68 Works

Data from: Influence of killing method on Lepidoptera DNA barcode recovery

Sandi Willows-Munro & M. Corrie Schoeman
The global DNA barcoding initiative has revolutionized the field of biodiversity research. Such large-scale sequencing projects require the collection of large numbers of specimens, which need to be killed and preserved in a way that is both DNA-friendly and which will keep voucher specimens in good condition for later study. Factors such as time since collection, correct storage (exposure to free water and heat) and DNA extraction protocol are known to play a role in...

Data from: Demography and social dynamics of an African elephant population 35 years after reintroduction as juveniles

Timothy R. Kuiper, Dave J. Druce & Heleen C. Druce
1. Given their vulnerability to local extinction, the reintroduction of megafauna species (often long-lived, ecologically-influential and highly-social) is an increasingly relevant conservation intervention. Studies that evaluate past megafauna reintroductions are both critical and rare. 2. Between 1981 and 1996, 12 cohorts of a total of 200 juvenile (<5 years old) African savanna elephants (Loxodonta africana africana) were re-introduced to Hluhluwe-iMfolozi Park (HiP), South Africa, after 100 years of absence. Here we model the population’s long...

Data from: Thermal resilience may shape population abundance of two sympatric congeneric Cotesia species (Hymenoptera: Braconidae)

Reyard Mutamiswa, Honest Machekano, Frank Chidawanyika & Casper Nyamukondiwa
Basal and plasticity of thermal tolerance determine abundance, biogeographical patterns and activity of insects over spatial and temporal scales. For coexisting stemborer parasitoids, offering synergistic impact to the efficacy of biological control, mismatches in thermal tolerance may influence their ultimate impact in biocontrol programs under climate variability. Using laboratory-reared congeneric parasitoid species Cotesia sesamiae and Cotesia flavipes Cameron (Hymenoptera: Braconidae), we examined basal thermal tolerance to understand potential impact of climate variability on their survival...

Data from: Cryptic diversity in black rats Rattus rattus of the Galápagos Islands, Ecuador

Sandi Willows-Munro, Robert C. Dowler, Michael R. Jarcho, Reese B. Phillips, Howard L. Snell, Tammy R. Wilbert & Cody W. Edwards
Human activity has facilitated the introduction of a number of alien mammal species to the Galápagos Archipelago. Understanding the phylogeographic history and population genetics of invasive species on the Archipelago is an important step in predicting future spread and designing effective management strategies. In this study, we describe the invasion pathway of Rattus rattus across the Galápagos using microsatellite data, coupled with historical knowledge. Microsatellite genotypes were generated for 581 R. rattus sampled from 15...

South African communal indigenous goats

Tlou Caswell Chokoe, Khanyisile Hadebe, Farai Muchadeyi, Edgar Dzomba, Khathutshelo Nephawe, Tumudi Mphahlele, Tlou Matelele & Bohani Mtileni
Indigenous goats form the majority of populations in smallholder; low input, low output production systems and are considered an important genetic resource due to their adaptability to different production environments and support communal farming. Effective population size (Ne), inbreeding levels, and the runs of homozygosity (ROHs) are effective tools for exploring the genetic diversity and understanding the demographic history in efforts to support breeding strategies to use and conserve genetic resources. Across populations, the current...

Data from: Foraging efficiency and size matching in a plant – pollinator community: the importance of sugar content and tongue length

Saskia G.T. Klumpers, Martina Stang & Peter G.L. Klinkhamer
A longstanding question in ecology is how species interactions are structured within communities. Although evolutionary theory predicts close size matching between floral nectar tube depth and pollinator proboscis length of interacting species, such size matching has seldom been shown and explained in multispecies assemblages. Here, we investigated the degree of size matching among Asteraceae and their pollinators and its relationship with foraging efficiency. The majority of pollinators, especially Hymenoptera, choose plant species on which they...

Data from: Fire frequency drives habitat selection by a diverse herbivore guild impacting top–down control of plant communities in an African savanna

Deron E. Burkepile, Dave I. Thompson, Richard W. S. Fynn, Sally E. Koerner, Stephanie Eby, Navashni Govender, Nicole Hagenah, Nathan P. Lemoine, Katherine J. Matchett, Kevin R. Wilcox, Scott L. Collins, Kevin P. Kirkman, Alan K. Knapp & Melinda D. Smith
In areas with diverse herbivore communities such as African savannas, the frequency of disturbance by fire may alter the top–down role of different herbivore species on plant community dynamics. In a seven year experiment in the Kruger National Park, South Africa, we examined the habitat use of nine common herbivore species across annually burned, triennially burned and unburned areas. We also used two types of exclosures (plus open access controls) to examine the impacts of...

Data from: The functional significance of complex floral colour pattern in a food-deceptive orchid

Xiaokai Ma, Jun Shi, Hans Banziger, Yangna Sun, Yanyan Guo, Zhongjian Liu, Steven D. Johnson & Yibo Luo
Many non-rewarding orchid species mimic the signals of co-occurring food flowers and thereby attract food-seeking animal pollinators. These signals are often visually complex with a colour pattern that contrasts between outer and central parts. The significance of this colour complexity for the pollination success of flowers of deceptive orchids has scarcely been investigated. We tested the effects of the colour patterns of the food-deceptive orchid Paphiopedilum micranthum on bumblebee visitation choices and pollination success using...

Phylogenomics and species delimitation for effective conservation of manta and devil rays

Emily Humble, Jane Hosegood, Rob Ogden, Mark De Bruyn, Simon Creer, Guy Stevens, Mohammed Abudaya, Kim Bassos-Hull, Ramon Bonfil, Daniel Fernando, Andrew Foote, Helen Hipperson, Rima Jabado, Jenny Kaden, Muhammad Moazzam, Lauren Peel, Stephen Pollett, Alessandro Ponzo, Marloes Poortvliet, Jehad Salah, Helen Senn, Joshua Stewart, Sabine Wintner & Gary Carvalho
Practical biodiversity conservation relies on delineation of biologically meaningful units. Manta and devil rays (Mobulidae) are threatened worldwide, yet morphological similarities and a succession of recent taxonomic changes impede the development of an effective conservation strategy. Here, we generate genome-wide single nucleotide polymorphism (SNP) data from a geographically and taxonomically representative set of manta and devil ray samples to reconstruct phylogenetic relationships and evaluate species boundaries under the general lineage concept. We show that nominal...

The role of plant-pollinator interactions in structuring nectar microbial communities

Clara De Vega, Sergio Álvarez-Pérez, Rafael G. Albaladejo, Sandy-Lynn Steenhuisen, Marc-André Lachance, Steve D. Johnson & Carlos M. Herrera
1. Floral nectar harbours a diverse microbiome of yeasts and bacteria that depend predominantly on animal visitors for their dispersal. Since pollinators visit specific sets of flowers and carry their own unique microbiota, we hypothesize that plant species visited by the same set of pollinators may support non-random nectar microbial communities linked together by the type of pollinator. 2. Here we explore the importance of plant-pollinator interactions in the assembly of nectar microbiome and study...

Discordance in a South African Memecylon clade (Melastomataceae): Evidence for reticulate evolution

Prabha Amarasinghe, Phuc Pham, Robert Douglas Stone & Nico Cellinese
Premise of research. Evergreen forests in eastern South Africa have high biodiversity but are limited in extent and have a highly fragmented distribution. Populations of forest plants are thus geographically isolated, and fine-scale evolutionary studies of these lineages might yield important insights into the history and assembly of the forests themselves. Despite their morphological diversity, a prior study showed that three South African Memecylon taxa in Melastomataceae (M. natalense, M. bachmannii, and M. australissimum) had...

The functional ecology of bat pollination in the African sausage tree Kigelia africana (Bignoniaceae)

Ethan Newman, Keeveshnee Govender, Sandy Van Niekerk & Steven D. Johnson
Plants often interact with a wide range of animal floral visitors that can vary in their pollination effectiveness. Flowers of the African sausage tree Kigelia africana are be visited by bats and bush babies during the night and by birds during the day. We studied floral traits (phenophases, scent, colour and nectar chemistry) and the visitation frequency and pollination effectiveness of different flower visitors to determine if K. africana is functionally specialized for bat-pollination. We...

Data from: Mapping polyclonal HIV-1 antibody responses via next-generation neutralization fingerprinting

Nicole A. Doria-Rose, Han R. Altae-Tran, Ryan S. Roark, Stephen D. Schmidt, Matthew S. Sutton, Mark K. Louder, Gwo-Yu Chuang, Robert T. Bailer, Valerie Cortez, Rui Kong, Krisha McKee, Sijy O'Dell, Felicia Wang, Salim S. Abdool Karim, James M. Binley, Mark Connors, Barton F. Haynes, Malcolm A. Martin, David C. Montefiori, Lynn Morris, Julie Overbaugh, Peter D. Kwong, John R. Mascola, Ivelin S. Georgiev & Sijy O’Dell
Computational neutralization fingerprinting, NFP, is an efficient and accurate method for predicting the epitope specificities of polyclonal antibody responses to HIV-1 infection. Here, we present next-generation NFP algorithms that substantially improve prediction accuracy for individual donors and enable serologic analysis for entire cohorts. Specifically, we developed algorithms for: (a) selection of optimized virus neutralization panels for NFP analysis, (b) estimation of NFP prediction confidence for each serum sample, and (c) identification of sera with potentially...

Data from: Geographical matching of volatile signals and pollinator olfactory responses in a cycad brood-site mutualism

Terence N. Suinyuy, John S. Donaldson & Steven D. Johnson
Brood-site mutualisms represent extreme levels of reciprocal specialization between plants and insect pollinators, raising questions about whether these mutualisms are mediated by volatile signals and whether these signals and insect responses to them covary geographically in a manner expected from coevolution. Cycads are an ancient plant lineage in which almost all extant species are pollinated through brood-site mutualisms with insects. We investigated whether volatile emissions and insect olfactory responses are matched across the distribution range...

Data from: Herbivores safeguard plant diversity by reducing variability in dominance

Brent Mortensen, Brent Danielson, Stan W. Harpole, Juan Alberti, Carlos Alberto Arnillas, Lori Biederman, Elizabeth T. Borer, Marc W. Cadotte, John M. Dwyer, Nicole Hagenah, Yann Hautier, Pablo Luis Peri, Eric W. Seabloom & W. Stanley Harpole
1. Reductions in community evenness can lead to local extinctions as dominant species exclude subordinate species; however, herbivores can prevent competitive exclusion by consuming otherwise dominant plant species, thus increasing evenness. While these predictions logically result from chronic, gradual reductions in evenness, rapid, temporary pulses of dominance may also reduce species richness. Short pulses of dominance can occur as biotic or abiotic conditions temporarily favor one or a few species, manifested as increased temporal variability...

Data from: Climate modifies response of non-native and native species richness to nutrient enrichment

Habacuc Flores-Moreno, Peter B. Reich, Eric M. Lind, Lauren L. Sullivan, Eric W. Seabloom, Laura Yahdjian, Andrew S. MacDougall, Lara G. Reichmann, Juan Alberti, Selene Báez, Jonathan D. Bakker, Marc W. Cadotte, Maria C. Caldeira, Enrique J. Chaneton, Carla M. D'Antonio, Philip A. Fay, Jennifer Firn, Nicole Hagenah, W. Stanley Harpole, Oscar Iribarne, Kevin P. Kirkman, Johannes M. H. Knops, Kimberly J. La Pierre, Ramesh Laungani, Andrew D. B. Leakey … & Elizabeth T. Borer
Ecosystem eutrophication often increases domination by non-natives and causes displacement of native taxa. However, variation in environmental conditions may affect the outcome of interactions between native and non-native taxa in environments where nutrient supply is elevated. We examined the interactive effects of eutrophication, climate variability and climate average conditions on the success of native and non-native plant species using experimental nutrient manipulations replicated at 32 grassland sites on four continents. We hypothesized that effects of...

Data from: Dung odours signal sex, age, territorial and oestrous state in white rhinos

Courtney Marneweck, Andreas Jürgens & Adrian M. Shrader
Mammals commonly communicate olfactorily via urine. However, the extent to which they communicate via dung, another waste product, is unknown. Behavioural studies suggest that mammals can obtain information from dung odours but are unclear about the information transmitted. Moreover, an understanding of the volatile organic compounds (VOCs) released from dung is limited. To address this, we analysed the odours emitted from the dung of free-ranging white rhinos, and found that 2,3-dimethylundecane signalled an individual's sex,...

Data from: Caching reduces kleptoparasitism in a solitary, large felid

Guy Balme, Jennifer R. B. Miller, Ross T. Pitman, Luke T. B. Hunter & Guy A. Balme
Food caching is a common strategy used by a diversity of animals, including carnivores, to store and/or secure food. Despite its prevalence, the drivers of caching behaviour, and its impacts on individuals, remain poorly understood, particularly for short-term food cachers. Leopards Panthera pardus exhibit a unique form of short-term food caching, regularly hoisting, storing and consuming prey in trees. We explored the factors motivating such behaviour among leopards in the Sabi Sand Game Reserve, South...

Data from: Floral community predicts pollinators' color preference: implications for Batesian floral mimicry

Michael R. Whitehead, Anne C. Gaskett, Steve D. Johnson & Steven D Johnson
Animals that rely on nectar are expected to display floral trait preferences correlating to the signals of nectar source flowers. Batesian mimicry evolves to exploit these pre-existing signal-receiver relationships, attracting pollinators through an adaptive resemblance to specific co-occurring rewarding species. The nectar-feeding long-proboscid flies of South Africa are pollinators for several deceptive orchid species that are putatively Batesian mimics. We tested whether flies’ measured color preference varied among communities providing different nectar-source diets, which would...

Data from: An African grassland responds similarly to long-term fertilization to the Park Grass experiment

David Ward, Kevin Kirkman & Zivanai Tsvuura
We compared the results of a long-term (65 years) experiment in a South African grassland with the world’s longest-running ecological experiment, the Park Grass study at Rothamsted, U.K. The climate is warm and humid in South Africa and cool and temperate in England. The African grassland has been fertilized with two forms of nitrogen applied at four levels, phosphorus and lime in a crossed design in 96 plots. In 1951, about 84% of plant cover...

Data from: DNA barcoding reveals the coral “laboratory-rat”, Stylophora pistillata encompasses multiple identities

Shashank Keshavmurthy, Sung-Yin Yang, Ada Alamaru, Yao-Yang Chuang, Michel Pichon, David Obura, Silvia Fontana, Stephane De Palmas, Fabrizio Stefani, Francesca Benzoni, Angus MacDonald, Annika M. E. Noreen, Chienshun Chen, Carden C. Wallace, Ruby M. Pillay, Vianney Denis, Affendi Yang Amri, James D. Reimer, Takuma Mezaki, Charles Sheppard, Yossi Loya, Avidor Abelson, Mohammed S. Mohammed, Andrew C. Baker, Pargol G. Mostafavi … & Chaolun A. Chen
Stylophora pistillata is a widely used coral “lab-rat” species with highly variable morphology and a broad biogeographic range (Red Sea to western central Pacific). Here we show, by analysing Cytochorme Oxidase I sequences, from 241 samples across this range, that this taxon in fact comprises four deeply divergent clades corresponding to the Pacific-Western Australia, Chagos-Madagascar-South Africa, Gulf of Aden-Zanzibar- Madagascar, and Red Sea-Persian/Arabian Gulf-Kenya. On the basis of the fossil record of Stylophora, these four...

Data from: Male interference with pollination efficiency in a hermaphroditic orchid

Karl J. Duffy & Steven D. Johnson
Hermaphroditism can lead to both intra- and inter-sexual conflict between male and female gender functions. However, the effect that such gender conflicts have on pollination efficiency has seldom been investigated. By artificially reducing the number of available male gametes on an individual, we quantified whether male interference with pollination efficiency occurs in the self-compatible, moth-pollinated orchid Satyrium longicauda. We partially emasculated S. longicauda inflorescences and compared pollination success and fecundity in these plants to intact...

Data from: Lion population dynamics: do nomadic males matter?

Natalia Borrego, Arpat Ozgul, Rob Slotow & Craig Packer
Key population processes are sometimes driven by male dynamics, but these drivers are often overlooked because of the scale over which they operate. Lions (Panthera leo) provide an ideal case study for investigating factors governing male dynamics and their influence on population sustainability. Lions display sexually selected infanticide, and resident males must defend their offspring from nomads that may have dispersed over long distances; factors affecting male-male competition over large spatial scales can have population...

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: Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis

Oliver Ratmann, M. Kate Grabowski, Matthew Hall, Tanya Golubchik, Chris Wymant, Lucie Abeler-Dörner, David Bonsall, Anne Hoppe, Andrew Leigh Brown, Tulio De Oliveira, Astrid Gall, Paul Kellam, Deenan Pillay, Joseph Kagaayi, Godfrey Kigozi, Thomas C. Quinn, Maria J. Wawer, Oliver Laeyendecker, David Serwadda, Ronald H. Gray, Christophe Fraser, &
To prevent new infections with human immunodeficiency virus type 1 (HIV-1) in sub-Saharan Africa, UNAIDS recommends targeting interventions to populations that are at high risk of acquiring and passing on the virus. Yet it is often unclear who and where these ‘source’ populations are. Here we demonstrate how viral deep-sequencing can be used to reconstruct HIV-1 transmission networks and to infer the direction of transmission in these networks. We are able to deep-sequence virus from...

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  • University of KwaZulu-Natal
  • University of California, Berkeley
  • University of Cape Town
  • University of Minnesota
  • Panthera Corporation
  • University of the Witwatersrand
  • University of Montana
  • University College London
  • Agricultural Research Council
  • Wageningen University & Research