Papers by Joseph Williamson
Frontiers in Ecology and the Environment
Agricultural expansion is a primary driver of biodiversity decline in forested regions of the tro... more Agricultural expansion is a primary driver of biodiversity decline in forested regions of the tropics. Consequently, it is important to understand the conservation value of remnant forests in production landscapes. In a tropical landscape dominated by oil palm (Elaeis guineensis), we characterized faunal communities across eight taxa occurring within riparian forest buffers, which are legally protected alongside rivers, and compared them to nearby recovering logged forest. Buffer width was the main predictor of species richness and abundance, with widths of 40–100 m on each side of the river supporting broadly equivalent levels of biodiversity as compared to logged forest. However, width responses varied markedly among taxa, and buffers often lacked forest‐dependent species. Much wider buffers than are currently mandated are needed to safeguard most species. The largest biodiversity gains are achieved by increasing relatively narrow buffers. To provide optimal conservation outcomes ...
Predicting the conditions under which rhizobacteria benefit plant growth remains challenging. Her... more Predicting the conditions under which rhizobacteria benefit plant growth remains challenging. Here we tested the hypothesis that benefits from inoculation with phosphate-solubilising rhizobacteria will depend upon two environmental conditions: phosphate availability and competition between bacteria. Maize-associated rhizobacteria with varying phosphate solubilisation ability were used in experiments in soil, sterilised soil and gnotobiotic microcosms under conditions of varying orthophosphate availability, while we manipulated intensity of competition by varying the number of isolates in plant inocula. Growth promotion by microbes did not depend on phosphate availability but was affected by interactions between inoculants: beneficial effects of one Serratia isolate were detectable only when plants were inoculated with a single strain and beneficial effects of a competition sensitive Rhizobium was only detectable in sterilised soil or in microcosms inoculated with single strains. Mor...
Proceedings. Biological sciences / The Royal Society, Jan 22, 2015
Successful establishment and range expansion of non-native species often require rapid accommodat... more Successful establishment and range expansion of non-native species often require rapid accommodation of novel environments. Here, we use common-garden experiments to demonstrate parallel adaptive evolutionary response to a cool climate in populations of wall lizards (Podarcis muralis) introduced from southern Europe into England. Low soil temperatures in the introduced range delay hatching, which generates directional selection for a shorter incubation period. Non-native lizards from two separate lineages have responded to this selection by retaining their embryos for longer before oviposition--hence reducing the time needed to complete embryogenesis in the nest--and by an increased developmental rate at low temperatures. This divergence mirrors local adaptation across latitudes and altitudes within widely distributed species and suggests that evolutionary responses to climate can be very rapid. When extrapolated to soil temperatures encountered in nests within the introduced range,...
<b>Description: </b>Dung beetle community at SAFE and LOMBOK rivers 2017/8<b>Pr... more <b>Description: </b>Dung beetle community at SAFE and LOMBOK rivers 2017/8<b>Project: </b>This dataset was collected as part of the following SAFE research project: <b>Effects of habitat modification and fragmentation on dung beetle biodiversity and associated ecosystem functioning</b><b>Funding: </b>These data were collected as part of research funded by: NERC (Human Modified Tropical Forests Programme, NE/K016407/1, http://lombok.nerc-hmtf.info/; http://nerc-hmtf.info/)British Council and Malaysian Industry Government Group for High Technology (Newton-Ungku Omar Fund, 216433953.0, http://www.newtonfund.ac.uk/about/about-partner-countries/malaysia/)This dataset is released under the CC-BY 4.0 licence, requiring that you cite the dataset in any outputs, but has the additional condition that you acknowledge the contribution of these funders in any outputs.<b>Permits: </b>These data were collected under permit from the following authorities:SaBC (Research licence Access licence number JKM/MBS.1000-2/2 JLD.6 (63))<b>XML metadata: </b>GEMINI compliant metadata for this dataset is available here<b>Files: </b>This consists of 1 file: SAFE_LOMBOK_Rivers_Dung_Beetle_2017_2018.xlsx<b>SAFE_LOMBOK_Rivers_Dung_Beetle_2017_2018.xlsx</b>This file contains dataset metadata and 1 data tables:<b>Dung beetle community dataset</b> (described in worksheet Dung_Beetles)Description: Abundance of beetle species at pitfall traps baited with human faecesNumber of fields: 56Number of data rows: 144Fields: <b>Site</b>: SAFE &amp; LOMBOK Rivers (Field type: location)<b>Date</b>: Date trap set to date collected (48 hours) (Field type: date)<b>Caccobius_bawangensis</b>: Baited pitfall trap (Field type: abundance)<b>Catharsius_dayacus</b>: Baited pitfall trap (Field type: abundance)<b>Catharsius_renaudpauliani</b>: Baited pitfall trap (Field type: abundance)<b>Copris_agnus</b>: Baited pitfall trap (Field type: abundance)<b>Copris_ramosiceps</b>: Baited pitfall trap (Field type: abundance)<b>Copris_sinicus</b>: Baited pitfall trap (Field type [...]
<b>Description: </b>Microclimate at SAFE and LOMBOK rivers<b>Project: </b>... more <b>Description: </b>Microclimate at SAFE and LOMBOK rivers<b>Project: </b>This dataset was collected as part of the following SAFE research project: <b>Do riparian buffer strips stabilise environmental conditions, conserve biodiversity, and maintain ecosystem functions in oil palm-dominated landscapes?</b><b>Funding: </b>These data were collected as part of research funded by: NERC (Human Modified Tropical Forests Programme, NE/K016407/1, http://lombok.nerc-hmtf.info/; http://nerc-hmtf.info/)British Council and Malaysian Industry Government Group for High Technology (Newton-Ungku Omar Fund, 216433953.0, http://www.newtonfund.ac.uk/about/about-partner-countries/malaysia/)This dataset is released under the CC-BY 4.0 licence, requiring that you cite the dataset in any outputs, but has the additional condition that you acknowledge the contribution of these funders in any outputs.<b>Permits: </b>These data were collected under permit from the following authorities:SaBC (Research licence JKM/MBS.1000-2/2JLD.5(13))<b>XML metadata: </b>GEMINI compliant metadata for this dataset is available here<b>Files: </b>This consists of 1 file: SAFE_LOMBOK_Rivers_Microclimate_JW.xlsx<b>SAFE_LOMBOK_Rivers_Microclimate_JW.xlsx</b>This file contains dataset metadata and 1 data tables:<b>Microclimate at SAFE and LOMBOK rivers</b> (described in worksheet Microclimate)Description: Microclimate at SAFE and LOMBOK rivers as recorded by dataloggers. Number of fields: 9Number of data rows: 198Fields: <b>Site</b>: SAFE &amp; LOMBOK Datalogger Points (Field type: location)<b>Position</b>: Position of datalogger within the sampling transect where buffer5-45m deisgnates distance from river within forest, bufferedge is within 10m of the edge of a riparian buffer (in forest) and op5-45m designate distance from river in ROP transects or distance from buffer edge in RR or SJI transects (Field type: categorical)<b>Date</b>: Date datalogger deployed (Field type: date)<b>maxTemp</b>: Mean daily maximum temperature (Field type: numeric)<b>meanTemp</b>: [...]
PeerJ, 2021
Invertebrate-derived DNA (iDNA) sampling in biodiversity surveys is becoming increasingly widespr... more Invertebrate-derived DNA (iDNA) sampling in biodiversity surveys is becoming increasingly widespread, with most terrestrial studies relying on DNA derived from the gut contents of blood-feeding invertebrates, such as leeches and mosquitoes. Dung beetles (superfamily Scarabaeoidea) primarily feed on the faecal matter of terrestrial vertebrates and offer several potential benefits over blood-feeding invertebrates as samplers of vertebrate DNA. Importantly, these beetles can be easily captured in large numbers using simple, inexpensive baited traps, are globally distributed, and occur in a wide range of habitats. To build on the few existing studies demonstrating the potential of dung beetles as sources of mammalian DNA, we subjected the large-bodied, Bornean dung beetle (Catharsius renaudpauliani) to a controlled feeding experiment. We analysed DNA from gut contents at different times after feeding using qPCR techniques. Here, we first describe the window of DNA persistence within a d...
<b>Description: </b>Dung beetle community and dung removal data at SAFE second order ... more <b>Description: </b>Dung beetle community and dung removal data at SAFE second order points 2015<b>Project: </b>This dataset was collected as part of the following SAFE research project: <b>Effects of habitat modification and fragmentation on dung beetle biodiversity and associated ecosystem functioning</b><b>Funding: </b>These data were collected as part of research funded by: NERC (Human Modified Tropical Forests Programme, NE/K016407/1, http://lombok.nerc-hmtf.info/; http://nerc-hmtf.info/)This dataset is released under the CC-BY 4.0 licence, requiring that you cite the dataset in any outputs, but has the additional condition that you acknowledge the contribution of these funders in any outputs.<b>Permits: </b>These data were collected under permit from the following authorities:SaBC (Research licence Access licence number JKM/MBS.1000-2/2(381))MBMC (Research licence Project number 129)<b>XML metadata: </b>GEMINI compliant metadata for this dataset is available here<b>Files: </b>This consists of 1 file: SAFE_database_dung_beetle_2015_data_final_uploaded_copy.xlsx<b>SAFE_database_dung_beetle_2015_data_final_uploaded_copy.xlsx</b>This file contains dataset metadata and 2 data tables:<b>Dung beetle community dataset</b> (described in worksheet Dung_Beetles)Description: Abundance of beetle species at pitfall traps baited with human faecesNumber of fields: 81Number of data rows: 197Fields: <b>Site</b>: SAFE points at second order (Field type: Location)<b>Date</b>: Date trap set to date collected (48 hours) (Field type: Date)<b>Caccobius_bawangensis</b>: Baited pitfall trap (Field type: Abundance)<b>Catharsius_dayacus</b>: Baited pitfall trap (Field type: Abundance)<b>Catharsius_renaudpauliani</b>: Baited pitfall trap (Field type: Abundance)<b>Copris_agnus</b>: Baited pitfall trap (Field type: Abundance)<b>Copris_ramosiceps</b>: Baited pitfall trap (Field type: Abundance)<b>Copris_sinicus</b>: Baited pitfall trap (Field type: Abundance)<b>Microcopris_doriae</b>: Baited pitfall trap (Field type: Abundance)<b>Microcop [...]
Molecular Biology and Evolution, 2021
Rhodopsin comprises an opsin attached to a retinal chromophore and is the only visual pigment con... more Rhodopsin comprises an opsin attached to a retinal chromophore and is the only visual pigment conferring dim-light vision in vertebrates. On activation by photons, the retinal group becomes detached from the opsin, which is then inactive until it is recharged. Of all vertebrate species, those that dive face unique visual challenges, experiencing rapid decreases in light level and hunting in near darkness. Here, we combine sequence analyses with functional assays to show that the rhodopsin pigments of four divergent lineages of deep-diving vertebrates have undergone convergent increases in their retinal release rate. We compare gene sequences and detect parallel amino acids between penguins and diving mammals and perform mutagenesis to show that a single critical residue fully explains the observed increases in retinal release rate in both the emperor penguin and beaked whale. At the same time, we find that other shared sites have no significant effect on retinal release, implying th...
Journal of Applied Ecology, 2020
This is an open access article under the terms of the Creative Commons Attribution License, which... more This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
Molecular Biology and Evolution, 2020
The transition to an aquatic lifestyle in cetaceans (whales and dolphins) resulted in a radical t... more The transition to an aquatic lifestyle in cetaceans (whales and dolphins) resulted in a radical transformation in their sensory systems. Toothed whales acquired specialized high-frequency hearing tied to the evolution of echolocation, whereas baleen whales evolved low-frequency hearing. More generally, all cetaceans show adaptations for hearing and seeing underwater. To determine the extent to which these phenotypic changes have been driven by molecular adaptation, we performed large-scale targeted sequence capture of 179 sensory genes across the Cetacea, incorporating up to 54 cetacean species from all major clades as well as their closest relatives, the hippopotamuses. We screened for positive selection in 167 loci related to vision and hearing and found that the diversification of cetaceans has been accompanied by pervasive molecular adaptations in both sets of genes, including several loci implicated in nonsyndromic hearing loss. Despite these findings, however, we found no dire...
Frontiers in Forests and Global Change, 2020
Logging and habitat fragmentation impact tropical forest ecosystems in numerous ways, perhaps the... more Logging and habitat fragmentation impact tropical forest ecosystems in numerous ways, perhaps the most striking of which is by altering the temperature, humidity, and light environment of the forest-its microclimate. Because local-scale microclimatic conditions directly influence the physiology, demography and behavior of most species, many of the impacts of land-use intensification on the biodiversity and ecosystem functioning of tropical forests have been attributed to changes in microclimate. However, the actual pathways through which altered microclimatic conditions reshape the ecology of these human-modified ecosystems remain largely unexplored. To bridge this knowledge gap, here we outline an agenda for future microclimate research in human-modified tropical ecosystems. We focus specifically on three main themes: the role of microclimate in shaping (i) species distributions, (ii) species interactions, and (iii) ecosystem functioning in tropical forests. In doing so we aim to highlight how a renewed focus on microclimate can help us not only better understand the ecology of human-modified tropical ecosystems, but also guide efforts to manage and protect them.
Journal of Applied Ecology, 2018
1. There is a weak evidence-base supporting the effective management of riparian ecosystems withi... more 1. There is a weak evidence-base supporting the effective management of riparian ecosystems within tropical agriculture. Policies to protect riparian buffers-strips of non-cultivated land alongside waterways-are vague and highly variable between countries. 2. From a rapid evidence appraisal we find that riparian buffers are beneficial for hydrology, water quality, biodiversity, and other ecosystem functions in tropical landscapes. However, effects on connectivity, carbon storage, and emissions reduction remain understudied. Riparian functions are mediated by buffer width and habitat quality, but explicit threshold recommendations are rare. 3. Policy implications. A one-size-fits-all width criterion, commonly applied, will be insufficient to provide all riparian functions in all circumstances. Context-specific guidelines for allocating, restoring, and managing riparian buffers are necessary to minimise continued degradation of biodiversity and ecosystem functioning in tropical agriculture.
Biotropica, 2019
Blood-feeding invertebrates are emerging model taxa in biodiversity assessments, both as indicato... more Blood-feeding invertebrates are emerging model taxa in biodiversity assessments, both as indicators of mammal abundance and also as sources of mammal DNA for identification. Among these, terrestrial leeches arguably offer the greatest promise; they are abundant and widespread in the humid tropics, and their blood meals can be easily assayed to establish diet. Unfortunately, terrestrial leeches are understudied, with little known about their ecology and behavior. Such information is needed to evaluate their utility as ecological indicators and to account for potential sampling biases that might arise from habitat preferences. By combining occupancy modeling and thermal tolerance assays, we determined the factors affecting species occurrence in the related terrestrial brown (Haemadipsa sumatrana) and tiger leech (Haemadipsa picta), both of which are widespread in tropical forests in Southeast Asia. We sampled both species across a degraded forest landscape in Sabah, Borneo, in wet and dry seasons, associating occurrence with habitat-level metrics. We found that, for both species, detection probability increased with canopy height regardless of season. Additionally, increased vegetation heterogeneity had a strong negative influence on brown leech occurrence in the dry season, implying an interaction between vegetation structure and climate. However, we found no difference in physiological thermal tolerance (CT MAX) between the two species. Finally, using a reduced dataset, we found a small improvement in brown leech model fit when including mammal abundance. Our results suggest that the presence of terrestrial leeches may act as useful ecological indicators of habitat quality and potentially mammalian abundance.
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Papers by Joseph Williamson