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Hypotheses about the origin of eukaryotic cells are classically framed within the context of a universal 'tree of life' based on conserved core genes. Vigorous ongoing debate about eukaryote origins is based on assertions that the topology of the tree of life depends on the taxa included and the choice and quality of genomic data analysed. Here we have reanalysed the evidence underpinning those claims and apply more data to the question by using supertree and coalescent methods to interrogate >3,000 gene families in archaea and eukaryotes. We find that eukaryotes consistently originate from within the archaea in a two-domains tree when due consideration is given to the fit between model and data. Our analyses support a close relationship between eukaryotes and Asgard archaea and identify the Heimdallarchaeota as the current best candidate for the closest archaeal relatives of the eukaryotic nuclear lineage.
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http://dx.doi.org/10.1038/s41559-019-1040-x | DOI Listing |
Biosystems
January 2025
The Ionian School, Early Evolution of Life Department, Genetic Code and tRNA Origin Laboratory, Via Roma 19, 67030, Alfedena, L'Aquila, Italy. Electronic address:
The length of the deepest branches of the tree of life would tend to support the hypothesis that the distance of the branch that separates the sequences of archaea from those of bacteria, i.e. the interdomain one, is longer than the intradomain ones, i.
View Article and Find Full Text PDFQRB Discov
January 2024
Independent Researcher, Uppsala, Sweden.
The formulation and testing of hypotheses using 'big biology data' often lie at the interface of computational biology and structural biology. The Protein Data Bank (PDB), which was established about 50 years ago, catalogs three-dimensional (3D) shapes of organic macromolecules and showcases a structural view of biology. The comparative analysis of the structures of homologs, particularly of proteins, from different species has significantly improved the in-depth analyses of molecular and cell biological questions.
View Article and Find Full Text PDFJ Affect Disord
June 2024
Department of Clinical and Experimental Medicine, University Hospital of Pisa, Psychiatry Unit 2, Pisa, Italy. Electronic address:
Background: Emotional dysregulation (ED) refers to the inability to manage emotional experiences or expressions hindering goal-oriented behavior. Moderate impairment on at least two domains among temper control, affective lability, and emotional over-reactivity has been proposed to identify ED in adults with attention-deficit/hyperactivity disorder (ADHD). No screening measure designed for use in diverse psychiatric samples exists.
View Article and Find Full Text PDFCurr Biol
December 2023
Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan; Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai 980-8578, Japan. Electronic address:
Temperature sensing is critical for the survival of living organisms. Thermosensitive transient receptor-potential (TRP) cation channels function as thermosensors in mammals. In contrast to animals, land plants lack TRP genes.
View Article and Find Full Text PDFSyst Biol
August 2023
Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, PO Box 22085, ES-46071 Valencia, Spain.
Cophylogeny represents a framework to understand how ecological and evolutionary process influence lineage diversification. The recently developed algorithm Random Tanglegram Partitions provides a directly interpretable statistic to quantify the strength of cophylogenetic signal and incorporates phylogenetic uncertainty into its estimation, and maps onto a tanglegram the contribution to cophylogenetic signal of individual host-symbiont associations. We introduce Rtapas, an R package to perform Random Tanglegram Partitions.
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