vortex R: an R package for post Vortex simulation analysis

1.Population viability analysis is an important tool for wildlife ecologists, geneticists and managers, which is used for the assessment of extinction risks, the evaluation of threatening processes and the establishment of conservation targets. 2.Vortex is among the leading population modelling software and the latest release includes an automated sensitivity test module. However, an equivalent automation of the post-simulation data inspection and analysis is currently missing. 3.vortexR is an R package to automate the analysis and visualisation of outputs from the population viability modelling software Vortex. vortexR facilitates collating Vortex output files, data visualisation and basic analyses (e.g. pairwise comparisons of scenarios), as well as providing more advanced statistics, such as searching for the best regression model(s) from a list of predictors to investigate the main effect and the interaction effects of the variables of interest. 4.This package speeds up and greatly facilitates the reproducibility and portability of post-simulation analysis results

dartR v2: An accessible genetic analysis platform for conservation, ecology and agriculture

Innumerable approaches to analyse genetic data are now available to guide conservation, ecological and agricultural projects. However, streamlined and accessible tools are needed to bring these approaches within the reach of a broader user base. dartR was released in 2018 to lessen the intrinsic complexity of analysing single nucleotide polymorphisms (SNPs) and dominant markers (presence/absence of amplified sequence tags) by providing user-friendly data quality control and marker selection functions. dartR users have grown steadily since its release and provided valuable feedback on their interaction with the package allowing us to enhance dartR capabilities. Here, we present Version 2 of dartR. In this version, we substantially increased the number of available functions from 45 to 144. In addition to improved functionality, we focused on enhancing the user experience by extending plot customisation, function standardisation, increasing user support and function speed. dartR provides functions for various stages in analysing genetic data, from data manipulation to reporting. dartR provides many functions for importing, exporting and linking to other packages, to provide an easy-to-navigate conduit between data generation and analysis options already available via other packages. We also implemented simulation functions whose results can be analysed seamlessly with several other dartR functions. As more methods and approaches mature to inform conservation, we envision that accessible platforms to analyse genetic data will play a crucial role in translating science into practice

Monitoring of Alarm Reactions of Red Deer (Cervus elaphus) in a Captive Population in Paneveggio Pale di San Martino Natural Park

Simple Summary After several years of inappropriate management, the pasture inside the enclosure for captive red deer in Paneveggio Pale di San Martino regional Park (TN, Italy) lost its nutritional value, due to the expansion of unpalatable tall grasses. Therefore, several measures to restore a suitable pasture composition were needed. The mowing activity represents a disturbance for the captive deer, which negatively affects the animals' well-being. To establish the more appropriate times/days to perform activities inside the enclosure, we observed the alarm reactions and relative intensity of animals exposed to different visual stimuli presented inside and outside the enclosure. Some differences were highlighted between the males and the nursery (females and fawns) groups. Considering the deer biology and the studied location, the best months in which it would be possible to plan activities inside the enclosure are March, April (if the snow is not present) and August. Data elaboration suggests that the best day to perform activities inside the enclosure is Wednesday because the animals showed less sensitivity to disturbances; Tuesday and Thursday may also be considered additional suitable days. The study analyzes red deer responses to disturbances during the day and different exposures to tourists, to establish the more appropriate times to carry out activities inside the Paneveggio deer enclosure. The alarm reactions of red deer were observed after presenting different types of visual stimuli inside and outside the fence, in order to answer some questions: Which stimuli produce the strongest reactions from the animals? Do animals differently react to stimuli presented outside and inside the fence? On which days and times are the animals more sensitive to disturbances? Are there different reactions between the males and females? The results suggest that the red deer adversely react to the disturbance at different degrees of intensity in relation to day, sex, tourist and where the stimuli are presented. It was observed that during the days with the highest tourist presence, the animals were particularly alarmed; discomfort accumulation produced the highest number of alarm reactions on Monday. For these reasons, it would be opportune to manage the pasture on Tuesday, Wednesday and Thursday, scheduled at specific times of day, preferably far from the estimated presence of tourists

Role of prolactin, growth hormone and insulin-like growth factor 1 in mammary gland involution in the dairy cow.

Bovine mammary involution, an important process for subsequent lactations, is characterized by loss of epithelial cells by apoptosis, but its hormonal regulation is still not well defined. Prolactin (PRL) and growth hormone (GH) play a specific role on rat mammary gland apoptosis, through insulin-like growth factor 1 (IGF-1) and the IGF binding protein (IGFBP) system. The purpose of our investigation was to determine the possible role of PRL, GH, and IGF-1 on cell survival and on IGFBP-5 expression in the bovine mammary gland. Mammary gland explants were cultured in the presence of cortisol, 17beta-estradiol, progesterone, insulin, PRL, GH, and IGF-1 and with the same treatment but without PRL, GH or IGF-1, respectively. After 24 h of culture, we determined the level of apoptosis through evaluation of DNA laddering in the oligonucleosomal fraction and examined IGFBP-5 messenger RNA (mRNA) expression. The results show a high level of DNA laddering and an increase in IGFBP-5 mRNA content in mammary explants cultured in the absence of PRL, GH, or IGF-I with respect to explants treated with all hormones. Moreover, explants cultured in presence of PRL, GH, or IGF-I show a low level of DNA laddering and IGFBP-5 expression with respect to explants cultured without any hormones. These data demonstrate a relationship between levels of apoptosis and IGFBP-5 mRNA expression in the bovine mammary gland and confirm the involvement of this binding protein programmed cell death and its relationship with the main lactogenic hormones

Detection and characterisation of an Endogenous Betaretrovirus in Australian Wild Deer

Endogenous retroviruses (ERVs) are the remnants of past retroviral infections that once invaded the host’s germline and were vertically transmitted. ERV sequences have been reported in mammals, but their distribution and diversity in cervids are unclear. Using next-generation sequencing, we identified a nearly complete genome of an endogenous betaretrovirus in fallow deer (Dama dama). Further genomic analysis showed that this provirus, tentatively named cervid endogenous betaretrovirus 1 (CERV β1), has typical betaretroviral genome features (gag-pro-pol-env) and the betaretrovirus-specific dUTPase domain. In addition, CERV β1 pol sequences were detected by PCR in the six non-native deer species with wild populations in Australia. Phylogenetic analyses demonstrated that CERV β1 sequences from subfamily Cervinae clustered as sister taxa to ERV-like sequences in species of subfamily Muntiacinae. These findings, therefore, suggest that CERV β1 endogenisation occurred after the split of these two subfamilies (between 3.3 and 5 million years ago). Our results provide important insights into the evolution of betaretroviruses in cervids

Genetic diversity loss in a biodiversity hotspot: ancient DNA quantifies genetic decline and former connectivity in a critically endangered marsupial

The extent of genetic diversity loss and former connectivity between fragmented populations are often unknown factors when studying endangered species. While genetic techniques are commonly applied in extant populations to assess temporal and spatial demographic changes, it is no substitute for directly measuring past diversity using ancient DNA (aDNA). We analysed both mitochondrial DNA (mtDNA) and nuclear microsatellite loci from 64 historical fossil and skin samples of the critically endangered Western Australian woylie (Bettongia penicillata ogilbyi), and compared them with 231 (n = 152 for mtDNA) modern samples. In modern woylie populations 15 mitochondrial control region (CR) haplotypes were identified. Interestingly, mtDNA CR data from only 29 historical samples demonstrated 15 previously unknown haplotypes and detected an extinct divergent clade. Through modelling, we estimated the loss of CR mtDNA diversity to be between 46% and 91% and estimated this to have occurred in the past 2000-4000 years in association with a dramatic population decline. In addition, we obtained near-complete 11-loci microsatellite profiles from 21 historical samples. In agreement with the mtDNA data, a number of 'new' microsatellite alleles was only detected in the historical populations despite extensive modern sampling, indicating a nuclear genetic diversity loss >20%. Calculations of genetic diversity (heterozygosity and allelic rarefaction) showed that these were significantly higher in the past and that there was a high degree of gene flow across the woylie's historical range. These findings have an immediate impact on how the extant populations are managed and we recommend the implementation of an assisted migration programme to prevent further loss of genetic diversity. Our study demonstrates the value of integrating aDNA data into current-day conservation strategies

Sonic hedgehog is expressed in human brain arteriovenous malformations and induces arteriovenous malformations in vivo

Abnormalities in arterial versus venous endothelial cell identity and dysregulation of angiogenesis are deemed important in the pathophysiology of brain arteriovenous malformations (AVMs). The Sonic hedgehog (Shh) pathway is crucial for both angiogenesis and arterial versus venous differentiation of endothelial cells, through its dual role on the vascular endothelial growth factor/Notch signaling and the nuclear orphan receptor COUP-TFII. In this study, we show that Shh, Gli1 (the main transcription factor of the Shh pathway), and COUP-TFII (a target of the non-canonical Shh pathway) are aberrantly expressed in human brain AVMs. We also show that implantation of pellets containing Shh in the cornea of Efnb2/LacZ mice induces growth of distinct arteries and veins, interconnected by complex sets of arteriovenous shunts, without an interposed capillary bed, as seen in AVMs. We also demonstrate that injection in the rat brain of a plasmid containing the human Shh gene induces the growth of tangles of tortuous and dilated vessels, in part positive and in part negative for the arterial marker \u3b1SMA, with direct connections between \u3b1SMA-positive and -negative vessels. In summary, we show that the Shh pathway is active in human brain AVMs and that Shh-induced angiogenesis has characteristics reminiscent of those seen in AVMs in humans

Understanding conflict among experts working on controversial species: A case study on the Australian dingo

Expert elicitation can be valuable for informing decision-makers on conservation and wildlife management issues. To date, studies eliciting expert opinions have primarily focused on identifying and building consensus on key issues. Nonetheless, there are drawbacks of a strict focus on consensus, and it is important to understand and emphasize dissent, too. This study adopts a dissensus-based Delphi to understand conflict among dingo experts. Twenty-eight experts participated in three rounds of investigation. We highlight disagreement on most of the issues explored. In particular, we find that disagreement is underpinned by what we call “conflict over values” and “conflict over evidence.” We also note the broader role played by distrust in influencing such conflicts. Understanding and recognizing the different elements shaping disagreement is critical for informing and improving decision-making and can also enable critique of dominant paradigms in current practices. We encourage greater reflexivity and open deliberation on these aspects and hope our study will inform similar investigations in other contexts.Valerio Donfrancesco, Benjamin L. Allen, Rob Appleby, Linda Behrendorff, Gabriel Conroy, Mathew S. Crowther, Christopher R. Dickman, Tim Doherty, Bronwyn A. Fancourt, Christopher E. Gordon, Stephen M. Jackson, Chris N. Johnson, Malcolm S. Kennedy, Loukas Koungoulos, Mike Letnic, Luke K.-P. Leung, Kieren J. Mitchell, Bradley Nesbitt, Thomas Newsome, Carlo Pacioni, Justine Phillip, Brad V. Purcell, Euan G. Ritchie, Bradley P. Smith, Danielle Stephens, Jack Tatler, Lily M. van Eeden, Kylie M. Cairn