Ancient co-speciation of simian foamy viruses and primates

@article{Switzer2005AncientCO,
  title={Ancient co-speciation of simian foamy viruses and primates},
  author={William M. Switzer and Marco Salemi and Vedapuri Shanmugam and Feng J. Gao and Mian-er Cong and Carla Kuiken and Vinod B Bhullar and Brigitte E. Beer and Dominique Vallet and Annie Gautier-hion and Zena J. Tooze and Francois J Villinger and Edward C. Holmes and Walid Heneine},
  journal={Nature},
  year={2005},
  volume={434},
  pages={376-380}
}
Although parasite–host co-speciation is a long-held hypothesis, convincing evidence for long-term co-speciation remains elusive, largely because of small numbers of hosts and parasites studied and uncertainty over rates of evolutionary change. Co-speciation is especially rare in RNA viruses, in which cross-species transfer is the dominant mode of evolution. Simian foamy viruses (SFVs) are ubiquitous, non-pathogenic retroviruses that infect all primates. Here we test the co-speciation hypothesis… 
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255 Citations
Highly Influential Citations
10
Background Citations
119
Methods Citations
13
Results Citations
10

255 Citations

Identification and evolution of avian endogenous foamy viruses
TLDR
By providing evidence that birds can be infected withfoamy viruses, this work fills the last major gap in the taxonomic distribution of foamy viruses and their animal hosts.
Identification and evolution of avian endogenous foamy viruses.
TLDR
By providing evidence that birds can be infected withfoamy viruses, this work fills the last major gap in the taxonomic distribution of foamy viruses and their animal hosts.
Wide distribution and ancient evolutionary history of simian foamy viruses in New World primates
TLDR
A broad distribution and stable co-speciation history of SFV in NWMs at the species level is demonstrated and the trees of NWM hosts and SFVs have remarkably similar topologies at the level of species and sub-populations suggestive of co- Speciation.
Secondary contact between diverged host lineages entails ecological speciation in a European hantavirus
TLDR
It is demonstrated that incipient speciation in a natural host species has generated distinct ecological niches leading to adaptive isolation in an RNA virus, and Evolutionary relationships between TULV clades indicate an emergence of these viruses through rapid differential adaptation to the previously diverged host lineages that resulted in levels of ecological isolation exceeding the progress of speciating in their vertebrate hosts.
Ancient DNA provides evidence of 27,000-year-old papillomavirus infection and long-term codivergence with rodents
TLDR
Viral sequences from ancient North American packrat middens are screened up to 27,000-years old and found evidence of papillomavirus (PV) infection in Neotoma cinerea (Bushy-tailed packrat).
A reptilian endogenous foamy virus sheds light on the early evolution of retroviruses
TLDR
A novel endogenous foamy virus is found in genome of the tuatara (Sphenodon punctatus), an endangered reptile species endemic to New Zealand, which fills a major gap in the fossil record of foamy viruses and provides important insights into the early evolution of retroviruses.
A Challenge to the Ancient Origin of SIVagm Based on African Green Monkey Mitochondrial Genomes
TLDR
This study substantially weakens the theory of ancient SIV infection followed by codivergence with its primate hosts and demonstrates that the SIVagm topology can be explained by a pattern of west-to-east transmission of the virus across existing AGM geographic ranges.
Multiple infiltration and cross-species transmission of foamy viruses across Paleozoic to Cenozoic era
TLDR
The multiple origin and complex evolution of amphibian FVs started from the Paleozoic era, and expressed FVs including a potential exogenous form were discovered, suggesting live FVs could be underestimated in nature.
Bayesian inference reveals ancient origin of simian foamy virus in orangutans.
Multiple Infiltration and Cross-Species Transmission of Foamy Viruses across the Paleozoic to the Cenozoic Era
TLDR
This study revealed the multiple origin and complex evolution of amphibian FVs started from the Paleozoic era, and revealed 412 FVs of 6 distinct lineages from three major orders of amphibians, including three distinct FV lineages had integrated into the genome of a salamander.
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References

SHOWING 1-10 OF 29 REFERENCES
A cophylogenetic perspective of RNA-virus evolution.
TLDR
It is demonstrated that RNA viruses are able to form stable associations with their hosts over evolutionary time scales and that the details of such associations are consistent with persistent infection being a necessary but not sufficient precondition.
Mosaic Genomes of the Six Major Primate Lentivirus Lineages Revealed by Phylogenetic Analyses
TLDR
Phylogeny reconstruction based on distance and maximum-likelihood algorithms followed by a number of statistical tests confirms the existence of at least five putative recombinant fragments in the PLV genome with different clustering patterns and implies that the six so-called pure PLVs have in fact mosaic genomes.
Resolution of the African hominoid trichotomy by use of a mitochondrial gene sequence.
TLDR
Comparisons of cytochrome oxidase subunit II gene sequences provide clear-cut evidence from the mitochondrial genome for the separation of the African ape trichotomy into two evolutionary lineages, one leading to gorillas and the other to humans and chimpanzees.
Mitochondrial DNA phylogeny of the Old-World monkey tribe Papionini.
The evolution of the Old World monkey tribe Papionini, composed of macaques, baboons, mandrills, drills, and mangabeys, was examined using mitochondrial DNA (mtDNA) sequence data on the cytochrome…
Constructing primate phylogenies from ancient retrovirus sequences.
  • W. E. Johnson, J. Coffin
  • Biology
    Proceedings of the National Academy of Sciences of the United States of America
  • 1999
TLDR
Trees are constructed with the noncoding long terminal repeats (LTRs) of several ERV loci to allow comparison of trees to a well established phylogenetic standard, that of the Old World primates.
Coevolution of persistently infecting small DNA viruses and their hosts linked to host-interactive regulatory domains.
  • F. Shadan, L. Villarreal
  • Biology
    Proceedings of the National Academy of Sciences of the United States of America
  • 1993
TLDR
The evolution of small-DNA-virus families may be tightly linked to host evolution and speciation by interaction with a subset of host regulatory proteins by identifying three specific regions of polyoma regulatory gene products as highly conserved.
Phylogeny of African monkeys based upon mitochondrial 12S rRNA sequences
TLDR
An extensive phylogeny based upon DNA evidence for 26 species of the major groups of African monkeys and apes and suggests rearrangements in traditional monkey taxonomy and evolution is constructed.
Mitochondrial COII sequences and modern human origins.
TLDR
The mitochondrial DNA sequence data from COII and ND4-5 regions therefore do not support this multiregional hypothesis for the emergence of modern humans and are compatible with a 1-Myr-old human mitochondrial ancestor.
Evolution of the primate cytochrome c oxidase subunit II gene
TLDR
In congruence with previous studies on COII, it was found that the monkeys and apes have undergone a nearly two-fold increase in the rate of amino acid replacement relative to other primates.
Historical Perspective of Foamy Virus Epidemiology and Infection
TLDR
While FV are ubiquitous in all nonhuman primates, they are only acquired as rare zoonotic infections in humans, as well as the lack of pathogenicity in natural, experimental, and zoonosis infections.
...
...