Detecting Traces of Prehistoric Human Migrations by Maps of Polyomavirus

[Euclides]

Journal of Molecular Evolution

Detecting Traces of Prehistoric Human Migrations by Geographic Synthetic Maps of Polyomavirus JC
Angelo Pavesi1

(1) Department of Genetics Anthropology Evolution, University of Parma, Parco Area delle Scienze 11/A, 1-43100 Parma, Italy

Received: 13 June 2003 Accepted: 19 September 2003

Abstract The polyomavirus JC (JCV) is a double-stranded DNA virus that is ubiquitous in human populations and is excreted in urine by a large percentage of individuals (20–70%). The strong genetic stability, combined with a mechanism of transmission mainly within the family, makes JCV a good marker of human migrations. In this study, the coevolution of JCV with its human host is investigated by using over a thousand nucleotide sequences deposited in the EMBL database; they correspond to the IG region, which is the genomic region with the highest rate of variation. The pattern of genetic diversity in JCV is evaluated by the principal coordinates analysis and the construction of synthetic maps. The first principal coordinate supports the existence of two distinct virus lineages, both arising from the ancestral African type. The first synthetic map suggests a two-migration model of the human dispersal out of Africa, thus implying a more complex picture than that known from human genes. The second principal coordinate points out the distinctiveness of strains coming from Asian/Amerind populations. The picture yielded by the second synthetic map appears to be more consistent with that known from human genes. In fact, it provides evidence of a deep split of the Asian lineage of JCV into two main branches: one diffusing in Japan and Americas, the other in Southeast Asia. The view that JCV, with its peculiar feature of a dual early emergence from Africa, can provide new information about the evolutionary history of our ancestors is discussed.

[Euclides]

African Origin of Polyomavirus JC and Implications for Prehistoric Human Migrations


Angelo Pavesi

A1 Department of Evolutionary and Functional Biology, University of Parma, Parco Area delle Scienze 11/A, I-43100 Parma, Italy


Abstract:


Abstract

The presence of distinctive types of JC virus (JCV) in the main ethnic groups suggests a close coevolution with the human host. However, phylogenetic trees of JCV show a basal clade of European lineages (Types 1/4), whereas trees of human genes are coherent in placing the first split between African and non-African populations. This discrepancy places into question the effectiveness of JCV as a marker of human population history. The present study investigates the evolution of JCV using a large set of fully sequenced strains. Their relationships are first elucidated by principal coordinates analysis. It is suggested that Type 6 from West Africa could represent the ancestral type, while the peculiar phylogeny of Types 1/4 could reflect their direct origin from the ancestral lineage. Further credit to the African origin of JCV is provided by a neighbor-joining analysis based on slow-evolving sites. Sequence analysis of fast-evolving sites reveals that the deep emergence of Types 1/4 in the tree does not reflect a real evolutionary divergence; rather it is the implicit result of a remarkably different G + C content. The hypothesis that Types 1/4 originated directly from Type 6 is confirmed by examining the pattern of variation at a few specific fast-evolving sites. On the basis of this approach, a twofold exit of JCV from Africa is hypothesized: one in the direction of the Eurasian continent and another limited to Europe. These findings suggest that two distinct migrations of individuals played a key role in the peopling of Europe during prehistoric times