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As more complete genomes are sequenced, phylogenetic analysis is entering a new era - that of phylogenomics. One branch of this expanding field aims to reconstruct the evolutionary history of organisms on the basis of the analysis of their genomes. Recent studies have demonstrated the power of this approach, which has the potential to provide answers to(More)
Until recently, molecular phylogenies based on a single or few orthologous genes often yielded contradictory results. Using multiple genes in a large concatenation was proposed to end these incongruences. Here we show that single-gene phylogenies often produce incongruences, albeit ones lacking statistically significant support. By contrast, the use of(More)
Tunicates or urochordates (appendicularians, salps and sea squirts), cephalochordates (lancelets) and vertebrates (including lamprey and hagfish) constitute the three extant groups of chordate animals. Traditionally, cephalochordates are considered as the closest living relatives of vertebrates, with tunicates representing the earliest chordate lineage.(More)
Gastropoda Hydrozoa Amoebozoa Ascomycota Basidiomycota Choanoflagellata Trichoplax_adhaerens Mammalia Calcarea Priapulida Annelida Hexapoda Cubozoa Excavata Ciliophora Echinodermata Demospongiae Hexactinellida Anthozoa 0.1 Amoebozoa Basidiomycota Ascomycota Choanoflagellata Placozoa Anthozoa Ctenophora Calcarea Scyphozoa Demospongiae Hexactinellida Mammalia(More)
Almost a decade ago, a new phylogeny of bilaterian animals was inferred from small-subunit ribosomal RNA (rRNA) that claimed the monophyly of two major groups of protostome animals: Ecdysozoa (e.g., arthropods, nematodes, onychophorans, and tardigrades) and Lophotrochozoa (e.g., annelids, molluscs, platyhelminths, brachiopods, and rotifers). However, it(More)
Between 1 and 1.5 billion years ago, eukaryotic organisms acquired the ability to convert light into chemical energy through endosymbiosis with a Cyanobacterium (e.g.,). This event gave rise to "primary" plastids, which are present in green plants, red algae, and glaucophytes ("Plantae" sensu Cavalier-Smith). The widely accepted view that primary plastids(More)
Thanks to the large amount of signal contained in genome-wide sequence alignments, phylogenomic analyses are converging towards highly supported trees. However, high statistical support does not imply that the tree is accurate. Systematic errors, such as the Long Branch Attraction (LBA) artefact, can be misleading, in particular when the taxon sampling is(More)
Genome-scale data sets result in an enhanced resolution of the phylogenetic inference by reducing stochastic errors. However, there is also an increase of systematic errors due to model violations, which can lead to erroneous phylogenies. Here, we explore the impact of systematic errors on the resolution of the eukaryotic phylogeny using a data set of 143(More)
For many genes, ray-finned fish (Actinopterygii) have two paralogous copies, where only one ortholog is present in tetrapods. The discovery of an additional, almost-complete set of Hox clusters in teleosts (zebrafish, pufferfish, medaka, and cichlid) but not in basal actinopterygian lineages (Polypterus) led to the formulation of the fish-specific genome(More)
More than 15 years ago, on the basis of phylogenetic analyses of a handful of anciently duplicated genes and of rRNA, Carl Woese proposed both a eubacterial rooting of the Tree of Life and a stepwise evolution of the eukaryotic cell. An important part of Woese's paradigm was the assumption that the so-called Archezoa were considered to be genuinely(More)