une phase d’identification de l’organisme sera entreprise. Les campagnes d’essais réalisées dans 3 villes ont permis de montrer une différence entre le contenu microbien de l’air dans des salles vides, des salles avec des activités classiques et des salles avec une simulation d’attaque biologique

Villes connectées : détection du risque biologique

International audienceLa sécurité dans les villes est un enjeu majeur dans les pays européens. Le projet IMPETUS vise à développer une plateforme numérique pour améliorer la gestion des évènements.Parmi les outils disponibles, il apparait des manques pour la sécurisation. Un outil pour détecter une attaque biologique est proposé. Il fonctionne en continu et analyse de manière régulière la concentration en bactéries dans l’air. Il permet d’alerter lorsqu’une concentration mesurée présente une valeur supérieure à un seuil. Suite à cette alerte, une phase d’identification de l’organisme sera entreprise. Les campagnes d’essais réalisées dans 3 villes ont permis de montrer une différence entre le contenu microbien de l’air dans des salles vides, des salles avec des activités classiques et des salles avec une simulation d’attaque biologique

Are aga-born obese adults more metabolically healhty than sga-born obese individuals?

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