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Michael A Charleston

Publications and source records attributed to Michael A Charleston.

6 recordsLinked to original sources
PubMed2006

Tracing the origin and co-phylogeny of the caliciviruses.

Caliciviruses infect a wide range of mammalian hosts and include the genus Norovirus, the major cause of food-borne viral gastroenteritis in humans. Using publicly available sequence data and phylogenetic analysis tools, the origins and virus-host co-phylogeny of these viruses were investigated. Here, evidence is presented in support of host switching by caliciviruses, but showing that zoonotic transfer does not appear to have occurred in the history of these viruses. The age or demography of the caliciviruses cannot yet be estimated with any firm degree of support, but further studies of this family, as new dated sequences become available, could provide key information of importance to human health and in understanding the emergence of food-borne disease.

Animals↗
PubMed2005

Traversing the tangle: algorithms and applications for cophylogenetic studies.

Cophylogenetic analysis supposes that two or more phylogenetic trees for linked groups have been constructed, and explores the relationships the trees have with each other. These types of analyses are most commonly used to assess relationships between hosts and their parasites, however the methodology can also be applied to diverse types of problems such as an examination of the phylogenies of genes with respect to those of organisms or those of geographic areas and the organisms that reside there. The working hypothesis is that the trees are correct, though sometimes attempts are made to take into account their uncertainty. Cophylogeny is computationally hard: that is, there are no known fast methods to compute relationships among such trees for any but the simplest of models. A review of methodology that has been developed to examine cophylogenetic relationships is presented and a brief discussion of some medically relevant examples is given.

Algorithms↗
PubMed2005

Host switch leads to emergence of Plasmodium vivax malaria in humans.

The geographical origin of Plasmodium vivax, the most widespread human malaria parasite, is controversial. Although genetic closeness to Asian primate malarias has been confirmed by phylogenetic analyses, genetic similarities between P. vivax and Plasmodium simium, a New World primate malaria, suggest that humans may have acquired P. vivax from New World monkeys or vice versa. Additionally, the near fixation of the Duffy-negative blood type (FY x B(null)/FY x B(null)) in West and Central Africa, consistent with directional selection, and the association of Duffy negativity with complete resistance to vivax malaria suggest a prolonged period of host-parasite coevolution in Africa. Here we use Bayesian and likelihood methods in conjunction with cophylogeny mapping to reconstruct the genetic and coevolutionary history of P. vivax from the complete mitochondrial genome of 176 isolates as well as several closely related Plasmodium species. Taken together, a haplotype network, parasite migration patterns, demographic history, and cophylogeny mapping support an Asian origin via a host switch from macaque monkeys.

Animals↗
PubMed2003

A cophylogenetic perspective of RNA-virus evolution.

The extent to which viruses and their hosts codiverge remains an open question, given that numerous cases of both "cospeciation" and horizontal switching have recently been documented. DNA viruses that form persistent infections are thought to be the most likely candidates for phylogenetic congruence. Phylogenetic reconciliation analysis was used to compare established phylogenies for four RNA viruses and their hosts. The analysis employs a cophylogeny mapping technique, implemented in TreeMap v2.0, to find the most parsimonious combinations of evolutionary events able to reconcile any incongruence. This technique is guaranteed to recover all potentially optimal solutions to the reconciled tree and specifically tests the null hypothesis that an associate phylogeny is no more congruent with a host phylogeny than would be a random tree with the same taxon set. Phylogenies for Hantavirus, Spumavirus, and avian sarcoma leukosis virus were found to be significantly similar to their host trees, whereas Lyssavirus and Arenavirus displayed no significant congruence. These results demonstrate 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.

Animals↗
PubMed2003

Recent results in cophylogeny mapping.

Virtually every problem in biology benefits from consideration within an evolutionary frame work. Parasitism has been part of life ever since one organism was able to provide an environment for another: questions of parasitology naturally lend themselves to consideration of the shared ancient history of parasites and hosts. The derivation of that shared history is therefore an area of great interest to theoreticians and practitioners alike. The most intuitive approach to this is by cophylogeny mapping. Mathematically the problem is that of optimally mapping the dependent tree into the independent one, e.g., parasite into host or gene tree into organismal phylogeny. This article describes some of the recent advances in cophylogenetic simulation, significance testing, and theoretical properties of maps. In simulation the author shows that the number of ways of mapping the parasite phylogeny into that of the hosts does indeed grow exponentially quickly in most cases and shows no close correlation with the similarity between the phylogenies, and that under a simple coevolutionary model, the range of behaviours of simulated parasite phylogenies is extremely broad and would appear to confound efforts to infer model parameters from observed cases. In the area of significance testing the author demonstrates that the maximal number of inferred codivergence events is not necessarily the best statistic for measuring cophylogenetic agreement, and that significance testing by randomisation which does not alter the parasite tree substantially biases results, and provides a new test to determine whether phylogenetic similarity is consistent with preferential host switching.

Animals↗