Kapli, P; Yang, Z; Telford, M; (2020) Phylogenetic tree building in the genomic age. Nature Reviews Genetics , 21 pp. 428-444. 10.1038/s41576-020-0233-0.

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Abstract

Knowing phylogenetic relationships among species is fundamental for many studies in biology. An accurate phylogenetic tree underpins our understanding of the major transitions in evolution such as the emergence of new body plans or metabolism and is key to inferring the origin of new genes, detecting molecular adaptation, understanding morphological character evolution, and reconstructing demographic changes in recently diverged species. While data are ever more plentiful and powerful analysis methods are available, there remain many challenges to reliable tree building. Here we discuss the major steps of phylogenetic analysis, including identification of orthologous genes or proteins, multiple sequence alignment and choice of substitution models and inference methodologies. Understanding different sources of errors and strategies to mitigate them is essential for assembling an accurate tree of life.

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