9 Works

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: 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: Local adaptation: mechanical fit between floral ecotypes of Nerine humilis (Amaryllidaceae) and pollinator communities

Ethan Newman, John Manning & Bruce Anderson
Geographic variation in floral morphology is often assumed to reflect geographic variation in pollinator communities and associated divergence in selective pressures. We studied populations of Nerine humilis (Amaryllidaceae) to assess whether geographic variation in floral form is the result of local adaptation to different pollinator communities. We first tested for associations between floral traits and visitor communities, and found that populations with similar floral morphologies were visited by similar insect communities. Mean style length in...

Data from: Limited dispersal in an ectoparasitic mite, Laelaps giganteus, contributes to significant phylogeographic congruence with their rodent hosts, Rhabdomys

Adriaan Engelbrecht, Sonja Matthee, Nina Du Toit, Conrad Matthee & Conrad A. Matthee
To explore how biogeography, parasite life history and host vagility influences evolutionary codivergences, we followed a comparative phylogeography approach using a host specific non-permanent mite, Laelaps giganteus that occurs on four rodent species within the genus Rhabdomys. A mtDNA COI haplotype network derived for 278 parasite specimens showed marked phylogeographic congruence with host distributions. Analysis of the less variable nuclear intron Tropomyosin was in part consistent with these results. Although distance-based cophylogenetic analyses in AXPARAFIT...

Data from: Lake Tanganyika - a 'melting pot' of ancient and young cichlid lineages (Teleostei: Cichlidae)?

Juliane D. Weiss, Fenton P. D. Cotterill & Ulrich K. Schliewen
A long history of research focused on the East Africa cichlid radiations (EAR) revealed discrepancies between mtDNA and nuclear phylogenies, suggesting that interspecific hybridisation may have been significant during the radiation of these fishes. The approximately 250 cichlid species of Lake Tanganyika have their roots in a monophyletic African cichlid assemblage, but controversies remain about the precise phylogenetic origin and placement of different lineages and consequently about L. Tanganyika colonization scenarios. 3312 AFLP loci and...

Data from: Energetic benefits and adaptations in mammalian limbs: scale effects and selective pressures

Brandon M. Kilbourne & Louwrens C. Hoffman
Differences in limb size and shape are fundamental to mammalian morphological diversity; however, their relevance to locomotor costs has long been subject to debate. In particular, it remains unknown if scale effects in whole limb morphology could partially underlie decreasing mass-specific locomotor costs with increasing limb length. Whole fore- and hindlimb inertial properties reflecting limb size and shape – moment of inertia (MOI), mass, mass distribution, and natural frequency – were regressed against limb length...

Data from: What doesn’t kill you might make you stronger: functional basis for variation in body armour

Chris Broeckhoven, Genevieve Diedericks & Pieter Le Fras N. Mouton
1. Predation has been proposed to be a selective agent in the evolution of morphological antipredator strategies in prey. Among vertebrates, one of the morphological traits that evolved multiple times is body armour, including carapaces, thickened keratinized scales and plates of dermal bone. 2. It has been generally assumed that body armour provides protection against a predatory attack; yet, few explicit tests of the hypothesis exist. Cordylidae, a relatively small family of southern African lizards,...

Data from: Indirect effects of habitat disturbance on invasion: nutritious litter from a grazing resistant plant favors alien over native Collembola

Hans Petter Leinaas, Jan Bengtsson, Charlene Janion-Scheepers & Steven L. Chown
Biological invasions are major threats to biodiversity, with impacts that may be compounded by other forms of environmental change. Observations of high density of the invasive springtail (Collembola), Hypogastrura manubrialis in heavily grazed renosterveld vegetation in the Western Cape, South Africa, raised the question of whether the invasion was favored by changes in plant litter quality associated with habitat disturbance in this vegetation type. To examine the likely mechanisms underlying the high abundance of H....

Data from: Exploring the impact of habitat size on phylogeographic patterning in the Overberg velvet worm Peripatopsis overbergiensis (Onychophora: Peripatopsidae)

Angus Macgregor Myburgh & Savel R. Daniels
Evolutionary relationships in the velvet worm species, Peripatopsis overbergiensis, were examined in 3 forest areas in the Overberg region of South Africa to explore the impact of historical habitat fragmentation on the population genetic structure of the species. We collected 84 P. overbergiensis specimens from Grootvadersbosch, Koppie Alleen, and Marloth Nature Reserves and sequenced all these specimens for the cytochrome c oxidase subunit I (COI) locus, whereas a subset of 13 specimens were also sequenced...

Registration Year

  • 2015

Resource Types

  • Dataset


  • Stellenbosch University
  • South African National Biodiversity Institute
  • Field Museum of Natural History
  • Oregon State University
  • United States Department of Agriculture
  • University of Oslo
  • Charles University
  • University of Chicago
  • Monash University
  • Swedish University of Agricultural Sciences