Novel Mathematical Aspects of Phylogenetic Estimation

摘要: In evolutionary biology, genetic sequences carry with them a trace of the underlying tree that describes their evolution from common ancestral sequence. Inferring this is challenging. We investigate some curious cases in which different methods like Maximum Parsimony, Likelihood and distance-based lead to trees. Moreover, we state cases, can be more reliably reconstructed when leaves are ignored – even if these close root. While all findings show problems inherent either assumed model or applied method, sometimes an inaccurate reconstruction simply due insufficient data. This particularly problematic rapid divergence event occurred distant past. analyze idealized form problem determine tight lower bound on growth rate for sequence length required resolve (independent any particular branch length). Finally, intermediates fossil record. The extent ‘gaps’ (missing transitional stages) has been used argue against gradual ancestor. take analytical approach demonstrate why, under certain sampling conditions, may not expect found.