Browsing by Subject "Phylogeography"

Now showing 1 - 8 of 8
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    Distribution of high-risk human papillomavirus genotypes among HIV-negative women with and without cervical intraepithelial neoplasia in South Africa
    (Public Library of Science, 2012) McDonald, Alicia C; Denny, Lynette; Wang, Chunhui; Tsai, Wei-Yann; Jr, Thomas C Wright; Kuhn, Louise
    Objective Large studies describing the profile of high-risk Human papillomavirus (hrHPV) genotypes among women in sub-Saharan Africa are lacking. Here we describe the prevalence and distribution of hrHPV genotypes among HIV-negative women in South Africa, with and without cervical intraepithelial neoplasia (CIN). METHODS: We report data on 8,050 HIV-negative women, aged 17-65 years, recruited into three sequential studies undertaken in Cape Town, South Africa. Women had no history of previous cervical cancer screening. Cervical samples were tested for hrHPV DNA using the Hybrid Capture 2 (HC2) assay and all positive samples were genotyped using a PCR-based assay (Line Blot). Women underwent colposcopy and biopsy/endocervical curettage to determine CIN status. The prevalence and distribution of specific hrHPV genotypes were examined by age and CIN status. RESULTS: Overall, 20.7% (95% CI, 19.9-21.6%) of women were hrHPV-positive by HC2, with women with CIN having the highest rates of positivity. Prevalence decreased with increasing age among women without CIN; but, a bimodal age curve was observed among women with CIN. HPV 16 and 35 were the most common hrHPV genotypes in all age and CIN groups. HPV 45 became more frequent among older women with CIN grade 2 or 3 (CIN2,3). Younger women (17-29 years) had more multiple hrHPV genotypes overall and in each cervical disease group than older women (40-65 years). CONCLUSION: HPV 16, 35, and 45 were the leading contributors to CIN 2,3. The current HPV vaccines could significantly reduce HPV-related cervical disease; however, next generation vaccines that include HPV 35 and 45 would further reduce cervical disease in this population.
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    Divergent evolutionary and epidemiological dynamics of cassava mosaic geminiviruses in Madagascar
    (2016) De Bruyn, Alexandre; Harimalala, Mireille; Zinga, Innocent; Mabvakure, Batsirai M; Hoareau, Murielle; Ravigné, Virginie; Walters, Matthew; Reynaud, Bernard; Varsani, Arvind; Harkins, Gordon W; Martin, Darren P; Lett, Jean-Michel; Lefeuvre, Pierre
    Abstract Background Cassava mosaic disease (CMD) in Madagascar is caused by a complex of at least six African cassava mosaic geminivirus (CMG) species. This provides a rare opportunity for a comparative study of the evolutionary and epidemiological dynamics of distinct pathogenic crop-infecting viral species that coexist within the same environment. The genetic and spatial structure of CMG populations in Madagascar was studied and Bayesian phylogeographic modelling was applied to infer the origins of Madagascan CMG populations within the epidemiological context of related populations situated on mainland Africa and other south western Indian Ocean (SWIO) islands. Results The isolation and analysis of 279 DNA-A and 117 DNA-B sequences revealed the presence in Madagascar of four prevalent CMG species (South African cassava mosaic virus, SACMV; African cassava mosaic virus, ACMV; East African cassava mosaic Kenya virus, EACMKV; and East African cassava mosaic Cameroon virus, EACMCV), and of numerous CMG recombinants that have, to date, only ever been detected on this island. SACMV and ACMV, the two most prevalent viruses, displayed low degrees of genetic diversity and have most likely been introduced to the island only once. By contrast, EACMV-like CMG populations (consisting of East African cassava mosaic virus, EAMCKV, EACMCV and complex recombinants of these) were more diverse, more spatially structured, and displayed evidence of at least three independent introductions from mainland Africa. Although there were no statistically supported virus movement events between Madagascar and the other SWIO islands, at least one mainland African ACMV variant likely originated in Madagascar. Conclusions Our study highlights both the complexity of CMD in Madagascar, and the distinct evolutionary and spatial dynamics of the different viral species that collectively are associated with this disease. Given that more distinct CMG species and recombinants have been found in Madagascar than any other similarly sized region of the world, the risks of recombinant CMG variants emerging on this island are likely to be higher than elsewhere. Evidence of an epidemiological link between Madagascan and mainland African CMGs suggests that the consequences of such emergence events could reach far beyond the shores of this island.
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    Diversification across an altitudinal gradient in the Tiny Greenbul (Phyllastrephus debilis) from the Eastern Arc Mountains of Africa
    (BioMed Central Ltd, 2011) Fuchs, Jérôme; Fjeldså, Jon; Bowie, Rauri
    BACKGROUND:The Eastern Arc Mountains of Africa have become one of the focal systems with which to explore the patterns and mechanisms of diversification among montane species and populations. One unresolved question is the extent to which populations inhabiting montane forest interact with those of adjacent lowland forest abutting the coast of eastern Africa. The Tiny Greenbul (Phyllastephus debilis) represents the only described bird species within the Eastern Arc/coastal forest mosaic, which is polytypic across an altitudinal gradient: the subspecies albigula (green head) is distributed in the montane Usambara and Nguru Mountains whereas the subspecies rabai (grey head) is found in Tanzanian lowland and foothill forest. Using a combination of morphological and genetic data, we aim to establish if the pattern of morphological differentiation in the Tiny Greenbul (Phyllastrephus debilis) is the result of disruptive selection along an altitudinal gradient or a consequence of secondary contact following population expansion of two differentiated lineages. RESULTS: We found significant biometric differences between the lowland (rabai) and montane (albigula) populations in Tanzania. The differences in shape are coupled with discrete differences in the coloration of the underparts. Using multi-locus data gathered from 124 individuals, we show that lowland and montane birds form two distinct genetic lineages. The divergence between the two forms occurred between 2.4 and 3.1 Myrs ago.Our coalescent analyses suggest that limited gene flow, mostly from the subspecies rabai to albigula, is taking place at three mid-altitude localities, where lowland and montane rainforest directly abut. The extent of this introgression appears to be limited and is likely a consequence of the recent expansion of rabai further inland. CONCLUSION: The clear altitudinal segregation in morphology found within the Tiny Greenbul is the result of secondary contact of two highly differentiated lineages rather than disruptive selection in plumage pattern across an altitudinal gradient. Based on our results, we recommend albigula be elevated to species rank.
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    Large-scale spatial distribution patterns of gastropod assemblages in rocky shores
    (Public Library of Science, 2013) Miloslavich, Patricia; Cruz-Motta, Juan José; Klein, Eduardo; Iken, Katrin; Weinberger, Vanessa; Konar, Brenda; Trott, Tom; Pohle, Gerhard; Bigatti, Gregorio; Benedetti-Cecchi, Lisandro
    Gastropod assemblages from nearshore rocky habitats were studied over large spatial scales to (1) describe broad-scale patterns in assemblage composition, including patterns by feeding modes, (2) identify latitudinal pattern of biodiversity, i.e., richness and abundance of gastropods and/or regional hotspots, and (3) identify potential environmental and anthropogenic drivers of these assemblages. Gastropods were sampled from 45 sites distributed within 12 Large Marine Ecosystem regions (LME) following the NaGISA (Natural Geography in Shore Areas) standard protocol ( www.nagisa.coml.org ). A total of 393 gastropod taxa from 87 families were collected. Eight of these families (9.2%) appeared in four or more different LMEs. Among these, the Littorinidae was the most widely distributed (8 LMEs) followed by the Trochidae and the Columbellidae (6 LMEs). In all regions, assemblages were dominated by few species, the most diverse and abundant of which were herbivores. No latitudinal gradients were evident in relation to species richness or densities among sampling sites. Highest diversity was found in the Mediterranean and in the Gulf of Alaska, while highest densities were found at different latitudes and represented by few species within one genus (e.g. Afrolittorina in the Agulhas Current, Littorina in the Scotian Shelf, and Lacuna in the Gulf of Alaska). No significant correlation was found between species composition and environmental variables (r≤0.355, p>0.05). Contributing variables to this low correlation included invasive species, inorganic pollution, SST anomalies, and chlorophyll-a anomalies. Despite data limitations in this study which restrict conclusions in a global context, this work represents the first effort to sample gastropod biodiversity on rocky shores using a standardized protocol across a wide scale. Our results will generate more work to build global databases allowing for large-scale diversity comparisons of rocky intertidal assemblages.
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    Nested clade analysis of geographic structure in the morphologically variable Themeda triandra in South Africa
    (2004) Oatley, Graeme; Bond, William J; Hedderson, Terry A
    The use of phylogeography in plant systems has been on the increase in recent years with the use of chloroplast DNA to detect sufficient intraspecific variation to reach significant conclusions about plant species histories, both temporally and spatially. In this study, the geographic structure and possible origin of the morphologically variable Themeda triandra is explored. The trnF - trnC and psbD - trnS gene regions of the cpDNA were used to find 12 haplotypes found in 11 populations of T. triandra that encompass the species large distributional range. A haplotype tree was constructed that showed the relationship of the 11 haplotypes (haplotype_H12 was excluded as it fell outside of the 95% confidence limit), with haplotype H6 inferred to be the ancestral haplotype. A nested clade analysis was performed with the results used to infer the geographic structure of T. triandra within South Africa. Significant results showed that there was restricted gene flow with nested clades involving the three Free State populations, indicating that there are barriers to gene flow with other haplotypes. The ancestral haplotype showed long distance colonisation, with a probable root of this colonisation being the Kruger National Park. This is the proposed point of introduction of T. triandra into South Africa, with results from this study supporting this proposal. A substantial amount of gene flow (25.49%; AMOV A) between populations is observed, with this probably being due to the widespread distribution of haplotypes H6 and H10. It is thought that T. triandra followed two migration routes within South Africa: one along the coast, with the other inland above the escarpment where populations became genetically isolated from populations below the escarpment. Further studies may look for a correlation between morphological variants of T. triandra and the cpDNA haplotypes found within the species.
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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.
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    Pleistocene aridification cycles shaped the contemporary genetic architecture of southern african baboons
    (Public Library of Science, 2015) Sithaldeen, Riashna; Ackermann, Rebecca Rogers; Bishop, Jacqueline M
    Plio-Pleistocene environmental change influenced the evolutionary history of many animal lineages in Africa, highlighting key roles for both climate and tectonics in the evolution of Africa’s faunal diversity. Here, we explore diversification in the southern African chacma baboon Papio ursinus sensu lato and reveal a dominant role for increasingly arid landscapes during past glacial cycles in shaping contemporary genetic structure. Recent work on baboons ( Papio spp.) supports complex lineage structuring with a dominant pulse of diversification occurring 1-2Ma, and yet the link to palaeoenvironmental change remains largely untested. Phylogeographic reconstruction based on mitochondrial DNA sequence data supports a scenario where chacma baboon populations were likely restricted to refugia during periods of regional cooling and drying through the Late Pleistocene. The two lineages of chacma baboon, ursinus and griseipes , are strongly geographically structured, and demographic reconstruction together with spatial analysis of genetic variation point to possible climate-driven isolating events where baboons may have retreated to more optimum conditions during cooler, drier periods. Our analysis highlights a period of continuous population growth beginning in the Middle to Late Pleistocene in both the ursinus and the PG2 griseipes lineages. All three clades identified in the study then enter a state of declining population size (Ne f ) through to the Holocene; this is particularly marked in the last 20,000 years, most likely coincident with the Last Glacial Maximum. The pattern recovered here conforms to expectations based on the dynamic regional climate trends in southern Africa through the Pleistocene and provides further support for complex patterns of diversification in the region’s biodiversity.
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    The spread of Tomato yellow leaf curl virus from the Middle East to the world
    (Public Library of Science, 2010) Lefeuvre, Pierre; Martin, Darren P; Harkins, Gordon; Lemey, Philippe; Gray, Alistair J A; Meredith, Sandra; Lakay, Francisco; Monjane, Adérito; Lett, Jean-Michel; Varsani, Arvind
    Author Summary Tomato yellow leaf curl virus (TYLCV) poses a serious threat to tomato production throughout the temperate regions of the world. Our analysis, using a suite of bioinformatic tools applied to all publically available TYLCV genome sequences, suggests that the virus probably arose somewhere in the Middle East between the 1930s and 1950s and that its global spread only began in the 1980s after the emergence of two strains - TYLCV-Mld and -IL. In agreement with others, we also find that the highly invasive TYLCV-IL strain has jumped at least twice to the Americas - once from the Mediterranean basin in the early 1990s and once from Asia in the early 2000s. Although our results corroborate historical accounts of TYLCV-like symptoms in tomato crops in the Jordan Valley in the late 1920s, they indicate that the region around Iran is both the current center of TYLCV diversity and is the site where the most intensive ongoing TYLCV evolution is taking place. However, our analysis indicates that this region is epidemiologically isolated suggesting that novel TYLCV variants found there are probably not direct global threats. Moreover, we identify the Mediterranean basin as the main launch-pad of global TYLCV movements.