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Phylogenomics: Constrained gene tree inference
Nature Ecology & Evolution, 2017Data from many genes across the genome are now being routinely used in the hope of reconstructing challenging parts of the tree of life, and a new method provides a practical way of resolving the phylogenetic trees suggested by different genes.
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Phylogenetics and Phylogenomics of the Fungal Tree of Life
2014Phylogenetic trees, once restricted to studies on systematics, are now used throughout all disciplines of fungal biology and provide the evolutionary context for a broad suite of studies that include understanding the evolution of major life forms, description of complex biotic communities, and predictive experimental biology.
Joseph W. Spatafora, Barbara Robbertse
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Phylogenomic interrogation resolves the backbone of the Pseudoscorpiones tree of life
Molecular Phylogenetics and Evolution, 2019Pseudoscorpiones, with nearly 3700 described species, are an ancient and globally distributed group of arachnids with a fossil record dating back to the Middle Devonian. Previous attempts to reconstruct their phylogenetic history have used morphology or a few amplicons, mostly of rRNAs and mitochondrial genes, which have not been able to completely ...
Ligia R, Benavides +3 more
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Broad phylogenomic sampling improves resolution of the animal tree of life
Nature, 2008Long-held ideas regarding the evolutionary relationships among animals have recently been upended by sometimes controversial hypotheses based largely on insights from molecular data. These new hypotheses include a clade of moulting animals (Ecdysozoa) and the close relationship of the lophophorates to molluscs and annelids (Lophotrochozoa).
Dunn, Casey W. +17 more
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An updated phylogenomic tree of Coleoptera (beetles)
Resolving deep phylogenetic relationships within Coleoptera remains challenging despite advances in phylogenomics. We present an updated phylogenomic dataset integrating available assemblies, reprocessed Sequence Read Archive (SRA) data, and newly generated genomes.Hehao Ye +4 more
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Phylogenomics resolves a congruent noctuoid Tree of Life
Zoological Journal of the Linnean SocietyAbstract Noctuoidea, the most diverse and economically significant superfamily of Lepidoptera (butterflies and moths), remain phylogenetically challenging due to the superfamily’s rapid radiation during the Late Cretaceous to Palaeogene.
Yehao Wang +2 more
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RETRACTED: Integrative phylogenomics positions sponges at the root of the animal tree
ScienceDetermining whether sponges or ctenophores root the animal tree has important implications for understanding early animal evolution. Here, we examined support for these competing hypotheses by constructing large and highly informative data matrices containing sequences from sponges, ctenophores, cnidarians, bilaterians, and diverse animal relatives ...
Jacob L. Steenwyk, Nicole King
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The Influence of the Number of Tree Searches on Maximum Likelihood Inference in Phylogenomics
Systematic BiologyAbstract Maximum likelihood (ML) phylogenetic inference is widely used in phylogenomics. As heuristic searches most likely find suboptimal trees, it is recommended to conduct multiple (e.g., 10) tree searches in phylogenetic analyses. However, beyond its positive role, how and to what extent multiple tree searches aid ML phylogenetic ...
Chao Liu +9 more
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