The DOI matches its Crossref record; 229 of the 229 references it cites were found in a registry or an index.
Incongruence in the phylogenomics era
Open accessAbstract
Genome-scale data and the development of novel statistical phylogenetic approaches have greatly aided the reconstruction of a broad sketch of the tree of life and resolved many of its branches. However, incongruence — the inference of conflicting evolutionary histories — remains pervasive in phylogenomic data, hampering our ability to reconstruct and interpret the tree of life. Biological factors, such as incomplete lineage sorting, horizontal gene transfer, hybridization, introgression, recombination and convergent molecular evolution, can lead to gene phylogenies that differ from the species tree. In addition, analytical factors, including stochastic, systematic and treatment errors, can drive incongruence. Here, we review these factors, discuss methodological advances to identify and handle incongruence, and highlight avenues for future research. Incongruence occurs when phylogenetic trees show conflicting evolutionary histories such as patterns of branching or relationships among taxa. This Review discusses the biological and analytical factors that lead to incongruence, methodological advances to identify and resolve incongruence, and avenues for future research.
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Revised evolutionary relationships within Brachycera and the early origin of bicoid in flies
Mulhair, P. O., Pennati, A., Herrera-Ubeda, C., & Holland, P. W. H. (2025) · Current Biology · doi:10.1016/j.cub.2025.09.051 · Cited by 2
Metadata
- Authors
- Steenwyk, J. L., Li, Y., Zhou, X., Shen, X.-X., & Rokas, A.
- Venue
- Nature Reviews Genetics
- Published
- 2023-06-27
- Volume
- 24
- Issue
- 12
- Pages
- 834-850
- ISSN
- 1471-0056 (ISSN-L)
- 1471-0064
- OpenAlex
- W4382248980
- Cited by
- 259
- References
- 229
- FWCI
- 6.47
- Type
- journal article
- Language
- en
- Open access
- green
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- Steenwyk, J. L., Li, Y., Zhou, X., Shen, X.-X., & Rokas, A. (2023). Incongruence in the phylogenomics era. Nature Reviews Genetics. https://doi.org/10.1038/s41576-023-00620-x
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