Molecular phylogeny of Duiker Antelope (Mammalia: Cephalophini)

Molecular sequence data, comparative cytogenetics, and fluorescence in situ hybridization (FISH) were employed to study evolutionary relationships within the duiker antelope (tribe Cephalophini). The results of the different data sets are highly concordant. Mitochondrial DNA sequences (the full cytochrome b gene and a 767 bp portion of the 12S rRNA) were analyzed from all 19 recognized species. Complete species representation and good cytochrome b resolution allowed for the retrieval of four adaptive lineages, the conservative dwarfs (Cephalophus monticola, C. maxwellii) which were the most basal clade, the savanna specialist (Sylvicapra grimmia) which groups apart from all the forest duiker, the giant duiker group (C. silvicultor, C. spadix, C. dorsalis, C. jentinki), and the red duiker lineage ( C. leucogaster, C. rufilatus, C. nigrifrons, C. natalensis, C. harveyi, C. callipygus, C. 'rveynsi, C. ogilbyi, C. rubidus, C. niger ). The placement of the endangered C. zebra and the enigmatic C. adersi remains obscure. Conventional chromosome banding showed a 2n=60 complement in C. spadix extending previous observations that speciation in duiker antelope does not involve euchromatic rearrangements or variation in diploid number. At a finer level, fluorescence in situ hybridization with species specific satellite fragments derived from the chromosomal DNA of C. marwellii and C. monticola, resulted in intense fluorescence to the centromeric regions of the autosomes of all species (S. grirnmia, C. dorsal is, C. rnarwellii, C. monticola, C. natalensis, C. silvicultor, C. spadix). However, variation in hybridization to the X and y chromosomes allowed for some distinction among taxa. These results are consistent with the delimitation of the four adaptive groups suggested by molecular analysis and the published morphological data which, when taken together, question and in some instances support several of the nomenclatural divisions in current use in duiker taxonomy. These include the recognition of Philantomba as genus name for C. monticola and C. mw..w ellii, an arrangement that would secure Cephalophus monophyly, and that C. harveyi be relegated to a subspecies of C. natalensis.Thesis (PhD (Zoology))--University of Pretoria, 1999.Zoology and EntomologyPhD (Zoology)Unrestricte

Genetic differentiation in Oxalis (Oxalidaceae): A tale of rarity and abundance in the Cape Floristic Region

AbstractOxalis L. is the largest and most diverse genus in the family Oxalidaceae. Within southern Africa, Oxalis is represented by ca. 270 taxa, the majority occurring in the Cape Region. Although many of the species are widespread, ca. 25% are considered rare. The aim of this paper is to assess the degree of genetic differentiation between two rare and highly localized species (Oxalis hygrophila Dreyer and Oxalis oligophylla Salter) and the more widespread Oxalis tomentosa L.f. For comparative purposes, we also include Oxalis purpurea L., one of the most widely distributed species in South Africa. Chloroplast sequences of the trnH/psbA spacer revealed low genetic diversity for O. oligophylla and O. tomentosa compared to the widespread O. purpurea. High genetic diversity in O. purpurea might, in combination with other ecological and reproductive factors, account for the success of this species. In contrast, low variation might contribute to rarity in O. oligophylla and ultimately ground O. tomentosa to become rare. The latter two species were not monophyletic with a shared haplotype. Coalescent modelling revealed low levels of gene flow (<1 migrant per generation) between them and we argue that the genetic pattern is the result of the retention of ancestral polymorphism following a recent divergence

Genetic evidence confirms the origin of the house mouse on sub-Antarctic Marion Island

Biological invasions and climate change are two of the largest threats to biodiversity, and this is especially true for island ecosystems that have largely evolved in isolation. The house mouse is considered to have been introduced to sub-Antarctic Marion Island by sealers in the early 1800s. It is currently widespread across the island and has a large impact on the indigenous biota. To date, little information is available on genetic aspects of biological invasions in the sub-Antarctic. Ten specimens of the house mouse were collected from two geographically separated localities on Marion Island. Sequences of the mitochondrial DNA control region revealed only two haplotypes, separated by a single site change. More importantly, these haplotypes are shared between the eastern and western side of Marion Island. By comparing our sequences to data available on GenBank, we provide evidence that house mice on Marion Island is Mus musculus domesticus (Rutty 1772), and most closely related to haplotypes characterizing this species from Denmark, Sweden, Finland, and northern Germany.Ctr Invas Bio

Evolutionary history of the Karoo bush rat, Myotomys unisulcatus (Rodentia: Muridae): disconcordance between morphology and genetics

Morphological characters have historically been used as the basis for mammalian taxonomic designations and, in a geographic context, subspecies descriptions. Geographic genetic structuring of a species, however, often reflects a contrasting classification for sampled populations. To investigate morphological and genetic congruence, geometric morphometrics and phylogeographic mitochondrial DNA sequence analyses of a South African plainsdwelling species, Myotomys unisulcatus, the Karoo bush rat, was performed across its range. A Bayesian population structure analysis identified two closely-related distinct genetic assemblages: the first contains populations from both the eastern, southern, and western parts of the species range (coastal lowland group), and the second comprises individuals from the Little Karoo (central interior group). Areas of sharp elevation (the Great Escarpment), coupled to vegetational differences, appeared to be the main factor limiting gene flow between these two groups. Geometric morphometric analyses on the ventral and dorsal views of the crania of M. unisulcatus failed to support the genetic groupings. Instead environmental factors in the respective biomes appeared to play a more important role in shaping the crania of both genders. The contrasting patterns obtained between morphology and genetics in M. unisulcatus is probably indicative of phenotypic plasticity throughout the range of the species, and it is hypothesized that regional environmental factors play a prominent role in explaining geographic morphological variation within the species

Population structure, propagule pressure, and conservation biogeography in the sub-Antarctic: lessons from indigenous and invasive springtails

The patterns in and the processes underlying the distribution of invertebrates among Southern Ocean islands and across vegetation types on these islands are reasonably well understood. However, few studies have examined the extent to which populations are genetically structured. Given that many sub-Antarctic islands experienced major glaciation and volcanic activity, it might be predicted that substantial population substructure and little genetic isolation-by-distance should characterize indigenous species. By contrast, substantially less population structure might be expected for introduced species. Here, we examine these predictions and their consequences for the conservation of diversity in the region. We do so by examining haplotype diversity based on mitochondrial cytochrome c oxidase subunit I sequence data, from two indigenous (Cryptopygus antarcticus travei, Tullbergia bisetosa) and two introduced (Isotomurus cf. palustris, Ceratophysella denticulata) springtail species from Marion Island. We find considerable genetic substructure in the indigenous species that is compatible with the geological and glacialogical history of the island. Moreover, by employing ecological techniques, we show that haplotype diversity is likely much higher than our sequenced samples suggest. No structure is found in the introduced species, with each being represented by a single haplotype only. This indicates that propagule pressure is not significant for these small animals unlike the situation for other, larger invasive species: a few individuals introduced once are likely to have initiated the invasion. These outcomes demonstrate that sampling must be more comprehensive if the population history of indigenous arthropods on these islands is to be comprehended, and that the risks of within- and among-island introductions are substantial. The latter means that, if biogeographical signal is to be retained in the region, great care must be taken to avoid inadvertent movement of indigenous species among and within islands. Thus, quarantine procedures should also focus on among-island movements.Ctr Invas Bio

Evolutionary history of Carnivora (Mammalia, Laurasiatheria) inferred from mitochondrial genomes

The order Carnivora, which currently includes 296 species classified into 16 families, is dis- tributed across all continents. The phylogeny and the timing of diversification of members of the order are still a matter of debate. Here, complete mitochondrial genomes were analysed to reconstruct the phylogenetic relationships and to estimate divergence times among spe- cies of Carnivora. We assembled 51 new mitogenomes from 13 families, and aligned them with available mitogenomes by selecting only those showing more than 1% of nucleotide divergence and excluding those suspected to be of low-quality or from misidentified taxa. Our final alignment included 220 taxa representing 2,442 mitogenomes. Our analyses led to a robust resolution of suprafamilial and intrafamilial relationships. We identified 21 fossil cali- bration points to estimate a molecular timescale for carnivorans. According to our diver- gence time estimates, crown carnivorans appeared during or just after the Early Eocene Climatic Optimum; all major groups of Caniformia (Cynoidea/Arctoidea; Ursidae; Musteloi- dea/Pinnipedia) diverged from each other during the Eocene, while all major groups of Feli- formia (Nandiniidae; Feloidea; Viverroidea) diversified more recently during the Oligocene, with a basal divergence of Nandinia at the Eocene/Oligocene transition; intrafamilial diver- gences occurred during the Miocene, except for the Procyonidae, as Potos separated from other genera during the Oligocene

Experimental characterization of the active and passive fast-ion H-alpha emission in W7-X using FIDASIM

This paper presents the first results from the analysis of Balmer-alpha spectra at Wendelstein 7-X which contain the broad charge exchange emission from fast-ions. The measured spectra are compared to synthetic spectra predicted by the FIDASIM code, which has been supplied with the 3D magnetic fields from VMEC, 5D fast-ion distribution functions from ASCOT, and a realistic Neutral Beam Injection geometry including beam particle blocking elements. Detailed modeling of the beam emission shows excellent agreement between measured beam emission spectra and predictions. In contrast, modeling of beam halo radiation and Fast-Ion H-Alpha signals (FIDA) is more challenging due to strong passive contributions. While about 50% of the halo radiation can be attributed to passive signals from edge neutrals, the FIDA emission—in particular for an edge-localized line of sights—is dominated by passive emission. This is in part explained by high neutral densities in the plasma edge and in part by edge-born fast-ion populations as demonstrated by detailed modeling of the edge fast-ion distribution