Resolution of Phylogenetic Conflict in Large Data Sets by Increased Taxon Sampling

Hedtke, Shannon M.; Townsend, Ted M.; Hillis, David M.

doi:10.1080/10635150600697358

Cited by 266 publications

(222 citation statements)

References 31 publications

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“…Studies have shown that taxon sampling is an important component for accurately estimating phylogenies (31,32). For example, a recent study in yeasts shows that increasing taxon sampling can resolve phylogenetic relationships that appear to be controversial using fewer taxa (33). The results of the present study suggest that, although taxon sampling remains important for phylogenetic analysis, it is also critical to gather sufficient numbers of loci to obtain a reliable phylogeny for eutherian mammals and other clades in the Tree of Life.…”

Section: Discussionmentioning

confidence: 60%

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

Song

Liu

Edwards

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

432

774

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The reconstruction of the Tree of Life has relied almost entirely on concatenation methods, which do not accommodate gene tree heterogeneity, a property that simulations and theory have identified as a likely cause of incongruent phylogenies. However, this incongruence has not yet been demonstrated in empirical studies. Several key relationships among eutherian mammals remain controversial and conflicting among previous studies, including the root of eutherian tree and the relationships within Euarchontoglires and Laurasiatheria. Both Bayesian and maximum-likelihood analysis of genome-wide data of 447 nuclear genes from 37 species show that concatenation methods indeed yield strong incongruence in the phylogeny of eutherian mammals, as revealed by subsampling analyses of loci and taxa, which produced strongly conflicting topologies. In contrast, the coalescent methods, which accommodate gene tree heterogeneity, yield a phylogeny that is robust to variable gene and taxon sampling and is congruent with geographic data. The data also demonstrate that incomplete lineage sorting, a major source of gene tree heterogeneity, is relevant to deep-level phylogenies, such as those among eutherian mammals. Our results firmly place the eutherian root between Atlantogenata and Boreoeutheria and support ungulate polyphyly and a sister-group relationship between Scandentia and Primates. This study demonstrates 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. Our analyses suggest that such incongruence can be resolved using phylogenomic data and coalescent methods that deal explicitly with gene tree heterogeneity.

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Section: Discussionmentioning

confidence: 60%

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

Song

Liu

Edwards

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

432

774

View full text Add to dashboard Cite

show abstract

“…The results of single-lineage analyses are also difficult to compare with the full analysis, because there is no principled statistical framework within which to evaluate whether attempting to place DPANN lineages individually ameliorates or aggravates potential phylogenetic artifacts, such as LBA. Better taxonomic sampling has been shown to improve phylogenetic inference (51)(52)(53), and there is no posterior support for these alternative placements from any of our analyses in which DPANN monophyly was tested directly, including our supertree analysis and the series of supermatrix analyses performed with methods commonly used to ameliorate LBA (23, 43, 54) (SI Appendix, Figs. S2-S5).…”

Section: Resultsmentioning

confidence: 99%

Integrative modeling of gene and genome evolution roots the archaeal tree of life

Williams

Szöllősi

Spang

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

216

212

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A root for the archaeal tree is essential for reconstructing the metabolism and ecology of early cells and for testing hypotheses that propose that the eukaryotic nuclear lineage originated from within the Archaea; however, published studies based on outgroup rooting disagree regarding the position of the archaeal root. Here we constructed a consensus unrooted archaeal topology using protein concatenation and a multigene supertree method based on 3,242 single gene trees, and then rooted this tree using a recently developed model of genome evolution. This model uses evidence from gene duplications, horizontal transfers, and gene losses contained in 31,236 archaeal gene families to identify the most likely root for the tree. Our analyses support the monophyly of DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, Nanohaloarchaea), a recently discovered cosmopolitan and genetically diverse lineage, and, in contrast to previous work, place the tree root between DPANN and all other Archaea. The sister group to DPANN comprises the Euryarchaeota and the TACK Archaea, including Lokiarchaeum, which our analyses suggest are monophyletic sister lineages. Metabolic reconstructions on the rooted tree suggest that early Archaea were anaerobes that may have had the ability to reduce CO 2 to acetate via the Wood-Ljungdahl pathway. In contrast to proposals suggesting that genome reduction has been the predominant mode of archaeal evolution, our analyses infer a relatively small-genomed archaeal ancestor that subsequently increased in complexity via gene duplication and horizontal gene transfer.evolution | phylogenetics | Archaea

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“…The Hillis group responded Pollock et al 2002;Hillis et al 2003), which led Rosenberg and Kumar (2003) to somewhat moderating their position. The debate on taxon sampling has continued to the present day, with additional simulations (Poe 2003;DeBry 2005;Hedtke et al 2006), review articles (Heath et al 2008a), and studies to understand the impact of taxon sampling on the inference of macroevolutionary processes (Heath et al 2008). The simulation literature in this area is considered important enough to even have a paper (Rannala et al 1998) about methodology for taxon-sampling simulations.…”

Section: Introductionmentioning

confidence: 99%

Polyhedral Geometry of Phylogenetic Rogue Taxa

Cueto

Matsen

2010

Bull Math Biol

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It is well known among phylogeneticists that adding an extra taxon (e.g. species) to a data set can alter the structure of the optimal phylogenetic tree in surprising ways. However, little is known about this "rogue taxon" effect. In this paper we characterize the behavior of balanced minimum evolution (BME) phylogenetics on data sets of this type using tools from polyhedral geometry. First we show that for any distance matrix there exist distances to a "rogue taxon" such that the BME-optimal tree for the data set with the new taxon does not contain any nontrivial splits (bipartitions) of the optimal tree for the original data. Second, we prove a theorem which restricts the topology of BME-optimal trees for data sets of this type, thus showing that a rogue taxon cannot have an arbitrary effect on the optimal tree. Third, we computationally construct polyhedral cones that give complete answers for BME rogue taxon behavior when our original data fits a tree on four, five, and six taxa. We use these cones to derive sufficient conditions for rogue taxon behavior for four taxa, and to understand the frequency of the rogue taxon effect via simulation.

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Resolution of Phylogenetic Conflict in Large Data Sets by Increased Taxon Sampling

Cited by 266 publications

References 31 publications

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

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

Integrative modeling of gene and genome evolution roots the archaeal tree of life

Polyhedral Geometry of Phylogenetic Rogue Taxa

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