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

  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},
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… 

Analysis of Phylogenomic Tree Space Resolves Relationships Among Marsupial Families

The methods provide an intuitive framework for improving the accuracy and precision of phylogenetic inference and molecular dating using genome‐scale data and show that incomplete lineage sorting can explain the division of loci into the two tree‐topology clusters, as found in the phylogenomic analysis of marsupials.

Whole-Genome Phylogenetic Reconstruction as a Powerful Tool to Reveal Homoplasy and Ancient Rapid Radiation in Waterflea Evolution

This work reconstructs the deep-rooted relationships of one of the oldest living arthropod clades, the branchiopod crustaceans, using a kaleidoscopic approach and supports the monophyly of the Cladocera and reveals remarkable homoplasy in their body plans.

Congruence and conflict in the higher-level phylogenetics of squamate reptiles: an expanded phylogenomic perspective.

It is found that rate and compositional heterogeneity drives discordance between gene trees and species tree and that conflicting loci rarely overlap across contentious nodes, and this locus-by-locus and node- by-node approach can be used to build consensus on which topological resolutions remain uncertain in phylogenomic studies of other contentious groups.

Expanded Taxonomic Sampling Coupled with Gene Genealogy Interrogation Provides Unambiguous Resolution for the Evolutionary Root of Angiosperms

A transcriptomic data set of 310 genes previously assembled is expanded to include data from seven species comprising two major lineages of flowering plants that were poorly represented or missing from the original study, and all multilocus analyses conducted provide overwhelming support for Amborella-sister topology regardless of data type.

From cacti to carnivores: Improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Caryophyllales.

It is demonstrated that phylogenomic data can provide unparalleled insight into the evolutionary history of Caryophyllales and a method for overcoming computational challenges associated with homolog clustering in large data sets is discussed.

Detecting introgression despite phylogenetic uncertainty: The case of the South American siskins.

This work inferred multiple introgression events within the Andean radiation of Spinus siskins in a way that was robust to phylogenetic uncertainty in the species tree, consistent with an emerging paradigm, thatintrogression tends to accompany the early stages of diversification.

Comparing Ultraconserved Elements and Exons for Phylogenomic Analyses of Middle American Cichlids: When Data Agree to Disagree

The causes of discordance between phylogenetic hypotheses obtained using a novel dataset of ultraconserved elements and a recently published exon dataset of the cichlid tribe Heroini are explored, demonstrating the robustness of phylogenomic methods to accommodate genomic markers with different biological and phylogenetic properties.

Ultra-Conserved Elements and morphology reciprocally illuminate conflicting phylogenetic hypotheses in Chalcididae (Hymenoptera, Chalcidoidea)

This joint analysis reveals that UCEs enable attainment of resolution between ancestry and convergent /divergent evolution when morphology is not informative enough, but also shows that a systematic exploration of bias with different analytical methods and a careful analysis of morphological features is required to prevent publication of artefactual results.

Testing the utility of alternative metrics of branch support to address the ancient evolutionary radiation of tunas, stromateoids, and allies (Teleostei: Pelagiaria).

The results demonstrate the limitations of employing current metrics of branch support and species-tree estimation when assessing the confidence of ancient evolutionary radiations and emphasize the necessity to embrace alternative measurements to explore phylogenetic uncertainty and discordance in phylogenomic datasets.



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.