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Multigene Phylogeny of the Green Lineage Reveals the Origin and Diversification of Land Plants

2012; Elsevier BV; Volume: 22; Issue: 15 Linguagem: Inglês

10.1016/j.cub.2012.07.021

1879-0445

Cédric Finet, Ruth Timme, Charles F. Delwiche, Ferdinand Marlétaz,

Plant Pathogens and Fungal Diseases

(Current Biology 20, 2217–2222; December 21, 2010) Following the publication of our multigene phylogeny of the green lineage, some studies have proposed a distinct branching pattern among algal relatives of land plants [1Wodniok S. Brinkmann H. Glöckner G. Heidel A.J. Philippe H. Melkonian M. Becker B. Origin of land plants: do conjugating green algae hold the key?.BMC Evol. Biol. 2011; 11: 104Crossref PubMed Scopus (241) Google Scholar, 2Timme R.E. Bachvaroff T.R. Delwiche C.F. Broad phylogenomic sampling and the sister lineage of land plants.PLoS ONE. 2012; 7: e29696Crossref PubMed Scopus (218) Google Scholar]. Most notably, these differences relate to the position of the taxon Coleochaete that we identified as a land plant sister group and the failure to recover the monophyly of Coleochaetales in our study. Recent exchanges of views with Hervé Philippe and colleagues have prompted us to investigate the possible cause of these inconsistencies. In particular, we searched for contaminations that had been identified by Philippe and colleagues ([3Laurin-Lemay S. Brinkmann H. Philippe H. Origin of land plants revisited in the light of sequence contamination and missing data.Curr. Biol. 2012; 22 (this issue): R593-R594Abstract Full Text Full Text PDF PubMed Scopus (93) Google Scholar], this issue of Current Biology). We identified cross-contaminations in two libraries sequenced for our study, corresponding to the species Chaetosphaeridium globosum and to a lesser extent Nitella hyalina. The contamination likely took place during library preparation or sequencing, because the samples were obtained from pure in-house algal cultures, and there is a correlation between time of sample processing at the sequence facility and levels of cross-contamination. It is also noteworthy that the most highly contaminated data set, with as much as 5% exogenous sequence, was from C. globosum, which was the one data set that was amplified prior to the sequencing reactions. C. globosum and N. hyalina had what appear to be erroneous sequences for 28 out of 77 genes, representing 47 out of 5,929 sequences in the data matrix. Unfortunately, the phylogenetic proximity of these taxa and the close similarity of these sequences caused the contaminant sequences to escape our validation protocol. To confirm the validity of our phylogenetic results, we set about evaluating the impact of the erroneous sequences on the reconstructed topology. We reconstructed independent trees with all significant hits (e value 1e−10) for the three concerned libraries and selected bona fide sequences among contaminants using a parsimony rule. We also included Chara data made recently available at the NCBI Sequence Read Archive [1Wodniok S. Brinkmann H. Glöckner G. Heidel A.J. Philippe H. Melkonian M. Becker B. Origin of land plants: do conjugating green algae hold the key?.BMC Evol. Biol. 2011; 11: 104Crossref PubMed Scopus (241) Google Scholar]. We then reassembled corrected ribosomal protein data sets and performed subsequent phylogenetic inference using maximum-likelihood and Bayesian inference. In agreement with the limited extent of the contamination, the tree topology was largely unaffected; however, there was one very interesting rearrangement among the lineages most closely related to embryophytes. In the corrected analyses, the sister taxon to embryophytes is a monophyletic group comprising both Coleochaetales and Zygnematales, although a single branch swap would yield either the same topology seen in our original study (except for the placement of Chaetosphaeridium) or else the topology reported previously [1Wodniok S. Brinkmann H. Glöckner G. Heidel A.J. Philippe H. Melkonian M. Becker B. Origin of land plants: do conjugating green algae hold the key?.BMC Evol. Biol. 2011; 11: 104Crossref PubMed Scopus (241) Google Scholar, 2Timme R.E. Bachvaroff T.R. Delwiche C.F. Broad phylogenomic sampling and the sister lineage of land plants.PLoS ONE. 2012; 7: e29696Crossref PubMed Scopus (218) Google Scholar] (Figure 1). Perhaps the most striking rearrangement is the emergence of a monophyletic Coleochaetales (i.e., Coleochaete and Chaetosphaeridium appear as sister taxa). We hypothesize that the possible introduction of Penium sequences into the Chaetosphaeridium cDNA library diminished the phylogenetic support for grouping Coleochaete and Chaetosphaeridium together. Importantly, regarding character orientation, it is noteworthy that the revised position of Coleochaete is consistent with the major conclusion of our paper that relatively simple algal forms may be the closest relatives of land plants, and that the whorled branches observed in Charales likely evolved convergently, a conclusion that is also supported by previous analyses [1Wodniok S. Brinkmann H. Glöckner G. Heidel A.J. Philippe H. Melkonian M. Becker B. Origin of land plants: do conjugating green algae hold the key?.BMC Evol. Biol. 2011; 11: 104Crossref PubMed Scopus (241) Google Scholar, 2Timme R.E. Bachvaroff T.R. Delwiche C.F. Broad phylogenomic sampling and the sister lineage of land plants.PLoS ONE. 2012; 7: e29696Crossref PubMed Scopus (218) Google Scholar]. Contamination has been a long-standing problem in molecular phylogenies and phylogenomics, especially when exploring new areas of biodiversity, and is particularly problematic in very large data sets that are difficult or impossible to fully curate manually. This case clearly pleads for further development of computational methods to detect contaminants in the growing amounts of sequence data generated for new taxa. Multigene Phylogeny of the Green Lineage Reveals the Origin and Diversification of Land PlantsFinet et al.Current BiologyDecember 9, 2010In BriefThe Viridiplantae (green plants) include land plants as well as the two distinct lineages of green algae, chlorophytes and charophytes. Despite their critical importance for identifying the closest living relatives of land plants, phylogenetic studies of charophytes have provided equivocal results [1–5]. In addition, many relationships remain unresolved among the land plants, such as the position of mosses, liverworts, and the enigmatic Gnetales. Phylogenomics has proven to be an insightful approach for resolving challenging phylogenetic issues, particularly concerning deep nodes [6–8]. Full-Text PDF Open ArchiveOrigin of land plants revisited in the light of sequence contamination and missing dataLaurin-Lemay et al.Current BiologyAugust 07, 2012In BriefKnowing the closest relatives of land plants is key to understanding the complex adaptations to terrestrial life. Unfortunately, multi-gene analyses have yielded highly incongruent results, suggesting, for instance, Charales [1], Zygnematales [2,3], or Coleochaete [4] as the sister-group of land plants. Such controversy may result from the real history of life, in particular closely spaced speciation events, incomplete lineage sorting, gene duplication or horizontal gene transfer. In such cases, the solution resides in improved taxon sampling and sophisticated models of evolution [5]. Full-Text PDF Open Archive