Current Approaches to Phylogenomic Reconstruction

Baurain, Denis; Piégay, Hervé

doi:10.1002/9780470570418.ch2

Cited by 5 publications

(5 citation statements)

References 160 publications

(215 reference statements)

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“…The variability in robustness across the tree (e.g., Figure 2) underscores the importance of clean phylogenomic datasets: whereas large amounts of phylogenetic signal usually drown out any non-phylogenetic signal, for nodes characterized by a scarce phylogenetic signal, even small amounts of non-phylogenetic signal may dominate and eventually yield incorrect results [10].…”

Section: Issues At the Level Of Sequence Alignmentsmentioning

confidence: 99%

“…Inferring phylogenies in difficult cases is akin to finding a needle (phylogenetic signal) in a haystack. Under the oversimplified assumption of an absence of non-phylogenetic signal, one can compute that the resolving power would increase from approximately 15 million years when using small subunit ribosomal RNA alone to less than 1 million years when using more than 50 genes [10] . At such levels of resolution, incomplete lineage sorting (i.e., the retention of ancestral polymorphisms over successive speciation events) should be taken into account as a potential source of phylogenetic error [11] .…”

Section: Hurdles To Phylogenomicsmentioning

confidence: 99%

“…In summary, analyzing the revised alignments from Schierwater et al [4] and Dunn et al [2] with their original taxon sampling and inference methods is sufficient to eliminate all significant incongruences among the three recent phylogenomic studies ( Figure 1 ). The variability in robustness across the tree (e.g., Figure 2 ) underscores the importance of clean phylogenomic datasets: whereas large amounts of phylogenetic signal usually drown out any non-phylogenetic signal, for nodes characterized by a scarce phylogenetic signal, even small amounts of non-phylogenetic signal may dominate and eventually yield incorrect results [10] .…”

Section: Issues At the Level Of Sequence Alignmentsmentioning

confidence: 99%

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Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough

et al. 2011

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Section: Issues At the Level Of Sequence Alignmentsmentioning

confidence: 99%

Section: Hurdles To Phylogenomicsmentioning

confidence: 99%

Section: Issues At the Level Of Sequence Alignmentsmentioning

confidence: 99%

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Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough

et al. 2011

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“…In addition, poor taxon sampling can often contribute to high branch support values (e.g. via resampling) or Bayesian posterior probabilities, a situation that can lead to misinterpretations in downstream applications (Baurain and Philippe, 2010; Philippe et al., 2011). Thus, simply taking branch support at face value on a phylogenomic tree can be dangerous; initial interpretation of support should be followed by a deeper investigation of phylogenetic signal.…”

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confidence: 99%

Plastid genomes and deep relationships among the commelinid monocot angiosperms

et al. 2012

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The commelinid monocots comprise the orders Arecales (A), Commelinales (C), Poales sensu Angiosperm Phylogeny Group III (APGIII) (P), Zingiberales (Z), plus the unplaced family Dasypogonaceae (D), collectively containing numerous economically and ecologically important species and encompassing enormous morphological diversity. Commelinids are supported as monophyletic based on anatomy and molecular data; however, relationships among major commelinid groupings conflict among previous studies, representing a long-standing problem in monocot systematics, with major implications for interpretations of character evolution. In more recent analyses, with whole-plastome sampling largely focused on Poales, areas of conflict remain, suggesting the need for closer investigation of relationships and support. Here, we increased sampling of plastomes among non-Poalean commelinid orders to investigate deep nodal support. Analysis of 83 plastid genes recovered relationships as ((A, D) (ZC, P)) with robust support, regardless of reconstruction method (parsimony ⁄ likelihood). However, conflict among genes was evident when grouped by genomic region. Cumulative analyses of genes ranked by decreasing numbers of informative characters indicated continued fluctuation in support, even as small genes were added to a nearly complete matrix, contrary to the expected pattern of stabilization in support. Topology tests among major commelinid groups suggested that the data were not powerful enough to reject all alternatives. This study provides clues to the limits of the plastid genome for resolving deep relationships among the commelinid monocots.

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“…In the Quest for Orthologs Benchmark 14 , the community benchmark for orthology inference, OMA Groups are consistently the most specific inference, although lacking in recall. As potentially missing genes are less detrimental to phylogenetic determination than false predictions are 24 , this is an appropriate choice of orthology inference method for this tutorial. Several phylogenies have already been published using OMA standalone or data from the OMA Browser, including those for archaea, sharks, spiders, worms, and insects, among others 25 – 29 .…”

Section: Discussionmentioning

confidence: 99%

How to build phylogenetic species trees with OMA

et al. 2022

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Knowledge of species phylogeny is critical to many fields of biology. In an era of genome data availability, the most common way to make a phylogenetic species tree is by using multiple protein-coding genes, conserved in multiple species. This methodology is composed of several steps: orthology inference, multiple sequence alignment and inference of the phylogeny with dedicated tools. This can be a difficult task, and orthology inference, in particular, is usually computationally intensive and error prone if done ad hoc. This tutorial provides protocols to make use of OMA Orthologous Groups, a set of genes all orthologous to each other, to infer a phylogenetic species tree. It is designed to be user-friendly and computationally inexpensive, by providing two options: (1) Using only precomputed groups with species available on the OMA Browser, or (2) Computing orthologs using OMA Standalone for additional species, with the option of using precomputed orthology relations for those present in OMA. A protocol for downstream analyses is provided as well, including creating a supermatrix, tree inference, and visualization. All protocols use publicly available software, and we provide scripts and code snippets to facilitate data handling. The protocols are accompanied with practical examples.

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Current Approaches to Phylogenomic Reconstruction

Cited by 5 publications

References 160 publications

Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough

Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough

Plastid genomes and deep relationships among the commelinid monocot angiosperms

How to build phylogenetic species trees with OMA

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