28 Works

Data from: Barriers to dispersal of rain forest butterflies in tropical agricultural landscapes

Sarah A. Scriven, Colin Michael Beale, Suzan Benedick & Jane K. Hill
Fragmentation of natural habitats can be detrimental for species if individuals fail to cross habitat boundaries to reach new locations, thereby reducing functional connectivity. Connectivity is crucial for species shifting their ranges under climate change, making it important to understand factors that might prevent movement through human-modified landscapes. In tropical regions, rain forests are being fragmented by agricultural expansion, potentially isolating populations of highly diverse forest-dependent species. The likelihood of crossing habitat boundaries is an...

Exploring the role of genetic diversity and relatedness in tree seedling growth and mortality: a multi‐species study in a Bornean rain forest

Chris Kettle, Claire Tito De Morais, C.D. Philipson, C.R. Maycock, D.F.R.P Burslem, E. Khoo & J. Ghazoul
Where conspecific seedlings occur at high densities, density dependent processes tend to depress their performance and survival relative to co‐occurring heterospecifics. We extend this observation to within‐species genetic diversity and relatedness. We posit that seedling growth and survival increase where there is higher genetic diversity, and lower relatedness, among seedling populations, under the expectation that increased genetic dissimilarity among conspecific seedlings affords greater resistance to pathogens. We used estimates of individual seedling genetic diversity (multilocus...

Data from: The value of biodiversity for the functioning of tropical forests: insurance effects during the first decade of the Sabah biodiversity experiment

Sean L. Tuck, Michael J. O'Brien, Christopher D. Philipson, Philippe Saner, Matteo Tanadini, Dzaeman Dzulkifli, H. Charles J. Godfray, Elia Godoong, Reuben Nilus, Robert C. Ong, Bernhard Schmid, Waidi Sinun, Jake L. Snaddon, Martijn Snoep, Hamzah Tangki, John Tay, Philip Ulok, Yap Sau Wai, Maja Weilenmann, Glen Reynolds & Andy Hector
One of the main environmental threats in the tropics is selective logging, which has degraded large areas of forest. In southeast Asia, enrichment planting with seedlings of the dominant group of dipterocarp tree species aims to accelerate restoration of forest structure and functioning. The role of tree diversity in forest restoration is still unclear, but the ‘insurance hypothesis’ predicts that in temporally and spatially varying environments planting mixtures may stabilize functioning owing to differences in...

Data from: Quaternary land bridges have not been universal conduits of gene flow

Emilie Cros, Balaji Chattopadhyay, Kritika M. Garg, Nathaniel Ng, Suzanne Tomassi, Suzan Benedick, David P. Edwards & Frank E. Rheindt
Quaternary climate oscillations are a well-known driver of animal diversification, but their effects are most well studied in areas where glaciations lead to habitat fragmentation. In large areas of the planet, however, glaciations have had the opposite effect, but here their impacts are much less well understood. This is especially true in Southeast Asia, where cyclical changes in land distribution have generated enormous land expansions during glacial periods. In this study, we selected a panel...

Change and persistence of hunting & dietary practices among Kadazandusun-Murut (KDM) bearded pig hunters in Sabah, Malaysia

David Kurz, Fiffy Saikim, Vanielie Justine, Jordan Bloem, Matthew Libassi, Matthew Luskin, Lauren Withey, Benoit Goossens, Justin Brashares & Matthew Potts
This dataset consists of 38 semi-structured interviews that we conducted with Kadazandusun-Murut (KDM) hunters in Sabah, Malaysian Borneo. The dataset is based on information shared during over 50 hours of time with the hunters. The data cover a variety of topics about the relationships between KDM hunters and bearded pigs, the favored game animal for this hunting group. We asked the hunters about their hunting and dietary practices, changes in hunting practices, and perceived changes...

Mammal occurrence identified from metabarcoding of two leech species from Sabah, Malaysia

R. Drinkwater, I.D. Schnell, K. Bohmann, H. Bernard, G. Veron, E. Clare, T.P. Gilbert & S.J. Rossiter
This dataset contains the results from a metabarcoding study of terrestrial leech blood meals to detect differences in the diets of two leech species, Haemadipsa picta and Haemadipsa sumatrana. Mammal taxa were identified using metabarcoding of 16s rRNA and comparisons of operational taxonomic units (OTUs) to a curated reference database from NCBI (National Center for Biotechnology Information) GenBank. All leeches were collected from the Stability of Altered Forest Ecosystems project (SAFE; www.SAFEproject.net) as part of...

Metabarcoding data from the guano of insectivorous bats in Sabah, Malaysia

D. Hemprich-Bennett, V. Kemp, J. Blackman, H. Bernard, S. Rossiter & E. Clare
This dataset includes capture data for insectivorous bats captured with harp traps in Sabah, Malaysia, and dietary metabarcoding data. The dietary data was generated through obtaining bat faeces, extracting the DNA, amplifying it using ZBJ-ArtF1c ZBJ-ArtR2c primers, and then sequencing it on an illumina miseq. Code to aid interpreting the data can be found at https://doi.org/10.17636/01044623 This data was collected as part of the NERC-funded LOMBOK HMTF project, also using a small grant from Bat...

Data from: Ant mosaics in Bornean primary rain forest high canopy depend on spatial scale, time of day, and sampling method

Kalsum M. Yusah, William A. Foster, Glen Reynolds & Tom M. Fayle
Background: Competitive interactions in biological communities can be thought of as giving rise to “assembly rules” that dictate the species that are able to co-exist. Ant communities in tropical canopies often display a particular pattern, an “ant mosaic”, in which competition between dominant ant species results in a patchwork of mutually exclusive territories. Although ant mosaics have been well-documented in plantation landscapes, their presence in pristine tropical forests remained contentious until recently. Here we assess...

Data from: Small logging roads do not restrict movements of forest rats in Bornean logged forests

Sui P. Heon, Philip M. Chapman, Henry Bernard & Robert M. Ewers.
Selective logging is driving the proliferation of roads throughout tropical rainforests, particularly narrow, unpaved logging roads. However, little is known about the extent of road edge effects or their influence on the movements of tropical understory animal species. Here, we used forest rats to address the following questions: (1) Does the occupancy of rats differ from road edges to forest interior within logged forests? (2) Do roads inhibit the movements of rats within these forests?...

Data from: Inter-annual dynamics and persistence of small mammal communities in a selectively logged tropical forest in Borneo

Philip M. Chapman, Oliver R. Wearn, Terhi Riutta, Chris Carbone, J. Marcus Rowcliffe, Henry Bernard, Robert M Ewers & Robert. M. Ewers
Understanding temporal change and long-term persistence of species and communities is vital if we are to accurately assess the relative values of human-modified habitats for biodiversity. Despite a large literature and emerging consensus demonstrating a high conservation value of selectively logged tropical rainforests, few studies have taken a long-term perspective. We resampled small mammals (≤1kg) in a heavily logged landscape in Sabah, Borneo between 2011 and 2016 to investigate temporal patterns of species-level changes in...

Management, yield, soil and vegetation data for oil palm smallholder farms in Sabah, Malaysian Borneo, 2019

S.Y. Gutierrez Al-Khudhairy, T.R. Howells, A. Bin Sailim, C.J. McClean, M.J.M. Senior, S. Benedick, J.K. Hill & R. Azmi
This dataset details information collected from smallholder oil palm farms in Sabah, Malaysian Borneo. Including: management practices, oil palm fruit yield, understorey vegetation, and soil chemical properties (SOC, total N, total P and available P). We collected data between August to November 2019 from 40 smallholdings (defined as farms < 50 ha) across six governance areas in Sabah. We used responses from face-to-face questionnaires to collect information about their management practices, including Best Management Practices...

High Carbon Stock stratification of the SAFE project site, Sabah, Malaysian Borneo, 2015 [HMTF]

N.J. Deere, G. Guillera-Arroita, E.L. Baking, H. Bernard, M. Pfeifer, G. Reynolds, O.R. Wearn, Z.G. Davies & M.J. Struebig
This data set provides a spatial stratification of forest cover into discrete vegetation classes according to the High Carbon Stock (HCS) Approach. The data set covers the Stability of Altered Forest Ecosystems (SAFE) project site located in Sabah, Malaysian Borneo. Data were collected in 2015 during a project which was included in the NERC Human-modified tropical forest (HMTF) programme.

Data from: Lowland biotic attrition revisited: body size and variation among climate change ‘winners’ and ‘losers’

Jedediah F. Brodie, Matthew Strimas-Mackey, Jayasilan Mohd-Azlan, Alys Granados, Henry Bernard, Anthony J. Giordano & Olga E. Helmy
The responses of lowland tropical communities to climate change will critically influence global biodiversity but remain poorly understood. If species in these systems are unable to tolerate warming, the communities—currently the most diverse on Earth—may become depauperate (‘biotic attrition’). In response to temperature changes, animals can adjust their distribution in space or their activity in time, but these two components of the niche are seldom considered together. We assessed the spatio-temporal niches of rainforest mammal...

Data from: Multiple stages of tree seedling recruitment are altered in tropical forests degraded by selective logging

Rajeev Pillay, Fangyuan Hua, Bette A. Loiselle, Henry Bernard & Robert J. Fletcher
Tropical forest degradation is a global environmental issue. In degraded forests, seedling recruitment of canopy trees is vital for forest regeneration and recovery. We investigated how selective logging, a pervasive driver of tropical forest degradation, impacts canopy tree seedling recruitment, focusing on an endemic dipterocarp Dryobalanops lanceolata in Sabah, Borneo. During a mast-fruiting event in intensively logged and nearby unlogged forest, we examined four stages of the seedling recruitment process: seed production, seed predation, and...

Data from: Habitat disturbance selects against both small and large species across varying climates

Heloise Gibb, Nathan J. Sanders, Robert R. Dunn, Xavier Arnan, Heraldo L. Vasconcellos, David A. Donoso, Alan N. Andersen, Rogerio R. Silva, Tom R. Bishop, Crisanto Gomez, Blair F. Grossman, Kalsum M. Yusah, Sarah H. Luke, Renata Pacheco, Jessica Pearce-Duvet, Javier Retana, Melanie Tista, Catherine L. Parr & H. L. Vasconcelos
Global extinction drivers, including habitat disturbance and climate change, are thought to affect larger species more than smaller species. However, it is unclear if such drivers interact to affect assemblage body size distributions. We asked how these two key global change drivers differentially affect the interspecific size distributions of ants, one of the most abundant and ubiquitous animal groups on earth. We also asked whether there is evidence of synergistic interactions and whether effects are...

Data from: Genetic diversity and distinctiveness of the proboscis monkeys (Nasalis larvatus) of the Klias Peninsula, Sabah, Malaysia

Jason Munshi-South & Henry Bernard
In this study, we sequenced a partial segment of the mitochondrial control region from 21 proboscis monkeys of the Klias peninsula, the last large population remaining on the west coast of Sabah, Malaysia. Our results showed that this population retains substantial genetic variation, and subpopulations from different river systems in the central and southern portions of the Klias share multiple haplotypes. We also compared our data with previously generated sequences from 2 eastern populations of...

Data from: Crossing the (Wallace) line: local abundance and distribution of mammals across biogeographic barriers

Jedediah F. Brodie, Olga Helmy, Margaretha Pangau-Adam, Giyarto Ugiek, Graden Froese, Alys Granados, Jayasilan Mohd-Azlan, Henry Bernard, Anthony J. Giordano, Muhammad Agil & Abdul Haris Mustari
Past and ongoing vertebrate introductions threaten to rearrange ecological communities in the Indo-Malay Archipelago, one of Earth's most biodiverse regions. But the consequences of these translocations are difficult to predict. We compared local abundance and distributions in four tropical mammal lineages that have crossed from Asia to Wallacea or New Guinea. The local abundance of macaques (Macaca spp.), which naturally crossed Wallace's Line, was higher in Sulawesi (east of the line; mean = 3.7 individuals...

Mammal detection data for the SAFE project site, Sabah, Malaysian Borneo, 2015 [HMTF]

N.J. Deere, G. Guillera-Arroita, E.L. Baking, H. Bernard, M. Pfeifer, G. Reynolds, O.R. Wearn, Z.G. Davies & M.J. Struebig
This data set contains stacked detection matrices for 28 recorded mammal species across 115 sampling locations at the Stability of Altered Forest Ecosystems (SAFE) project site located in Sabah, Malaysian Borneo. Information for each camera trap sampling location, including spatial information and sampling effort is included. Data were collected in order to determine the contribution of carbon-based policies to biodiversity conservation in agricultural land-use mosaics. These data are essential to the development of the occupancy...

Vegetation and habitat data for fragmented and continuous forest sites in Sabah, Malaysian Borneo, 2017

E.H. Waddell, S. Fleiss, B. Bala Ola, A. Bin Sailim, A. Jelling, K.L. Yeong, J. Tangah, S. Benedick, H. King, M. Hughes, C.J. McClean, D.S. Chapman, J.K. Hill & L.F. Banin
This dataset contains records for vegetation in 49 plots across 14 fragmented forest sites and 4 continuous forest sites in Sabah, Malaysian Borneo. Living vegetation and deadwood were surveyed in two or three 0.28-ha plots in each of the 18 sites. In addition to vegetation data, the dataset contains topsoil parameters, measurements of forest structure, and metrics of the degree of forest fragmentation in the landscape surrounding the plots. These data were collected in order...

Glucocorticoids link forest type to local abundance in tropical birds

Simone Messina, David Edwards, Valeria Marasco, Virginie Canoine, Cindy Cosset, Suzanne Tomassi, Suzan Benedick, Marcel Eens & David Costantini
Selective logging is a major driver of environmental changes in the tropics. Recently, there has been increasing interest in understanding which traits make bird species resilient or vulnerable to such changes. Physiological stress mediated by the steroid hormone corticosterone (CORT) might underlie changes in local abundance of species because it regulates a range of body functions and behaviours to maintain homeostasis in changing environments. We conducted a three-year study to assess: (i) the variation in...

Brevity is not a universal in animal communication: evidence for compression depends on the unit of analysis in small ape vocalizations

Dena Clink, Abdul Hamid Ahmad & Holger Klinck
Evidence for compression, or minimization of code length, has been found across biological systems from genomes to human language and music. Two linguistic laws—Menzerath’s law (which states that longer sequences consist of shorter constituents) and Zipf’s law of abbreviation (a negative relationship between signal length and frequency of use) are predictions of compression. It has been proposed that compression is a universal in animal communication, but there have been mixed results, particularly in reference to...

Data from: Selective logging in tropical forests decreases the robustness of liana-tree interaction networks to the loss of host tree species

Ainhoa Magrach, Rebecca A. Senior, Andrew Rogers, Deddy Nurdin, Suzan Benedick, William F. Laurance, Luis Santamaría & David P. Edwards
Selective logging is one of the major drivers of tropical forest degradation, causing important shifts in species composition. Whether such changes modify interactions between species and the networks in which they are embedded remain fundamental questions to assess the ‘health’ and ecosystem functionality of logged forests. We focus on interactions between lianas and their tree hosts within primary and selectively logged forests in the biodiversity hotspot of Malaysian Borneo. We found that lianas were more...

Data from: Contrasting patterns of local richness of seedlings, saplings and trees may have implications for regeneration in rainforest remnants

Gail Stride, Chris D. Thomas, Suzan Benedick, Jenny A. Hodgson, Ahmad Jelling, Michael J.M. Senior & Jane K. Hill
Remnants of lowland rainforest remain following deforestation, but the longer-term effects of fragmentation remain poorly understood, partly due to the long generation times of trees. We study rainforest trees in three size classes: seedlings (<1 cm dbh), saplings (1-5 cm dbh) and trees (>5 cm), that broadly reflect pre- and post-fragmentation communities, and we examine the impacts of fragmentation on forest regeneration in Sabah, Malaysian Borneo. We found that seedling richness (measured as the number...

Data from: Limited contributions of plant pathogens to density-dependent seedling mortality of mast fruiting Bornean trees

Patrick Cannon, Michael O'Brien, Kalsum Yasah, David Edwards & Robert Freckleton
Fungal pathogens are implicated in driving tropical plant diversity by facilitating strong, negative density-dependent mortality of conspecific seedlings (C-NDD). Assessment of the role of fungal pathogens in mediating coexistence derives from relatively few tree species and predominantly the Neotropics, limiting our understanding of their role in maintaining hyper-diversity in many tropical forests. A key question is whether fungal pathogen-mediated C-NDD seedling mortality is ubiquitous across diverse plant communities. Using a manipulative shadehouse experiment, we tested...

Data from: Models for assessing local-scale co-abundance of animal species while accounting for differential detectability and varied responses to the environment

Jedediah F. Brodie, Olga E. Helmy, Jayasilan Mohd-Azlan, Alys Granados, Henry Bernard, Anthony J. Giordano & Elise Zipkin
We developed a new modeling framework to assess how the local abundance of one species influences the local abundance of a potential competitor while explicitly accounting for differential responses to environmental conditions. Our models also incorporate imperfect detection as well as abundance estimation error for both species. As a case study, we applied the model to four pairs of mammal species in Borneo, surveyed by extensive and spatially widespread camera trapping. We detected different responses...

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  • Universiti of Malaysia Sabah
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  • Universiti Malaysia Sabah
  • University of York
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  • University of Cambridge
  • Universiti Malaysia Sarawak
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