Genome-wide interrogation advances resolution of recalcitrant groups in the tree of life

@article{Arcila2017GenomewideIA,
  title={Genome-wide interrogation advances resolution of recalcitrant groups in the tree of life},
  author={Dahiana Arcila and Guillermo Ort{\'i} and Richard P. Vari and Jonathan W. Armbruster and Melanie L J Stiassny and Kyung Dae Ko and Mark Henry Sabaj and John G. Lundberg and Liam J. Revell and Ricardo Betancur-R},
  journal={Nature Ecology \&Evolution},
  year={2017},
  volume={1}
}
Much progress has been achieved in disentangling evolutionary relationships among species in the tree of life, but some taxonomic groups remain difficult to resolve despite increasing availability of genome-scale data sets. Here we present a practical approach to studying ancient divergences in the face of high levels of conflict, based on explicit gene genealogy interrogation (GGI). We show its efficacy in resolving the controversial relationships within the largest freshwater fish radiation… 
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173 Citations

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References

SHOWING 1-10 OF 82 REFERENCES

Genome-scale approaches to resolving incongruence in molecular phylogenies

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.

Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model

It is demonstrated that the incongruence introduced by concatenation methods is a major cause of long-standing uncertainty in the phylogeny of eutherian mammals, and the same may apply to other clades and the analyses suggest that such incONGruence can be resolved using phylogenomic data and coalescent methods that deal explicitly with gene tree heterogeneity.

Phylogenomic interrogation of arachnida reveals systemic conflicts in phylogenetic signal.

It is shown that phylogenetic signal for the monophyly of Arachnida is restricted to the 500 slowest-evolving genes in the data set, and that outgroup selection without regard for branch length distribution exacerbates long-branch attraction artifacts and does not mitigate gene-tree discordance, regardless of high gene representation for outgroups that are model organisms.

A practical approach to phylogenomics: the phylogeny of ray-finned fish (Actinopterygii) as a case study

A practical approach that systematically compares whole genome sequences to identify single-copy nuclear gene markers for inferring phylogeny is presented and is an improvement over traditional approaches because it uses genomic information and automates the process to identify large numbers of candidate makers.

Whole-genome analyses resolve early branches in the tree of life of modern birds

A genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves recovered a highly resolved tree that confirms previously controversial sister or close relationships and identifies the first divergence in Neoaves, two groups the authors named Passerea and Columbea.

Irrational exuberance for resolved species trees

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.

Less is more in mammalian phylogenomics: AT-rich genes minimize tree conflicts and unravel the root of placental mammals.

It is argued that the GC content-because it is a reliable indicator of the long-term recombination rate-is an informative criterion that could help in identifying the most reliable molecular markers for species tree inference.

Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough

Three recent large-scale phylogenomics studies, which deal with the early diversification of animals, produced highly incongruent findings despite the use of considerable sequence data, suggesting that merely adding more sequences is not enough to resolve the inconsistencies.

The gene tree delusion.

Phylogenetic analysis at deep timescales: unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum.

...