Phylogenetic tree building in the genomic age
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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Partitioning is generally thought to offer an improvement over unpartitioned analyses by accommodating inter-gene evolutionary heterogeneity.
“In phylogenomics, partitioning is generally thought to offer an improvement over unpartitioned analyses by accommodating inter-gene evolutionary heterogeneity38,59.”
From Evidence for sponges as sister to all other animals from partitioned phylogenomics with mixture models and recoding (2021) · cites this paper as [59]
Distinguishing orthologs and paralogs is a fundamental problem in evolutionary and molecular biology and a prerequisite for many genomic analyses.
“Distinguishing orthologs and paralogs is a fundamental problem in evolutionary and molecular biology (1) and a prerequisite for many genomic analyses, including reconstructing phylogenetic trees, predicting gene function, investigating molecular and genome evolution, and discovering differences in genes that underlie phenotypes of the sequenced species (2–6).”
From Integrating gene annotation with orthology inference at scale (2023) · cites this paper as [2]
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“It presents ample information on evolutionary events among organisms [73].”
- Authors
- Kapli, P., Yang, Z., & Telford, M. J.
- Affiliations
- University College London (GB)
- Corresponding author
- Telford, Maximilian J.
- Venue
- Nature Reviews Genetics
- Published
- 2020-05-18
- Volume
- 21
- Issue
- 7
- Pages
- 428-444
- ISSN
- 1471-0056 (ISSN-L)
- 1471-0064
- OpenAlex
- W3025857586
- Cited by
- 533
- References
- 14
- Citations by year
- 2026: 75 · 2025: 101 · 2024: 128 · 2023: 89 · 2022: 71 · 2021: 48 · 2020: 20 · 2013: 1
- FWCI
- 5.55
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Nature Reviews Genetics (publishedVersion)
- PubMed (publishedVersion)
- UCL Discovery (University College London) (submittedVersion)
- Funders
- Biotechnology and Biological Sciences Research Council (BB/R016240/1)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology Studies
- Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Plant Diversity and Evolution
- Keywords
- phylogenetic tree construction, ortholog identification, multiple sequence alignment, substitution models, phylogenetic inference, genomic data, molecular adaptation, gene origin
- MeSH terms
- Animals, Crosses, Genetic, Humans, Models, Genetic, Phylogeny, Genome, Genetic Heterogeneity, Evolution, Molecular, Computational Biology, Genomics, Databases, Genetic
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