Manuscript Topics

Deep phylogenies are difficult to recover. Anyone who has worked on deep phylogenies would have experienced the frustrating situation in which different research groups have generated “robustly supported” phylogenies that unfortunately are totally incompatible with each other. Some methodologies or analyses must be severely flawed. Various attempts have been made to 1) increase the amount of data to augument the weak phylogenetic signals in each individual gene, 2) diversify molecular data to incorporate conservation of gene interaction pathways, 3) improve the sequence alignment, 4) develop more realistic substitution models and more rigorous statistical tests of alternative topologies, 5) design new algorithms to search the tree space more thoroughly to avoid local optima, and 6) evaluate the biological relevance of resulting phylogenies by its power to explain phenotypic differences and evolutionary and adaptive trajectories in response to natural selection mediated by environmental differences. This special issue aims to attract research articles on, and reviews of, methods and applications in these six categories leading to better resolution of deep phylogenies (which do not necessarily imply the reconstruction of speciation or gene duplication events that occurred billions of years ago, as some viral phylogenies could be quite “deep” going back less than a million years). We particularly encourage submission of papers that identify the flaws in previous publications leading to resolution of existing controversies. Papers mainly on dating may be considered but are not the prime focus of this issue (unless they are explicitly hypothesis-driven).

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