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From Sequence Data incl. Orthologs, Paralogs, and Xenologs to Gene and Species Trees
Phylogenetic reconstruction aims at finding plausible hypotheses of the evolutionary history of genes or species based on genomic sequence information. The distinction of orthologous genes (genes having a common ancestry and diverged after a speciation) is crucial and lies at the heart of many genomic studies. However, existing methods that rely only on 1:1 orthologs to infer species trees are strongly restricted to a small set of allowed genes that provide information about the species tree. The use of larger gene sets that additionally consist of non-orthologous genes (e.g., so-called paralogous or xenologous genes) considerably increases the information about the evolutionary history of the respective species. In this work, we introduce a novel method to compute species phylogenies based on sequence data including orthologs, paralogs, or even xenologs.
21 Sep 2016
[HW16] Hellmuth, M., and Wieseke, N.: From Sequence Data incl. Orthologs, Paralogs, and Xenologs to Gene and Species Trees. Chapter in Evolutionary Biology: Convergent Evolution, Evolution of Complex Traits, Concepts and Methods, Ed. Pierre Pontarotti, Springer, p. 373-392, ISBN 978-3-319-41323-5, 2016