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    Island biogeography and human practices drive ecological connectivity in mosquito species richness in the Lakshadweep Archipelago

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    Exceptional longevity in northern peripheral populations of Wels catfish (Siluris glanis)

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    A global inventory of animal diversity measured in different grazing treatments

    Synthesis and data extractionData were collected using a literature search of Web of Science for peer-reviewed journal articles published between 1970 and November 2019. We conducted two sets of searches to capture grazing with discrete comparisons (e.g., grazed/ungrazed, moderate vs. heavy intensity grazing) and a range of grazing intensities. The search terms used for each were as follows 1) (graz* OR livestock) AND (exclosure* OR exclusion OR exclude* OR ungrazed OR retire* OR fallow* OR fence* OR paddock*), 2) (“grazing intensity” OR “grazing gradient” OR “stocking rate” OR “rotation*grazing”). Our synthesis includes domesticated and wild grazer species, with the latter defined as an undomesticated species naturally occurring in the study area during the study. Wild grazers are typically native species to the region (e.g., the American bison in Western North America) but can include non-native species that are naturalized in the area (e.g., feral horses on Sable Island).We excluded any study that did not test the effect of grazing animals. A grazer was defined using the definition provided by the authors of the respective study to account for the proportion of forage types in a herbivore’s diet that varies between seasons and habitats. For example, we included animals where their diet is assumed to come from all (e.g., cattle, sheep), most (e.g., wapiti, kangaroos), or some (e.g., deer species) grass species. However, within the included studies, these animals were classified as grazers as most of their diet was grass for the duration of the study. For added clarity about the herbivore composition in each study, we extracted a list of any herbivores listed in the paper regardless of foraging type or if any data was provided.We only included studies that measured animal diversity or abundance as a response variable and included data we could extract or contact the author to obtain9. We included any study with a grazing treatment and included observations within these studies of any grazed and ungrazed sites. All studies with grazing included a comparison to either ungrazed sites, different grazing practices (e.g., cattle vs. sheep), and/or differences in intensities (e.g., heavy/light, extensive/intensive). Studies that only measured plants or soil biota were excluded because syntheses of grazing effects on these groups have already been conducted7,11,12, and our goal was to provide a robust inventory of animal diversity. However, if a study included plants, lichens, or fungi in addition to animals, we included this data. Studies discussing marine grazing or aquatic systems were also excluded. From these preliminary filters, we identified 3,489 published manuscripts. We reviewed these 3,489 published articles and found 245 studies that surveyed animals in grazed sites. In total, we extracted 16,105 observations for over 1,200 species.We extracted 28 variables that focus on management systems, assemblages of grazer species, ecosystem characteristics, and survey type (Table 1). The latitudes, longitudes, and elevations of each study were included when provided for use with geospatial data. In addition, we included variables about the study site’s disturbance history, including last time grazed, if a flood event or fire had occurred, if fertilization was used, if the area was open or fenced off, and if the area was publicly or privately owned. Furthermore, the timeline for the study (i.e., the years the authors initiated and completed the study) was also provided. Study initiation was described by the authors and could include when the grazing treatment started, another treatment was applied, and/or animal surveys began. These timeline columns can be useful in identifying long-term studies and differentiating single grazing events or multi-year experiments. Finally, we generalized the characteristics of the ecosystem of the sites used in each study based on the climate and dominant vegetation.Table 1 The attributes and description of the metadata.csv file that lists the general characteristics of each study.Full size tableWithin the grazing data, we included information about the grazer when provided, including any measurement of the intensity of grazing (e.g., animals per hectare, the height of residual vegetation). We also provided two columns that detailed whether the study tested grazing effects using a discrete comparison or gradient of intensities (Table 2). The value for the target specimens extracted may represent either a single observation or a summarized statistic (e.g., mean animals per site). We identify unique observations as “count” and summarized statistics by the metric used, such as mean, median, standard deviation (column stat in grazingData.csv). When possible, we also included any record of other grazers that co-occurred with the observed grazer species. The data for these variables were extracted from the papers by a single researcher who read through each paper and filled in available data on the mentioned variables.Table 2 The attributes and description of the grazingData.csv file that has the extracted data from each study.Full size tableWe extracted information about the target specimen, site, year, experimental replicate, and response estimate (Table 2). We included multiple categorizations of the target species to assist future users in synthesizing similar taxa (Table 2). When a species name or genus was provided, we conducted a search query (see detailedTaxa.r) through the global biodiversity information facility (GBIF.org) to determine the taxonomic classification of the species, including kingdom, phylum, order, class, and family. When a species name was not included, we provided the lowest taxonomic resolution available. We also included a broader classification of ‘higherTaxon’ to distinguish plants, fungi, vertebrates, and invertebrates. These columns may help group similar species together for community-level analyses. Lastly, we included the characteristic of the plant community (i.e., planted or self-assembled, tilled, and its vegetation class) when plant data was reported.Patterns among studiesMost of the studies took place in the United States (26%), Australia (9%), and the United Kingdom (7%) (Fig. 1). As expected, most studies were conducted in grasslands (n = 206), followed by forests (n = 92) and shrublands (n = 82) (Fig. 2). We included publications from the entire range of years (i.e., 1970–2019), but most were published after 2000 (76%). The number of sites in a study and the study duration showed a bimodal distribution with a long tail (Fig. 3). Most studies included one to eight different sites, and few were conducted longer than five years (Fig. 3). A few studies were highly replicated, while many were limited in their replication (Fig. 3).Fig. 1The locations of studies that measured the response of animals to domestic or wild grazing.Full size imageFig. 2The number of grazing studies conducted in ecosystems around the world. We generalized the characteristics of the ecosystem of the sites used in each study based on the climate and dominant vegetation community. We separated grassland communities into those that were (a) semi-natural without recent cultivation or seeding (self-assembled), (b) recently cultivated or had supplemental seeding (planted/cultivated), and (c) a combination of both. In most grasslands, the cultivation history was unclear.Full size imageFig. 3The number of independent sites surveyed and the duration of each study. Most studies were conducted at either a single site or with some replication (e.g., 6–8 sites). Similarly, most studies were either conducted in one year ( >30%) or over a few years (e.g., 3–6 years). Very few studies (32) or lasted longer than 15 years.Full size imageSite and management data were not reported in all studies, as found in other reviews of grazing impacts on ecological processes10. Of the studies that mentioned the ownership status of the land used, 46% were on private land, 42% were on public land, and 12% had a history of both public and private ownership. Most studies included binary comparisons (56%) of grazed vs. ungrazed plots or sites, though some also included a discrete (22%) or a continuous estimate of grazing intensities (18%).Of the studies that reported plant community origin, 76% were self-assembled, 17% were planted communities, and the remaining included sites were a combination of the two. Domesticated grazers as the focal herbivore made up 67% of the studies, with 12% of the studies having wild grazers as the focal herbivore, and 21% having both present. Domesticated livestock were the most frequently surveyed grazers including cattle (n = 164), sheep (n = 83), and horses (n = 21), but studies are included that examined wild grazers, such as kangaroos (n = 6), elephants (n = 5), and pronghorn (n = 5) (Fig. 4).Fig. 4The frequency in which a study reported herbivores. We included any mention of herbivores regardless of being a grazer, browser, granivore, or other class. This list was obtained by the text within the manuscript and is different than the representation of species in the database (i.e., the measured species).Full size image More

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    Intolerant baboons avoid observer proximity, creating biased inter-individual association patterns

    All research methods included in this study were performed in accordance with the relevant guidelines and regulations, under ZA/LP/81996 research permit, with ethical approval from the Animal Welfare Ethical Review Board (AWERB) at Durham University. The authors confirm the study was carried out in compliance with ARRIVE guidelines.All inter-individual association data was collected between June 2018 and June 2019 on a wild habituated group of Afro-montane chacma baboons in the western Soutpansberg Mountains, South Africa (central coordinates S29.44031°, E23.02217°) (for study site description see2). The study group was habituated circa 2005 and was the focus of intermittent research attention until 2014. The study area experienced long-term anthropogenic activities (local farming, forestry, and residences) prior to 2005, as such, consistent interactions with humans have been ongoing with this population for some time. From 2007 onwards numerous researchers were able to collect expansive datasets on the study group (e.g. Refs.17,18), indicating that habituation was at a typical level found elsewhere (also validated by AA and RH, who had researched chacma baboons elsewhere). From 2014 the group received full day (dawn until dusk) follows 3–4 days a week, with occasional gaps of up to 5 weeks in duration. These gaps did not appear to effect habituation levels, likely due to the presence of other researchers at the field site who always tried to act benignly when encountering the habituated group. The follow schedule was designed so that the study group retained as much of their natural interactions with predators as possible by ensuring the baboons spent significant time without observers who may influence the frequency and nature of predator–prey interactions19.The study site was located in a private nature reserve and the study group was not hunted during observation gaps or engaged in any conflict with humans, other than occasionally being scared (chasing, yelling, throwing stones etc.) from a small plantation by local workers, usually resulting in alarm barks and fleeing responses. However, the study group appeared adept at recognising the differences between researchers and these threats20. The majority of the study group’s home-range typically overlapped with the core area of the Lajuma Research Centre, and as a result, interactions with staff living in the area, unfamiliar researchers, and tourists were frequent. However, the baboons had not engaged in ‘raiding’ residences, threatening humans, or any other potentially negative symptom of habituation before the end of this study.Sampling methodology for proximity associations30-s focal sampling was used to collect proximity associations between all group members (excluding infants). All data was collected between June and December 2018 and January and June 2019; the majority of 2018s data was collected during the wet season, whilst most of 2019s data was collected during the dry season. To account for time of day, each day was split into four time-periods that were seasonally adjusted ensuring each period accounted for 25% of the current day length. A randomly ordered list of individuals was produced for each day, the first individual identified from the top 15 (approx. 20% of group size) individuals on the list was sampled immediately. Individuals could only be sampled once per time period per day, and a maximum of twice total per day. All individuals received at least 14 focal observations per time period (56 total) across the study period (see below for how we handled uneven sampling for some individuals). A video camera was used by AA (the only observer to collect this data) to record all focal observations (Panasonic HC-W580 Camcorder). At the end of the 30-s focal observation the identities of all neighbouring conspecifics within 5 m, 2.5 m, 1 m, and touching the focal animal were recorded (audibly by AA). We chose the end of the focal observation to record this data as this was most likely to reflect the conditions during the focal, i.e., the observer had been in proximity for at least 30 s.Neighbour information was extracted from video footage and entered manually by AA and AW. Data was split into separate years to reflect an observation gap of several weeks and to understand whether there was consistency in the hypothesized effects through time and to reflect underlying differences in environmental conditions during the two study periods; during the dry season fruits and seeds are scarce and day lengths are several hours shorter than in the wet season such that day journey lengths are often shorter in the dry season and animals are much more sedentary which could impact inter-individual spacings. In 2018 each individual was sampled between 28 and 30 times; 28 focals were randomly selected from each individual to make sampling even. For 2019 there were between 25 and 27 focals per individual; 25 samples of each individual were randomly selected. Observations were undertaken at a range of distances. For both years the median end observer distance was 4.5 m; data was thus split into close focal observations of less than or equal to 4.5 m (2018: n = 918, 2019: n = 809), and observations greater than 4.5 m (2018: n = 902 2019: n = 816). See supporting information Table S1 for summary statistics of the observation distances of each individual.We did not make any attempt to record our focal data evenly across the various habitats at our field site (see Supporting information text S1 for complete habitat descriptions) as our previous research indicated there was little difference in general spatial cohesion/inter-individual proximity patterns across these habitats (see Supporting information text S2 and Table S2). As a result, we considered it unlikely that there were fundamental differences in inter-individual association patterns across habitats, or that observers struggled to reliably detect or identify neighbours in dense habitats. We do acknowledge, however, that there will always be an element of bias with such methods, as observations were avoided, aborted, or excluded if visual obstructions (e.g., cliffs, rocks, walls, buildings, very dense vegetation etc.) prohibited accurate assessments; the observations used in the current study are from occasions when these factors were not an issue.During this study the group contained between 85 and 92 individuals. Age-sex class was defined according to secondary sexual characteristics (e.g., testes descending/enlarging, sexual swelling, canine eruption) and changes in pelage throughout juvenile development (see Supporting information text S3 for full descriptions). All 65 non-infant individuals that were present during 2017 (when displacement tolerances were calculated) and still remaining in the group by the end of 2019 were used in this study (4 individuals from the prior FID study were no longer present). There were a high number of births between 2018 and 2019, but none were independent by the time either of our sampling periods begun in 2018 or 2019. There was no immigration of foreign individuals, but two individuals disappeared, both during the 2018 focal sampling period. As a result, we had a very consistent pool of individuals to sample from during this study. We removed all data associated with the two individuals who disappeared as their occurrences as neighbours would have been poorly sampled (due to missing more than half the study) relative to the rest of the group which would have led to statistical biases21.Flight initiation distance procedureIndividual displacement tolerance estimates were previously quantified in our previous research2 using a flight initiation distance (FID) procedure22 that was completed between October 2017 and April 2018, prior and independent to the commencement of proximity association focal sampling in June 2018. Individual baboons were approached by an observer, and the distance at which the animal displaced away from the observer measured (see Supporting information Table S2 for summary statistics). This procedure was repeated 24 times for each individual baboon, with approaches spread evenly across two observers differing in familiarity. At the beginning of each approach we also recorded several behavioural, social, and environmental factors that could have hypothetically influenced an individual’s FID2 including whether the animal was engaged (e.g., digging or grooming) or not engaged (e.g., resting, chewing food, being groomed), habitat type (open/closed: see Supporting text S1), whether the animal was on the ground or sat on a low branch or rock within 50 cm of the ground, the number of conspecifics within 5 m of the focal animal, and whether there had been any external events within the preceding 5 min (e.g., alarm calls, aggressions, encountering another group or predator). During the approach, we also recorded the visual orientation distance (the distance at which the focal animal directed its line of vision towards the head of the approaching observer) and whether one of the focal animal’s neighbours had displaced/fled before the focal animal. Although all but neighbour flee first and external events showed some importance for predicting looking (see Table S4), FID was found to be distinct amongst individuals and repeatable within each individual, evidence that displacement tolerance may be an individual level trait2. Full details of methods, statistical analysis, and results (including comparison to the original model) for this updated model are in Supporting information text S4, with model summary results for the previous and updated models in Tables S3 and S4.The notion of an observer approaching a habituated primate may be considered atypical or likely to result in habituation/sensitization effects or agonistic behaviours being directed towards the approaching observers. However, our previous study2 showed that almost all approaches resulted in the animal passively relocating (98.85%), a very benign response identical to the behaviours of subordinate baboons displacing away from dominant conspecifics. This suggests that in this group, observers may be considered equivalent to a high-level social threat2. Throughout observation periods on habituated animals, observers are likely to approach or displace animals either incidentally or accidentally multiple times throughout the day, especially during lengthy focal observations. As such, the approach methodology is unlikely to represent a stimulus outside of the norm for our study animals. This may explain why displacement responses were so passive and why there was no evidence of habituation or sensitization effects across the group or individually through a range of temporal periods2 or after life-threatening events20. As a result, our situation was possible without risk of causing stress or anxiety in the study subjects, eliciting agonistic behaviours towards observers, or interfering with their prior habituation levels.Statistical analysisInfluence of tolerance and observer distance on inter-individual association patternsQuantifying displacement toleranceTo quantify displacement tolerance towards observers we extracted the individual conditional modes from the updated FID model using the ranef function in brms. Conditional modes are often referred to as Best Linear Unbiased Predictors (BLUPs) and are the difference between the predicted mean population-level response for a given set of treatments (i.e., population-level effects) and the predicted responses for each individual, and therefore infer the extent to which each individual differs from the population mean. The conditional modes and their associated standard deviations can be found in supporting information Table S5.To validate that the conditional modes from the updated model were both representative of the individual’s flight responses and in line with the estimates produced from our previous study2 we performed additional tests. Firstly, we performed a Pearson’s correlation between the conditional modes from the updated model and the conditional modes from the previous article. Individual tolerance estimates were consistent (r(63) = 0.915, p  More