137 Works

Impacts of invasive Australian acacias on soil bacterial community composition, microbial enzymatic activities, and nutrient availability in fynbos soils

Jan-Hendrik Keet
Invasive nitrogen-fixing plants often impact the soils they invade, notably through changes in soil chemistry and microbial community composition, which in turn could lead to alterations in soil functionality. We aimed to determine the impacts that invasive Australian Acacia trees have on soil chemistry and function (carbon, nitrogen, and phosphorus cycling) in South Africa’s Core Cape Subregion, and whether any differences in soil function are linked to differences in soil chemical properties and bacterial community...

Data from: Defining functional biomes and monitoring their change globally

Steven I. Higgins, Robert Buitenwerf, Glenn Moncrieff & Glenn R. Moncrieff
Biomes are important constructs for organizing understanding of how the worlds’ major terrestrial ecosystems differ from one another and for monitoring change in these ecosystems. Yet existing biome schemes have been criticized for being overly subjective and for explicitly or implicitly invoking climate. We propose a new biome map and classification scheme that uses information on (i) an index of vegetation productivity, (ii) whether the minimum of vegetation activity is in the driest or coldest...

Data from: Phylogenetic marker development for target enrichment from transcriptome and genome skim data: the pipeline and its application in southern African Oxalis (Oxalidaceae)

Roswitha Schmickl, Aaron Liston, Vojtěch Zeisek, Kenneth Oberlander, Kevin Weitemier, Shannon C. K. Straub, Richard C. Cronn, Léanne L. Dreyer & Jan Suda
Phylogenetics benefits from using a large number of putatively independent nuclear loci and their combination with other sources of information, such as the plastid and mitochondrial genomes. To facilitate the selection of orthologous low-copy nuclear (LCN) loci for phylogenetics in nonmodel organisms, we created an automated and interactive script to select hundreds of LCN loci by a comparison between transcriptome and genome skim data. We used our script to obtain LCN genes for southern African...

Data from: Bird and bat species' global vulnerability to collision mortality at wind farms revealed through a trait-based assessment

Chris B. Thaxter, Graeme M. Buchanan, Carr Jamie, Stuart H.M. Butchart, Tim Newbold, Rhys E. Green, Joseph A. Tobias, Wendy B. Foden, Sue O'Brien & James W. Pearce-Higgins
Mitigation of anthropogenic climate change involves deployments of renewable energy worldwide, including wind farms, which can pose a significant collision risk to volant animals. Most studies into the collision risk between species and wind turbines, however, have taken place in industrialized countries. Potential effects for many locations and species therefore remain unclear. To redress this gap, we conducted a systematic literature review of recorded collisions between birds and bats and wind turbines within developed countries....

Data from: The ghost of introduction past: spatial and temporal variability in the genetic diversity of invasive smallmouth bass

Genevieve Diedericks, Romina Henriques, Sophie Von Der Heyden, Olaf Weyl & Cang Hui
Understanding the demographic history of introduced populations is essential for unravelling their invasive potential and adaptability to a novel environment. To this end, levels of genetic diversity within the native and invasive range of a species are often compared. Most studies, however, focus solely on contemporary samples, relying heavily on the premise that the historic population structure within the native range has been maintained over time. Here, we assess this assumption by conducting a three-way...

Data from: Impacts of environmental variability on desiccation rate, plastic responses and population dynamics of Glossina pallidipes

E. Kleynhans, Susana Clusella-Trullas & John S. Terblanche
Physiological responses to transient conditions may result in costly responses with little fitness benefits, and therefore, a trade-off must exist between the speed of response and the duration of exposure to new conditions. Here, using the puparia of an important insect disease vector, Glossina pallidipes, we examine this potential trade-off using a novel combination of an experimental approach and a population dynamics model. Specifically, we explore and dissect the interactions between plastic physiological responses, treatment-duration...

Character displacement drives floral variation in Pelargonium (Geraniaceae) communities

Ethan Newman & Bruce Anderson
Interactions between plant community members are an underexplored driver of angiosperm floral variation. We investigate character displacement as a potential contributor to floral variation in Pelargonium communities. Pelargoniums all place pollen on the ventral sides of their pollinators, potentially leading to interspecific pollen transfer (IPT) in sympatry. We show that the positions of pollen placement and receipt are determined by anther and style exsertion lengths. Using field experiments, we demonstrate that heterospecific species experience high...

The effect of storage conditions on microbial communities in stool

Kristien Nel Van Zyl
Microbiome research has experienced a surge of interest in recent years due to the advances and reduced cost of next-generation sequencing technology. The production of high quality and comparable data is dependent on proper sample collection and storage and should be standardized as far as possible. However, this becomes challenging when samples are collected in the field, especially in resource-limited settings. We investigated the impact of different stool storage methods common to the TB-CHAMP clinical...

The evolutionary potential of an insect invader under climate change

Michael Logan, Ingrid Minnaar, Kaitlin Keegan & Susana Clusella-Trullas
Although the impacts of climate change and invasive species are typically studied in isolation, they likely interact to reduce the viability of plant and animal populations. Indeed, invasive species, by definition, have succeeded in areas outside of their native range and may therefore have higher adaptive capacity relative to native species. Nevertheless, the genetic architecture of the thermal niche, which sets a limit to the potential for populations to evolve rapidly under climate change, has...

Data for: Calibration of individual-based models to epidemiological data: a systematic review

C. Marijn Hazelbag, Jonathan Dushoff, Emanuel M. Dominic, Zinhle E. Mthombothi & Wim Delva
Calibrating or fitting an individual-based model (IBM) to data is a crucial step in model development. We performed a systematic review to provide an overview of calibration methods used in IBMs modelling infectious disease spread. We included articles if models stored individual-specific information and calibration involved running the model and comparing model output to population-level targets expressed as summary statistics. The dataset contains information for each of the included articles on model calibration methods, including;...

Data From: Phylogenomics reveals accelerated late Cretaceous diversification of bee flies (Diptera: Bombyliidae)

Xuankun Li, Luisa C. Teasdale, Keith M. Bayless, Allan G. Ellis, Brian M. Wiegmann, Carlos José E. Lamas, Christine L. Lambkin, Neal L. Evenhuis, James A. Nicholls, Diana Hartley, Seunggwan Shin, Michelle Trautwein, Andreas Zwick, Bryan D. Lessard & David K. Yeates
Bombyliidae is a very species-rich and widespread family of parasitoid flies with more than 250 genera classified into 17 extant subfamilies. However, little is known about their evolutionary history or how their present-day diversity was shaped. Transcriptomes of 15 species and anchored hybrid enrichment (AHE) sequence captures of 86 species, representing 94 bee fly species and 14 subfamilies, were used to reconstruct the phylogeny of Bombyliidae. We integrated data from transcriptomes across each of the...

A new sectional classification of Lachenalia (Asparagaceae) based on a multilocus DNA phylogeny

Graham D. Duncan, Carl D. Schlichting, Felix Forest, Allan G. Ellis, Alan R. Lemmon, Emily Moriarty Lemmon & G. Anthony Verboom
Lachenalia J.Jacq. ex Murray (Asparagaceae; Scilloideae; Hyacintheae) is a large and morphologically diverse genus of more than 140 bulbous species endemic to southern Africa. Previous attempts to infer a well resolved and robustly supported phylogeny of Lachenalia using Sanger sequencing of candidate loci and/or morphological characters have been largely unsuccessful. Consequently, the current infrageneric classification is artificial and there is a need to explore alternative avenues to produce a phylogenetic classification. In this paper we...

Amphibian diversity in the Amazonian floating meadows: a Hanski core-satellite species system (scripts and codes)

Luis Fernando Marin Da Fonte, Guillaume Latombe, Marcelo Gordo, Marcelo Menin, Alexandre Pinheiro De Almeida, Cang Hui & Stefan Lötters
The Amazon catchment is the largest river basin on earth, and up to 30% of its waters flow across floodplains. In its open waters, floating plants known as floating meadows abound. They can act as vectors of dispersal for their associated fauna and, therefore, can be important for the spatial structure of communities. Here, we focus on amphibian diversity in the Amazonian floating meadows over large spatial scales. We recorded 50 amphibian species over 57...

Fragmented landscapes affect honeybee colony strength at diverse spatial scales in agro-ecological landscapes in Kenya

Pamela Ochungo, Ruan Veldtman, Elfatih Abdel-Rahman, Eliud Muli, James Ng'ang'a, Henri Tonnang & Tobias Landmann
Landscape fragmentation and habitat loss at multiple scales directly affect species abundance, diversity and their productivity. There is a paucity of information about the effect of the landscape structure and diversity on honeybee colony strength in Africa. Here, we present new insights into the relationship between landscape metrics such as patch size, shape, connectivity, composition and configuration and honeybee (Apis mellifera) colony strength characteristics. Remote sensing-based landscape variables were linked to honeybee colony strength variables...

Data from: Rethinking the scale and formulation of indices assessing organism vulnerability to warmer habitats

Raquel A. Garcia, Jessica L. Allen & Susana Clusella-Trullas
Ecologists often use indices or proxies to communicate complex ecological entities. Indices commonly known as Thermal Safety Margin, Habitat Thermal Quality and Hours of Restriction describe species' vulnerability to climate change by comparing organisms' thermal limits or preferences to available habitat temperatures. Ready access to temperature data, from global gridded datasets or limited in situ measurements, has made these indices popular for vulnerability assessments across taxonomic groups and regions. However, such coarse descriptions of thermal...

Data from: Frequency dependence of pollinator visitation rates suggests that pollination niches can allow plant species coexistence

Gita Benadi & Anton Pauw
1. How do many species coexist within a trophic level? Resource niches are the classical answer, but in plants which share a small set of abiotic resources the possibilities for resource partitioning are limited. One possible explanation is that plant species have different pollination niches, with each species specialized to a subset of the available animal species. If this pollinator partitioning results in negative frequency dependence such that each plant species’ reproduction is reduced when...

Data from: Proximate causes of variation in dermal armour: insights from armadillo lizards

Chris Broeckhoven, P. L. Le Fras N. Mouton & Cang Hui
Although it is widely assumed that body armour in animals evolved to thwart predator attacks, assessing the role that predators may play in shaping defensive morphologies has proven to be difficult. Recent studies suggest that body armour might be influenced by additional factors besides predation, and/or even by sexual selection. We investigated variation in dermal armour in 13 populations of armadillo lizards (Ouroborus cataphractus), spanning the entire distribution range of the species. We obtained thickness...

Data from: Fitness costs of rapid cold-hardening in Ceratitis capitata

C Helene Basson, Casper Nyamukondiwa & John S Terblanche
Rapid cold-hardening (RCH) is a unique form of phenotypic plasticity which confers survival advantages at low temperature. The fitness costs of RCH are generally poorly elucidated and are important to understanding the evolution of plastic physiology. This study examined whether RCH responses, induced by ecologically relevant diel temperature fluctuations, carry metabolic, survival or fecundity costs. We predicted that potential costs in RCH would be manifested as differences in metabolic rate, fecundity or survival in flies...

Data from: Costs of deception and learned resistance in deceptive interactions

Marinus L. De Jager & Allan G. Ellis
The costs that species suffer when deceived are expected to drive learned resistance, although this relationship has seldom been studied experimentally. Flowers that elicit mating behaviour from male insects by mimicking conspecific females provide an ideal system for such investigation. Here, we explore interactions between a sexually deceptive daisy with multiple floral forms that vary in deceptiveness, and the male flies that pollinate it. We show that male pollinators are negatively impacted by the interaction,...

Data from: Life table invasion models: spatial progression and species-specific partitioning

Zihua Zhao, Cang Hui, Richard E. Plant, Min Su, Tim Carpenter, Nikos Papadopoulos, Zhihong Li & James R. Carey
Biological invasions are increasingly being considered important spatial processes that drive global changes, threatening biodiversity, regional economies, and ecosystem functions. A unifying conceptual model of the invasion dynamics could serve as a useful tool for comparison and classification of invasion processes involving different species across large geographic ranges. By dividing these geographic ranges that are subject to invasions into discrete spatial units we here conceptualize the invasion process as the transition from pristine to invaded...

Data from: Cultivation shapes genetic novelty in a globally important invader

Genevieve D. Thompson, Dirk U. Bellstedt, Margaret Byrne, Melissa A. Millar, David M. Richardson, John Ross U. Wilson & Johannes J. Le Roux
Acacia saligna is a species complex that has become invasive in a number of countries worldwide where it has caused substantial environmental and economic impacts. Understanding genetic and other factors contributing to its success may allow managers to limit future invasions of closely related species. We used three molecular markers to compare the introduced range (South Africa) to the native range (Western Australia). Nuclear markers showed that invasive populations are divergent from native populations and...

Data from: Urban nectarivorous bird communities in Cape Town, South Africa, are structured by ecological generalisation and resource distribution

Anina Coetzee, Phoebe Barnard & Anton Pauw
Biological communities are increasingly faced with novel urban habitats and their response may depend on a combination of biological and habitat traits. The response of pollinator species to urban habitats are of particular importance because all species involved in the pollination mutualism may be affected. Nectarivorous bird communities worldwide show varying tolerances to urban areas, but studies from Africa are lacking. We investigated nectarivorous bird communities in a medium-sized South African city and asked which...

Data from: Between the Cape Fold Mountains and the deep blue sea: comparative phylogeography of selected codistributed ectotherms reveals asynchronous cladogenesis. Sampling locations and MaxEnt input files

Angus Myburgh
We compare the phylogeographic structure of thirteen codistributed ectotherms including four reptiles (a snake, a legless skink and two tortoise species) and nine invertebrates (six freshwater crabs and three velvet worm species) to test the presence of congruent evolutionary histories. Phylogenies were estimated and dated using maximum likelihood and Bayesian methods with combined mitochondrial and nuclear DNA sequence datasets. All taxa demonstrated a marked east/west phylogeographic division, separated by the Cape Fold Mountain range. Phylogeographic...

Data from: Emergence of weak‐intransitive competition through adaptive diversification and eco‐evolutionary feedbacks

Laure Gallien, Pietro Landi, Cang Hui & David M. Richardson
Indirect biotic interactions—such as intransitive competition—are increasingly recognized as being important in shaping ecological patterns in natural systems. Over long time‐scales, such indirect interactions may affect the evolution of species phenotypes, which in turn can modify these interactions, thereby begetting eco‐evolutionary feedbacks. If indirect intransitive interactions can emerge in situ during lineage diversification, they could profoundly affect species’ phenotypic diversity, temporal stability, and subsequent diversification rates. We address these questions by investigating the conditions under...

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  • Stellenbosch University
  • South African National Biodiversity Institute
  • University of Cape Town
  • University of Pretoria
  • Monash University
  • Oregon State University
  • Rhodes University
  • German Center for Integrative Biodiversity Research
  • Charles University
  • African Institute for Mathematical Sciences