Phylogenetic Analysis: Basic Concepts and Its Use as a Tool for Virology and Molecular Epidemiology

Eloiza Teles Caldart, Helena Mata, Cláudio Wageck Canal, Ana Paula Ravazzolo


Background: Phylogenetic analyses are an essential part in the exploratory assessment of nucleic acid and amino acid sequences. Particularly in virology, they are able to delineate the evolution and epidemiology of disease etiologic agents and/or the evolutionary path of their hosts. The objective of this review is to help researchers who want to use phylogenetic analyses as a tool in virology and molecular epidemiology studies, presenting the most commonly used methodologies, describing the importance of the different techniques, their peculiar vocabulary and some examples of their use in virology.

Review: This article starts presenting basic concepts of molecular epidemiology and molecular evolution, emphasizing their relevance in the context of viral infectious diseases. It presents a session on the vocabulary relevant to the subject, bringing readers to a minimum level of knowledge needed throughout this literature review. Within its main subject, the text explains what a molecular phylogenetic analysis is, starting from a multiple alignment of nucleotide or amino acid sequences. The different software used to perform multiple alignments may apply different algorithms. To build a phylogeny based on amino acid or nucleotide sequences it is necessary to produce a data matrix based on a model for nucleotide or amino acid replacement, also called evolutionary model. There are a number of evolutionary models available, varying in complexity according to the number of parameters (transition, transversion, GC content, nucleotide position in the codon, among others). Some papers presented herein provide techniques that can be used to choose evolutionary models. After the model is chosen, the next step is to opt for a phylogenetic reconstruction method that best fits the available data and the selected model. Here we present the most common reconstruction methods currently used, describing their principles, advantages and disadvantages. Distance methods, for example, are simpler and faster, however, they do not provide reliable estimations when the sequences are highly divergent. The accuracy of the analysis with probabilistic models (neighbour joining, maximum likelihood and bayesian inference) strongly depends on the adherence of the actual data to the chosen development model. Finally, we also explore topology confidence tests, especially the most used one, the bootstrap. To assist the reader, this review presents figures to explain specific situations discussed in the text and numerous examples of previously published scientific articles in virology that demonstrate the importance of the techniques discussed herein, as well as their judicious use.

Conclusion: The DNA sequence is not only a record of phylogeny and divergence times, but also keeps signs of how the evolutionary process has shaped its history and also the elapsed time in the evolutionary process of the population. Analyses of genomic sequences by molecular phylogeny have demonstrated a broad spectrum of applications. It is important to note that for the different available data and different purposes of phylogenies, reconstruction methods and evolutionary models should be wisely chosen. This review provides theoretical basis for the choice of evolutionary models and phylogenetic reconstruction methods best suited to each situation. In addition, it presents examples of diverse applications of molecular phylogeny in virology.


evolution; evolutionary models; molecular epidemiology; phylogeny; phylogenetic reconstruction methods.

Full Text:



Aamir U.B., Wernery U., Ilyushina N. & Webster R.G. 2007. Characterization of avian H9N2 influenza viruses from United Arab Emirates 2000 to 2003. Virology. 361(1): 45-55.

Abascal F., Zardoya R. & Posada D. 2005. ProtTest: selection of best-fit models of protein evolution. Bioinformatics. 21(9): 2104-2105.

Antunes A., Troyer J.L., Roelke M.E., Pecon-Slattery J., Packer C., Winterbach C., Winterbach H., Hemson G., Frank L., Stander P., Siefert L., Driciru M., Funston P. J., Alexander K.A., Prager K.C., Mills G., Wildt D., Bush M., O’Brien S.J. & Johnson W.E. 2008. The evolutionary dynamics of the lion (Panthera leo) revealed by host and viral population genomics. PLOS Genetics. 4(11): e1000251.

Batista W.C., Kashima S., Marques A.C. & Figueiredo L.T.M. 2001. Phylogenetic analysis of Brazilian Flavivirus using nucleotide sequences of parts of NS5 gene and 3´non-coding regions. Virus Research. 75(1): 35-42.

Bayes T. 1763. An essay towards solving in the doctrine of chances. Philosophical Transactions of the Royal Society London. 53(1): 370-418.

Bhullar K., Waglechner N., Pawlowski A., Koteva K. & Banks E.D. 2012. Antibiotic Resistance Is Prevalent in an Isolated Cave Microbiome. PLoS ONE. 7(4): e34953.

Biek R., Drummond A.J. & Poss M. 2006. A virus reveals population structure and recent demographic history of its carnivore host. Science. 311(5760): 538-541.

Brandão P.E., Gregori F., Richtzenhain L.J., Rosales C.A.R., Villareal L.Y.B. & Jerez J.A. 2006. Molecular diversity of Brazilian strains of bovine coronavirus (BCoV) reveals a deletion within the hypervariable region of the S1 subunit of the spike glycoprotein also found in human coronavirus OC43. Archives of Virology. 151(9): 1735-1748.

Brandão P.E., Scheffer K., Villarreal L.Y., Achkar S., Oliveira R.N., Fahl W.O., Castilho J.G., Kotait I. & Richtzenhain L.J. 2008. A coronavirus detected in the vampire bat Desmodus rotundus. Brazilian Journal of Infectious Diseases. 12(6): 466-468.

Brandão P.E., Villareal L.Y.B., Gregori F., Souza S.L.P., Lopes M.A.E., Gomes C.R., Sforsin A.J., Sanches A.A., Rosales C.A.R Richtzenhain L.J., Ferreira A.J.P. & Jerez J.A. 2007. On the etiology of an outbreak of winter dysentery in dairy cows in Brazil. Pesquisa Veterinária Brasileira. 27(10): 398-402.

Brocchieri L. 2001. Phylogenetic Inferences from Molecular Sequences: Review and Critique. Theoretical Population Biology. 59(1): 27-40.

Budaszewski R.F., Pinto L.D., Weber M.N., Caldart E.T., Alves C.D.B.T., Martellac V., Ikutad N., Lunged V.R. & Canal C.W. 2014. Genotyping of canine distemper virus strains circulating in Brazil from 2008 to 2012. Virus Research. 180(1): 76-83. DOI: 10.1016/j.virusres.2013.12.024.

Carnieli Jr. P., Brandão P.E., Carrieri M.L., Castilho J.G., Macedo C.I., Machado L.M., Rangel N., de Carvalho R.C., de Carvalho V.A., Montebello L., Wada M. & Kotait I. 2006. Molecular epidemiology of rabies virus strains isolated from wild canids in Northeastern Brazil. Virus Research. 120(1-2):113-120.

Cavalli-Sforza L.L. & Edwards A.W.F. 1967. Phylogenetic Analysis Models and Estimation Procedures. American Journal of Human Genetics. 19(3): 233-257.

Chen R. & Holmes E.C. 2006. Avian Influenza Virus exhibits rapid evolutionary dynamics. Molecular Biology and Evolution. 23(12): 2336-2341.

Choi Y.K., Goyal S.M., Farnham M.W. & Joo H.S. 2002. Phylogenetic analysis of H1N2 isolates of Influenza A Virus from pigs in the United States. Virus Research. 87(2): 173-179.

Cisterna D., Bonaventura R., Caillou S., Pozo O., Andreau M.L., Fontana L.D., Echegoyen C., de Mattos C., de Mattos C., Russo S., Novaro L., Elbergerh D. & Freire M.C. 2005. Antigenic and molecular characterization of rabies virus in Argentina. Virus Research. 109(2): 139-147.

Davies J. & Davies D. 2010. Origins and Evolution of Antibiotic Resistance. Microbiology and Molecular Biology Reviews. 74(3): 417-433.

De Robertis E.M.F. & Hib J. 2006. Bases da biologia celular e molecular. 4.ed. Rio de Janeiro: Guanabara Koogan, 389p.

Dorman J.S. 2000. Molecular epidemiology: The impact of molecular biology in epidemiology research. Revista Medica de Chile. 128(11): 1261-1268.

Edwards A.W.F. 1972. Likelihood. An Account of the Statistical Concept of Likelihood and Its Application to Scientific Inference. New York: Cambridge University Press, 236p.

Efron B. 1979. Bootstrap methods: another look at the jackknife. The Annals of Statistics. 7(1): 1-26.

Étienne J., Millot F. & Cerqueira A.J. 2003. Bioquímica genética e biologia molecular. 6.ed. São Paulo: Livraria & Editora, 504p.

Ewald P.W. 2004. Evolution of virulence. Infectious Disease Clinics of North America. 18(1): 1-15.

Ewing B. & Green P. 1998. Base-calling of automated sequencer traces using Phred. II. Error probabilities. Genome Research. 8(1): 186-194.

Ewing B., Hillier L. & Wendl M.C. 1998. Base-calling of automated sequencer traces usingPhred. I. Accuracy assessment. Genome Research. 8(1): 175-185.

Feitosa A.L.V.L., da Silva Teixeira M.F., Pinheiro R.R., da Cunha R.M.S., Lima J.P.M.S., Andrioli A. & Pinheiro D.C.S.N. 2010. Phylogenetic analysis of small ruminant lentiviruses from Northern Brazil. Small Ruminant Research. 94(1): 205-209.

Felsenstein J. 1978. Cases in which parsimony or compatibility methods will be positively misleading. Systematic Zoology. 27(4): 401-410.

Felsenstein J. 1981. Evolutionary trees from DNA sequences: a máximum likelihood approach. Journal of Molecular Evolution. 17(6): 368-376.

Felsenstein J. 1985. Confidence limits on Phylogenies: An Approach Using the Bootstrap. Evolution. 39(4): 783-791.

Felsenstein J. 2004. Inferring Phylogenies. 2nd edn. Sunderland: Sinauer Associates Inc., 664p.

Ferreira H.B., Passaglia L.M.P. & Zaha A. 2003. Biologia molecular básica. 3.ed. Porto Alegre: Mercado Aberto, 421p.

Forattini O.P. 2004. Conceitos básicos de epidemiologia molecular. São Paulo: Editora da Universidade de São Paulo, 98p.

Fraga A.P., Balestrin E., Ikuta N., Fonseca A.S.K., Spilki F.R., Canal C.W. & Lunge V.R. 2013. Emergence of a New Genotype of Avian Infectious Bronchitis Virus in Brazil. Avian Diseases. 57(2): 225-232.

Frost S.D.W., Pybus O.G., Gog J.R., Viboud C., Bonhoeffer S. & Bedford T. 2015. Eight challenges in phylodynamic inference. Epidemics. 10: 88-92.

Garcia M. 2007. Uma filogenia mitocondrial de metazoários. 212f. Petrópolis, RJ. Dissertação (Mestrado em Modelagem Computacional com Ênfase em Bioinformática) - Programa de Pós-graduação em Modelagem Computacional, Universidade Federal do Rio de Janeiro.

Gilks W.R., Richardson S. & Spiegelhalter D.J. 1996. Markov Chain Monte Carlo in Practice. London: Chapman & Hall, 512p.

Goldman N. & Whelan S. 2000. Statistical tests of γ-distributed rate heterogeneity in models of sequence evolution in phylogenetics. Molecular Biology and Evolution. 17(1): 974-978.

Grego E., Profiti M., Giammarioli M., Giannino L., Rutili D., Woodall C., & Rosati S. 2002. Genetic heterogeneity of small ruminant lentiviruses involves immunodominant epitope of capsid antigen and affects sensitivity of singlestrain-based immunoassay. Clinical and diagnostic laboratory immunology. 9(4): 828-832.

Hasegawa M., Kishino H. & Yano T. 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution. 22(2): 160-174.

Hillis D.M. & Bull J.J. 1993. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Systematic Biology. 42(2): 182-192.

Holder M. & Lewis P.O. 2003. Phylogeny estimation: traditional and Bayesian approaches. Nature. 4(4): 275-284.

Holmes E.C. 1998. Molecular epidemiology and evolution of emerging infectious diseases. British Medical Bulletin. 54(3): 533-543.

Holmes E.C., Ghedin E., Miller N., Taylor J., Bao Y., George K.S., Grenfell B.T., Salzberg S.L., Fraser C.M., Lipman D.J. & Taubenberger J.K. 2005. Whole-genome analysis of Human Influenza A Virus reveals multiple persistent lineages and reassortment among recent H3N2 Virus. PLoSI. 3(9): 1579-1589.

Hu X., Javadian A., Gagneux P. & Robertson B.H. 2001. Paired chinpanze hepatitis B virus (ChHBV) and mtDNA sequences suggest different ChHBV genetic variants are found in geographically distinct chimpanzee subspecies. Virus Research. 79(1): 103-108.

Huelsenbeck J.P., Ronquist F., Nielsen R. & Bollback J.P. 2001. Bayesian inference of phylogeny and its impact on evolutionary biology. Science. 294(5550): 2310-2314.

Hussain A.I., Shanmugam V., Bhullar V.B., Beer B.E., Vallet D., Gautier-Hion A., Wolfe N.D., Karesh W.B., Kilbourn A.M., Tooze Z., Heneine W. & Switzer W.E. 2003. Screening of simian foamy virus infection by using a combined antigen western blot assay: evidence for a wide distribution among old world primates and identification of four new divergent viruses. Virology. 309(2): 248-257.

Jakab F., Horváth G., Ferenczi E., Sebók J., Varecza Z. & Szúcs G. 2007. Detection of Dobrava hantaviruses in Apodemus agrarius mice in the Transdanubian region of Hungary. Virus Research. 128(1-2): 149-152.

Jukes T.H. & Cantor C.R. 1969. Evolution of Protein Molecules. In: Munro H.N. (Ed). Mammalian Protein Metabolism. 3rd edn. New York: Academic Press, pp.21-132.

Junqueira L.C.U. & Carneiro J. 2005. Biologia celular e molecular. 8.ed. Rio de Janeiro: Guanabara Koogan, 332p.

Karr B. M., Chebloune Y., Leung K. & Narayan O. 1996. Genetic characterization of two phenotypically distinct North American ovine lentiviruses and their possible origin from caprine arthritis-encephalitis virus. Virology. 225(1): 1-10.

Katzourakis A., Aiewsakun P., Jia H., Wolfe N.D., LeBreton M. & Yoder A.D. 2014. Discovery of prosimian and afrotherian foamy viruses and potential cross species transmissions amidst stable and ancient mammalian co-evolution. Retrovirology. 11(1): 1.

Khuner M.K. & Felsenstein J. 1994. A Simulation Comparison of Phylogeny Algorithms Under Equal and Unequal Evolutionary Rates. Molecular Biology and Evolution. 11(3): 459-468.

Kimura M. 1980. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution. 16(1): 111-120.

Kinsella E., Martin S.G., Grolla A., Czub M., Feldmann H. & Flicka R. 2004. Sequence determination of the Crimean-Congo hemorrhagic fever vírus L segment. Virology. 321(1): 23-28.

Knowles N.J., Dickinson N.D., Wilsden G., Carra E., Brocchi E. & De Simone F. 1998. Molecular analysis of encephalomyocarditis viruses isolated from pigs and rodents in Italy. Virus Research. 57(X): 53-62.

Leroux C., Chastang J., Greenland T. & Mornex J.F. 1997. Genomic heterogeneity of small ruminant lentiviruses: existenceof heterogeneous populations in sheep and of the samelentiviral genotypes in sheep and goats. Archives of virology. 142(6): 1125-1137.

Leser W. 1985. Elementos em epidemiologia geral. Rio de Janeiro: Atheneu, 178p.

Levin B.R., Lipsitch M. & Bonhoeffer S. 1999. Population Biology, Evolution, and Infectious Disease: Convergence and Synthesis. Science. 283(5403): 806-809.

Liegeois F., Courgnaud V., Switzer W.M., Murphy H.W., Loul S., Aghokeng A., Pourrut X., Mpoudi-Ngole E., Delaporte E. & Peeters M. 2006. Molecular characterization of a novel simian imunodeficiency virus lineage (SIVtal) from northern talapoins (Miopithecus ogouensis). Virology. 349(1): 55-65.

Mata H., Fontana C.S., Maurício G.N., Bornschein M.R., de Vasconcelos M.F. & Bonatto S.L. 2009. Molecular phylogeny and biogeography of the eastern Tapaculos (Aves: Rhinocryptidae: Scytalopus, Eleoscytalopus): Cryptic diversification in Brazilian Atlantic Forest. Molecular Phylogenetics and Evolution. 53(2): 450-462. DOI:10.1016/j. ympev.2009.07.017.

Mata H., Gongora J., Eizirik E., Alves B.M., Soares M.A. & Ravazzolo A.P. 2015. Identification and characterization of diverse groups of endogenous retroviruses in felids. Retrovirology. Mar 15;12:26. DOI: 10.1186/s12977-015-0152-x.

Mata H., Gongora J. & Ravazzolo A.P. 2013. Molecular Characterization of SINEs Integrated in Endogenous Retrovirus Sequences from Leopardus geoff royi and Puma concolor. Acta Scientiae Veterinariae. 41(1): 1133.

Matioli S.R. 2001. Biologia molecular e evolução. Ribeirão Preto: Holos, 202p.

Maruyama S.R., Castro-Jorge L.A., Ribeiro J.M.C., Gardinassi L.G., Garcia G.R., Brandão L.G., Rodrigues A.R., Okada M.I., Abrão E.P., Ferreira B.R., Fonseca B.A.L. & Miranda-Santos I.K.F. 2014. Characterisation of divergent flavivirus NS3 and NS5 protein sequences detected in Rhipicephalus microplus ticks from Brazil. Memórias do Instituto Oswaldo Cruz. 109(1): 38-50.

Maurício G.N., Mata H., Bornschein M.R., Cadena C.D., Alvarenga H. & Bonatto S.L. 2008. Hidden generic diversity in Neotropical birds: Molecular and anatomical data support a new genus for the ‘‘Scytalopus” indigoticus species-group (Aves: Rhinocryptidae). Molecular Phylogenetics and Evolution. 49(1): 125-135.

Metzker M.L., Mindell D.P., Liu X-M., Ptak R.G., Gibbs R.A. & Hillis D.M. 2002. Molecular evidence of HIV-1 transmission in a criminal case. PNAS. 99(22): 14292-14297.

Nei M. 1996. Phylogenetic Analysis in Molecular Evolutionary Genetics. Annual Review of Genetics. 30(1): 371-403.

O´Brien S.J., Troyerb J.L., Roelkeb M., Markerc L. & Pecon-Slattery J. 2006. Plagues and adaptation: lessons from the felidae models for SARS and AIDS. Biological Conservation. 131(2): 255-267.

Ota R., Waddell P.J., Hasegawa M., Shimodaira H. & Kishino H. 2000. Appropriate likelihood ratio tests and marginal distributions for evolutionary tree models with constraints on parameters. Molecular Biology and Evolution. 17(5): 798-803.

Ou C.Y., Ciesielski C.A., Myers G., Bandea C.I., Luo C.-C., Korber B.T.M., Mullins J.I., Schochetman G., Berkelman R.L., Economou A.N., Witte J.J., Furman L.J., Satten G.A., Maclnnes K.A., Curran J.W. & Jaffe H.W. 1992. Molecular epidemiology of HIV transmission in a dental practice. Science. 256(5060): 1165-1171.

Page R.D.M. & Holmes E.C. 1998. Molecular evolution: a Phylogenetic Approach. Oxford: Blackwell Science Ltd., 352p.

Pennings P.S. 2012. Standing Genetic Variation and the Evolution of Drug Resistance in HIV. PLoS Computacional Biology. 8(6): e1002527.

Pinto L.D., Barros I.N., Budaszewski R.F., Weber M.N., Mata H., Antunes J.R., Boabaid F.M., Wouters A.T.B., Driemeier D., Brandão P.E. & Canal C.W. 2014. Characterization of pantropic canine coronavirus from Brazil. The Veterinary Journal. 202(3): 659-662. DOI:10.1016/j.tvjl.2014.09.006.

Pisoni G., Bertoni G., Boettcher P., Ponti W.A. & Moroni P. 2006. Phylogenetic analysis of the gag region encoding the matriz protein of small ruminant lentiviruses: comparative analysis and molecular epidemiological applications. Virus Research. 116(1): 159-167.

Pisoni G., Bertoni G., Puricelli M., Maccalli M. & Moroni P. 2007. Demonstration of coinfection with and recombination by caprine arthritis-encephalitis virus and maedi-visna virus in naturally infected goats. Journal of Virology. 81(10): 4948-4955.

Posada D. 2008. jModelTest: Phylogenetic Model Averaging. Molecular Biology and Evolution. 25(7): 1253-1256.

Posada D. 2009. Selecting models of evolution. In: Salemi M. (Ed). The Phylogenetic Handbook: A Practical Approach to DNA and Protein Phylogeny. 2nd edn. Cambridge: Cambridge University Press, pp.256-282.

Posada D. & Crandall K.A. 2001. Selecting the best-fit model of nucleotide substitution. Systematic Biology. 50(4): 580-601.

Rannala B. & Yang Z. 1996. Probability Distribution of Molecular Evolutionary Trees: A New Method of Phylogenetic Inference. Journal of Molecular Evolution. 43(3): 304-311.

Ravazzolo A.P., Reischak D., Peterhans E. & Zanoni R. 2001. Phylogenetic analysis of small ruminant lentiviruses from Southern Brazil. Virus Research. 79(1): 117-123. DOI:10.1016/S0168-1702(01)00339-2.

Real L.A. & Biek R. 2007. Spatial dynamics and genetics of infectious diseases on heterogeneous landscapes. Journal of the Royal Society. 4(16): 935-948.

Riley L.W. 2004. Molecular epidemiology of infectious diseases: principles and practices. Washington: ASM Press, 348p.

Rodenbusch C.R., Baptistotte C., Werneck M.R., Pires T.T., Melo M.T.D., de Ataíde M.W., dos Reis K.D.H.L., Testa P., Alievi M.M. & Canal C.W. 2014. Fibropapillomatosis in green turtles Chelonia mydas in Brazil: characteristics of tumors and virus. Diseases of Aquatic Organisms. 111(3): 207-217. DOI:10.3354/dao02782.

Rokas A. & Carrol S.B. 2005. More Genes or More Taxa? The Relative Contribution of Gene Number and Taxon Number to Phylogenetic Accuracy. Molecular Biology and Evolution. 22(5): 1337-1344.

Ronquist F. & Deans A.R. 2010. Bayesian phylogenetics and its influence on insect systematics. Annual Review of Entomology. 55(1): 189-206.

Ronquist F., Huelsenbeck J.P. & Britton T. 2004. Bayesian supertrees. In: Bininda-Emonds O.R.P. (Ed). Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life. Amsterdam: Kluwer, pp.193-224.

Ronquist F., Teslenko M., Mark P.V.D., Ayres D.L., Darling A., Höhna S., Larget B., Liu L., Suchard M.A. & Huelsenbeck J.P. 2012. MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space. Systematic Biology. 61(3): 539-542.

Rost B. 1999. Twilight zone of protein sequence alignments. Protein Engineering. 12(2): 85-94.

Russel B. 1946. A History of Western Phylosophy. London: Routledge, 895p.

Saitou N. & Imanishi T. 1989. Relative Efficiences of Fitch-Margoliash, Maximum-Parsimony, Maximum-Likelihood, Minimum-Evolution, and Neighbor-Joining Methods of Phylogenetic Tree Construction in Obtaining the Correct Tree. Molecular Biology and Evolution. 4(4): 406-425.

Saitou N. & Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution. 4(4): 406-425.

Saltarelli M., Querat G., Konings D.A., Vigne R. & Clements J.E. 1990. Nucleotide sequence and transcriptional analysis of molecular clones of CAEV which generate infectious virus. Virology. 179(1): 347-364.

Schneider H. 2003. Métodos de Análise filogenética: um guia prático. Ribeirão Preto: Holos Editora, 162p.

Schumann T., Hotzel H., Otto P. & Johne R. 2009. Evidences of interespecies transmission and reassortment among avian group A rotaviruses. Virology. 386(2): 334-343.

Shah C., Böni J., Huder J.B., Vogt H.R., Mühlherr J., Zanoni R. & Schüpbach J. 2004. Phylogenetic analysis and reclassification of caprine and ovine lentiviruses based on 104 new isolates: evidence for regular sheep-to-goat transmission and worldwide propagation through livestock trade. Virology. 319(1): 12-26.

Simionatto S., Lima-Rosa C.A.V., Binneck E., Ravazzolo A.P. & Canal C.W. 2006. Characterization and phylogenetic analysis of Brazilian chicken anaemia vírus. Virus Genes. 33(1): 5-10. DOI: 10.1007/s11262-005-0033-9.

Smith G.J.D., Vijaykrishna D., Bahl J., Lycett S.J., Worobey M., Pybus O.G., Ma S.M., Cheung C.L., Raghwani J., Bhatt S., Peiris J.S.M. & Guan Y., Rambaut A. 2009. Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic. Nature. 459(7250): 1122-1126.

Sonigo P., Alizon M., Staskus K., Klatzmann D., Cole S., Danos O., Retzel E., Tiollais P., Haase A. & Wain-Hobson S. 1985. Nucleotide sequence of the visna lentivirus: relationship to the AIDS virus. Cell. 42(1): 369-382.

Sounis E. 1985. Epidemiologia geral. São Paulo: Atheneu, 178p.

Steel M. & Penny D. 2000. Parsimony, likelihood, and the role of models in molecular phylogenetics. Molecular Biology and Evolution. 17(6): 839-850.

Studier J.A. & Keppler K.J. 1988. A note on the neighbor-joining algorithm of Saitou and Nei. Molecular Biology and Evolution. 5(6): 729-731.

Tajima F. & Nei M. 1984. Estimation of evolutionary distance between nucleotide sequences. Molecular Biology and Evolution. 1(3): 269-285.

Takahashi K. & Nei M. 2000. Efficiencies of Fast Algorithms of Phylogenetic Inference Under the Criteria of Maximum Parsimony, Minimum Evolution, and Maximum Likelihood When a Large Number of Sequences Are Used. Molecular Biology and Evolution. 17(3): 1251-1258.

Tamura K. 1992. Estimation of the number of nucleotide substitutions when there are strong transition-transversion and GC-content biases. Molecular Biology and Evolution. 9(4): 678-687.

Tamura K. & Nei M. 1993. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Molecular Biology and Evolution. 10(3): 512-526.

Thrusfield M. 2004. Epidemiologia Veterinária. 2.ed. São Paulo: Roca, 556p.

Turner P.C. & Motta P.A. 2004. Biologia molecular. Rio de Janeiro: Guanabara Koogan, 287p.

Troy C.S. MacHugh D.E., Bailey J.F., Magee D.A., Loftus R.T., Cunningham P., Chamberlain A.T., Sykes B.C. & Bradley D.G. 2001. Genetic evidence for Near-Eastern origins of European cattle. Nature. 410(6832): 1091-1110.

Vandamme A.M. 2009. Basic Concepts of Molecular Evolution. In: Salemi M. (Ed). The Phylogenetic Handbook: A Practical Approach to DNA and Protein Phylogeny. 2nd edn. Cambridge: Cambridge University Press, pp.1-23.

Villareal L.Y.B., Brandão P.E., Chacón J.L., Saidenberg A.B.S., Assayag A.S., Jones R.C. & Ferreira A.J.P. 2007. Molecular characterization of infectious bronchitis virus strains isolated from the enteric contents of brazilian laying hens and broilers. Avian Diseases. 51(4): 974-978.

Weber M.N., Silveira S., Machado G., Groffc F.H.S., Mósena A.C.S., Budaszewski R.F., Dupont P.M., Corbellini L.G. & Canal C.W. 2014. High frequency of bovine viral diarrhea virus type 2 in Southern Brazil. Virus Research. 191: 197-124.

Weber M.N., Streck A.F., Silveira S., Mósena A.C.S., da Silva M.S. & Canal C.W. 2015. Homologous recombination in pestiviruses: Identification of three putative novel events between different subtypes/genogroups. Infection, Genetics and Evolution. 30: 219-224. DOI:10.1016/j.meegid.2014.12.032.

Whelan S., Liò P. & Goldman N. 2001. Molecular phylogenetics: state-of-the art methods for looking into the past. Trends in Genetics. 17(5): 262-272.

World Health Organization (WHO). 2016. Disponível em: . [Accessed April 2016.]

Xia X. & Xie Z. 2001. DAMBE: data analysis in molecular biology and evolution. Journal of Heredity. 92(4): 371-373.

Yang Z. 1994. Estimating the pattern of nucleotide substitution. Journal of Molecular Evolution. 39(1): 105-111.

Zharkikh A. & Li W.-H. 1992. Statistical properties of bootstrap estimation of phylogenetic variability from nucleotide sequences. I. Four taxa with a molecular clock. Journal of Molecular Evolution. 9(6): 1119-1147.


Copyright (c) 2018 Eloiza Teles Caldart, Helena Mata, Cláudio Wageck Canal, Ana Paula Ravazzolo

Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License.