Limits...
A challenge to the ancient origin of SIVagm based on African green monkey mitochondrial genomes.

Wertheim JO, Worobey M - PLoS Pathog. (2007)

Bottom Line: Here, we present well-resolved phylogenies based on full-length AGM mitochondrial genomes and seven previously published SIVagm genomes; these allowed us to perform the first rigorous phylogenetic test to our knowledge of the hypothesis that SIVagm codiverged with the AGMs. Using the Shimodaira-Hasegawa test, we show that the AGM mitochondrial genomes and SIVagm did not evolve along the same topology.Using a relaxed molecular clock, we also provide a date for the most recent common ancestor of the AGMs at approximately 3 million years ago.This study substantially weakens the theory of ancient SIV infection followed by codivergence with its primate hosts.

View Article: PubMed Central - PubMed

Affiliation: Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, United States of America. wertheim@email.arizona.edu

ABSTRACT
While the circumstances surrounding the origin and spread of HIV are becoming clearer, the particulars of the origin of simian immunodeficiency virus (SIV) are still unknown. Specifically, the age of SIV, whether it is an ancient or recent infection, has not been resolved. Although many instances of cross-species transmission of SIV have been documented, the similarity between the African green monkey (AGM) and SIVagm phylogenies has long been held as suggestive of ancient codivergence between SIVs and their primate hosts. Here, we present well-resolved phylogenies based on full-length AGM mitochondrial genomes and seven previously published SIVagm genomes; these allowed us to perform the first rigorous phylogenetic test to our knowledge of the hypothesis that SIVagm codiverged with the AGMs. Using the Shimodaira-Hasegawa test, we show that the AGM mitochondrial genomes and SIVagm did not evolve along the same topology. Furthermore, we demonstrate that the SIVagm topology can be explained by a pattern of west-to-east transmission of the virus across existing AGM geographic ranges. Using a relaxed molecular clock, we also provide a date for the most recent common ancestor of the AGMs at approximately 3 million years ago. This study substantially weakens the theory of ancient SIV infection followed by codivergence with its primate hosts.

Show MeSH

Related in: MedlinePlus

Phylogenetic Relationships among AGM Nuclear Loci(A) CD4 phylogeny and (B) CCR5 phylogeny. Both trees are midpoint rooted. ML nonparametric bootstrap support values (>50) are shown on nodes. “C. unknown” in (A) refers to a taxon with no published species-specific information.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC1904472&req=5

ppat-0030095-g002: Phylogenetic Relationships among AGM Nuclear Loci(A) CD4 phylogeny and (B) CCR5 phylogeny. Both trees are midpoint rooted. ML nonparametric bootstrap support values (>50) are shown on nodes. “C. unknown” in (A) refers to a taxon with no published species-specific information.

Mentions: To determine if available sequence data were sufficient to infer the branching order among the AGM species, we constructed phylogenies using the CD4 and CCR5 genes. Although available 12s rRNA data have proven useful for differentiating AGM species, they were not sufficient for resolving the phylogeny with statistical confidence. Furthermore, additional nuclear gene data have accumulated recently but have not yet been subjected to phylogenetic analysis. Despite earlier studies with fewer sequences, which seemed to determine the AGM topology, our results with the most complete alignments of nuclear gene sequences indicated that coding nuclear loci do not sufficiently resolve the AGM phylogeny. According to the CD4 topology, AGM species are not reciprocally monophyletic (Figure 2A). There is low bootstrap support across the entire CD4 tree. We were also unable to resolve the branching order using CCR5 (Figure 2B). All AGM species for which more than one CCR5 allele was analyzed exhibited paraphyly. Moreover, the only CCR5 allele from C. tantalus is identical to one of the C. sabaeus alleles, implying that CCR5 is not useful in distinguishing AGM species, let alone their phylogenetic relationships.


A challenge to the ancient origin of SIVagm based on African green monkey mitochondrial genomes.

Wertheim JO, Worobey M - PLoS Pathog. (2007)

Phylogenetic Relationships among AGM Nuclear Loci(A) CD4 phylogeny and (B) CCR5 phylogeny. Both trees are midpoint rooted. ML nonparametric bootstrap support values (>50) are shown on nodes. “C. unknown” in (A) refers to a taxon with no published species-specific information.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC1904472&req=5

ppat-0030095-g002: Phylogenetic Relationships among AGM Nuclear Loci(A) CD4 phylogeny and (B) CCR5 phylogeny. Both trees are midpoint rooted. ML nonparametric bootstrap support values (>50) are shown on nodes. “C. unknown” in (A) refers to a taxon with no published species-specific information.
Mentions: To determine if available sequence data were sufficient to infer the branching order among the AGM species, we constructed phylogenies using the CD4 and CCR5 genes. Although available 12s rRNA data have proven useful for differentiating AGM species, they were not sufficient for resolving the phylogeny with statistical confidence. Furthermore, additional nuclear gene data have accumulated recently but have not yet been subjected to phylogenetic analysis. Despite earlier studies with fewer sequences, which seemed to determine the AGM topology, our results with the most complete alignments of nuclear gene sequences indicated that coding nuclear loci do not sufficiently resolve the AGM phylogeny. According to the CD4 topology, AGM species are not reciprocally monophyletic (Figure 2A). There is low bootstrap support across the entire CD4 tree. We were also unable to resolve the branching order using CCR5 (Figure 2B). All AGM species for which more than one CCR5 allele was analyzed exhibited paraphyly. Moreover, the only CCR5 allele from C. tantalus is identical to one of the C. sabaeus alleles, implying that CCR5 is not useful in distinguishing AGM species, let alone their phylogenetic relationships.

Bottom Line: Here, we present well-resolved phylogenies based on full-length AGM mitochondrial genomes and seven previously published SIVagm genomes; these allowed us to perform the first rigorous phylogenetic test to our knowledge of the hypothesis that SIVagm codiverged with the AGMs. Using the Shimodaira-Hasegawa test, we show that the AGM mitochondrial genomes and SIVagm did not evolve along the same topology.Using a relaxed molecular clock, we also provide a date for the most recent common ancestor of the AGMs at approximately 3 million years ago.This study substantially weakens the theory of ancient SIV infection followed by codivergence with its primate hosts.

View Article: PubMed Central - PubMed

Affiliation: Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, United States of America. wertheim@email.arizona.edu

ABSTRACT
While the circumstances surrounding the origin and spread of HIV are becoming clearer, the particulars of the origin of simian immunodeficiency virus (SIV) are still unknown. Specifically, the age of SIV, whether it is an ancient or recent infection, has not been resolved. Although many instances of cross-species transmission of SIV have been documented, the similarity between the African green monkey (AGM) and SIVagm phylogenies has long been held as suggestive of ancient codivergence between SIVs and their primate hosts. Here, we present well-resolved phylogenies based on full-length AGM mitochondrial genomes and seven previously published SIVagm genomes; these allowed us to perform the first rigorous phylogenetic test to our knowledge of the hypothesis that SIVagm codiverged with the AGMs. Using the Shimodaira-Hasegawa test, we show that the AGM mitochondrial genomes and SIVagm did not evolve along the same topology. Furthermore, we demonstrate that the SIVagm topology can be explained by a pattern of west-to-east transmission of the virus across existing AGM geographic ranges. Using a relaxed molecular clock, we also provide a date for the most recent common ancestor of the AGMs at approximately 3 million years ago. This study substantially weakens the theory of ancient SIV infection followed by codivergence with its primate hosts.

Show MeSH
Related in: MedlinePlus