Browsing by Author "Bloomer, Paulette"

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    Open Access
    Facilitating golden mole conservation in South African highland grasslands : a predictive modelling approach
    (2016) Rampartab, Chanel; Bronner, Gary N; Bennett, Nigel C; Bloomer, Paulette; Robertson, M P
    Golden moles are subterranean mammals endemic to sub-Saharan Africa and threatened by anthropogenic habitat loss. At present, little is known about the biology, taxonomy, distribution and severity of threats faced by many of these taxa. In an attempt to raise awareness of these elusive grassland flagship taxa, the Endangered Wildlife Trust's Threatened Grassland Species Programme (EWT-TGSP) identified the need for more information on the distributions and conservation status of four poorly-known golden mole taxa (Amblysomus hottentotus longiceps, A. h. meesteri, A. robustus, A. septentrionalis) that are endemic to the Grassland Biome, and which may be heavily impacted by anthropogenic habitat alteration in the Highveld regions of Mpumalanga Province. This study employed species distribution modelling to predict the distributional ranges of these taxa, and involved four main processes: (i) creating initial models trained on sparse museum data records; (ii) ground-truthing field surveys during austral spring/summer to gather additional specimens at additional localities; (iii) genetic analyses (using cytochrome-b) to determine the species identities of the newly-acquired specimens, as these taxa are morphologically indistinguishable; and (iv) refining the models and determining the conservation status of these Highveld golden moles. Initial species distribution models were developed using occurrence records for 38 specimens, based on interpolated data for 19 bioclimatic variables, continuous altitude data, as well as categorical spatial data for landtypes, WWF ecoregions and vegetation types. These initial models helped to effectively focus survey efforts within a vast study area, with surveying during the austral spring-summer of 2013-4 resulting in the acquisition of 25 specimens from across Mpumalanga, nine individuals of which (A. h. meesteri n = 2; A. septentrionalis n = 5; unknown n = 2) were captured in five new quarter-degree-squares (QDSs) where no previous golden moles have been recorded. Additionally, observed activity was also recorded in nine new QDSs (see Appendix 3), showing that the model refinement methods used (variable selection, auto-correlation, non-repeated versus cross-validated models, jackknife of variable importance and localities, independent data testing) were effective in locating golden mole populations. By using genetically-identified historical golden mole records, predictive distribution models were calibrated in maximum entropy (MaxEnt) software to focus ground-truthing efforts.
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    How attractive is the girl next door? An assessment of spatial mate acquisition and paternity in the solitary Cape dune mole-Rat, Bathyergus suillus
    (Public Library of Science, 2012) Bray, Timothy C; Bloomer, Paulette; O'Riain, M Justin; Bennett, Nigel C
    Behavioural observations of reproduction and mate choice in wild fossorial rodents are extremely limited and consequently indirect methods are typically used to infer mating strategies. We use a combination of morphological, reproductive, spatial, and genetic data to investigate the reproductive strategy of a solitary endemic species, the Cape dune mole-rat Bathyergus suillus. These data provide the first account on the population dynamics of this species. Marked sexual dimorphism was apparent with males being both significantly larger and heavier than females. Of all females sampled 36% had previously reproduced and 12% were pregnant at the time of capture. Post-partum sex ratio was found to be significantly skewed in favour of females. The paternity of fifteen litters (n = 37) was calculated, with sires assigned to progeny using both categorical and full probability methods, and including a distance function. The maximum distance between progeny and a putative sire was determined as 2149 m with males moving between sub-populations. We suggest that above-ground movement should not be ignored in the consideration of mate acquisition behaviour of subterranean mammals. Estimated levels of multiple paternity were shown to be potentially as high as 26%, as determined using sibship and sire assignment methods. Such high levels of multiple paternity have not been found in other solitary mole-rat species. The data therefore suggest polyandry with no evidence as yet for polygyny.
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    Multidisciplinary investigation into stock structure of small pelagic fishes in southern Africa
    (2014) Hampton, Shannon; Moloney, Coleen; Bloomer, Paulette; Van der Lingen, Carl D
    Three abundant small pelagic fish species co-occur in the Benguela upwelling ecosystem off southern Africa: sardine (Sardinops sagax), anchovy (Engraulis encrasicolus) and round herring (Etrumeus whiteheadi). It is hypothesised that populations of these species have a complex structure that reflects the complexity of their varying habitats. On the basis of the locality and timing of spawning, and morphological, meristic and parasite studies, it has been proposed that there are separate stocks of sardine in South African waters west and east of Cape Agulhas. Consequently, new operational procedures for managing the fishery are based on the premise of two such stocks, termed the west and south coast stocks respectively. In this study, it is hypothesized that the factors causing purported stock differences in sardine should also apply to anchovy and redeye. Three different approaches were used to further test the multi-stock hypothesis for sardine in southern Africa and to provide new information for understanding possible stock differences in anchovy and round herring. The population structure of sardine was investigated through studies on samples taken from the Cape west and south coasts as well as from Namibia and KwaZulu-Natal. Two dimensionless otolith shape indices, otolith elemental signatures, seven microsatellite loci and the mitochondrial DNA marker, ND2, were used to supplement existing information on sardine. Otolith shape, while influenced by fish length and season of capture, distinguished the east coast samples from those taken elsewhere, while the otolith elemental signatures indicated differentiation among sites on a small scale and between samples taken from the west and south coast for certain elements. Both genetic indicators showed high levels of genetic diversity and variation among individuals. There were some genetic differences among sites within a single year, but overall the results suggest that the South African sardine population is well mixed, with weak evidence of genetic patchiness that is not temporally stable. This genetic pattern is evidence of sweepstake recruitment. For anchovy, two spawning locations have been identified in South African waters, but there have been no previous investigations into stock structure. The current study aimed to apply different methods to anchovy samples to determine their usefulness for differentiating population structure,. An analysis of otolith shape revealed that it was primarily influenced by the length of the fish, with no differentiation among sites, whereas an investigation into genetic differentiation using five microsatellite markers revealed high levels of genetic diversity and differentiation among sites. Since there were relatively few samples for a study of this sort, further work is recommended to investigate stock structure in South African anchovy. For round herring, only otolith shape was analysed to test for stock structure. Otolith shape was found to be primarily related to the length of the fish (as in anchovy) and sex, but no significant difference was found between coasts. There were different magnitudes of variability in the results for the three species using different methods. It is likely that the complex, variable environment causes complex patterns of mixing and micro-structuring within all three species, linked to their different niches.
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    A phylogenetic estimate for golden moles (Mammalia, Afrotheria, Chrysochloridae)
    (BioMed Central Ltd, 2010) Asher, Robert; Maree, Sarita; Bronner, Gary; Bennett, Nigel C; Bloomer, Paulette; Czechowski, Paul; Meyer, Matthias; Hofreiter, Michael
    BACKGROUND: Golden moles (Chrysochloridae) are small, subterranean, afrotherian mammals from South Africa and neighboring regions. Of the 21 species now recognized, some (e.g., Chrysochloris asiatica, Amblysomus hottentotus) are relatively common, whereas others (e.g., species of Chrysospalax, Cryptochloris, Neamblysomus) are rare and endangered. Here, we use a combined analysis of partial sequences of the nuclear GHR gene and morphological characters to derive a phylogeny of species in the family Chrysochloridae. RESULTS: Although not all nodes of the combined analysis have high support values, the overall pattern of relationships obtained from different methods of phylogeny reconstruction allow us to make several recommendations regarding the current taxonomy of golden moles. We elevate Huetia to generic status to include the species leucorhinus and confirm the use of the Linnean binomial Carpitalpa arendsi, which belongs within Amblysominae along with Amblysomus and Neamblysomus. A second group, Chrysochlorinae, includes Chrysochloris, Cryptochloris, Huetia, Eremitalpa, Chrysospalax, and Calcochloris. Bayesian methods make chrysochlorines paraphyletic by placing the root within them, coinciding with root positions favored by a majority of randomly-generated outgroup taxa. Maximum Parsimony (MP) places the root either between chrysochlorines and amblysomines (with Chlorotalpa as sister taxon to amblysomines), or at Chlorotalpa, with the former two groups reconstructed as monophyletic in all optimal MP trees. CONCLUSIONS: The inclusion of additional genetic loci for this clade is important to confirm our taxonomic results and resolve the chrysochlorid root. Nevertheless, our optimal topologies support a division of chrysochlorids into amblysomines and chrysochlorines, with Chlorotalpa intermediate between the two. Furthermore, evolution of the chrysochlorid malleus exhibits homoplasy. The elongate malleus has evolved just once in the Cryptochloris-Chrysochloris group; other changes in shape have occurred at multiple nodes, regardless of how the root is resolved.
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    The phylogenetics and evolution of Africa's larks (Alaudidae)
    (2007) Barnes, Keith N; Ryan, Peter G; Bloomer, Paulette
    The larks are a group of dull coloured birds that are conservative in plumage coloration and pattern due to the requirements for camouflage in open habitats. Because many species inhabit structurally similar habitats the group is also characterised by a great deal of morphological convergence. Variation in plumage and morphology is frequently as great within species as it is between species, leading to many inconsistent and controversial taxonomic treatments and classifications at an intra- and inter-generic level, and when defining specific and sub-specific boundaries. The advent of genetic techniques and success at applying these to species complexes in southern Africa suggested that a molecular phylogeny of the family would elucidate relationships that could not be determined via traditional taxonomic practices. In this study 2009 nucleotides of two mitochondrial DNA genes, cytochrome b and 16S rRNA (Chapter 2), and 2872 nucleotides of the nuclear exon RAG-l (Chapter 3) were used to generate a robust phylogeny of the family Alaudidae. The former analysis included 55 species and the latter 25. These data were also combined to construct a combined evidence phylogeny (Chapter 7). Within the family, several genera recognised by more traditional taxonomies are polyphyletic, including Ammomanes, Eremalauda .and Certhilauda. Two other genera, Calandrella and Mirafra, are best treated as multiple genera (Chapter 2). The sampled Alaudidae can be divided into three main radiations, the ammomanid larks, mirafrid larks and alaudid larks (Chapter 3). Within the ammomanid larks, there is strong support for: (1) a southern African' radiation comprising Chersomanes, the Long-billed Lark complex (Certhilauda) and Ammomanes (Ammomanopsis) grayi ,with Alaemon allied to this radiation; and (2) a .Saharo-Sindian radiation comprising Ramphocoris c1otbey, Ammomanes cinc(urus, and A. deserti sister to the Afro-Sindian sparrowlark Eremopterix clade. The Madagascan endemic Mirafra hova was a surprise basal member of Eremopterix.
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    Phylogeography of a morphologically cryptic golden mole assemblage from South-Eastern Africa
    (Public Library of Science, 2015) Mynhardt, Samantha; Maree, Sarita; Pelser, Illona; Bennett, Nigel C; Bronner, Gary N; Wilson, John W; Bloomer, Paulette
    The Greater Maputaland-Pondoland-Albany (GMPA) region of southern Africa was recently designated as a centre of vertebrate endemism. The phylogeography of the vertebrate taxa occupying this region may provide insights into the evolution of faunal endemism in south-eastern Africa. Here we investigate the phylogeographic patterns of an understudied small mammal species assemblage ( Amblysomus ) endemic to the GMPA, to test for cryptic diversity within the genus, and to better understand diversification across the region. We sampled specimens from 50 sites across the distributional range of Amblysomus , with emphasis on the widespread A . hottentotus , to analyse geographic patterns of genetic diversity using mitochondrial DNA (mtDNA) and nuclear intron data. Molecular dating was used to elucidate the evolutionary and phylogeographic history of Amblysomus . Our phylogenetic reconstructions show that A . hottentotus comprises several distinct lineages, or evolutionarily significant units (ESUs), some with restricted geographic ranges and thus worthy of conservation attention. Divergence of the major lineages dated to the early Pliocene, with later radiations in the GMPA during the late-Pliocene to early-Pleistocene. Evolutionary diversification within Amblysomus may have been driven by uplift of the Great Escarpment c. 5-3 million years ago (Ma), habitat changes associated with intensification of the east-west rainfall gradient across South Africa and the influence of subsequent global climatic cycles. These drivers possibly facilitated geographic spread of ancestral lineages, local adaptation and vicariant isolation. Our study adds to growing empirical evidence identifying East and southern Africa as cradles of vertebrate diversity.