Contentious relationships in phylogenomic studies can be driven by a handful of genes

@article{Shen2017ContentiousRI,
  title={Contentious relationships in phylogenomic studies can be driven by a handful of genes},
  author={Xing-Xing Shen and C. T. Hittinger and A. Rokas},
  journal={Nature ecology \& evolution},
  year={2017},
  volume={1},
  pages={126 - 126}
}
Phylogenomic studies have resolved countless branches of the tree of life, but remain strongly contradictory on certain, contentious relationships. Here, we use a maximum likelihood framework to quantify the distribution of phylogenetic signal among genes and sites for 17 contentious branches and 6 well-established control branches in plant, animal and fungal phylogenomic data matrices. We find that resolution in some of these 17 branches rests on a single gene or a few sites, and that removal… Expand
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Phylogenomics, the use of large datasets to examine phylogeny, has revolutionized the study of evolutionary relationships. However, genome-scale data have not been able to resolve all relationshipsExpand
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References

SHOWING 1-10 OF 63 REFERENCES
Addressing Inter-Gene Heterogeneity in Maximum Likelihood Phylogenomic Analysis: Yeasts Revisited
TLDR
This work has investigated the use of appropriate evolutionary models to address inter-gene heterogeneities and the scalability and validity of supermatrix analysis as the phylogenetic problem becomes more difficult and the number of genes analysed approaches truly phylogenomic dimensions. Expand
Assessing the root of bilaterian animals with scalable phylogenomic methods
  • A. Hejnol, M. Obst, +14 authors C. Dunn
  • Biology, Medicine
  • Proceedings of the Royal Society B: Biological Sciences
  • 2009
TLDR
New sequence data and methods strongly uphold previous suggestions that Acoelomorpha is sister clade to all other bilaterian animals, find diminishing evidence for the placement of the enigmatic Xenoturbella within Deuterostomia, and place Cycliophora with Entoprocta and EctoproCTa. Expand
Broad phylogenomic sampling improves resolution of the animal tree of life
TLDR
This data reinforce several previously identified clades that split deeply in the animal tree, unambiguously resolve multiple long-standing issues for which there was strong conflicting support in earlier studies with less data, and provide molecular support for the monophyly of molluscs, a group long recognized by morphologists. Expand
Genome-scale approaches to resolving incongruence in molecular phylogenies
TLDR
The results suggest that data sets consisting of single or a small number of concatenated genes have a significant probability of supporting conflicting topologies, and have important implications for resolving branches of the tree of life. Expand
Selecting Question-Specific Genes to Reduce Incongruence in Phylogenomics: A Case Study of Jawed Vertebrate Backbone Phylogeny.
TLDR
This study highlights the importance of gene selection in phylogenomic analyses, suggesting that simply using a large amount of data cannot guarantee correct results, and constructing question-specific data sets may be more powerful for resolving problematic nodes. Expand
Deep metazoan phylogeny: when different genes tell different stories.
TLDR
The accuracy of phylogenetic inference may be substantially improved by selecting genes that evolve slowly across the Metazoa and applying more realistic substitution models, as well as modifying gene sampling and the taxonomic composition of the outgroup. Expand
Irrational exuberance for resolved species trees
TLDR
Several ways in which the possible presence of hemiplasy can be diagnosed are offered, and multiple approaches to dealing with the problems presented by underlying gene tree discordance when carrying out character mapping are discussed. Expand
The gene tree delusion.
TLDR
It is argued that it is illogical to apply coalescence methods to complete protein-coding sequences and distorted true gene tree stoichiometry that is required for accurate species tree inference, and contradict the central rationale for applying coalescent methods to difficult phylogenetic problems. Expand
Improved Phylogenomic Taxon Sampling Noticeably Affects Nonbilaterian Relationships
TLDR
This work recovers monophyletic Porifera as the sister group to all other Metazoa and suggests that the basal position of the fast-evolving Ctenophora proposed by Dunn et al. was due to LBA and that broad taxon sampling is of fundamental importance to metazoan phylogenomic analyses. Expand
Extracting phylogenetic signal and accounting for bias in whole-genome data sets supports the Ctenophora as sister to remaining Metazoa
TLDR
The phylogeny supports the still-controversial position of ctenophores as sister group to all other metazoans and provides a workflow and computational tools for minimizing systematic bias in genome-based phylogenetic analyses. Expand
...
1
2
3
4
5
...