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Data for: Love thy neighbour: feral buffalo show greater space use, resource overlap and encounters during the wet season in the Northern Territory
<p>The code, data, and R objects in this repository accompany a paper titled 'Love thy neighbour: feral buffalo show greater space use, resource overlap and encounters during the wet season in the Northern Territory'.</p> <p>In this paper we used spatially explicit movement models to understand buffalo movement and social behaviour to provide decision support to wildlife managers. We used continuous time movement models to produce autocorrelated kernel density estimates of buffalo home ranges and encounter space from 126,567 locations from 17 buffalo GPS tracked from November 2018 to April 2019. We compared the movement, space use and social behaviour of buffalo between the wet and dry season of the Djelk area, when resource availability is vastly different in the wetland areas of the Northern Territory. Results from these models can be used by land holders, traditional owners, and wildlife managers to make evidence-based decisions to optimize buffalo management in respect to disease risk, sustainable harvest, and damage to environmental and cultural assets.</p> <p>The R Markdown, and accompanying data detail the modelling process from data pre-processing, fitting home ranges, comparing home range overalp and estimating social encounter area for the buffalo over three seasonal periods. Estimating home ranges can be computationally taxing and re-creating home range estimates for each buffalo can take several hours depending on the computing power of the user so intermediate outputs have also been included. </p>
Fig. 1 in Occurrence of Amblyomma mixtum on the water buffalo (Bubalus bubalis) in Mexico
Fig. 1. Occurrence of Amblyomma mixtum in the perianal region of a water buffalo (adult stage).
Figure 1 in Investigation of GH and GHR Alu I gene polymorphisms on meat yields in Anatolian water buffalo breed using PCR-RFLP method
Figure 1. PCR products of exons 4 and 5 of the GH gene (428-bp band, M: 100-bp DNA ladder).
Figure2 in Comparative Study in Habitat Suitability Analysis of Wild Water Buffalo (Bubalus arnee) in Two Flood Plains of Chitwan National Park (CNP), Nepal
Figure2. Methodological Flow Diagram
Figure6 in Comparative Study in Habitat Suitability Analysis of Wild Water Buffalo (Bubalus arnee) in Two Flood Plains of Chitwan National Park (CNP), Nepal
Figure6. IVI of Tree Species in Western Sector
Figure5 in Comparative Study in Habitat Suitability Analysis of Wild Water Buffalo (Bubalus arnee) in Two Flood Plains of Chitwan National Park (CNP), Nepal
Figure5. IVI of Tree Species in Eastern Sector
Figure1 in Comparative Study in Habitat Suitability Analysis of Wild Water Buffalo (Bubalus arnee) in Two Flood Plains of Chitwan National Park (CNP), Nepal
Figure1. Study Area
Figure4 in Comparative Study in Habitat Suitability Analysis of Wild Water Buffalo (Bubalus arnee) in Two Flood Plains of Chitwan National Park (CNP), Nepal
Figure4. IVI of Grass Species in Western Sector
Figure3 in Comparative Study in Habitat Suitability Analysis of Wild Water Buffalo (Bubalus arnee) in Two Flood Plains of Chitwan National Park (CNP), Nepal
Figure3. IVI of Grass Species in Eastern Sector
Figure8 in Comparative Study in Habitat Suitability Analysis of Wild Water Buffalo (Bubalus arnee) in Two Flood Plains of Chitwan National Park (CNP), Nepal
Figure8. Habitat Suitability Map of Western Flood Plain
Figure7 in Comparative Study in Habitat Suitability Analysis of Wild Water Buffalo (Bubalus arnee) in Two Flood Plains of Chitwan National Park (CNP), Nepal
Figure7. Habitat Suitability Map of Eastern Flood Plain
African buffalo helminth β-diversity
<p>Concepts of β-diversity originally developed for use in free-living communities have been widely applied to parasite communities to gain insight into how infection risk changes with local conditions by comparing parasite communities across abiotic and biotic gradients. Factors shaping β-diversity in communities of immature parasites, such as larvae, are largely unknown. This is a key knowledge gap as larvae are frequently the infective life stage and understanding variation in these larval communities is thus key for disease prevention. Our goal was to uncover links between β-diversity of parasite communities at different life stages; therefore, we used gastrointestinal nematodes infecting African buffalo in Kruger National Park, South Africa to investigate within-host and extra-host drivers of adult and larval parasite community similarity.</p>
Buffalo close association matrices: Kruger National Park, South Africa
<div class="ListContainerWrapper SCXW115066823 BCX0"> <ol class="NumberListStyle1 SCXW115066823 BCX0"> <li class="OutlineElement Ltr SCXW115066823 BCX0"> <p class="Paragraph SCXW115066823 BCX0"><span class="TextRun SCXW115066823 BCX0"><span class="NormalTextRun SCXW115066823 BCX0">Many infectious pathogens are shared through social interactions, and examining host connectivity has offered valuable insights for understanding patterns of pathogen transmission across wildlife species. African buffalo are social ungulates and i</span><span class="NormalTextRun SCXW115066823 BCX0">mportant reservoirs of </span><span class="ContextualSpellingAndGrammarError SCXW115066823 BCX0">directly-transmitted</span><span class="NormalTextRun SCXW115066823 BCX0"> pathogens that impact numerous wildlife and livestock species. </span></span><span class="EOP SCXW115066823 BCX0"> </span></p> </li> </ol> </div> <div class="ListContainerWrapper SCXW115066823 BCX0"> <ol class="NumberListStyle1 SCXW115066823 BCX0"> <li class="OutlineElement Ltr SCXW115066823 BCX0"> <p class="Paragraph SCXW115066823 BCX0"><span class="TextRun SCXW115066823 BCX0"><span class="NormalTextRun SCXW115066823 BCX0">Here, we analyzed African buffalo social networks to quantify variation in close contacts, examined drivers of contact heterogeneity, and investigat</span><span class="NormalTextRun SCXW115066823 BCX0">ed how the observed contact patterns affect pathogen invasion likelihoods for a wild social ungulate. </span></span><span class="EOP SCXW115066823 BCX0"> </span></p> </li> </ol> </div> <div class="ListContainerWrapper SCXW115066823 BCX0"> <ol class="NumberListStyle1 SCXW115066823 BCX0"> <li class="OutlineElement Ltr SCXW115066823 BCX0"> <p class="Paragraph SCXW115066823 BCX0"><span class="TextRun SCXW115066823 BCX0"><span class="NormalTextRun SCXW115066823 BCX0">We collected continuous association data using proximity collars and sampled host traits approximately every two months during a 15-month study period in</span><span class="NormalTextRun SCXW115066823 BCX0"> Kruger National Park, South Africa. </span></span><span class="EOP SCXW115066823 BCX0"> </span></p> </li> </ol> </div> <div class="ListContainerWrapper SCXW115066823 BCX0"> <ol class="NumberListStyle1 SCXW115066823 BCX0"> <li class="OutlineElement Ltr SCXW115066823 BCX0"> <p class="Paragraph SCXW115066823 BCX0"><span class="TextRun SCXW115066823 BCX0"><span class="NormalTextRun SCXW115066823 BCX0">Although the observed herd was well connected, with most individuals contacting each other during each bimonthly interval, our analyses revealed striking heterogeneity in close-contact associations among herd members. </span><span class="NormalTextRun SCXW115066823 BCX0">Network analysis showed that individual connectivity was stable over time and that individual age, sex, reproductive status, and pairwise genetic relatedness were important predictors of buffalo connectivity. Calves were the most connected members of the h</span><span class="NormalTextRun SCXW115066823 BCX0">erd, and adult males were the least connected. These findings highlight the role susceptible calves may play in the transmission of pathogens within the herd. We also demonstrate that, at time scales relevant to infectious pathogens found in nature, the ob</span><span class="NormalTextRun SCXW115066823 BCX0">served level of connectivity affects pathogen invasion likelihoods for a wide range of infectious periods and </span><span class="SpellingError SCXW115066823 BCX0">transmissibilities</span><span class="NormalTextRun SCXW115066823 BCX0">. </span></span><span class="EOP SCXW115066823 BCX0"> </span></p> </li> </ol> </div> <div class="ListContainerWrapper SCXW115066823 BCX0"> <ol class="NumberListStyle1 SCXW115066823 BCX0"> <li class="OutlineElement Ltr SCXW115066823 BCX0"> <p class="Paragraph SCXW115066823 BCX0"><span class="TextRun SCXW115066823 BCX0"><span class="NormalTextRun SCXW115066823 BCX0">Ultimately, our study identifies key predictors of social connectivity in a social ungulate and illustrates how contact heter</span><span class="NormalTextRun SCXW115066823 BCX0">ogeneity, even within a highly connected herd, can shape pathogen invasion likelihoods. </span></span><span class="EOP SCXW115066823 BCX0"> </span></p> </li> </ol> </div>
African buffalo helminth β-diversity
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Buffalo close association matrices: Kruger National Park, South Africa
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Data from: A natural gene drive system influences bovine tuberculosis susceptibility in African buffalo: possible implications for disease management
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Data from: Why did the buffalo cross the park? Resource shortages, but not infections, drive dispersal in female African buffalo (Syncerus caffer)
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Pathogen group-specific risk factors for intra-mammary infection in water buffalo
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Spermatozoa RRBS data: Post-Bismark aligned files extracted for the methylation call for every single C in the CpG context of sperm cells of Murrah buffalo bulls under heat stress
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Data from: Host immunity, nutrition and coinfection alter longitudinal infection patterns of schistosomes in a free ranging African buffalo population
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.