Biology subjects

Hamede, R. K.

Publications and source records attributed to Hamede, R. K..

6 recordsLinked to original sources

bioRxiv2023

Reference genome of the endangered eastern quoll (Dasyurus viverrinus)

The eastern quoll (Dasyurus viverrinus) is an endangered marsupial mesopredator native to Australia. Since the extirpation of the last mainland Australian populations in the late 20th century, wild populations of this species have been restricted to two islands at the far southern end of its historical range. Eastern quolls are the subject of captive breeding programs and attempts have recently been made to re-establish a population in mainland Australia through translocations. However, few resources currently exist to guide the genetic management of this species. Here, we generated a chromosome-scale reference genome for the eastern quoll, along with gene annotations supported by multi-tissue transcriptomes. Through comparisons with related species, we find that our reference genome is among the most complete marsupial assemblies currently available. Using this assembly, we infer the species demographic history and identify potential evidence of a long-term decline beginning in the late Pleistocene. Finally, we identify a deletion at the ASIP locus that likely drives differences in pelage color between the eastern quoll and the closely related Tasmanian devil (Sarcophilus harrisii). The genomic resources we present are valuable new tools for evolutionary and conservation genomic studies.

genomics↗

bioRxiv2023

A systematic global review of mammalian carnivore responses to production forests

O_LIUnmodified forests are increasingly rare worldwide, with forestry a major contributor to habitat modification. Extending conservation practices beyond protected areas is important to conserve forest ecosystems. C_LIO_LIWe investigate the response of native mammalian carnivores (both Order Carnivora and Family Dasyuridae) to production forests globally, including harvested native forest and timber plantations. We examine how carnivores recorded in production forests use these forests versus other land uses, particularly native and unharvested forest; how habitat use relates to threatened status, body size, diet, and harvesting method; carnivore responses to habitat features within production forests; and carnivore denning, breeding, and predation behaviour in production forests. C_LIO_LIWe review 294 studies recording 132 carnivore species in production forests. Carnivores generally show higher use of native and unharvested forests and lower use of agricultural land than production forests. Threatened species and large carnivores respond more negatively to production forests than non-threatened species and small carnivores respectively. Hypercarnivores respond more negatively than omnivores to plantations compared to native forest, but there was no difference in the use of harvested and unharvested native forest between these dietary groups. C_LIO_LISurprisingly, a high proportion of carnivore species use clearfelled more than unharvested native forest. In forest with partial harvesting or reduced-impact logging, most species show no difference in use between harvested and unharvested forest. C_LIO_LICarnivores generally respond positively to habitat features such as riparian areas and coarse woody debris. Several carnivores were recorded denning and breeding in production forests. Production forests often influence the prey availability, hunting success, and diet of carnivores. C_LIO_LIWe show that many carnivores use production forests, and how they respond to production forestry varies with species traits. We recommend that production forests are managed as valuable carnivore habitat, and highlight strategies to enhance the use of these forests by carnivores. C_LI

ecology↗

bioRxiv2023

Portable X-ray fluorescence for identifying harmful lead exposure in wild mammals through hair analysis

Lead exposure threatens scavenging wildlife globally. For inexpensive estimation of lead concentration in bones from avian scavengers, portable X-ray fluorescence (XRF) devices have been trialed. However, portable XRF has not been validated for tissue lead measurement in non-human mammalian scavengers. We evaluated portable XRF for hair lead measurement in the endangered Tasmanian devil (Sarcophilus harrisii). We first analyzed large ([~]1.0 g) hair samples from 39 deceased animals from southeastern Tasmania via portable XRF and then inductively-coupled plasma mass spectrometry (ICP-MS) (validation study). We then measured lead concentrations via portable XRF only in 61 small ([~]0.1 g) hair samples from live devils from a plantation landscape (plantation study). Portable XRF measures of hair lead levels were positively correlated with ICP-MS values (R2 = 0.61). In the validation study, 95% of sampled Tasmanian devils had relatively low lead levels (< 2 mg/kg), but the remaining two showed elevated lead levels (> 15 mg/kg). Mean lead levels in the plantation study and validation study were not significantly different. Our preliminary results suggest that portable XRF can provide a useful measure of differences in lead levels in wildife hair over a coarse scale. We provide recommendations for further research and refinement of this method. SynopsisPortable XRF can provide inexpensive and non-destructive analysis of environmental contaminants in wildlife. We present the first evaluation of portable XRF for analysis of lead contamination in mammalian scavenger hair.

ecology↗

bioRxiv2023

Movements and habitat selection of a marsupial carnivore in a modified landscape

Landscape modification is a major threat to carnivores worldwide, but modified landscapes can also provide important habitat for these species, as protected areas alone are insufficient. Understanding how carnivores use modified landscapes, such as production forests, can inform management strategies to improve the value of these landscapes to carnivores. Little is known about habitat selection by marsupial carnivores in production forests, where they occupy a similar ecological niche to their more well-studied eutherian counterparts. We used GPS tracking, Hidden Markov Models, and Manlys selection ratios to identify the habitat selected in 3 behavioral states by the largest marsupial carnivore, the Tasmanian devil (Sarcophilus harrisii), in a timber plantation-dominated landscape. Behavioral states were approximated as: state 1, resting or feeding at a carcass; state 2, foraging; and state 3, travel. Devils did not show preferences for any of native forest, native grassland, and plantation in any behavioral state. Within plantations, devils preferred a plantation age of 4-7 years (selection ratio [wi] = 1.52). Devils preferred roads (state 1: wi = 2.71, state 2: wi = 2.48, state 3: wi = 2.97) and plantation edges (state 1: wi = 2.38, state 2: wi = 2.24, state 3: wi = 2.78) in all behavioral states, and moved faster on roads and edges than away from them. Together, our results indicate devils use road and edges for foraging (scavenging and hunting) and travel. No measured habitat variables influenced devil home range size. To support devils in plantation landscapes, we recommend maintaining a heterogeneous landscape of different plantation ages and native remnants and reducing the risk of vehicle collisions by minimizing forestry traffic at night. Tasmanian devils share similar adaptable traits to generalist eutherian carnivore species in their use of modified landscapes. Plantations can provide valuable habitat for this and other threatened predator species.

ecology↗

bioRxiv2023

Faecal glucocorticoid metabolite levels of intensive captive, free-range captive, and wild Tasmanian devils

Captivity can alter the stress physiology and behaviour of an animal in both the short- and long-term through repetitive exposure to novel stressors and, subsequently, may reduce the success of conservation efforts such as translocation and reintroduction. The Tasmanian devil (Sarcophilus harrisii) is threatened with extinction from a fatal facial tumour disease which has led to the establishment of an insurance meta-population designed for future reintroductions of disease-free devils. The meta-population is comprised of intensive captive and free-range captive environments; however, no study has yet examined the long-term physiological implications of captivity on devils. We used non-invasive faecal glucocorticoid metabolite (FGM) monitoring to determine if there were any differences in adrenal activity between intensive captive, free-range captive, and wild devils. FGMs were not age- or sexdependent, and we found that all population-types had similar intra-population variability and mean FGMs. In conclusion, both types of captive environment maintain stress profiles similar to wild devils.

zoology↗

bioRxiv2018

Individual and temporal variation in pathogen load predicts long-term impacts of an emerging infectious disease

Emerging infectious diseases increasingly threaten wildlife populations. Most studies focus on managing short-term epidemic properties, such as controlling early outbreaks. Predicting long-term endemic characteristics with limited retrospective data is more challenging. We used individual-based modelling informed by individual variation in pathogen load and transmissibility to predict long-term impacts of a lethal, transmissible cancer on Tasmanian devil (Sarcophilus harrisii) populations. For this, we employed Approximate Bayesian Computation to identify model scenarios that best matched known epidemiological and demographic system properties derived from ten years of data after disease emergence, enabling us to forecast future system dynamics. We show that the dramatic devil population declines observed thus far are likely attributable to transient dynamics. Only 21% of matching scenarios led to devil extinction within 100 years following devil facial tumour disease (DFTD) introduction, whereas DFTD faded out in 57% of simulations. In the remaining 22% of simulations, disease and host coexisted for at least 100 years, usually with long-period oscillations. Our findings show that pathogen extirpation or host-pathogen coexistence are much more likely than the DFTD-induced devil extinction, with crucial management ramifications. Accounting for individual-level disease progression and the long-term outcome of devil-DFTD interactions at the population-level, our findings suggest that immediate management interventions are unlikely to be necessary to ensure the persistence of Tasmanian devil populations. This is because strong population declines of devils after disease emergence do not necessarily translate into long-term population declines at equilibria. Our modelling approach is widely applicable to other host-pathogen systems to predict disease impact beyond transient dynamics.

epidemiology↗