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Phylogenetic tree building in the genomic age

Nature Reviews Genetics volume 21, pages 428–444 (2020)Cite this article

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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. Although 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 the different sources of errors and the strategies to mitigate them is essential for assembling an accurate tree of life.

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Fig. 1: Phylogenomic pipeline.
Fig. 2: Distinguishing orthologous and paralogous relationships between genes.
Fig. 3: Heterogeneous rates across lineages and long-branch attraction.
Fig. 4: Heterogeneous substitution rates and patterns across sites.
Fig. 5: Heterogeneities across time or lineages.
Fig. 6: Homogeneous partition and mixture models.
Fig. 7: Gene-tree–species-tree incongruence.

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Acknowledgements

The authors thank members of the Z. Yang and M. Telford laboratories as well as the three reviewers for valuable feedback on previous versions of the manuscript. The writing of this Review was supported by BBSRC grant reference BB/R016240/1.

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  1. Centre for Life’s Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK

    Paschalia Kapli, Ziheng Yang & Maximilian J. Telford

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K.P., Z.Y. and M.J.T. contributed to all aspects of the article.

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Correspondence to Maximilian J. Telford.

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Glossary

Homologous

When features, including morphological characters and gene loci, are inherited from a common ancestor, for example, a gene in two species originating from a single ancestral gene.

Orthologous

Homologous sequences that have diverged due to speciation events.

Substitution models

Continuous time Markov Chain probabilistic models that describe changes between nucleotides or amino acids over evolutionary time.

Species tree

A phylogenetic tree for a set of species that underlies the gene trees at individual loci.

Paralogy

Homologous sequences that have diverged due to duplication events so that both copies have descended side by side during the history of an organism.

Xenology

Homologous sequences originating from horizontal gene transfer (also known as lateral gene transfer).

Alignment

Insertion of gaps in homologous sequences so that nucleotides or amino acids in the same column are homologous.

Gene tree

The phylogenetic or genealogical tree of sequences at a gene locus or genomic region.

Systematic errors

Errors due to incorrect model assumptions.

Incomplete lineage sorting

Discordance of gene trees from the species tree due to ancestral polymorphism.

Topology

The branching pattern of a phylogenetic tree indicating relationships between taxa.

Long-branch attraction

(LBA). The phenomenon of inferring an incorrect tree in which taxa with long branches are grouped together.

Clades

A clade is a group of taxa on a tree that includes their most recent common ancestor and all its descendants, also known as a monophyletic group.

Stochastic errors

Errors due to the finite length of sequences in the alignment.

Homogeneous-process model

A model that assumes the same substitution rate or process across alignment sites, taxa and time.

Compositional homogeneity

Homogeneity in nucleotide or amino acid frequencies across lineages of a phylogeny.

Mixture models

Models that assume different substitution rates or processes across sites of the alignment.

Profile mixture models

Models that assume multiple sets of state frequencies for sites (for example, CAT, C10–C60).

Coalescence

The process of lineage joining when one traces the history of a sample of sequences backwards in time.

Genetic drift

The process of random changes in allele frequencies over generations due to the stochastic nature of reproduction.

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Kapli, P., Yang, Z. & Telford, M.J. Phylogenetic tree building in the genomic age. Nat Rev Genet 21, 428–444 (2020). https://doi.org/10.1038/s41576-020-0233-0

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