Targeted conservation genetics of the endangered chimpanzee

Populations of the common chimpanzee (Pan troglodytes) are in an impending risk of going extinct in the wild as a consequence of damaging anthropogenic impact on their natural habitat and illegal pet and bushmeat trade. Conservation management programmes for the chimpanzee have been established outside their natural range (ex situ), and chimpanzees from these programmes could potentially be used to supplement future conservation initiatives in the wild (in situ). However, these programmes have often suffered from inadequate information about the geographical origin and subspecies ancestry of the founders. Here, we present a newly designed capture array with ~60,000 ancestry informative markers used to infer ancestry of individual chimpanzees in ex situ populations and determine geographical origin of confiscated sanctuary individuals. From a test panel of 167 chimpanzees with unknown origins or subspecies labels, we identify 90 suitable non-admixed individuals in the European Association of Zoos and Aquaria (EAZA) Ex situ Programme (EEP). Equally important, another 46 individuals have been identified with admixed subspecies ancestries, which therefore over time, should be naturally phased out of the breeding populations. With potential for future re-introduction to the wild, we determine the geographical origin of 31 individuals that were confiscated from the illegal trade and demonstrate the promises of using non-invasive sampling in future conservation action plans. Collectively, our genomic approach provides an exemplar for ex situ management of endangered species and offers an efficient tool in future in situ efforts to combat the illegal wildlife trade.PF is supported by the Innovation Fund Denmark doctoral fellowship programme and the Candys Foundation. CF is supported by “la Caixa” doctoral fellowship programme. TSK is funded by Carlsberg grant CF19-0712 prepared within the framework of the HSE University Basic Research Program. TMB is supported by BFU2017-86471-P (MINECO/FEDER, UE), U01 MH106874 grant, Howard Hughes International Early Career, Obra Social “La Caixa” and Secretaria d’Universitats i Recerca and CERCA Programme del Departament d’Economia i Coneixement de la Generalitat de Catalunya (GRC 2017 SGR 880). EL is supported by CGL2017-82654-P (MINECO/FEDER, UE).Peer reviewe

Data and code for: The welfare problems of wide-ranging Carnivora reflect naturally itinerant lifestyles

Carnivora with naturally small annual home ranges can adjust well to the evolutionarily new environment of captivity, but wider-ranging species are vulnerable to stress. To investigate why, we identified eight correlates of home range size (reflecting energetic needs, movement, intra-specific interactions, and itinerant lifestyles). We systematically assessed whether these correlates predict welfare better than range size itself, using data on captive juvenile mortality (from 13,518 individuals across 42 species) and stereotypic route-tracing (456 individuals, 27 species). Rather than large ranges per se, itinerant lifestyles (quantified via ratios of daily to annual travel distances in nature) were found to confer risk, predicting greater captive juvenile losses and stereotypic time-budgets. This result advances our understanding of the evolutionary basis for welfare problems in captive Carnivora, helping to explain why naturally sedentary species (e.g. American mink) may breed even in intensive farm conditions, while others (e.g. polar bears, giant pandas) can struggle even in modern zoos/breeding centres. Naturally itinerant lifestyles involve decision-making and strategic shifts to new locations, suggesting that supplying more novelty, cognitive challenge and/or opportunities for control will be effective ways to meet these animals' motivational needs in captivity. Such findings could therefore assist with both collection planning and enclosure design

Data and code for: Feeding, mating, and animal wellbeing: New insights from Phylogenetic Comparative Methods

Some species tend to thrive in captivity, while others risk health and reproductive problems. This enables the use of Phylogenetic Comparative Methods (PCMs) to identify aspects of natural biology that predispose species to faring poorly or well. Risk factors can then suggest new ways to improve animal care. A steady trickle of studies has applied PCMs to animal welfare over the last two decades, Lewis et al. (1) providing the latest. Here we contextualise this new work and suggest further research it might inspire. Provided here are the data and R code for Figure 1 provided in a commentary on: (1) Lewis, K., M.O. Parker, L. Proops, and S.D. McBride, Risk factors for stereotypic behaviour in captive ungulates. Proceedings of the Royal Society B: Biological Sciences, 2022. 289(1983): p. 20221311

Communication Skills

PAPER PUBLICATION: This data set is linked to the following paper: The future of veterinary communication: partnership or persuasion? A qualitative investigation of veterinary communication in the pursuit of client behaviour change. Alison M. Bard, David C.J. Main, Anne M. Haase, Helen R. Whay, Emma J. Roe, Kristen K. Reyher. Accepted for publication in PLOS ONE January 2017: Journal reference PONE-D-16-35222R2. DATA: Data are comprised of 15 transcripts of role-play interactions between cattle veterinarians an an actress. The consent form completed by participants is also included for reference. These documents can be opened in any operating system that supports .txt files. ABSTRACT: Client behaviour change is at the heart of veterinary practice, where promoting animal health and welfare is often synonymous with engaging clients in animal management practices. In the medical realm, extensive research points to the link between practitioner communication and patient behavioural outcomes, suggesting that the veterinary industry could benefit from a deeper understanding of veterinarian communication and its effects on client motivation. Whilst extensive studies have quantified language components typical of the veterinary consultation, the literature is lacking in-depth qualitative analysis in this context. The objective of this study was to address this deficit, and offer new critical insight into veterinary communication strategies in the pursuit of client behaviour change. Role-play interactions (n=15) between UK cattle veterinarians and an actress experienced in medical and veterinary education were recorded, transcribed and analysed thematically. Analysis revealed that, overall, veterinarians tend to communicate in a directive style (minimal eliciting of client opinion, dominating the consultation agenda, prioritising instrumental support), reflecting a paternalistic role in the consultation interaction. Given this finding, recommendations for progress in the veterinary industry are made; namely, the integration of evidence-based medical communication methodologies into clinical training. Use of these types of methodologies may facilitate the adoption of more mutualistic, relationship-centred communication in veterinary practice, supporting core psychological elements of client motivation and resultant behaviour change

Communication Skills

PAPER PUBLICATION: This data set is linked to the following paper: The future of veterinary communication: partnership or persuasion? A qualitative investigation of veterinary communication in the pursuit of client behaviour change. Alison M. Bard, David C.J. Main, Anne M. Haase, Helen R. Whay, Emma J. Roe, Kristen K. Reyher. Accepted for publication in PLOS ONE January 2017: Journal reference PONE-D-16-35222R2. DATA: Data are comprised of 15 transcripts of role-play interactions between cattle veterinarians an an actress. The consent form completed by participants is also included for reference. These documents can be opened in any operating system that supports .txt files. ABSTRACT: Client behaviour change is at the heart of veterinary practice, where promoting animal health and welfare is often synonymous with engaging clients in animal management practices. In the medical realm, extensive research points to the link between practitioner communication and patient behavioural outcomes, suggesting that the veterinary industry could benefit from a deeper understanding of veterinarian communication and its effects on client motivation. Whilst extensive studies have quantified language components typical of the veterinary consultation, the literature is lacking in-depth qualitative analysis in this context. The objective of this study was to address this deficit, and offer new critical insight into veterinary communication strategies in the pursuit of client behaviour change. Role-play interactions (n=15) between UK cattle veterinarians and an actress experienced in medical and veterinary education were recorded, transcribed and analysed thematically. Analysis revealed that, overall, veterinarians tend to communicate in a directive style (minimal eliciting of client opinion, dominating the consultation agenda, prioritising instrumental support), reflecting a paternalistic role in the consultation interaction. Given this finding, recommendations for progress in the veterinary industry are made; namely, the integration of evidence-based medical communication methodologies into clinical training. Use of these types of methodologies may facilitate the adoption of more mutualistic, relationship-centred communication in veterinary practice, supporting core psychological elements of client motivation and resultant behaviour change

Some aspects of the antibacterial activity of bovine neutrophils in relation to staphylococcal mastitis /

Diss. Ph.D.: veterinary medicin

Beak lengths of young laying hens (pullets) from flocks provided with potential beak-blunting materials and from control flocks

Injurious Pecking, commonly controlled by beak trimming (BT) is a widespread issue in laying hens associated with thwarted foraging. This controlled study compared the effect in intact and beak-trimmed pullets of providing pecking pans to 8 treatment flocks from 6 weeks of age. Flocks (mean size 6,843) comprised 8 British Blacktail, 6 Lohmann Brown and 2 Bovans Brown. All young birds (6-7 weeks) pecked more frequently at the pecking pans (mean 40.4) than older pullets (mean 26.0, 23.3 pecks/bird/minute at 10-11 weeks and 14-15 weeks respectively) (

Data and R script for Neville, Andrews, Nettle and Bateson, 'Dissociating the effects of alternative early-life feeding schedules on the development of adult depression-like phenotypes'

The R script and raw data files for the paper 'Dissociating the effects of alternative early-life feeding schedules on the development of adult depression-like phenotypes', by Vikki Neville, Clare Andrews, Daniel Nettle and Melissa Bateson

The Camouflage Machine: Optimising protective colouration using deep learning with genetic algorithms

Evolutionary biologists frequently wish to measure the fitness of alternative phenotypes using behavioural experiments. However, many phenotypes are complex. For example colouration: camouflage aims to make detection harder, while conspicuous signals (e.g. for warning or mate attraction) require the opposite. Identifying the hardest and easiest to find patterns is essential for understanding the evolutionary forces that shape protective colouration, but the parameter space of potential patterns (coloured visual textures) is vast, limiting previous empirical studies to a narrow range of phenotypes. Here we demonstrate how deep learning combined with genetic algorithms can be used to augment behavioural experiments, identifying both the best camouflage and the most conspicuous signal(s) from an arbitrarily vast array of patterns. To show the generality of our approach, we do so for both trichromatic (e.g. human) and dichromat (e.g. typical mammalian) visual systems, in two different habitats. The patterns identified were validated using human participants; those identified as the best for camouflage were significantly harder to find than a tried-and-tested military design, while those identified as most conspicuous were significantly easier than other patterns. More generally, our method, dubbed the ‘Camouflage Machine’, will be a useful tool for identifying the optimal phenotype in high dimensional state-spaces