Dataset Information

The Global Phylogeography of Lyssaviruses - Challenging the 'Out of Africa' Hypothesis.

ABSTRACT: Rabies virus kills tens of thousands of people globally each year, especially in resource-limited countries. Yet, there are genetically- and antigenically-related lyssaviruses, all capable of causing the disease rabies, circulating globally among bats without causing conspicuous disease outbreaks. The species richness and greater genetic diversity of African lyssaviruses, along with the lack of antibody cross-reactivity among them, has led to the hypothesis that Africa is the origin of lyssaviruses. This hypothesis was tested using a probabilistic phylogeographical approach. The nucleoprotein gene sequences from 153 representatives of 16 lyssavirus species, collected between 1956 and 2015, were used to develop a phylogenetic tree which incorporated relevant geographic and temporal data relating to the viruses. In addition, complete genome sequences from all 16 (putative) species were analysed. The most probable ancestral distribution for the internal nodes was inferred using three different approaches and was confirmed by analysis of complete genomes. These results support a Palearctic origin for lyssaviruses (posterior probability = 0.85), challenging the 'out of Africa' hypothesis, and suggest three independent transmission events to the Afrotropical region, representing the three phylogroups that form the three major lyssavirus clades.

SUBMITTER: Hayman DT

PROVIDER: S-EPMC5231386 | biostudies-other | 2016 Dec

REPOSITORIES: biostudies-other

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The Global Phylogeography of Lyssaviruses - Challenging the 'Out of Africa' Hypothesis.

Hayman David T S DT Fooks Anthony R AR Marston Denise A DA Garcia-R Juan C JC

PLoS neglected tropical diseases 20161230 12

Rabies virus kills tens of thousands of people globally each year, especially in resource-limited countries. Yet, there are genetically- and antigenically-related lyssaviruses, all capable of causing the disease rabies, circulating globally among bats without causing conspicuous disease outbreaks. The species richness and greater genetic diversity of African lyssaviruses, along with the lack of antibody cross-reactivity among them, has led to the hypothesis that Africa is the origin of lyssaviru ...[more]

PMID: 28036390

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Project description:Comparative phylogeography is an effective approach to assess the evolutionary history of biological communities. We used comparative phylogeography in fourteen tree taxa from Lower Guinea (Atlantic Equatorial Africa) to test for congruence with two simple evolutionary scenarios based on physio-climatic features 1) the W-E environmental gradient and 2) the N-S seasonal inversion, which determine climatic and seasonality differences in the region. We sequenced the trnC-ycf6 plastid DNA region using a dual sampling strategy: fourteen taxa with small sample sizes (dataset 1, mean n?=?16/taxon), to assess whether a strong general pattern of allele endemism and genetic differentiation emerged; and four taxonomically well-studied species with larger sample sizes (dataset 2, mean n?=?109/species) to detect the presence of particular shared phylogeographic patterns. When grouping the samples into two alternative sets of two populations, W and E, vs. N and S, neither dataset exhibited a strong pattern of allelic endemism, suggesting that none of the considered regions consistently harboured older populations. Differentiation in dataset 1 was similarly strong between W and E as between N and S, with 3-5 significant F ST tests out of 14 tests in each scenario. Coalescent simulations indicated that, given the power of the data, this result probably reflects idiosyncratic histories of the taxa, or a weak common differentiation pattern (possibly with population substructure) undetectable across taxa in dataset 1. Dataset 2 identified a common genetic break separating the northern and southern populations of Greenwayodendron suaveolens subsp. suaveolens var. suaveolens, Milicia excelsa, Symphonia globulifera and Trichoscypha acuminata in Lower Guinea, in agreement with differentiation across the N-S seasonal inversion. Our work suggests that currently recognized tree taxa or suspected species complexes can contain strongly differentiated genetic lineages, which could lead to misinterpretation of phylogeographic patterns. Therefore the evolutionary processes of such taxa require further study in African tropical rainforests.

Project description:Background and aimsUnderstanding the factors that shape variation in genetic diversity across the geographic ranges of species is an important challenge in the effort to conserve evolutionary processes sustaining biodiversity. The historical influences leading to a central-marginal organization of genetic diversity have been explored for species whose range is known to have expanded from refugia after glacial events. However, this question has rarely been addressed for Mediterranean endemic plants of azonal habitats such as rocky slopes or screes. In this context, this comprehensive study examined molecular and field data from Arenaria provincialis (Caryophyllaceae), a narrow endemic plant of south-eastern France.MethodsAcross the whole geographic range, an investigation was made of whether high levels of abundance and genetic diversity (estimated from amplified fragment length polymorphism markers) are centrally distributed, to evaluate the relevance of the central-marginal hypothesis. Phylogeographic patterns inferred from chloroplast DNA (cpDNA) were used, applying Bayesian methods to test the influence of past biogeographic events. Multivariate analysis combining phylogeographic and ecological data was used to reveal the historical and ecological distinctiveness of populations.Key resultsDespite the narrow distribution of A. provincialis, a high level of nucleotide variation is found within cpDNA loci, supporting its persistence throughout the Pleistocene period. The area characterized by the highest genetic diversity is centrally located. Structured phylogeography and Bayesian factor analysis supported the hypothesis that the central area of the distribution was the source of both westward and eastward migrations, probably during arid periods of the Pleistocene, and more recently was a crossroads of backward migrations. By contrast, the two areas located today at the range limits are younger, have reduced genetic diversity and are marginal in the ecological gradients.ConclusionsThis study highlights a case of strong population distinctiveness within a narrow range. Phylogeography sheds light on the historical role of the areas centrally situated in the distribution. The current range size and abundance patterns are not sufficient to predict the organization of genetic diversity.

Dataset Information

The Global Phylogeography of Lyssaviruses - Challenging the 'Out of Africa' Hypothesis.

Publications

The Global Phylogeography of Lyssaviruses - Challenging the 'Out of Africa' Hypothesis.

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