Statistical Methods in Phylogenetic and Evolutionary Inferences
DOI:
https://doi.org/10.6092/issn.1973-2201/3556Abstract
Molecular instruments are the most accurate methods in organisms’identification and characterization. Biologists are often involved in studies where the main goal is to identify relationships among individuals. In this framework, it is very important to know and apply the most robust approaches to infer correctly these relationships, allowing the right conclusions about phylogeny. In this review, we will introduce the reader to the most used statistical methods in phylogenetic analyses, the Maximum Likelihood and the Bayesian approaches, considering for simplicity only analyses regardingDNA sequences. Several studieswill be showed as examples in order to demonstrate how the correct phylogenetic inference can lead the scientists to highlight very peculiar features in pathogens biology and evolution.References
G. AMORE, L. BERTOLOTTI,G. L. HAMER, U. D. KITRON, E. D.WALKER,M. O. RUIZ, J. D. BRAWN, T. L. GOLDBERG (in press). Multi-year evolutionary dynamics of west nile virus in suburban chicago, usa, 2005-2007. Philosophical Transactions of the Royal Society B.
G. BARNARD, T. BAYES (1958). Studies in the history of probability and statistics: Ix. thomas bayes’s essay towards solving a problem in the doctrine of chances. Biometrika, 45, no. 3, pp. 293–315.
L. BERTOLOTTI, U. KITRON, T. L. GOLDBERG (2007). Diversity and evolution of west nile virus in illinois and the united states, 2002-2005. Virology, 360, no. 1, pp. 143–149.
L. BERTOLOTTI,U. D. KITRON, E. D. WALKER, M. O. RUIZ, J. D. BRAWN, S. R. LOSS, G. L. HAMER, T. L. GOLDBERG (2008). Fine-scale genetic variation and evolution of west nile virus in a transmission "hot spot" in suburban chicago, usa. Virology, 374, no. 2, pp. 381–389.
G. CARPI, L. BERTOLOTTI, E. PECCHIOLI, F. CAGNACCI, A. RIZZOLI (2009). Anaplasma phagocytophilum groel gene heterogeneity in ixodes ricinus larvae feeding on roe deer in northeastern italy. Vector Borne Zoonotic Dis, 9, no. 2, pp. 179–184.
F. CERUTTI, L. BERTOLOTTI, T. L. GOLDBERG,M. GIACOBINI (2010a). Adding vertical meaning to phylogenetic trees by artificial evolution. In Advances in Artificial Life: 10th European Conference, ECAL 2009. Budapest, Hungary. In press.
F. CERUTTI, L. BERTOLOTTI, T. L. GOLDBERG, M. GIACOBINI (2010b). Investigating populational evolutionary algorithms to add vertical meaning in phylogenetic trees. In 8th European Conference on Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics. Istanbul, Turkey.
A. EIBEN, J. SMITH (2003). Introduction to evolutionary computing. Springer Verlag.
J. FELSENSTEIN (1973). Maximum likelihood and minimum-steps methods for estimating evolutionary trees from data on discrete characters. Systematic Zoology, pp. 240–249.
J. FELSENSTEIN (1981). Evolutionary trees from dna sequences: a maximum likelihood approach. Journal of molecular evolution, 17, no. 6, pp. 368–376.
J. FELSENSTEIN (2004). Inferring phytogenies. Sinauer Associates, Sunderland,Massachusetts.
R. FISHER (1912). On an absolute criterion for fitting frequency curves. Messengers ofMathematic, 41, pp. 155–160.
A. FUSARO,M. NELSON, T. JOANNIS, L. BERTOLOTTI, I. MONNE, A. SALVIATO, O. OLALEYE, I. SHITTU, L. SULAIMAN, L. LOMBIN, et al. (2010). Evolutionary dynamics of multiple sublineages of h5n1 influenza viruses in nigeria, 2006-2008. Journal of Virolog, 84, no. 7, pp. 3239–47.
C. GEYER (1992). In Computing Science and Statistics: Proceedings of the 23rd Symposium on the Interface. Keramidas, EM, Ed.
G. GONNET, S. BENNER, S. ZURICH (1996). Probabilistic ancestral sequences and multiple alignments. In Algorithm theory: SWAT’96: 5th Scandinavian Workshop on Algorithm Theory, Reykjavík, Iceland, July 3-5, 1996: proceedings. Springer, p. 380.
P. GREEN (1995). Reversible jump markov chain monte carlo computation and bayesian model determination. Biometrika, 82, no. 4, p. 711.
E. GREGO, L. BERTOLOTTI, S. PELETTO, G. AMORE, L. TOMASSONE,A.MANNELLI (2007). Borrelia lusitaniae ospa gene heterogeneity in mediterranean basin area. Journal of Molecular Evolution, 65, no. 5, pp. 512–518.
W. HASTINGS (1970). Monte carlo sampling methods using markov chains and their applications. Biometrika, , no. 57, pp. 97–109.
P. LEMEY, A. RAMBAUT, A. DRUMMOND,M. SUCHARD (2009). Bayesian phylogeography finds its roots. PLoS Computational Biology, 5, no. 9.
W. MADDISON (1989). Reconstructing character evolution on polytomous cladograms. Cladistics, 5, pp. 365–377.
N. METROPOLIS, A. ROSENBLUTH, M. ROSENBLUTH, A. TELLER, E. TELLER, et al. (1953). Equation of state calculations by fast computing machines. The journal of chemical physics, 21, no. 6, p. 1087.
M. PRICE (1763). An essay towards solving a problem in the doctrine of chances. by the late rev. mr. bayes, frs communicated bymr. price, in a letter to john canton, amfrs. Philosophical Transactions (1683-1775), 53, pp. 370–418.
A. TETTAMANZI, M. TOMASSINI (2001). Soft computing: integrating evolutionary, neural, and fuzzy systems. Springer Verlag.
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