Evolution moléculaire et phylogénie M2 – EcoSciences/5BIM INSA Céline Brochier ([email protected]) 2015-2016 (http://www.frangun.org) Evolution moléculaire et phylogénie (Céline Brochier-Armanet 2015-2016) Phylogeny of Eucarya (eighties) Crown Based on SSU rRNA A well resolved asymmetric base An unresolved crown Late emergence of multicellular eukaryotes Early emergence of amitochondriate lineages Asymmetric (Archezoa) base Gradual complexity of the eukaryotic cell (Adapted from Sogin Early evolution and the origin of eukaryotes - Curr. Opin. Genet. Dev. – 1991) Evolution moléculaire et phylogénie (Céline Brochier-Armanet 2015-2016) Origin of the mitochondria (From Keeling A kingdom’s progress: Archezoa and the origin of eukaryotes – BioEssays - 1998) Evolution moléculaire et phylogénie (Céline Brochier-Armanet 2015-2016) Archezoa Cavalier-Smith Eukaryotes with no mitochondria – Nature - 1987 Cavalier-Smith Archaebacteria and Archezoa - Nature - 1989 Metamonad Archamoeba Parabasalia Microsporidia Retortamonas Pelomyxa Trichomonas Nosema (From Keeling A kingdom’s progress: Archezoa and the origin of eukaryotes – BioEssays - 1998) Evolution moléculaire et phylogénie (Céline Brochier-Armanet 2015-2016) The archezoa hypothesis “Archezoa are eukaryotes which primitively lack mitochondria” The nucleus originated before the mitochondrial endosymbiosis The first eukaryotes were anaerobes Archezoans might provide insights into the nature of ancestral eukaryotic genomes and biology Evolution moléculaire et phylogénie (Céline Brochier-Armanet 2015-2016) The archezoa hypothesis “Archezoa are eukaryotes which primitively lack mitochondria” The nucleus originated before the mitochondrial endosymbiosis The first eukaryotes were anaerobes Archezoans might provide insights into the nature of ancestral eukaryotic genomes and biology BUT… the hypothesis would fall if We find mitochondrial genes in archezoan genomes We find that archezoans branch among aerobic species with mitochondria Mitochondrion-derived organelles are found in archezoans Evolution moléculaire et phylogénie (Céline Brochier-Armanet 2015-2016) Evolution moléculaire et phylogénie (Céline Brochier-Armanet 2015-2016) Mol. Biol. Evol. 2001 Mitochondrial genes Parabasalia Trichomonas vaginalis 1 (Hydrogenosomes) Trichomonas vaginalis 2 Giardia intestinalis Metamonads (Mitosomes) Mitochondrial genes Proteobacteria Evolution moléculaire et phylogénie (Céline Brochier-Armanet 2015-2016) The archezoa hypothesis “Archezoa are eukaryotes which primitively lack mitochondria” The nucleus originated before the mitochondrial endosymbiosis The first eukaryotes were anaerobes Archezoans might provide insights into the nature of ancestral eukaryotic genomes and biology BUT… the hypothesis would fall if We find mitochondrial genes in archezoan genomes We find that archezoans branch among aerobic species with mitochondria Mitochondrion-derived organelles are found in archezoans Evolution moléculaire et phylogénie (Céline Brochier-Armanet 2015-2016) Conflicting phylogenetic signals SSU rRNA Actin b-Tubulin (Philippe H. et al. Early-branching or fast-evolving eukaryotes? - Proc. Biol. Sci. - 2000) Evolution moléculaire et phylogénie (Céline Brochier-Armanet 2015-2016) The phylogeny of Eucarya is severely affected by tree reconstruction artefacts B C B C q q p<q2 p A D A D Evolution moléculaire et phylogénie (Céline Brochier-Armanet 2015-2016) Microsporidia are related to Fungi The use of accurate evolutionary models (S/F, removal of invariant sites, Gamma corrections, etc.) and methods (ML, Bayesian) disentangles the phylogenetic position of Microsporidia ML – V-ATPase ML – RPB1 (Vivares et al. Curr Opin Microbiol. 2002) (Hirt et al. PNAS 2001) Evolution moléculaire et phylogénie (Céline Brochier-Armanet 2015-2016) The archezoa hypothesis “Archezoa are eukaryotes which primitively lack mitochondria” The nucleus originated before the mitochondrial endosymbiosis The first eukaryotes were anaerobes Archezoans might provide insights into the nature of ancestral eukaryotic genomes and biology BUT… the hypothesis would fall if We find mitochondrial genes in archezoan genomes We find that archezoans branch among aerobic species with mitochondria Mitochondrion-derived organelles are found in archezoans Evolution moléculaire et phylogénie (Céline Brochier-Armanet 2015-2016) Hydrogenosomes and Mitosomes are mitochondria remnants 50 nm 50 nm (2002) (2003) 50 nm 1 μm (Nyctotherus, 2005) Evolution moléculaire et phylogénie (Céline Brochier-Armanet 2015-2016) Evolution moléculaire et phylogénie (Céline Brochier-Armanet 2015-2016) The archezoa hypothesis “Archezoa are eukaryotes which primitively lack mitochondria” The nucleus originated before the mitochondrial endosymbiosis The first eukaryotes were anaerobes Archezoans might provide insights into the nature of ancestral eukaryotic genomes and biology BUT… the hypothesis would fall if We find mitochondrial genes in archezoan genomes We find that archezoans branch among aerobic species with mitochondria Mitochondrion-derived organelles are found in archezoans Evolution moléculaire et phylogénie (Céline Brochier-Armanet 2015-2016) Origin of the mitochondria (From Keeling A kingdom’s progress: Archezoa and the origin of eukaryotes – BioEssays - 1998) Evolution moléculaire et phylogénie (Céline Brochier-Armanet 2015-2016) Phylogeny of Eucarya (nineties) Microsporidia Crown ? Evolution moléculaire et phylogénie (Céline Brochier-Armanet 2015-2016) Why such a lack of resolution? Radiation Too few phylogenetic signal has been recorded in sequences Dt short (Gribaldo and Brochier - Phylogeny of prokaryotes: does it exist and why should we care? - Res Micro - 2009) Evolution moléculaire et phylogénie (Céline Brochier-Armanet 2015-2016) Why such a lack of resolution? Radiation Too few phylogenetic signal has been recorded in sequences Dt short Substitutional saturation The ancient phylogenetic signal is progressively erased by multiple substitutions Observed substitutions Real number of substitutions (Gribaldo and Brochier - Phylogeny of prokaryotes: does it exist and why should we care? - Res Micro - 2009) Evolution moléculaire et phylogénie (Céline Brochier-Armanet 2015-2016) How can we overcome the lack of signal? Improve methods of reconstruction and evolutionary models (Van de Peer, Ben Ali, Meyer – Gene - 2000) Evolution moléculaire et phylogénie (Céline Brochier-Armanet 2015-2016) How can we overcome the lack of signal? Improve the taxonomic sampling to avoid tree reconstruction artefact & reduce saturation 28S rRNA of 31 Gnathostoma (parsimony – 529 positions) (Lecointre et al. – Mol. Phyl. Evol. - 1993) Evolution moléculaire et phylogénie (Céline Brochier-Armanet 2015-2016) How can we overcome the lack of signal? Increase the amount of data Evolution moléculaire et phylogénie (Céline Brochier-Armanet 2015-2016) Improving the amount of data is not sufficient The use of inaccurate evolutionary models can deadly bias phylogenetic inferences (~70 nuclear genes 17807 amino acid positions) Fungi Fungi Deuterostoma Deuterostoma Arthropoda Arthropoda Nematoda Nematoda WAG+F+Γ CAT+F+Γ (Lartillot, Brinkmann and Philippe – BMC Evol. Biol. - 2007) Evolution moléculaire et phylogénie (Céline Brochier-Armanet 2015-2016) Improving the amount of data is not sufficient The use of inaccurate taxonomic sampling can deadly bias phylogenetic inferences (~70 nuclear proteins,17807 amino acid positions) Fungi Fungi Deuterostoma Cnidaria+Choano Deuterostoma Arthropoda Arthropoda Nematoda Nematoda WAG+F+Γ (Lartillot, Brinkmann and Philippe – BMC Evol. Biol. - 2007) Evolution moléculaire et phylogénie (Céline Brochier-Armanet 2015-2016) Improving the amount of data is not sufficient Break the long branches to avoid Long Branch Attraction artefacts 146 nuclear proteins (35,346 amino-acid positions), ML (JTT+Γ) (Delsuc, Brinkmann and Philippe – Nat. Rev. Micro. - 2005) Evolution moléculaire et phylogénie (Céline Brochier-Armanet 2015-2016) Improving the amount of data is not sufficient Compositional biases and multiple substitutions can deadly affect tree inference… 46 r-prot, 137 proteobacterial species, 15372 nucleic acid positions (Ramulu et al. – Mol. Phylogent. Evol. - 2014) Evolution moléculaire et phylogénie (Céline Brochier-Armanet 2015-2016) Improving the amount of data is not sufficient especially when using inaccurate evolutionary models e e GG+Γ d a GTR+Γ a d b b g g 46 r-prot, 137 proteobacterial species, 15372 nucleic acid positions (Ramulu et al. – Mol. Phylogenet. Evol. - 2014) Evolution moléculaire et phylogénie (Céline Brochier-Armanet 2015-2016) Garbage in, garbage out The recoding of multiple alignments can help to overcome systematic biases 4 mitochondrial genes (3 729 nucleic acid positions) ML (GTR+I+Γ) Recoding RY + ML (CF+I+Γ) Ticks emerge with A+T rich insects Ticks emerge within other chelicerates (Delsuc, Brinkmann and Philippe – Nat. Rev. Micro. - 2005) Evolution moléculaire et phylogénie (Céline Brochier-Armanet 2015-2016) Garbage in, garbage out The removal of fastest evolving sites can help to overcome systematic biases and to detect Long Branch Attraction artefacts 146 nuclear genes (35371 amino acid positions), ML (JTT + Γ) Slow-Fast method (Delsuc, Brinkmann and Philippe – Nat. Rev. Micro. - 2005) Evolution moléculaire et phylogénie (Céline Brochier-Armanet 2015-2016) Supermatrix approaches have improved our knowledge of eukaryotic phylogeny Year Author Number Main results