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

Arcila, Dahiana; Ortı́, Guillermo; Vari, Richard P.; Armbruster, Jonathan W.; Stiassny, Melanie L. J.; Ko, Kyung Dae; Sabaj, Mark H.; Lundberg, John G.; Revell, Liam J.; Betancur‐R, Ricardo

doi:10.1038/s41559-016-0020

Cited by 224 publications

(291 citation statements)

References 71 publications

Supporting

Mentioning

270

Contrasting

Unclassified

Order By: Relevance

“…Since then, more than a dozen conflicting phylogenomic analyses have offered support for the ctenophores-sister hypothesis [2, 3, 7, 32, 38–40], the sponges-sister hypothesis [34–37, 41, 42] or (much more rarely) neither [43] (Figure 2). …”

Section: Enter the Phylogenomics Eramentioning

confidence: 99%

“…In the case of the metazoan controversy, analyses employing site-homogeneous models of protein evolution with partitioning (a different model for each gene) tend to recover ctenophores as the sister branch ([2, 3, 7, 32, 33, 38–40], but see [35, 42]). In contrast, analyses employing site-heterogeneous models (and in particular the CAT model [47]) typically recover sponges as the sister branch ([34–37, 41, 42], but see [38, 40, 48]).…”

Section: Enter the Phylogenomics Eramentioning

confidence: 99%

“…To generate phylogenies, gene or protein sequence alignments can be interrogated to separate phylogenetic signal (sequence changes that reflect the evolutionary relationships among species) from noise. In the post-genomics era, the analysis of hundreds or thousands of genes using powerful models and computational algorithms has dramatically improved the accuracy with which the evolutionary relationships among living organisms can be deduced, but certain key branches have remained recalcitrant and sparked controversy [1–3]. …”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Embracing Uncertainty in Reconstructing Early Animal Evolution

2017

View full text Add to dashboard Cite

The origin of metazoans, one of the major transitions in evolution, remains mysterious. While many key aspects of metazoan origins can be reconstructed by comparing living organisms within a robust phylogenetic framework, uncertainty regarding the evolutionary relationships among sponges, ctenophores and the remainder of metazoan diversity has proven to be a major barrier. Comparative morphology and some phylogenomic analyses support the view that sponges represent the sister lineage to the rest of the metazoans, while other competing phylogenomic analyses strongly support ctenophores, a phylum of carnivorous, gelatinous marine organisms, as the sister lineage. Here, we explore why different phylogenomic studies yield different answers and discuss the implications of the two alternative hypotheses for understanding the origin of metazoan multicellularity. Reconstruction of ancient evolutionary radiations, like the one that gave rise to metazoans, is devilishly difficult and will likely require broader sampling of sponge and ctenophore genomes, improved analytical strategies, and critical analyses of the phylogenetic distribution and molecular mechanisms underlying apparently conserved traits. Rather than staking out positions in favor of the ctenophore-sister or the sponge-sister hypothesis, we submit that research programs aimed at understanding the biology of the first metazoans should embrace the uncertainty surrounding early metazoan evolution in their experimental designs.

show abstract

Section: Enter the Phylogenomics Eramentioning

confidence: 99%

Section: Enter the Phylogenomics Eramentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Embracing Uncertainty in Reconstructing Early Animal Evolution

2017

View full text Add to dashboard Cite

show abstract

“…For example, statistical procedures for identifying sets of loci Lith similar tree properties that might be used for phylogenetic inference, but Lhich are agnostic Lith respect to the biological processes, have been proposed (e.g., Arcila et al, 2017;de Vienne et al, 2012;Fong et al, 2012;Weyenberg et al, 2014). This contrasts Lith our approach in Lhich subsets of data for phylogenetic inference are identified Lith respect to the biological processes generating the discord.…”

Section: Introductionmentioning

confidence: 95%

“…Coalescent theory makes it possible to effectively model ILS and construct a species tree conditioned on a distribution of gene trees in empirical data (Ane et al, 2007;KnoLles, 2009;KnoLles and Kubatko, 2011;KnoLles et al, 2012;Liu et al, 2009;Mirarab et al, 2014). HoLever, ILS may not be the primary contributor to patterns of gene tree discord in phylogenomics (e.g., Arcila et al, 2017). There are many other factors related to evolutionary history (e.g., lateral gene transfer [LGT], hybridization [H], gene duplication and loss [DL];Maddison (1997)) and molecular evolution (e.g., noise/lack of signal in the sequences, and nonstationarity in base composition) that can contribute to gene tree discord.…”

Section: Introductionmentioning

confidence: 99%

Cause of gene tree discord? Distinguishing incomplete lineage sorting and lateral gene transfer in phylogenetics

Huang

Sukumaran

Smith

et al. 2017

Preprint

View full text Add to dashboard Cite

Despite recent efforts that have produced data sets with hundreds and thousands of gene regions to resolve regions of the tree of life, recalcitrant nodes persist and disagreement among genes as well as disagreement between individual gene trees and species trees are common. There are a number of evolutionary processes that contribute to these conflicts between gene trees and species trees, including deep coalescence (lineage sorting), horizontal gene transfer or hybridization, etc. While for some of these processes, we have very powerful and sophisticated models that uses the conflict in the gene trees as information that contributes materially to correctly inferring the species tree, such as the multispecies coalescent (MSC). However, usage of these models require a priori recognition of relevant processes, which is often unknown for empirical dataset. Here we propose a new perspective to not only identify the cause of discord among gene trees, but also use it to classify loci by the underlying cause of discord to identify subsets of loci for analysis with the goal of improving phylogenetic accuracy. This approach differs fundamentally from all other criteria used for making decisions about which loci to include in a phylogenetic analysis. In particular, the choice of loci in this framework is based on identifying those that reflect descent from a common ancestor (as opposed to other processes), and thereby can minimize problems with model misspecification. We present preliminary results that demonstrate the potential of this framework in distinguishing the lateral gene transfer (LGT) from incomplete lineage sorting (ILS) process, as implemented in a new software package CLASSIPHY, while also highlighting areas for further development and testing. We discussed why such methods (i) are critical to improving phylogenetic accuracy with the increased complexity of genomic/transcriptomic datasets, and that (ii) characterizing patterns of discordance and the contribution of different processes to this discordance is itself of interest for generating hypotheses about the role of lateral gene transfer, gene duplication, and incomplete lineage sorting during the divergence of different taxa. correctly inferring the species tree, such as the multispecies coalescent (MSC). HoLever, usage of these models require a priori recognition of relevant processes, Lhich is often unknoLn for empirical dataset. Here Le propose a neL perspective to not only identify the cause of discord among gene trees, but also use it to classify loci by the underlying cause of discord to identify subsets of loci for analysis Lith the goal of improving phylogenetic accuracy. This approach differs fundamentally from all other criteria used for making decisions about Lhich loci to include in a phylogenetic analysis. In particular, the choice of loci in this frameLork is based on identifying those that reflect descent from a common ancestor (as opposed to other processes), and thereby can minimize problems Lith model misspecification. We present prel...

show abstract

New prospects in the detection and comparative analysis of hybridization in the tree of life

Folk

Soltis

et al. 2018

American J of Botany

131

108

View full text Add to dashboard Cite

Assessing the relative importance of the various pathways to diversification is a central goal of biodiversity researchers. For plant biologists, and increasingly across the spectrum of biological sciences, among these pathways of interest is hybridization. New methodological developments are moving the field away from questions of whether natural hybridization occurs or hybrids can persist and toward more direct assessments of the long-term impact of hybridization on diversification and genome organization. Advances in theory and new data, especially phylogenomic data, have changed the face of this field, revealing extensive occurrences of hybridization at both shallow and deep levels, but lacking is a synthesis of these advancements. Here we provide an overview of methods that have been proposed for detecting hybridization with molecular data and advocate a time-extended, comparative view of reticulate evolution. In particular, we pose three overarching questions, newly placed within reach, that are critical for advancing our understanding of hybridization pattern and process: (1) How often is introgression biased toward certain genomes and loci, and is this bias selectively neutral? (2) What are the relative rates of formation of hybrid species and introgressants, and how does this compare to their subsequent fates? (3) Has the frequency of hybridization increased under historical periods of greater dynamism in climate and geographic range, such as the Pleistocene?

show abstract

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

Cited by 224 publications

References 71 publications

Embracing Uncertainty in Reconstructing Early Animal Evolution

Embracing Uncertainty in Reconstructing Early Animal Evolution

Cause of gene tree discord? Distinguishing incomplete lineage sorting and lateral gene transfer in phylogenetics

New prospects in the detection and comparative analysis of hybridization in the tree of life

Contact Info

Product

Resources

About