@ARTICLE{TreeBASE2Ref25028,
author = {Silvia Restrepo and Juan Enciso and Javier F Tabima and Diego Mauricio Riano-Pachon},
title = {Phylogenomics of the Kingdom Protista},
year = {2015},
keywords = {Phylogenomics, Markovian Ortholog Clustering, Opisthokonta,Stramenopila, Alveolata},
doi = {},
url = {http://},
pmid = {},
journal = {Academia},
volume = {},
number = {},
pages = {},
abstract = {The lack of organisation of discrete lineages in the phylogeny and taxonomy of protists has precluded the understanding of the group?s evolutionary history and trait comparison among members of the group. We used a phylogenomics approach to establish phylogenetic hypotheses of the protist group. We used an automatic orthologous clustering (OrthoMCL)-based strategy to recover 72 clusters of orthologues from 73 eukaryotic species. A maximum likelihood tree was inferred from the supermatrix. Overall, we obtained consistent inferences, but some unexpected branching patterns were poorly supported. Despite the large quantity of genes from the Opisthokonta groups, this clade appeared to be polyphyletic. The monophyly of the Excavata was recovered for all but three species that were expected to group within it but were found scattered, most likely because of long-branch attraction artefacts. A second dataset was constructed after removing the fast-evolving/saturated sites, and a Shimodaira-Hasegawa test was performed to verify whether our data allowed us to reject branching patterns that were previously reported. The results of these tests suggested that the competing tree topologies were not significantly better than our recovered topologies. Novel relationships were shown inside the Opisthokonta, for two genera, Thecamonas trahens and Capsaspora owczarzaki. Additionally, some controversial phylogenetic positions among several eukaryotic groups were found using this phylogenomics approach.
}
}
Citation for Study 18190
Citation title:
"Phylogenomics of the Kingdom Protista".
Study name:
"Phylogenomics of the Kingdom Protista".
This study is part of submission 18190
(Status: Published).
Citation
Restrepo S., Enciso J., Tabima J.F., & Riano-pachon D. 2015. Phylogenomics of the Kingdom Protista. Academia, .
Authors
-
Restrepo S.
-
Enciso J.
+57 3192569896
-
Tabima J.F.
(submitter)
7143335200
-
Riano-pachon D.
Abstract
The lack of organisation of discrete lineages in the phylogeny and taxonomy of protists has precluded the understanding of the group?s evolutionary history and trait comparison among members of the group. We used a phylogenomics approach to establish phylogenetic hypotheses of the protist group. We used an automatic orthologous clustering (OrthoMCL)-based strategy to recover 72 clusters of orthologues from 73 eukaryotic species. A maximum likelihood tree was inferred from the supermatrix. Overall, we obtained consistent inferences, but some unexpected branching patterns were poorly supported. Despite the large quantity of genes from the Opisthokonta groups, this clade appeared to be polyphyletic. The monophyly of the Excavata was recovered for all but three species that were expected to group within it but were found scattered, most likely because of long-branch attraction artefacts. A second dataset was constructed after removing the fast-evolving/saturated sites, and a Shimodaira-Hasegawa test was performed to verify whether our data allowed us to reject branching patterns that were previously reported. The results of these tests suggested that the competing tree topologies were not significantly better than our recovered topologies. Novel relationships were shown inside the Opisthokonta, for two genera, Thecamonas trahens and Capsaspora owczarzaki. Additionally, some controversial phylogenetic positions among several eukaryotic groups were found using this phylogenomics approach.
Keywords
Phylogenomics, Markovian Ortholog Clustering, Opisthokonta,Stramenopila, Alveolata
External links
About this resource
- Canonical resource URI:
http://purl.org/phylo/treebase/phylows/study/TB2:S18190
- Other versions:
Nexus
NeXML
- Show BibTeX reference
@ARTICLE{TreeBASE2Ref25028,
author = {Silvia Restrepo and Juan Enciso and Javier F Tabima and Diego Mauricio Riano-Pachon},
title = {Phylogenomics of the Kingdom Protista},
year = {2015},
keywords = {Phylogenomics, Markovian Ortholog Clustering, Opisthokonta,Stramenopila, Alveolata},
doi = {},
url = {http://},
pmid = {},
journal = {Academia},
volume = {},
number = {},
pages = {},
abstract = {The lack of organisation of discrete lineages in the phylogeny and taxonomy of protists has precluded the understanding of the group?s evolutionary history and trait comparison among members of the group. We used a phylogenomics approach to establish phylogenetic hypotheses of the protist group. We used an automatic orthologous clustering (OrthoMCL)-based strategy to recover 72 clusters of orthologues from 73 eukaryotic species. A maximum likelihood tree was inferred from the supermatrix. Overall, we obtained consistent inferences, but some unexpected branching patterns were poorly supported. Despite the large quantity of genes from the Opisthokonta groups, this clade appeared to be polyphyletic. The monophyly of the Excavata was recovered for all but three species that were expected to group within it but were found scattered, most likely because of long-branch attraction artefacts. A second dataset was constructed after removing the fast-evolving/saturated sites, and a Shimodaira-Hasegawa test was performed to verify whether our data allowed us to reject branching patterns that were previously reported. The results of these tests suggested that the competing tree topologies were not significantly better than our recovered topologies. Novel relationships were shown inside the Opisthokonta, for two genera, Thecamonas trahens and Capsaspora owczarzaki. Additionally, some controversial phylogenetic positions among several eukaryotic groups were found using this phylogenomics approach.
}
}
- Show RIS reference
TY - JOUR
ID - 25028
AU - Restrepo,Silvia
AU - Enciso,Juan
AU - Tabima,Javier F
AU - Riano-Pachon,Diego Mauricio
T1 - Phylogenomics of the Kingdom Protista
PY - 2015
KW - Phylogenomics
KW - Markovian Ortholog Clustering
KW - Opisthokonta
KW - Stramenopila
KW - Alveolata
UR - http://dx.doi.org/
N2 - The lack of organisation of discrete lineages in the phylogeny and taxonomy of protists has precluded the understanding of the group?s evolutionary history and trait comparison among members of the group. We used a phylogenomics approach to establish phylogenetic hypotheses of the protist group. We used an automatic orthologous clustering (OrthoMCL)-based strategy to recover 72 clusters of orthologues from 73 eukaryotic species. A maximum likelihood tree was inferred from the supermatrix. Overall, we obtained consistent inferences, but some unexpected branching patterns were poorly supported. Despite the large quantity of genes from the Opisthokonta groups, this clade appeared to be polyphyletic. The monophyly of the Excavata was recovered for all but three species that were expected to group within it but were found scattered, most likely because of long-branch attraction artefacts. A second dataset was constructed after removing the fast-evolving/saturated sites, and a Shimodaira-Hasegawa test was performed to verify whether our data allowed us to reject branching patterns that were previously reported. The results of these tests suggested that the competing tree topologies were not significantly better than our recovered topologies. Novel relationships were shown inside the Opisthokonta, for two genera, Thecamonas trahens and Capsaspora owczarzaki. Additionally, some controversial phylogenetic positions among several eukaryotic groups were found using this phylogenomics approach.
L3 -
JF - Academia
VL -
IS -
ER -
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