Andrew J. Hearn

Bio: Andrew J. Hearn is an academic researcher from University of Oxford. The author has contributed to research in topics: Leopard & Neofelis diardi. The author has an hindex of 14, co-authored 44 publications receiving 1317 citations.

The importance of correcting for sampling bias in MaxEnt species distribution models

Abstract: Aim Advancement in ecological methods predicting species distributions is a crucial precondition for deriving sound management actions. Maximum entropy (MaxEnt) models are a popular tool to predict species distributions, as they are considered able to cope well with sparse, irregularly sampled data and minor location errors. Although a fundamental assumption of MaxEnt is that the entire area of interest has been systematically sampled, in practice, MaxEnt models are usually built from occurrence records that are spatially biased towards better-surveyed areas. Two common, yet not compared, strategies to cope with uneven sampling effort are spatial filtering of occurrence data and background manipulation using environmental data with the same spatial bias as occurrence data. We tested these strategies using simulated data and a recently collated dataset on Malay civet Viverra tangalunga in Borneo. Location Borneo, Southeast Asia. Methods We collated 504 occurrence records of Malay civets from Borneo of which 291 records were from 2001 to 2011 and used them in the MaxEnt analysis (baseline scenario) together with 25 environmental input variables. We simulated datasets for two virtual species (similar to a range-restricted highland and a lowland species) using the same number of records for model building. As occurrence records were biased towards north-eastern Borneo, we investigated the efficacy of spatial filtering versus background manipulation to reduce overprediction or underprediction in specific areas. Results Spatial filtering minimized omission errors (false negatives) and commission errors (false positives). We recommend that when sample size is insufficient to allow spatial filtering, manipulation of the background dataset is preferable to not correcting for sampling bias, although predictions were comparatively weak and commission errors increased. Main Conclusions We conclude that a substantial improvement in the quality of model predictions can be achieved if uneven sampling effort is taken into account, thereby improving the efficacy of species conservation planning.

Orangutan distribution, density, abundance and impacts of disturbance

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Modelling the species distribution of flat-headed cats (Prionailurus planiceps), an endangered South-East Asian small felid.

Abstract: Background: The flat-headed cat (Prionailurus planiceps) is one of the world's least known, highly threatened felids with a distribution restricted to tropical lowland rainforests in Peninsular Thailand/Malaysia, Borneo and Sumatra. Throughout its geographic range large-scale anthropogenic transformation processes, including the pollution of fresh-water river systems and landscape fragmentation, raise concerns regarding its conservation status. Despite an increasing number of camera-trapping field surveys for carnivores in South-East Asia during the past two decades, few of these studies recorded the flat-headed cat. Methodology/Principal Findings: In this study, we designed a predictive species distribution model using the Maximum Entropy (MaxEnt) algorithm to reassess the potential current distribution and conservation status of the flat-headed cat. Eighty-eight independent species occurrence records were gathered from field surveys, literature records, and museum collections. These current and historical records were analysed in relation to bioclimatic variables (WorldClim), altitude (SRTM) and minimum distance to larger water resources (Digital Chart of the World). Distance to water was identified as the key predictor for the occurrence of flat-headed cats (>50% explanation). In addition, we used different land cover maps (GLC2000, GlobCover and SarVision LLC for Borneo), information on protected areas and regional human population density data to extract suitable habitats from the potential distribution predicted by the MaxEnt model. Between 54% and 68% of suitable habitat has already been converted to unsuitable land cover types (e. g. croplands, plantations), and only between 10% and 20% of suitable land cover is categorised as fully protected according to the IUCN criteria. The remaining habitats are highly fragmented and only a few larger forest patches remain. Conclusion/Significance: Based on our findings, we recommend that future conservation efforts for the flat-headed cat should focus on the identified remaining key localities and be implemented through a continuous dialogue between local stakeholders, conservationists and scientists to ensure its long-term survival. The flat-headed cat can serve as a flagship species for the protection of several other endangered species associated with the threatened tropical lowland forests and surface fresh-water sources in this region.

Coming down from the trees: Is terrestrial activity in Bornean orangutans natural or disturbance driven?

Abstract: The orangutan is the world's largest arboreal mammal, and images of the red ape moving through the tropical forest canopy symbolise its typical arboreal behaviour. Records of terrestrial behaviour are scarce and often associated with habitat disturbance. We conducted a large-scale species-level analysis of ground-based camera-trapping data to evaluate the extent to which Bornean orangutans Pongo pygmaeus come down from the trees to travel terrestrially, and whether they are indeed forced to the ground primarily by anthropogenic forest disturbances. Although the degree of forest disturbance and canopy gap size influenced terrestriality, orangutans were recorded on the ground as frequently in heavily degraded habitats as in primary forests. Furthermore, all age-sex classes were recorded on the ground (flanged males more often). This suggests that terrestrial locomotion is part of the Bornean orangutan's natural behavioural repertoire to a much greater extent than previously thought, and is only modified by habitat disturbance. The capacity of orangutans to come down from the trees may increase their ability to cope with at least smaller-scale forest fragmentation, and to cross moderately open spaces in mosaic landscapes, although the extent of this versatility remains to be investigated.

Activity patterns and temporal avoidance by prey in response to Sunda clouded leopard predation risk

Abstract: Little is known about the activity patterns of Bornean ungulates, or the temporal interactions of these species with the Sunda clouded leopard Neofelis diardi. In this study, we use photographic capture data to quantify the activity patterns for the Sunda clouded leopard and six potential prey species: bearded pig Sus barbatus, Bornean yellow muntjac Muntiacus atherodes, red muntjac Muntiacusmuntjak, lesser mouse deer Tragulus kanchil, greater mouse deer Tragulusnapu, and sambar deer Rusa unicolor, and to calculate the overlap in activity patterns between these species. This is the first insight into the temporal interactions between the Sunda clouded leopard and its potential prey. Sunda clouded leopards' activity patterns overlapped most with those of sambar deer and greater mouse deer. In the absence of clouded leopards, we report a significant difference in activity patterns for bearded pigs which show greater nocturnal activity in the absence of this predator. This suggests that bearded pigs may be prey species for clouded leopards and they are capable of altering their activity pattern in response to this risk. © 2013 The Zoological Society of London.

spThin: an R package for spatial thinning of species occurrence records for use in ecological niche models

Abstract: Spatial thinning of species occurrence records can help address problems associated with spatial sampling biases. Ideally, thinning removes the fewest records necessary to substantially reduce the effects of sampling bias, while simultaneously retaining the greatest amount of useful information. Spatial thinning can be done manually; however, this is prohibitively time consuming for large datasets. Using a randomization approach, the ‘thin’ function in the spThin R package returns a dataset with the maximum number of records for a given thinning distance, when run for sufficient iterations. We here provide a worked example for the Caribbean spiny pocket mouse, where the results obtained match those of manual thinning.

The importance of correcting for sampling bias in MaxEnt species distribution models

Abstract: Aim Advancement in ecological methods predicting species distributions is a crucial precondition for deriving sound management actions. Maximum entropy (MaxEnt) models are a popular tool to predict species distributions, as they are considered able to cope well with sparse, irregularly sampled data and minor location errors. Although a fundamental assumption of MaxEnt is that the entire area of interest has been systematically sampled, in practice, MaxEnt models are usually built from occurrence records that are spatially biased towards better-surveyed areas. Two common, yet not compared, strategies to cope with uneven sampling effort are spatial filtering of occurrence data and background manipulation using environmental data with the same spatial bias as occurrence data. We tested these strategies using simulated data and a recently collated dataset on Malay civet Viverra tangalunga in Borneo. Location Borneo, Southeast Asia. Methods We collated 504 occurrence records of Malay civets from Borneo of which 291 records were from 2001 to 2011 and used them in the MaxEnt analysis (baseline scenario) together with 25 environmental input variables. We simulated datasets for two virtual species (similar to a range-restricted highland and a lowland species) using the same number of records for model building. As occurrence records were biased towards north-eastern Borneo, we investigated the efficacy of spatial filtering versus background manipulation to reduce overprediction or underprediction in specific areas. Results Spatial filtering minimized omission errors (false negatives) and commission errors (false positives). We recommend that when sample size is insufficient to allow spatial filtering, manipulation of the background dataset is preferable to not correcting for sampling bias, although predictions were comparatively weak and commission errors increased. Main Conclusions We conclude that a substantial improvement in the quality of model predictions can be achieved if uneven sampling effort is taken into account, thereby improving the efficacy of species conservation planning.

Mapping species distributions with MAXENT using a geographically biased sample of presence data: a performance assessment of methods for correcting sampling bias.

Abstract: MAXENT is now a common species distribution modeling (SDM) tool used by conservation practitioners for predicting the distribution of a species from a set of records and environmental predictors. However, datasets of species occurrence used to train the model are often biased in the geographical space because of unequal sampling effort across the study area. This bias may be a source of strong inaccuracy in the resulting model and could lead to incorrect predictions. Although a number of sampling bias correction methods have been proposed, there is no consensual guideline to account for it. We compared here the performance of five methods of bias correction on three datasets of species occurrence: one “virtual” derived from a land cover map, and two actual datasets for a turtle (Chrysemys picta) and a salamander (Plethodon cylindraceus). We subjected these datasets to four types of sampling biases corresponding to potential types of empirical biases. We applied five correction methods to the biased samples and compared the outputs of distribution models to unbiased datasets to assess the overall correction performance of each method. The results revealed that the ability of methods to correct the initial sampling bias varied greatly depending on bias type, bias intensity and species. However, the simple systematic sampling of records consistently ranked among the best performing across the range of conditions tested, whereas other methods performed more poorly in most cases. The strong effect of initial conditions on correction performance highlights the need for further research to develop a step-by-step guideline to account for sampling bias. However, this method seems to be the most efficient in correcting sampling bias and should be advised in most cases.

Is my species distribution model fit for purpose? Matching data and models to applications

Abstract: Species distribution models (SDMs) are used to inform a range of ecological, biogeographical and conservation applications. However, users often underestimate the strong links between data type, model output and suitability for end-use. We synthesize current knowledge and provide a simple framework that summarizes how interactions between data type and the sampling process (i.e. imperfect detection and sampling bias) determine the quantity that is estimated by a SDM. We then draw upon the published literature and simulations to illustrate and evaluate the information needs of the most common ecological, biogeographical and conservation applications of SDM outputs. We find that, while predictions of models fitted to the most commonly available observational data (presence records) suffice for some applications, others require estimates of occurrence probabilities, which are unattainable without reliable absence records. Our literature review and simulations reveal that, while converting continuous SDM outputs into categories of assumed presence or absence is common practice, it is seldom clearly justified by the application's objective and it usually degrades inference. Matching SDMs to the needs of particular applications is critical to avoid poor scientific inference and management outcomes. This paper aims to help modellers and users assess whether their intended SDM outputs are indeed fit for purpose.