Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants

Stephen A. Smith, Michael J. Moore, Joseph W. Brown, Ya Yang

Research output: Contribution to journalArticlepeer-review

158 Scopus citations


Background: The use of transcriptomic and genomic datasets for phylogenetic reconstruction has become increasingly common as researchers attempt to resolve recalcitrant nodes with increasing amounts of data. The large size and complexity of these datasets introduce significant phylogenetic noise and conflict into subsequent analyses. The sources of conflict may include hybridization, incomplete lineage sorting, or horizontal gene transfer, and may vary across the phylogeny. For phylogenetic analysis, this noise and conflict has been accommodated in one of several ways: by binning gene regions into subsets to isolate consistent phylogenetic signal; by using gene-tree methods for reconstruction, where conflict is presumed to be explained by incomplete lineage sorting (ILS); or through concatenation, where noise is presumed to be the dominant source of conflict. The results provided herein emphasize that analysis of individual homologous gene regions can greatly improve our understanding of the underlying conflict within these datasets. Results: Here we examined two published transcriptomic datasets, the angiosperm group Caryophyllales and the aculeate Hymenoptera, for the presence of conflict, concordance, and gene duplications in individual homologs across the phylogeny. We found significant conflict throughout the phylogeny in both datasets and in particular along the backbone. While some nodes in each phylogeny showed patterns of conflict similar to what might be expected with ILS alone, the backbone nodes also exhibited low levels of phylogenetic signal. In addition, certain nodes, especially in the Caryophyllales, had highly elevated levels of strongly supported conflict that cannot be explained by ILS alone. Conclusion: This study demonstrates that phylogenetic signal is highly variable in phylogenomic data sampled across related species and poses challenges when conducting species tree analyses on large genomic and transcriptomic datasets. Further insight into the conflict and processes underlying these complex datasets is necessary to improve and develop adequate models for sequence analysis and downstream applications. To aid this effort, we developed the open source software phyparts (, which calculates unique, conflicting, and concordant bipartitions, maps gene duplications, and outputs summary statistics such as internode certainy (ICA) scores and node-specific counts of gene duplications.

Original languageEnglish (US)
Article number150
JournalBMC evolutionary biology
Issue number1
StatePublished - Aug 5 2015

Bibliographical note

Funding Information:
We would like to thank Cody Hinchliff„ Caroline Parins-Fukuchi, and Joseph Walker for helpful discussions. Support came from a National Science Foundation award (DEB 1352907 and DEB 1354048) to SAS and MJM, and a MCubed initiative award to SAS.

Publisher Copyright:
© 2015 Smith et al.


  • Gene duplication
  • Gene tree conflict
  • Incomplete lineage sorting
  • Phylogenomics
  • Transcriptome


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