164 Works

Environmental heterogeneity explains contrasting plant species richness between the South African Cape and southwestern Australia

Ruan Van Mazijk, Michael D. Cramer & G. Anthony Verboom
Aim: To assess whether a difference in species richness per unit area between two mediterranean-type biodiversity hotspots is explained by differences in environmental heterogeneity. Location: The Greater Cape Floristic Region, South Africa (GCFR) and Southwest Australian Floristic Region (SWAFR). Taxon: Vascular plants (tracheophytes). Methods: Comparable, geospatially explicit environmental and species occurrence data were obtained for both regions and used to generate environmental heterogeneity and species richness raster layers. Heterogeneity in multiple environmental variables and species...

Data from: Continuous-time spatially explicit capture-recapture models, with an application to a jaguar camera-trap survey.

Rebecca Foster, Bart Harmsen, Lorenzo Milazzo, Greg Distiller & David Borchers
1. Many capture-recapture surveys of wildlife populations operate in continuous time but detections are typically aggregated into occasions for analysis, even when exact detection times are available. This discards information and introduces subjectivity, in the form of decisions about occasion definition. 2. We develop a spatio-temporal Poisson process model for spatially explicit capture-recapture (SECR) surveys that operate continuously and record exact detection times. We show that, except in some special cases (including the case in...

Sustainable Cities Survey 2019, Maputo

Sylvia Croese

Township Smoking Study

OHS-LFS Consistent Series Weights 1994-2007

Nicola Branson

Allometric modelling of plant biomass from drone-acquired photographs: drone images, ground control marker coordinates and biomass data from 36 sites, 2016-2020

A. Cunliffe, K. Anderson, F. Boschetti, H. Graham, R. Brazier, I. Myers-Smith, T. Astor, M. Boer, L. Calvo, P. Clark, M. Cramer, M. Encinas-Lara, S. Escarzaga, J. Fernández-Guisuraga, A. Fisher, K. Gdulová, B. Gillespie, A. Griebel, N. Hanan, M. Hanggito, S. Haselberger, C. Havrilla, W. Ji, J. Karl, M. Kirchhoff … & R. Wojcikiewicz
This dataset contains RGB photographs acquired from drone surveys. There are 741 harvest plots from 38 surveys at 36 sites around the world. Each site was approximately 1 ha in area. Included with the photographic images are the coordinates of ground control markers, biomass, taxonomic and location data for harvest plots and ancillary metadata. The observations can be used to obtain allometric size-biomass models. This work was supported by the Natural Environment Research Council award...

Data from: Strong trans-Pacific break and local conservation units in the Galapagos shark (Carcharhinus galapagensis) revealed by genome-wide cytonuclear markers

Diana A. Pazmiño, Gregory E. Maes, Madeline E. Green, Colin A. Simpfendorfer, Mauricio Hoyos-Padilla, Clinton J.A. Duffy, Carl G. Meyer, Sven E. Kerwath, Pelayo Salinas-De-León & Lynne Van Herwerden
The application of genome-wide cytonuclear molecular data to identify management and adaptive units at various spatio-temporal levels is particularly important for overharvested large predatory organisms, often characterized by smaller, localized populations. Despite being “near threatened”, current understanding of habitat use and population structure of Carcharhinus galapagensis is limited to specific areas within its distribution. We evaluated population structure and connectivity across the Pacific Ocean using genome-wide Single Nucleotide Polymorphisms (~7200 SNPs) and mitochondrial Control Region...

Data from: Genome-wide expression reveals multiple systemic effects associated with detection of anticoagulant poisons in bobcats (Lynx rufus)

Devaughn Fraser, Alice Mouton, Laurel E.K. Serieys, Steve Cole, Scott Carver, Sue Vandewoude, Michael Lappin, Seth P.D. Riley, Robert Wayne & Laurel E. K. Serieys
Anticoagulant rodenticides (ARs) are indiscriminate toxicants that threaten non-target predatory and scavenger species through secondary poisoning. Accumulating evidence suggests that AR exposure may have disruptive sublethal consequences on individuals that can affect fitness. We evaluated AR-related effects on genome wide expression patterns in a population of bobcats in southern California. We identify differential expression of genes involved in xenobiotic metabolism, endoplasmic reticulum stress response, epithelial integrity, and both adaptive and innate immune function. Further, we...

Data from: Contrasting global patterns of spatially periodic fairy circles and regular insect nests in drylands

Stephan Getzin, Hezi Yizhaq, Michael D. Cramer & Walter R. Tschinkel
Numerical analysis of spatial pattern is widely used in ecology to describe the characteristics of floral and faunal distributions. These methods allow attribution of pattern to causal mechanisms by uncovering the specific signatures of patterns and causal agents. For example, grassland‐gap patterns called fairy circles (FCs) in Namibia and Australia are characterized by highly regular and homogenous distributions across landscapes that show spatially periodic ordering. These FCs have been suggested to be caused by both...

Metabolic rate is negatively linked to adult survival but does not explain latitudinal differences in songbirds

Andy Boyce, James C. Mouton, Penn Lloyd, Blair O. Wolf & Thomas E. Martin
Survival rates vary dramatically among species and predictably across latitudes, but causes of this variation are unclear. The rate of living hypothesis posits that physiological damage from metabolism causes species with faster metabolic rates to exhibit lower survival rates. However, whether increased survival commonly observed in tropical and south temperate latitudes is associated with slower metabolic rate remains unclear. We compared metabolic rates and annual survival rates across 46 species that we measured, and 147...

Data from: Dated plant phylogenies resolve Neogene climate and landscape evolution in the Cape Floristic Region

Vera Hoffmann, G. Anthony Verboom & Fenton P. D. Cotterill
In the context of molecularly-dated phylogenies, inferences informed by ancestral habitat reconstruction can yield valuable insights into the origins of biomes, palaeoenvironments and landforms. In this paper, we use dated phylogenies of 12 plant clades from the Cape Floristic Region (CFR) in southern Africa to test hypotheses of Neogene climatic and geomorphic evolution. Our combined dataset for the CFR strengthens and refines previous palaeoenvironmental reconstructions based on a sparse, mostly offshore fossil record. Our reconstructions...

Data from: Lions and leopards coexist without spatial, temporal or demographic effects of interspecific competition

Jennifer R.B. Miller, Ross T. Pitman, Gareth K.H. Mann, Angela K. Fuller, Guy A. Balme, Jennifer R. B. Miller & Gareth K. H. Mann
1. Although interspecific competition plays a principle role in shaping species behaviour and demography, little is known about the population-level outcomes of competition between large carnivores, and the mechanisms that facilitate coexistence. 2. We conducted a multi-landscape analysis of two widely distributed, threatened large carnivore competitors to offer insight into coexistence strategies and assist with species-level conservation. 3. We evaluated how interference competition affects occupancy, temporal activity and population density of a dominant competitor, the...

Data from: First record of the Mesozoic scroll coprolites: classification, characteristics, elemental composition and probable producers

Nibedita Rakshit, Mohd Shafi Bhat, Debarati Mukherjee & Sanghamitra Ray
Multiple, small, cylindrical scroll coprolites having rounded and tapering ends and pertaining to a new ichnotaxon have been recovered from the Upper Triassic Tiki Formation of India. This is the first record of scroll coprolites from the Mesozoic. Based on cross‐sectional geometry, external surface textures, and internal morphology, these coprolites are subdivided into three morphotypes. The coprolites contain several kinds of undigested food material in the form of ganoid fish scales, teeth, lower jaw and...

Data from: Dynamic multi-species occupancy models reveal individualistic habitat preferences in a high-altitude grassland bird community

David H. Maphisa, Hanneline Smit-Robinson & Res Altwegg
Moist, high-altitude grasslands of eastern South African harbour rich avian diversity and endemism. This area is also threatened by increasingly intensive agriculture and land conversion for energy production. This conflict is particularly evident at Ingula, an Important Bird and Biodiversity Area located within the least conserved high-altitude grasslands and which is also the site of a new Pumped Storage Scheme. The new management seeks to maximise biodiversity through manipulation of the key habitat variables: grass...

Data from: Local forage fish abundance influences foraging effort and offspring condition in an Endangered marine predator

Kate J. Campbell, Antje Steinfurth, Les G. Underhill, Janet C. Coetzee, Bruce M. Dyer, Katrin Ludynia, Azwianewi B. Makhado, Dagmar Merkle, Johan Rademan, Leshia Upfold & Richard B. Sherley
1. Understanding the functional relationship between marine predators and their prey is vital to inform ecosystem-based management. However, collecting concurrent data on predator behaviour and their prey at relevant scales is challenging. Moreover, opportunities to study these relationships in the absence of industrial fishing are extremely rare. 2. We took advantage of an experimental fisheries closure to study how local prey abundance influences foraging success and chick condition of Endangered African penguins Spheniscus demersus in...

Data from: Are forest‐shrubland mosaics of the Cape Floristic Region an example of alternate stable states?

Michael D. Cramer, Simon C. Power, Anastas Belev, Lindsay Gillson, William J. Bond, Michael Timm Hoffman, Lars O. Hedin & Lindsey Gillson
The idea of alternate stable states (ASS) has been used to explain the juxtaposition of distinct vegetation types within the same climate regime. ASS may explain the co‐existence of relatively inflammable closed‐canopy Afrotemperate Forest patches (“Forest”) within fire‐prone open‐canopy Fynbos in the Cape Floristic Region (CFR) on sandstone‐derived soils. We evaluated the hypothesis that although fire and local topography and hydrology likely determined the paleogeographic boundaries of Forest, present‐day boundaries are additionally imposed by emergent...

Data from: Seascape genetics of the spiny lobster Panulirus homarus in the Western Indian Ocean: understanding how oceanographic features shape the genetic structure of species with high larval dispersal potential

Sohana P. Singh, Johan C. Groeneveld, Michael G. Hart-Davis, Björn C. Backeberg & Sandi Willows-Munro
This study examines the fine-scale population genetic structure and phylogeography of the spiny lobster Panulirus homarus in the Western Indian Ocean. A seascape genetics approach was used to relate the observed genetic structure based on 21 microsatellite loci to ocean circulation patterns, and to determine the influence of latitude, sea surface temperature (SST) and ocean turbidity (KD490) on population-level processes. At a geospatial level, the genetic clusters recovered corresponded to three putative subspecies, P. h....

Data from: The contribution of land tenure diversity to the spatial resilience of protected area networks

Alta De Vos & Graeme S. Cumming
1. The relationship between diversity and resilience is relatively well-established for ecological systems, but remains much less explored for socioeconomic systems. Institutional diversity may have particular relevance for protected areas, whose managerial responses to environmental change depend on their legal basis, ability to make and enforce rules, and socio-political acceptance and endorsement. 2. Protected area expansion strategies are increasingly turning to private land conservation to increase the configuration and connectivity of national protected area networks....

Data from: Factors affecting carcass detection at wind farms using dogs and human searchers

Jon Domínguez Del Valle, Francisco Cervantes Peralta & María Isabel Jaquero Arjona
1. The use of detection dogs to effectively monitor bird and bat fatalities at wind farms is becoming increasingly popular. All studies to date agree that dogs outperform human searchers at finding bird and bat carcasses around wind turbines; however, it remains unclear how particular conditions during the search may influence carcass detection. 2. We investigate the effect of carcass size, habitat characteristics and weather conditions on carcass detection probability, for both dogs and humans,...

Camera trap survey of jaguars from Cockscomb Basin Wildlife Sanctuary in Belize

Greg Distiller, David Borchers, Rebecca Foster & Bart Harmsen
These data are from a camera trap survey of jaguars in Cockscomb Basin Wildlife Sanctuary in Belize that ran for a 6 month period from August 2013 until February 2014. The associated manuscript contains analyses of these data using continuous-time spatial capture-recapture models, and demonstrates how one can make inference about animal activity patterns. The data include 287 detections of 19 individual male jaguars, and 44 detections of 8 individual female jaguars.

Faunal input at host plants: can Camelthorn trees use nutrients imported by resident Sociable weavers?

Kervin Prayag, Carla Du Toit, Michael Cramer & Robert Thomson
“Islands of fertility” result from the focussing of water and nutrients around many shrub- or tree species due to plants foraging for resources. Plant-animal feedbacks may amplify the development of such islands through environmental modification due to, for example, faunal deposition of nutrients and seeds. Fauna residing within vegetation clumps are likely to exert stronger feedbacks on their hosts than itinerant species. We studied the interaction between camelthorn trees (Vachellia erioloba) and the colonial nests...

Data from: Just Google it: assessing the use of Google Images to describe geographical variation in visible traits of organisms

Gabriella R. M. Leighton, Pierre S. Hugo, Alexandre Roulin & Arjun Amar
Describing spatial patterns of phenotypic traits can be important for evolutionary and ecological studies. However, traditional approaches, such as fieldwork, can be time-consuming and expensive. Information technologies, such as Internet search engines, could facilitate the collection of these data. Google Images is one such technology that might offer an opportunity to rapidly collect information on spatial patterns of phenotypic traits. We investigated the use of Google Images in extracting data on geographical variation in phenotypic...

Data from: Evaluation of Xpert® MTB/RIF assay in induced sputum and gastric lavage samples from young children with suspected tuberculosis from the MVA85A TB vaccine trial

Erick Wekesa Bunyasi, Michele Tameris, Hennie Geldenhuys, Bey-Marrie Schmidt, Angelique Kany Kany Luabeya, Humphrey Mulenga, Thomas J. Scriba, Willem A. Hanekom, Hassan Mahomed, Helen McShane & Mark Hatherill
Objective: Diagnosis of childhood tuberculosis is limited by the paucibacillary respiratory samples obtained from young children with pulmonary disease. We aimed to compare accuracy of the Xpert® MTB/RIF assay, an automated nucleic acid amplification test, between induced sputum and gastric lavage samples from young children in a tuberculosis endemic setting. Methods: We analyzed standardized diagnostic data from HIV negative children younger than four years of age who were investigated for tuberculosis disease near Cape Town,...

Data from: Wood warblers copy settlement decisions of poor quality conspecifics: support for the tradeoff between the benefit of social information use and competition avoidance

Jakub Szymkowiak, Robert L. Thomson & Lechosław Kuczyński
Social information use in songbird habitat selection commonly involves a conspecific attraction strategy. Individuals copy the breeding-site choices of conspecifics, that is, bias their own settlement decisions towards sites (tracts of spatially limited habitat with similar structure) already occupied by others. In order to be adaptive, social information use has to be discriminative. Especially the decisions of good quality individuals, i.e. measuring high at observable fitness correlates, should be copied more frequently than those of...

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  • University of Cape Town
  • University of Cambridge
  • French National Centre for Scientific Research
  • University of Pretoria
  • Stellenbosch University
  • South African National Biodiversity Institute
  • Royal Society for the Protection of Birds
  • Nelson Mandela University
  • University of the Witwatersrand
  • Panthera Corporation