Genetic structure of the common impala (Aepyceros melampus melampus) in South Africa: phylogeography and implications for conservation

Schwab, Patrick; Debes, Paul V.; Witt, Thorsten; Hartl, Günther B.; Hmwe, San San; Zachos, Frank E.; Grobler, J. Paul

doi:10.1111/j.1439-0469.2011.00638.x

Cited by 13 publications

(9 citation statements)

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“…This same pattern, which includes a northern coastal population with an otherwise inland group, has also been described in impala ( Aepyceros melampus ) by Schwab et al (2012) and other South African mammals (Lawes et al, 2007). Cooke (1962), Van Zinderen Bakker (1978) and Scott (2002) suggested that evergreen forest may have stretched from the northern region (NE1/NE2) into KwaZulu-Natal (NC1) before and after the last glacial maxima, 16,000–18,000 years before present.…”

Section: Discussionsupporting

confidence: 69%

Localized population divergence of vervet monkeys (Chlorocebusspp.) in South Africa: Evidence from mtDNA

Turner

Coetzer

Schmitt

et al. 2015

American J Phys Anthropol

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Objectives Vervet monkeys are common in most tree-rich areas of South Africa, but their absence from grassland and semi-desert areas of the country suggest potentially restricted and mosaic local population patterns that may have relevance to local phenotype patterns and selection. A portion of the mtDNA control region was sequenced to study patterns of genetic differentiation. Materials and Methods DNA was extracted and mtDNA sequences were obtained from 101 vervet monkeys at 15 localities which represent both an extensive (widely across the distribution range) and intensive (more than one troop at most of the localities) sampling strategy. Analyses utilized Arlequin 3.1, MEGA 6, BEAST v1.5.2 and Network V3.6.1 Results The dataset contained 26 distinct haplotypes, with six populations fixed for single haplotypes. Pairwise P-distance among population pairs showed significant differentiation among most population pairs, but with non-significant differences among populations within some regions. Populations were grouped into three broad clusters in a maximum likelihood phylogenetic tree and a haplotype network. These clusters correspond to (i) north-western, northern and north-eastern parts of the distribution range as well as the northern coastal belt; (ii) central areas of the country; and (iii) southern part of the Indian Ocean coastal belt, and adjacent inland areas. Discussion Apparent patterns of genetic structure correspond to current and past distribution of suitable habitat, geographic barriers to gene flow, geographic distance and female philopatry. However, further work on nuclear markers and other genomic data is necessary to confirm these results.

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Section: Discussionsupporting

confidence: 69%

Localized population divergence of vervet monkeys (Chlorocebusspp.) in South Africa: Evidence from mtDNA

Turner

Coetzer

Schmitt

et al. 2015

American J Phys Anthropol

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“…Both cytb and D-loop detect continental and regional (South Africa) phylogeographic structure respectively [43,44]. The COI phylogenetic tree reflects a similar continental pattern to that of cytb [43].…”

Section: Resultsmentioning

confidence: 99%

Where is the game? Wild meat products authentication in South Africa: a case study

et al. 2013

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BackgroundWild animals’ meat is extensively consumed in South Africa, being obtained either from ranching, farming or hunting. To test the authenticity of the commercial labels of meat products in the local market, we obtained DNA sequence information from 146 samples (14 beef and 132 game labels) for barcoding cytochrome c oxidase subunit I and partial cytochrome b and mitochondrial fragments. The reliability of species assignments were evaluated using BLAST searches in GenBank, maximum likelihood phylogenetic analysis and the character-based method implemented in BLOG. The Kimura-2-parameter intra- and interspecific variation was evaluated for all matched species.ResultsThe combined application of similarity, phylogenetic and character-based methods proved successful in species identification. Game meat samples showed 76.5% substitution, no beef samples were substituted. The substitutions showed a variety of domestic species (cattle, horse, pig, lamb), common game species in the market (kudu, gemsbok, ostrich, impala, springbok), uncommon species in the market (giraffe, waterbuck, bushbuck, duiker, mountain zebra) and extra-continental species (kangaroo). The mountain zebra Equus zebra is an International Union for Conservation of Nature (IUCN) red listed species. We also detected Damaliscus pygargus, which is composed of two subspecies with one listed by IUCN as ‘near threatened’; however, these mitochondrial fragments were insufficient to distinguish between the subspecies. The genetic distance between African ungulate species often overlaps with within-species distance in cases of recent speciation events, and strong phylogeographic structure determines within-species distances that are similar to the commonly accepted distances between species.ConclusionsThe reliability of commercial labeling of game meat in South Africa is very poor. The extensive substitution of wild game has important implications for conservation and commerce, and for the consumers making decisions on the basis of health, religious beliefs or personal choices.Distance would be a poor indicator for identification of African ungulates species. The efficiency of the character-based method is reliant upon availability of large reference data. The current higher availability of cytochrome b data would make this the marker of choice for African ungulates. The encountered problems of incomplete or erroneous information in databases are discussed.

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“…The Drakensberg Mountains are very old, with an estimated age of 280 million years, which implies that a separation of the vervet populations could have occurred in a time frame ranging from 3 million years ago (during the AGM spread throughout sub-Saharan Africa) to 100,000 years go (during the mass migrations that occurred in the Plio-Pleistocene glacial periods). The Drakensberg Mountains may also have acted as an effective barrier to separate different populations of at least two other species, the common impala ( Aepyceros melampus melampus ) [113] and the chacma baboon ( Papio ursinus ) [114]. We therefore performed relaxed molecular clock analyses to specify TMRCA of the SIVagm samples surrounding the Drakensberg Mountains range to a time-frame spanning 100,000 to 3,000,000 years since the present for the env tree, and in the pol tree we additionally included SIV strains of several species and further calibrated the tree based on isolates from Bioko Island [2].…”

Section: Discussionmentioning

confidence: 99%

SIVagm Infection in Wild African Green Monkeys from South Africa: Epidemiology, Natural History, and Evolutionary Considerations

et al. 2013

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Pathogenesis studies of SIV infection have not been performed to date in wild monkeys due to difficulty in collecting and storing samples on site and the lack of analytical reagents covering the extensive SIV diversity. We performed a large scale study of molecular epidemiology and natural history of SIVagm infection in 225 free-ranging AGMs from multiple locations in South Africa. SIV prevalence (established by sequencing pol, env, and gag) varied dramatically between infant/juvenile (7%) and adult animals (68%) (p<0.0001), and between adult females (78%) and males (57%). Phylogenetic analyses revealed an extensive genetic diversity, including frequent recombination events. Some AGMs harbored epidemiologically linked viruses. Viruses infecting AGMs in the Free State, which are separated from those on the coastal side by the Drakensberg Mountains, formed a separate cluster in the phylogenetic trees; this observation supports a long standing presence of SIV in AGMs, at least from the time of their speciation to their Plio-Pleistocene migration. Specific primers/probes were synthesized based on the pol sequence data and viral loads (VLs) were quantified. VLs were of 104–106 RNA copies/ml, in the range of those observed in experimentally-infected monkeys, validating the experimental approaches in natural hosts. VLs were significantly higher (107–108 RNA copies/ml) in 10 AGMs diagnosed as acutely infected based on SIV seronegativity (Fiebig II), which suggests a very active transmission of SIVagm in the wild. Neither cytokine levels (as biomarkers of immune activation) nor sCD14 levels (a biomarker of microbial translocation) were different between SIV-infected and SIV-uninfected monkeys. This complex algorithm combining sequencing and phylogeny, VL quantification, serology, and testing of surrogate markers of microbial translocation and immune activation permits a systematic investigation of the epidemiology, viral diversity and natural history of SIV infection in wild African natural hosts.

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Genetic structure of the common impala (Aepyceros melampus melampus) in South Africa: phylogeography and implications for conservation

Cited by 13 publications

References 50 publications

Localized population divergence of vervet monkeys (Chlorocebusspp.) in South Africa: Evidence from mtDNA

Localized population divergence of vervet monkeys (Chlorocebusspp.) in South Africa: Evidence from mtDNA

Where is the game? Wild meat products authentication in South Africa: a case study

SIVagm Infection in Wild African Green Monkeys from South Africa: Epidemiology, Natural History, and Evolutionary Considerations

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