Challenges of phylogenetic analyses of aDNA sequences

• Main Authors: Katharina Dittmar, Sheila Mendonça de Souza, Adauto Araújo
• Format: Article
• Language: English
• Published: Instituto Oswaldo Cruz, Ministério da Saúde 2006-12-01
• Series: Memórias do Instituto Oswaldo Cruz.
• Subjects: phylogenetics; methods; informative characters; missing data; aDNA
• Online Access: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0074-02762006001000003
• ISSN: 0074-0276; 1678-8060

One of the crucial steps of authentication of aDNA sequences is phylogenetic consistency. Amplified sequences should fit into the phylogenetic framework of their supposed origin. An inherent property of aDNA sequences however, is their short sequence length. Additionally, genes for aDNA studies are often chosen by their preservation potential rather than by phylogenetically informative content. This poses potential challenges regarding their analyses, and might result in an inaccurate reflection of the supposed phylogenetic history of the sequence or organism under study. In this paper some fundamental problems of phylogenetic analysis and interpretation of aDNA datasets are discussed. Suggestions for character sampling and treatment of missing data are made. The publication is the result of a talk from the 1st PAMINSA Meeting in Rio de Janeiro, July 2005.