The Experts below are selected from a list of 132 Experts worldwide ranked by ideXlab platform
Martin Kolisko - One of the best experts on this subject based on the ideXlab platform.
-
Supplementary Materials Description from Combined morphological and phylogenomic re-examination of malawimonads, a critical taxon for inferring the evolutionary history of eukaryotes
2018Co-Authors: Aaron A. Heiss, Andrew J. Roger, Martin Kolisko, Fleming Ekelund, Matthew W. Brown, Alastair G. B. SimpsonAbstract:Modern syntheses of eukaryote diversity assign almost all taxa to one of three groups: Amorphea, Diaphoretickes and Excavata (comprising Discoba and Metamonada). The most glaring exception is Malawimonadidae, small heterotrophic flagellates that resemble Excavata by morphology, but group with Amorphea in most phylogenomic analyses. However, just one malawimonad, Malawimonas jakobiformis, has been studied with both morphological and molecular-phylogenetic approaches, raising the spectre of interpretation errors and phylogenetic artefacts from low taxon sampling. We report a morphological and phylogenomic study of a new deep-branching malawimonad, Gefionella okellyi n. gen. n. sp. Electron microscopy revealed all canonical features of ‘typical excavates’, including two opposed flagellar vanes (unlike M. jakobiformis but like many metamonads) and a composite fibre. Initial phylogenomic analyses grouped malawimonads with the Amorphea-related orphan lineage Collodictyon, separate from a Metamonada+Discoba clade. However, support for this topology weakened when more sophisticated evolutionary models were used, and/or fast-evolving sites and long-branching taxa (FS/LB) were excluded. Analyses of ‘-FS/LB’ datasets instead suggested a relationship between malawimonads and metamonads. The ‘malawimonad+metamonad signal’ in morphological and molecular data argues against a Metamonada+Discoba clade (i.e. the predominant concept of Excavata). A Metamonad+Discoba clade should therefore not be assumed when inferring deep-level evolutionary history in eukaryotes
-
Supplementary Figure 6 from Combined morphological and phylogenomic re-examination of malawimonads, a critical taxon for inferring the evolutionary history of eukaryotes
2018Co-Authors: Aaron A. Heiss, Andrew J. Roger, Martin Kolisko, Fleming Ekelund, Matthew W. Brown, Alastair G. B. SimpsonAbstract:Heat map showing RAxML rapid bootstrap support for clade of Discoba and Metamonada with removal of fast-evolving sites (X-axis, in thousands) and fast-evolving taxa (Y-axis)
-
arginine deiminase pathway enzymes evolutionary history in metamonads and other eukaryotes
BMC Evolutionary Biology, 2016Co-Authors: Lukáš Novák, Alastair G. B. Simpson, Zuzana Zubáčová, Anna Karnkowska, Martin Kolisko, Miluše Hroudová, Courtney W. Stairs, Patrick J KeelingAbstract:Multiple prokaryotic lineages use the arginine deiminase (ADI) pathway for anaerobic energy production by arginine degradation. The distribution of this pathway among eukaryotes has been thought to be very limited, with only two specialized groups living in low oxygen environments (Parabasalia and Diplomonadida) known to possess the complete set of all three enzymes. We have performed an extensive survey of available sequence data in order to map the distribution of these enzymes among eukaryotes and to reconstruct their phylogenies. We have found genes for the complete pathway in almost all examined representatives of Metamonada, the anaerobic protist group that includes parabasalids and diplomonads. Phylogenetic analyses indicate the presence of the complete pathway in the last common ancestor of metamonads and heterologous transformation experiments suggest its cytosolic localization in the metamonad ancestor. Outside Metamonada, the complete pathway occurs rarely, nevertheless, it was found in representatives of most major eukaryotic clades. Phylogenetic relationships of complete pathways are consistent with the presence of the Archaea-derived ADI pathway in the last common ancestor of all eukaryotes, although other evolutionary scenarios remain possible. The presence of the incomplete set of enzymes is relatively common among eukaryotes and it may be related to the fact that these enzymes are involved in other cellular processes, such as the ornithine-urea cycle. Single protein phylogenies suggest that the evolutionary history of all three enzymes has been shaped by frequent gene losses and horizontal transfers, which may sometimes be connected with their diverse roles in cellular metabolism.
-
Additional file 2: of Arginine deiminase pathway enzymes: evolutionary history in metamonads and other eukaryotes
2016Co-Authors: Lukáš Novák, Zuzana Zubáčová, Anna Karnkowska, Martin Kolisko, Miluše Hroudová, Courtney W. Stairs, Alastair Simpson, Patrick Keeling, Andrew Roger, Ivan ČepičkaAbstract:Phylogenetic tree of CK sequences. The tree based on a 251 positions long protein alignment of 256 sequences was constructed in RAxML using the LG4X+ Γ model of substitution. Eukaryotic taxa are highlighted in different colors according to the major group they belong to. The color code is the same as in Fig. 1. The values at nodes represent RAxML bootstrap support/IQ-TREE bootstrap support. Only values above 50 % are shown. Black circles indicate support of 100 %/100 %. Vertical black bars indicate well-supported eukaryotic clades: Ch – Chlorophyta; Din – Dinoflagellata; Dip – Diplomonadida; Pa – Parabasalia; Pr – Preaxostyla. Species with multiple sequences included: Giardia intestinalis 1 – GSB 16453; Giardia intestinalis 2 – GL50803 16453; Thalassiosira pseudonana 1 – GI 223995860; Thalassiosira pseudonana 2 – GI 224000745; Trichomonas vaginalis 1 – TVAG 420500; Trichomonas vaginalis 2 – TVAG 261970; Trichomonas vaginalis 3 – TVAG 420510. The tree is unrooted. (PDF 482 kb
-
Additional file 1: of Arginine deiminase pathway enzymes: evolutionary history in metamonads and other eukaryotes
2016Co-Authors: Lukáš Novák, Zuzana Zubáčová, Anna Karnkowska, Martin Kolisko, Miluše Hroudová, Alastair Simpson, Patrick Keeling, Andrew Roger, Courtney Stairs, Ivan ČepičkaAbstract:Phylogenetic tree of OTC sequences. The tree based on a 242 positions long protein alignment of 444 sequences was constructed in RAxML using the LG4X + Γ model of substitution. Eukaryotic taxa are highlighted in different colors according to the major group they belong to. The color code is the same as in Fig. 1. The values at nodes represent RAxML bootstrap support/IQ-TREE bootstrap support. Only values above 50 % are shown. Black circles indicate support of 100 %/100 %. Species with multiple sequences included: Alexandrium tamarense 1 – CAMPEP 0186340278; Alexandrium tamarense 2 – CAMPEP 0186191854; Alexandrium tamarense 3 – CAMPEP 0186247540; Durinskia baltica 1 – CAMPEP 0200033980; Durinskia baltica 2 – CAMPEP 0200081736; Euglena gracilis 1 – c20598 g1 i1; Euglena gracilis 2 – c34673 g1 i6; Eutreptiella gymnastica-like 1 – CAMPEP 0200420840; Eutreptiella gymnastica-like 2 – CAMPEP 0200409666; Karenia brevis 1 – CAMPEP 0188881430; Karenia brevis 2 – CAMPEP 0188950444; Karlodinium micrum 1 – CAMPEP 0200795676; Karlodinium micrum 2 – CAMPEP 0200767534. The tree is rooted with sequences of bacterial aspartate carbamoyltransferase (ATC; EC 2.1.3.2). (PDF 506 kb
Anna Karnkowska - One of the best experts on this subject based on the ideXlab platform.
-
arginine deiminase pathway enzymes evolutionary history in metamonads and other eukaryotes
BMC Evolutionary Biology, 2016Co-Authors: Lukáš Novák, Alastair G. B. Simpson, Zuzana Zubáčová, Anna Karnkowska, Martin Kolisko, Miluše Hroudová, Courtney W. Stairs, Patrick J KeelingAbstract:Multiple prokaryotic lineages use the arginine deiminase (ADI) pathway for anaerobic energy production by arginine degradation. The distribution of this pathway among eukaryotes has been thought to be very limited, with only two specialized groups living in low oxygen environments (Parabasalia and Diplomonadida) known to possess the complete set of all three enzymes. We have performed an extensive survey of available sequence data in order to map the distribution of these enzymes among eukaryotes and to reconstruct their phylogenies. We have found genes for the complete pathway in almost all examined representatives of Metamonada, the anaerobic protist group that includes parabasalids and diplomonads. Phylogenetic analyses indicate the presence of the complete pathway in the last common ancestor of metamonads and heterologous transformation experiments suggest its cytosolic localization in the metamonad ancestor. Outside Metamonada, the complete pathway occurs rarely, nevertheless, it was found in representatives of most major eukaryotic clades. Phylogenetic relationships of complete pathways are consistent with the presence of the Archaea-derived ADI pathway in the last common ancestor of all eukaryotes, although other evolutionary scenarios remain possible. The presence of the incomplete set of enzymes is relatively common among eukaryotes and it may be related to the fact that these enzymes are involved in other cellular processes, such as the ornithine-urea cycle. Single protein phylogenies suggest that the evolutionary history of all three enzymes has been shaped by frequent gene losses and horizontal transfers, which may sometimes be connected with their diverse roles in cellular metabolism.
-
Additional file 2: of Arginine deiminase pathway enzymes: evolutionary history in metamonads and other eukaryotes
2016Co-Authors: Lukáš Novák, Zuzana Zubáčová, Anna Karnkowska, Martin Kolisko, Miluše Hroudová, Courtney W. Stairs, Alastair Simpson, Patrick Keeling, Andrew Roger, Ivan ČepičkaAbstract:Phylogenetic tree of CK sequences. The tree based on a 251 positions long protein alignment of 256 sequences was constructed in RAxML using the LG4X+ Γ model of substitution. Eukaryotic taxa are highlighted in different colors according to the major group they belong to. The color code is the same as in Fig. 1. The values at nodes represent RAxML bootstrap support/IQ-TREE bootstrap support. Only values above 50 % are shown. Black circles indicate support of 100 %/100 %. Vertical black bars indicate well-supported eukaryotic clades: Ch – Chlorophyta; Din – Dinoflagellata; Dip – Diplomonadida; Pa – Parabasalia; Pr – Preaxostyla. Species with multiple sequences included: Giardia intestinalis 1 – GSB 16453; Giardia intestinalis 2 – GL50803 16453; Thalassiosira pseudonana 1 – GI 223995860; Thalassiosira pseudonana 2 – GI 224000745; Trichomonas vaginalis 1 – TVAG 420500; Trichomonas vaginalis 2 – TVAG 261970; Trichomonas vaginalis 3 – TVAG 420510. The tree is unrooted. (PDF 482 kb
-
Additional file 1: of Arginine deiminase pathway enzymes: evolutionary history in metamonads and other eukaryotes
2016Co-Authors: Lukáš Novák, Zuzana Zubáčová, Anna Karnkowska, Martin Kolisko, Miluše Hroudová, Alastair Simpson, Patrick Keeling, Andrew Roger, Courtney Stairs, Ivan ČepičkaAbstract:Phylogenetic tree of OTC sequences. The tree based on a 242 positions long protein alignment of 444 sequences was constructed in RAxML using the LG4X + Γ model of substitution. Eukaryotic taxa are highlighted in different colors according to the major group they belong to. The color code is the same as in Fig. 1. The values at nodes represent RAxML bootstrap support/IQ-TREE bootstrap support. Only values above 50 % are shown. Black circles indicate support of 100 %/100 %. Species with multiple sequences included: Alexandrium tamarense 1 – CAMPEP 0186340278; Alexandrium tamarense 2 – CAMPEP 0186191854; Alexandrium tamarense 3 – CAMPEP 0186247540; Durinskia baltica 1 – CAMPEP 0200033980; Durinskia baltica 2 – CAMPEP 0200081736; Euglena gracilis 1 – c20598 g1 i1; Euglena gracilis 2 – c34673 g1 i6; Eutreptiella gymnastica-like 1 – CAMPEP 0200420840; Eutreptiella gymnastica-like 2 – CAMPEP 0200409666; Karenia brevis 1 – CAMPEP 0188881430; Karenia brevis 2 – CAMPEP 0188950444; Karlodinium micrum 1 – CAMPEP 0200795676; Karlodinium micrum 2 – CAMPEP 0200767534. The tree is rooted with sequences of bacterial aspartate carbamoyltransferase (ATC; EC 2.1.3.2). (PDF 506 kb
Patrick J Keeling - One of the best experts on this subject based on the ideXlab platform.
-
arginine deiminase pathway enzymes evolutionary history in metamonads and other eukaryotes
BMC Evolutionary Biology, 2016Co-Authors: Lukáš Novák, Alastair G. B. Simpson, Zuzana Zubáčová, Anna Karnkowska, Martin Kolisko, Miluše Hroudová, Courtney W. Stairs, Patrick J KeelingAbstract:Multiple prokaryotic lineages use the arginine deiminase (ADI) pathway for anaerobic energy production by arginine degradation. The distribution of this pathway among eukaryotes has been thought to be very limited, with only two specialized groups living in low oxygen environments (Parabasalia and Diplomonadida) known to possess the complete set of all three enzymes. We have performed an extensive survey of available sequence data in order to map the distribution of these enzymes among eukaryotes and to reconstruct their phylogenies. We have found genes for the complete pathway in almost all examined representatives of Metamonada, the anaerobic protist group that includes parabasalids and diplomonads. Phylogenetic analyses indicate the presence of the complete pathway in the last common ancestor of metamonads and heterologous transformation experiments suggest its cytosolic localization in the metamonad ancestor. Outside Metamonada, the complete pathway occurs rarely, nevertheless, it was found in representatives of most major eukaryotic clades. Phylogenetic relationships of complete pathways are consistent with the presence of the Archaea-derived ADI pathway in the last common ancestor of all eukaryotes, although other evolutionary scenarios remain possible. The presence of the incomplete set of enzymes is relatively common among eukaryotes and it may be related to the fact that these enzymes are involved in other cellular processes, such as the ornithine-urea cycle. Single protein phylogenies suggest that the evolutionary history of all three enzymes has been shaped by frequent gene losses and horizontal transfers, which may sometimes be connected with their diverse roles in cellular metabolism.
Lukáš Novák - One of the best experts on this subject based on the ideXlab platform.
-
arginine deiminase pathway enzymes evolutionary history in metamonads and other eukaryotes
BMC Evolutionary Biology, 2016Co-Authors: Lukáš Novák, Alastair G. B. Simpson, Zuzana Zubáčová, Anna Karnkowska, Martin Kolisko, Miluše Hroudová, Courtney W. Stairs, Patrick J KeelingAbstract:Multiple prokaryotic lineages use the arginine deiminase (ADI) pathway for anaerobic energy production by arginine degradation. The distribution of this pathway among eukaryotes has been thought to be very limited, with only two specialized groups living in low oxygen environments (Parabasalia and Diplomonadida) known to possess the complete set of all three enzymes. We have performed an extensive survey of available sequence data in order to map the distribution of these enzymes among eukaryotes and to reconstruct their phylogenies. We have found genes for the complete pathway in almost all examined representatives of Metamonada, the anaerobic protist group that includes parabasalids and diplomonads. Phylogenetic analyses indicate the presence of the complete pathway in the last common ancestor of metamonads and heterologous transformation experiments suggest its cytosolic localization in the metamonad ancestor. Outside Metamonada, the complete pathway occurs rarely, nevertheless, it was found in representatives of most major eukaryotic clades. Phylogenetic relationships of complete pathways are consistent with the presence of the Archaea-derived ADI pathway in the last common ancestor of all eukaryotes, although other evolutionary scenarios remain possible. The presence of the incomplete set of enzymes is relatively common among eukaryotes and it may be related to the fact that these enzymes are involved in other cellular processes, such as the ornithine-urea cycle. Single protein phylogenies suggest that the evolutionary history of all three enzymes has been shaped by frequent gene losses and horizontal transfers, which may sometimes be connected with their diverse roles in cellular metabolism.
-
Additional file 2: of Arginine deiminase pathway enzymes: evolutionary history in metamonads and other eukaryotes
2016Co-Authors: Lukáš Novák, Zuzana Zubáčová, Anna Karnkowska, Martin Kolisko, Miluše Hroudová, Courtney W. Stairs, Alastair Simpson, Patrick Keeling, Andrew Roger, Ivan ČepičkaAbstract:Phylogenetic tree of CK sequences. The tree based on a 251 positions long protein alignment of 256 sequences was constructed in RAxML using the LG4X+ Γ model of substitution. Eukaryotic taxa are highlighted in different colors according to the major group they belong to. The color code is the same as in Fig. 1. The values at nodes represent RAxML bootstrap support/IQ-TREE bootstrap support. Only values above 50 % are shown. Black circles indicate support of 100 %/100 %. Vertical black bars indicate well-supported eukaryotic clades: Ch – Chlorophyta; Din – Dinoflagellata; Dip – Diplomonadida; Pa – Parabasalia; Pr – Preaxostyla. Species with multiple sequences included: Giardia intestinalis 1 – GSB 16453; Giardia intestinalis 2 – GL50803 16453; Thalassiosira pseudonana 1 – GI 223995860; Thalassiosira pseudonana 2 – GI 224000745; Trichomonas vaginalis 1 – TVAG 420500; Trichomonas vaginalis 2 – TVAG 261970; Trichomonas vaginalis 3 – TVAG 420510. The tree is unrooted. (PDF 482 kb
-
Additional file 1: of Arginine deiminase pathway enzymes: evolutionary history in metamonads and other eukaryotes
2016Co-Authors: Lukáš Novák, Zuzana Zubáčová, Anna Karnkowska, Martin Kolisko, Miluše Hroudová, Alastair Simpson, Patrick Keeling, Andrew Roger, Courtney Stairs, Ivan ČepičkaAbstract:Phylogenetic tree of OTC sequences. The tree based on a 242 positions long protein alignment of 444 sequences was constructed in RAxML using the LG4X + Γ model of substitution. Eukaryotic taxa are highlighted in different colors according to the major group they belong to. The color code is the same as in Fig. 1. The values at nodes represent RAxML bootstrap support/IQ-TREE bootstrap support. Only values above 50 % are shown. Black circles indicate support of 100 %/100 %. Species with multiple sequences included: Alexandrium tamarense 1 – CAMPEP 0186340278; Alexandrium tamarense 2 – CAMPEP 0186191854; Alexandrium tamarense 3 – CAMPEP 0186247540; Durinskia baltica 1 – CAMPEP 0200033980; Durinskia baltica 2 – CAMPEP 0200081736; Euglena gracilis 1 – c20598 g1 i1; Euglena gracilis 2 – c34673 g1 i6; Eutreptiella gymnastica-like 1 – CAMPEP 0200420840; Eutreptiella gymnastica-like 2 – CAMPEP 0200409666; Karenia brevis 1 – CAMPEP 0188881430; Karenia brevis 2 – CAMPEP 0188950444; Karlodinium micrum 1 – CAMPEP 0200795676; Karlodinium micrum 2 – CAMPEP 0200767534. The tree is rooted with sequences of bacterial aspartate carbamoyltransferase (ATC; EC 2.1.3.2). (PDF 506 kb
-
The mitochondrion-like organelle of Trimastix pyriformis contains the complete glycine cleavage system.
Public Library of Science (PLoS), 2026Co-Authors: Zuzana Zubáčová, Lukáš Novák, Jitka Bublíková, Vojtěch Vacek, Jan Fousek, Jakub Rídl, Jan Tachezy, Pavel Doležal, Cestmír Vlček, Vladimír HamplAbstract:All eukaryotic organisms contain mitochondria or organelles that evolved from the same endosymbiotic event like classical mitochondria. Organisms inhabiting low oxygen environments often contain mitochondrial derivates known as hydrogenosomes, mitosomes or neutrally as mitochondrion-like organelles. The detailed investigation has shown unexpected evolutionary plasticity in the biochemistry and protein composition of these organelles in various protists. We investigated the mitochondrion-like organelle in Trimastix pyriformis, a free-living member of one of the three lineages of anaerobic group Metamonada. Using 454 sequencing we have obtained 7 037 contigs from its transcriptome and on the basis of sequence homology and presence of N-terminal extensions we have selected contigs coding for proteins that putatively function in the organelle. Together with the results of a previous transcriptome survey, the list now consists of 23 proteins - mostly enzymes involved in amino acid metabolism, transporters and maturases of proteins and transporters of metabolites. We have no evidence of the production of ATP in the mitochondrion-like organelle of Trimastix but we have obtained experimental evidence for the presence of enzymes of the glycine cleavage system (GCS), which is part of amino acid metabolism. Using homologous antibody we have shown that H-protein of GCS localizes into vesicles in the cell of Trimastix. When overexpressed in yeast, H- and P-protein of GCS and cpn60 were transported into mitochondrion. In case of H-protein we have demonstrated that the first 16 amino acids are necessary for this transport. Glycine cleavage system is at the moment the only experimentally localized pathway in the mitochondrial derivate of Trimastix pyriformis
Alastair G. B. Simpson - One of the best experts on this subject based on the ideXlab platform.
-
Supplementary Materials Description from Combined morphological and phylogenomic re-examination of malawimonads, a critical taxon for inferring the evolutionary history of eukaryotes
2018Co-Authors: Aaron A. Heiss, Andrew J. Roger, Martin Kolisko, Fleming Ekelund, Matthew W. Brown, Alastair G. B. SimpsonAbstract:Modern syntheses of eukaryote diversity assign almost all taxa to one of three groups: Amorphea, Diaphoretickes and Excavata (comprising Discoba and Metamonada). The most glaring exception is Malawimonadidae, small heterotrophic flagellates that resemble Excavata by morphology, but group with Amorphea in most phylogenomic analyses. However, just one malawimonad, Malawimonas jakobiformis, has been studied with both morphological and molecular-phylogenetic approaches, raising the spectre of interpretation errors and phylogenetic artefacts from low taxon sampling. We report a morphological and phylogenomic study of a new deep-branching malawimonad, Gefionella okellyi n. gen. n. sp. Electron microscopy revealed all canonical features of ‘typical excavates’, including two opposed flagellar vanes (unlike M. jakobiformis but like many metamonads) and a composite fibre. Initial phylogenomic analyses grouped malawimonads with the Amorphea-related orphan lineage Collodictyon, separate from a Metamonada+Discoba clade. However, support for this topology weakened when more sophisticated evolutionary models were used, and/or fast-evolving sites and long-branching taxa (FS/LB) were excluded. Analyses of ‘-FS/LB’ datasets instead suggested a relationship between malawimonads and metamonads. The ‘malawimonad+metamonad signal’ in morphological and molecular data argues against a Metamonada+Discoba clade (i.e. the predominant concept of Excavata). A Metamonad+Discoba clade should therefore not be assumed when inferring deep-level evolutionary history in eukaryotes
-
Supplementary Figure 6 from Combined morphological and phylogenomic re-examination of malawimonads, a critical taxon for inferring the evolutionary history of eukaryotes
2018Co-Authors: Aaron A. Heiss, Andrew J. Roger, Martin Kolisko, Fleming Ekelund, Matthew W. Brown, Alastair G. B. SimpsonAbstract:Heat map showing RAxML rapid bootstrap support for clade of Discoba and Metamonada with removal of fast-evolving sites (X-axis, in thousands) and fast-evolving taxa (Y-axis)
-
arginine deiminase pathway enzymes evolutionary history in metamonads and other eukaryotes
BMC Evolutionary Biology, 2016Co-Authors: Lukáš Novák, Alastair G. B. Simpson, Zuzana Zubáčová, Anna Karnkowska, Martin Kolisko, Miluše Hroudová, Courtney W. Stairs, Patrick J KeelingAbstract:Multiple prokaryotic lineages use the arginine deiminase (ADI) pathway for anaerobic energy production by arginine degradation. The distribution of this pathway among eukaryotes has been thought to be very limited, with only two specialized groups living in low oxygen environments (Parabasalia and Diplomonadida) known to possess the complete set of all three enzymes. We have performed an extensive survey of available sequence data in order to map the distribution of these enzymes among eukaryotes and to reconstruct their phylogenies. We have found genes for the complete pathway in almost all examined representatives of Metamonada, the anaerobic protist group that includes parabasalids and diplomonads. Phylogenetic analyses indicate the presence of the complete pathway in the last common ancestor of metamonads and heterologous transformation experiments suggest its cytosolic localization in the metamonad ancestor. Outside Metamonada, the complete pathway occurs rarely, nevertheless, it was found in representatives of most major eukaryotic clades. Phylogenetic relationships of complete pathways are consistent with the presence of the Archaea-derived ADI pathway in the last common ancestor of all eukaryotes, although other evolutionary scenarios remain possible. The presence of the incomplete set of enzymes is relatively common among eukaryotes and it may be related to the fact that these enzymes are involved in other cellular processes, such as the ornithine-urea cycle. Single protein phylogenies suggest that the evolutionary history of all three enzymes has been shaped by frequent gene losses and horizontal transfers, which may sometimes be connected with their diverse roles in cellular metabolism.
-
phylogenomic analyses support the monophyly of excavata and resolve relationships among eukaryotic supergroups
Proceedings of the National Academy of Sciences of the United States of America, 2009Co-Authors: Vladimír Hampl, Alastair G. B. Simpson, Jessica W Leigh, Franz B Lang, Joel B. Dacks, Andrew J. RogerAbstract:Nearly all of eukaryotic diversity has been classified into 6 suprakingdom-level groups (supergroups) based on molecular and morphological/cell-biological evidence; these are Opisthokonta, Amoebozoa, Archaeplastida, Rhizaria, Chromalveolata, and Excavata. However, molecular phylogeny has not provided clear evidence that either Chromalveolata or Excavata is monophyletic, nor has it resolved the relationships among the supergroups. To establish the affinities of Excavata, which contains parasites of global importance and organisms regarded previously as primitive eukaryotes, we conducted a phylogenomic analysis of a dataset of 143 proteins and 48 taxa, including 19 excavates. Previous phylogenomic studies have not included all major subgroups of Excavata, and thus have not definitively addressed their interrelationships. The enigmatic flagellate Andalucia is sister to typical jakobids. Jakobids (including Andalucia), Euglenozoa and Heterolobosea form a major clade that we name Discoba. Analyses of the complete dataset group Discoba with the mitochondrion-lacking excavates or “metamonads” (diplomonads, parabasalids, and Preaxostyla), but not with the final excavate group, Malawimonas. This separation likely results from a long-branch attraction artifact. Gradual removal of rapidly-evolving taxa from the dataset leads to moderate bootstrap support (69%) for the monophyly of all Excavata, and 90% support once all metamonads are removed. Most importantly, Excavata robustly emerges between unikonts (Amoebozoa + Opisthokonta) and “megagrouping” of Archaeplastida, Rhizaria, and chromalveolates. Our analyses indicate that Excavata forms a monophyletic suprakingdom-level group that is one of the 3 primary divisions within eukaryotes, along with unikonts and a megagroup of Archaeplastida, Rhizaria, and the chromalveolate lineages.