Department of Genetics Anthropology & Evolution, University of Parma, Parco Area delle Scienze 11/A, I-43100 Parma, Italy
Correspondence
Angelo Pavesi
angelo.pavesi{at}unipr.it
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ABSTRACT |
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INTRODUCTION |
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Sequencing of JCV has revealed the existence of several distinct genotypes. Types 1 and 4, closely interrelated to each other, were found not only in Europe (Agostini et al., 2001a), but also in indigenous populations living in northern Japan, North-East Siberia and northern Canada (Sugimoto et al., 2002a
; Yogo et al., 2003
). Types 3 and 6 are characteristic of sub-Saharan Africa: type 3 was isolated in Ethiopia (Sugimoto et al., 2002b
), Tanzania (Agostini et al., 1997b
) and South Africa (Venter et al., 2004
), and type 6 in Ghana (Guo et al., 1996
; Kato et al., 2000
). Both genotypes were also found in the Biaka Pygmies and Bantus from Central Africa (Chima et al., 1998
). Types 2 and 7 show a large geographical distribution (Sugimoto et al., 1997
). Type 2 includes several variants, with subtype 2A mainly in the Japanese population and native Americans (excluding Inuits), 2B in Eurasians, 2D in Indians, and 2E in Australians and western Pacific populations (Fernandez-Cobo et al., 2002
; Yanagihara et al., 2002
; Zheng et al., 2003
; Miranda et al., 2004
; Takasaka et al., 2004
). Subtype 7A was found to be characteristic of southern China and South-East Asia (Saruwatari et al., 2002
), while subtype 7B of northern China, Mongolia and Japan (Sugimoto et al., 2002b
; Zheng et al., 2004a
). A third subtype (7C), spread throughout northern and southern China, has recently been characterized by Cui et al. (2004)
. Finally, type 8 was found in Papua New Guinea and the Pacific Islands (Jobes et al., 2001
; Yanagihara et al., 2002
).
The ubiquitous distribution of JCV, combined with a transmission mechanism largely within families or populations (Kunitake et al., 1995; Kato et al., 1997
; Suzuki et al., 2002
; Zheng et al., 2004b
), make it an attractive candidate for reconstructing human migrations dating to prehistoric times. The close relationship of JCV found in native Americans with that in North-East Asia is consistent with the migration of Amerindian ancestors from Asia across the Bering land bridge (Agostini et al., 1997a
). Doubts regarding the reliability of JCV as a marker of human evolution (Wooding, 2001
) have recently been dispelled by a whole-genome phylogenetic analysis focused on the distinction between slow- and fast-evolving sites (Pavesi, 2003
). By this approach, it was proposed that the association of JCV with humans originated in Africa, since type 6 was found to be the putative ancestral genotype. It was also demonstrated how type 6 gave rise to two independent evolutionary lineages: one including types 1 and 4, the other including types 2, 3, 7 and 8 (Pavesi, 2003
).
The diffusion in the world of both lineages was elucidated through the analysis of over 1000 sequences of the genomic region of JCV with the highest variation rate (Pavesi, 2004). By using synthetic geographical maps, it was hypothesized that the expansion of Homo sapiens from Africa was mediated by two migration waves, each carrying a different virus lineage (Pavesi, 2004
). This finding is a valuable one, because it sheds new light on the pattern of human evolution yielded so far by human genes, supporting the hypothesis of one single expansion from Africa into Asia and from there to the other continents (reviewed by Cavalli-Sforza & Feldman, 2003
).
The view that the dual exit of JCV from Africa mirrors two migrations on the part of our ancestors is appealing. However, the objection can be raised that the present genetic diversity between the two virus lineages one (types 1 and 4) mainly diffused in the northern areas of the world and the other (types 2, 3, 7, and 8) in the central and southern areas is the result of selective pressures favouring adaptation to different climates. In this case, large-scale inferences concerning human evolution should be treated with caution, since a reliable reconstruction of human history is based on phenomena such as genetic drift or migration, and not natural selection (Cavalli-Sforza et al., 1994). A possible response to this objection could be a more subtle analysis of the genome sequence of JCV, with the aim of characterizing the type of nucleotide substitutions causing the deep divergence between the two virus lineages.
In this study, I propose to illustrate an approach to investigate the evolution of JCV based on correspondence analysis (Lebart et al., 1984). The main advantage of this method derives from a mathematically adequate representation of a set of related sequences. It allows not only an elucidation of the evolutionary relationships between sequences, as do the standard phylogenetic methods, but also the identification of those nucleotide positions where systematic changes have occurred in the past. Correspondence analysis was also applied to a large set of complete mitochondrial genomes, whose sequence has been made available by recent studies on global mitochondrial DNA (mtDNA) diversity in humans (Ingman et al., 2000
; Mishmar et al., 2003
; Ingman & Gyllensten, 2003
). Thanks to the elevated analytical power of the method, a detailed comparison between the patterns of change underlying the evolution of JCV and human mtDNA is presented.
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METHODS |
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The accession numbers of the JCV sequences under examination are as follows: AB038249AB038255, AB048545AB048582, AB074575AB074591, AB077855AB077879, AB081005AB081030, AB081600AB081618, AB081654, AB092578AB092587, AB103387, AB103402AB103423, AB104487, AF004349AF004350, AF015526AF015537, AF030085, AF281599AF281626, AF295731AF295739, AF300945AF300967, AF363830AF363834, AF396422AF396435, AY121907AY121915, J02226, U61771 and U73500U73502. Five sequences (AB038254, AB038255, AF015537, AF030085 and AF004350) derived from patients, died of progressive multifocal leukoencephalopathy. The inclusion of these sequences does not affect the present analysis, since no amino acid substitutions that could be correlated with disease have been detected so far (Kato et al., 2000). The nomenclature system of JCV was in accordance with Agostini et al. (2001b)
. The correlation between Agostini's classification and that developed by Sugimoto et al. (2002b)
is reported by Cui et al. (2004)
. The accession numbers of the mtDNA sequences are AY195745AY195792, AF346963AF347015, AY289051AY289102, D38112, J01415 and X93334.
Data analysis.
The 275 genome sequences of JCV were aligned using the CLUSTAL W program (Thompson et al., 1994). A multiple alignment of 4867 nt positions was obtained. Two sequences were excluded, because of the presence of a large deletion in the VP2 gene (63 bp in the sequence AB103402) or in the small t antigen gene (38 bp in the sequence AB103407). CLUSTAL W was also used to align the 156 mtDNA sequences, yielding a multiple alignment of 15 465 sites. Each alignment was examined to detect variable sites. A total of 1030 variable sites were found in JCV, 944 of them without gaps. The mtDNA sequence showed a total of 1035 variable sites, 994 of them without gaps.
Correspondence analysis was carried out on the JCV sequences formed by nucleotides at the variable sites lacking gaps. Each sequence was converted into a vector consisting of 1s and 0s, depending on whether a given nucleotide is present at a given position or not. For example, the most variable position of JCV (122 A, 10 T, 133 G and 8 C) was represented as a string of four binary characters: for the 122 sequences with A the string is 1000, for the 10 sequences with T the string is 0100, for the 133 sequences with G the string is 0010 and for the 8 sequences with C the string is 0001. Those positions containing only two or three types of nucleotide were converted into a string of two and three binary characters, respectively. According to these rules, each viral sequence was represented as a vector of 2032 binary characters. This yielded the matrix A (273 rows and 2032 columns) with elements aij. The matrix P with elements pij was computed as follows:
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The matrix D with elements dij was computed as follows:
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The product between the transpose of the matrix D (DT with 2032 rows and 273 columns) and the matrix D itself (273 rows and 2032 columns) yielded the matrix E (2032 rows and 2032 columns). Eigenvectors and eigenvalues of the matrix E were calculated with the EIGEN subroutine from the statistical language R (Ihaca & Gentleman, 1996; www.r-project.org). Only the first 10 eigenvectors were taken into consideration, yielding the matrix F (2032 rows and 10 columns). The product between the matrix D and the matrix F gave the matrix G (273 rows and 10 columns).
The information carried by the matrix G is crucial, since it provides the position coordinates of the 273 JCV sequences on the first 10 axes of ordination. The percentage variation fraction associated with each axis was calculated as the ratio of the corresponding eigenvalue to the sum of all eigenvalues. The evolutionary relationships between sequences were visualized by the construction of bidimensional plots.
The information carried by the first 10 eigenvectors (matrix F) is also very valuable, since it reveals the nucleotide positions that maximally contribute to the JCV clustering at each axis of ordination. To obtain this information, the absolute values of the 2032 elements of each eigenvector were sorted in increasing order. The highest values correspond to the important positions, whose phylogenetic relevance was evaluated further with the 2 test. The eigenvectors were finally used to draw bidimensional plots, in which the variable sites were represented as a heterogeneous cloud of points.
Correspondence analysis was also applied to the 156 human mtDNA sequences. Each sequence, consisting of 994 variable sites, was converted into a vector of 2000 binary characters, and then subjected to the same processes of calculation described above.
Finally, by using the method of Nei & Gojobori (1986), the rates of synonymous and non-synonymous substitutions in the protein-coding regions of both JCV and mitochondrial genomes were estimated. The degree of similarity between individual amino acid residues was evaluated with the BLOSUM 62 substitution matrix (Henikoff & Henikoff, 1992
).
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RESULTS |
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By choosing as the threshold a 2 value of 1·07 (P<0·30 for 1 d.f.), a total of 61 nt positions with a pattern of change determining the distinctiveness of the virus lineage formed by types 1 and 4 were found (Table 1
). In particular, five sites were localized in the intergenic regions or in the intron of the large T antigen gene. The great majority of sites (48) were characterized by synonymous substitutions. Only eight positions showed a non-synonymous change, most of them determining a conservative substitution (Asn vs His, Ala vs Val, Ala vs Ser, Asp vs Glu, Glu vs Asp, Arg vs Lys and Asn vs Ser). The only point mutation yielding a non-conservative amino acid exchange (the hydrophilic Gln residue vs the hydrophobic Leu residue) was located in the second exon of the large T antigen gene. Interestingly, such a substitution occurs in close proximity to the T antigen zinc finger motif, which is essential for the replication of viral DNA (Swenson et al., 1996
).
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Correspondence analysis of the human mtDNA sequences
The map in Fig. 2(a) was obtained from the first two axes of ordination, which accounted for 4·6 and 3·3 %, respectively, of the total variation. It yielded evidence for a grouping of the 156 mtDNA sequences into four clusters. In particular, the projection of points on axis 1 assigned marked negative values (from 0·031 to 0·064) to a fairly heterogeneous set of 17 sequences, thus stressing their separation from the rest. Such sequences, which were isolated from indigenous populations living in sub-Saharan Africa, belong to haplogroups L0 and L1.
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Overall, the correspondence analysis of the human mtDNA highlighted the pattern of variation responsible for the divergence of three of four African haplogroups (L0, L1, L2 and L3). Like the analysis of JCV, this pattern appeared to be poorly affected by natural selection, being characterized mainly by nucleotide substitutions of the synonymous type.
Comparison between the patterns of synonymous and non-synonymous substitutions in the protein-coding regions of JCV and human mtDNA
The exclusion of the non-coding region from each viral sequence led to a sequence formed by the six protein-coding genes, having a length of 4572 bp. The exclusion from each mtDNA sequence of the genes encoding rRNAs or tRNAs, as well as of the intergenic regions, yielded a sequence of 11 334 bp long and included the 13 protein-coding genes.
Using the method by Nei & Gojobori (1986), the 273 sequences of JCV were compared to each other. In each comparison, the number of synonymous (Sd) and non-synonymous (Nd) differences was evaluated. At the end of the calculation, a mean value of Sd equal to 47·4, with a standard deviation (SD) of 27·6, was found. The mean value of Nd was 12·2, with a SD of 6·1. The same process of calculation was carried out on the 156 mtDNA sequences. A mean value of Sd equal to 22·4 (SD=14·6) and a mean value of nd equal to 8·2 (SD=3·7) were obtained.
Although the virus contains a protein-coding region over two times shorter than mtDNA, it exhibited a mean amount of synonymous changes over twice as great. This remarkable difference was investigated further by comparing the mean number of synonymous substitutions per site observed in JCV (Ks=0·0516, SD=0·0034) with that found in mtDNA (Ks=0·0082, SD=0·0010).
The trend of the mean number of synonymous substitutions per site (Ks), averaged over a sliding-window region of 100 codons, was evaluated along the entire coding sequences of both JCV and mitochondrial genomes (Fig. 3). The examination of the two profiles evidenced a considerably higher rate of synonymous substitution in JCV. In particular, it was found that most of the coding region of JCV exhibits a Ks value invariably more elevated with respect to the highest Ks value observed in the mtDNA sequence.
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DISCUSSION |
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The clustering of the 273 genome sequences of JCV along the first axis of ordination of the correspondence analysis (Fig. 1a) resembles that provided by a principal coordinate analysis of about 100 genome sequences (Pavesi, 2003
) or over 1000 sequences of the genomic region with the highest variation rate (Pavesi, 2004
). Similar to what has been found using standard phylogenetic methods (Cui et al., 2004
; Yogo et al., 2004
and references therein), such a clustering confirms an important feature of the evolutionary history of JCV, namely an early emergence of two different lineages from the common root given by the ancestral African genotype (type 6). One lineage includes the 52 strains of types 1 and 4 (see right side of axis 1), the other includes the 214 strains of types 2, 3, 7 and 8 (see left side of axis 1).
The first point to stress is the geographical distribution of the 52 strains of types 1 and 4. Half of them were found in Europe. One strain was found in Morocco. Six strains were isolated in North America from individuals of European origin. Eight strains were isolated from autochthonous populations inhabiting the northeastern edge of Siberia, such as the Nanais, Koryaks, Chukchis, Luskys and Yukaghirs. Two strains were found in the Canadian Inuits, an indigenous Arctic populace speaking an Eskimo-Aleut language (Ruhlen, 1991). The remaining nine strains were found in Japan: four of them belong to the Ainu, a pre-agricultural native population of great anthropological interest (Bannai et al., 2000
).
Since it has been proved that types 1 and 4 arose from type 6 as an independent lineage (Pavesi, 2003), its geographical distribution could reflect a prehistoric migration of humans from Africa into Europe and from there to northern Asia. The hypothesis that types 1 and 4 were acquired by modern humans when they migrated into Europe and came in contact with archaic populations (Homo neanderthalensis) seems to be rather unlikely. The transmission of JCV, in fact, requires close and prolonged contact between individuals living in the same ethnic group (Kunitake et al., 1995
), as proved by the lack of transmission between populations inhabiting the same geographical area yet only occasionally intermingling with each other (Kato et al., 1997
). The geographical distribution of the other lineage of JCV (East Africa, Eurasia, Asia, Americas, Oceania and the Pacific Islands) is compatible with the pattern of migration yielded by human genes (Cavalli-Sforza & Feldman, 2003
).
The finding that the divergence of the Caucasian lineage of JCV (types 1 and 4) was accompanied by synonymous, rather than non-synonymous substitutions (Table 1) seems to exclude the hypothesis of a divergence due to selective pressures favouring adaptation to cold climates. The hypothesis of an additional early expansion of humans from Africa to the northern areas of the world (Fig. 4
), previously suggested by synthetic maps (Pavesi, 2004
) or phylogenetic trees (Yanagihara et al., 2002
; Sugimoto et al., 2002a
, b
; Yogo et al., 2003
), seems to be substantiated by the virtual lack of marks of natural selection in the divergence of types 1 and 4. The only adaptation change is probably a non-conservative amino acid replacement (Gln vs Leu) found in the T antigen gene. Besides the Caucasian lineage, this substitution also occurs in five viral strains of subtype 2B, belonging to the alternative lineage yet showing a geographical distribution similar to that of types 1 and 4. Thus, the Gln
Leu change seems to be affected by selection, although its functional significance remains to be determined.
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Correspondence analysis of the human mtDNA yielded a first axis of ordination which separated the sequences according to the following order: the haplogroups L0, L1, L2 and finally the remaining haplogroups (Fig. 2a). This clustering is similar to the topology of the consensus phylogenetic trees including more or less the same sequences and constructed with the neighbour-joining method (Ingman et al., 2000
; Mishmar et al., 2003
). Both trees, in fact, show a basal branching pattern where the deepest branch is represented by the haplogroup L0. The following two deepest branches include the haplogroup L1 and L2, respectively.
By comparing the pattern of change peculiar to mtDNA with that of JCV, some relevant differences can be appreciated. The first difference lies in the fact that the first axis of ordination of JCV situates the ancestral type 6 in the middle, between the two lineages arising from it (Fig. 1a). The first axis of mtDNA, on the other hand, places the ancestral haplogroup L0 at the extreme left, since it gave rise to one sole lineage (Fig. 2a
).
The second difference stems from the finding that the various axes of ordination are much more informative in JCV than in mtDNA. Indeed, the peopling of the world by humans carrying different types or subtypes of JCV can be correlated with most of the first 10 axes of ordination (Table 2). In the case of mtDNA, the phylogenetic information is limited, however, to the more ancient African haplogroups L0, L1 and L2 (Table 4
). The lack of discrimination of the fourth African haplogroup (L3) is consistent with the fact that such a haplogroup usually features, in the consensus trees, with the non-African haplogroups (Ingman et al., 2000
; Mishmar et al., 2003
).
The third difference depends on the rate of substitution found in the protein-coding region of JCV and mtDNA. Although JCV is known to be a very slowly evolving virus, it shows a mean nucleotide diversity (59·6) double that of mtDNA (30·6). By removing the bias due to the different length of the protein-coding region (4572 bp in JCV and 11 334 bp in mtDNA), it was found that the mean number of synonymous substitutions per site of JCV (Ks=0·0516) is over six times higher than that of mtDNA (Ks=0·0082). The difference between the substitution rates can explain why the number of the important nucleotide positions, which is those positions where systematic changes have occurred in the past, was much higher in JCV with respect to the human mtDNA (see first three axes of ordination in Tables 2 and 4). The greater amount of silent changes in JCV can be appreciated by comparing the trends of the mean synonymous diversity shown in Fig. 3
.
The findings reported here support the hypothesis that the human mtDNA, unlike JCV, shows a nucleotide diversity too low to trace the pattern of migrations subsequent to the split between African and non-African populations. Since it is known that mtDNA evolves at a speed 510 times higher than the nuclear DNA (Vawter & Brown, 1986), it is likely that a reconstruction of human history based on the nucleotide sequence of DNA fragments from autosomal or sex-linked loci is an even more difficult task.
It is important to note, however, that improved methods for a large-scale characterization of human genome diversity have provided in the last years valuable information concerning the small nuclear polymorphism or the microsatellite loci. For example, Zhivotovsky et al. (2003) studied 377 autosomal microsatellite polymorphisms in 52 world populations and constructed a phylogenetic tree whose two oldest branches include, respectively, hunter-gatherer and farmer populations from sub-Saharan Africa.
Nevertheless, a ubiquitous, usually harmless, symbiote co-evolving with the human host and showing a sufficiently sensitive variation rate could be an alternative approach. A few viruses have been used for inferences about human evolution, such as the hepatitis G virus (Pavesi, 2001), the papillomavirus (Ho et al., 1993
; Ong et al., 1993
) and the T-cell lymphotropic virus (Miura et al., 1994
; Salemi et al., 1999
). In the case of the latter two, the main drawback is a transmission mechanism prevalently horizontal. Although the hepatitis G virus does not cause liver disease and is largely transmitted from mother to infant, the finding that it can recombine raises doubts on its ability to trace human history (Worobey & Holmes, 2001
). Finally, and most importantly, what we expect from a virus are novel clues on human history, rather than a pure replication of the pattern yielded by human genes.
The JC polyomavirus, exhibiting the unusual feature of a twofold exit from Africa (Pavesi, 2003), could shed new light on the number of migrations leading to the peopling of the various continents. The virtual lack of pathogen power (the virus can cause disease only in 5 % of severely immunocompromised patients), the absence of genetic recombination (the unique strain whose sequence suggested recombination has now been discredited due to the inability to repeat the result in the same patient), the strong ethnicity due to a transmission mechanism within the family or in the same community, and the easy detection in individuals due to the high frequency of urinary excretion support the effectiveness of JCV in tracing the history of human populations. The findings reported here, supporting the virtual absence of marks of natural selection in JCV evolution, would encourage further sampling of virus isolates from historical populations, thus providing a more exhaustive picture of our past.
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ACKNOWLEDGEMENTS |
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Received 29 September 2004;
accepted 3 February 2005.
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