Limits...
Collodictyon--an ancient lineage in the tree of eukaryotes.

Zhao S, Burki F, Bråte J, Keeling PJ, Klaveness D, Shalchian-Tabrizi K - Mol. Biol. Evol. (2012)

Bottom Line: Collodictyon shares cellular characteristics with Excavata and Amoebozoa, such as ventral feeding groove supported by microtubular structures and the ability to form thin and broad pseudopods.These may therefore be ancient morphological features among eukaryotes.Overall, this shows that Collodictyon is a key lineage to understand early eukaryote evolution.

View Article: PubMed Central - PubMed

Affiliation: Microbial Evolution Research Group, Department of Biology, University of Oslo, Oslo, Norway.

ABSTRACT
The current consensus for the eukaryote tree of life consists of several large assemblages (supergroups) that are hypothesized to describe the existing diversity. Phylogenomic analyses have shed light on the evolutionary relationships within and between supergroups as well as placed newly sequenced enigmatic species close to known lineages. Yet, a few eukaryote species remain of unknown origin and could represent key evolutionary forms for inferring ancient genomic and cellular characteristics of eukaryotes. Here, we investigate the evolutionary origin of the poorly studied protist Collodictyon (subphylum Diphyllatia) by sequencing a cDNA library as well as the 18S and 28S ribosomal DNA (rDNA) genes. Phylogenomic trees inferred from 124 genes placed Collodictyon close to the bifurcation of the "unikont" and "bikont" groups, either alone or as sister to the potentially contentious excavate Malawimonas. Phylogenies based on rDNA genes confirmed that Collodictyon is closely related to another genus, Diphylleia, and revealed a very low diversity in environmental DNA samples. The early and distinct origin of Collodictyon suggests that it constitutes a new lineage in the global eukaryote phylogeny. Collodictyon shares cellular characteristics with Excavata and Amoebozoa, such as ventral feeding groove supported by microtubular structures and the ability to form thin and broad pseudopods. These may therefore be ancient morphological features among eukaryotes. Overall, this shows that Collodictyon is a key lineage to understand early eukaryote evolution.

Show MeSH
Phylogenomic position of Collodictyon inferred from 124 genes under the CAT mixture model in PhyloBayes v3.2. Branches that received 1.00 PP are marked by filled circles. The branch length of Entamoeba is shortened by 50% to save space. (A) Tree topology constructed with 79 taxa from the saved 18,000 trees after discarding the first 6,000 cycles as burn-in (maxdiff = 0.137). Missing data for each taxon is shown as a color barplot (left bar: missing number of genes; right bar: missing percentage of characters). Bars marked by “*” indicate the missing percentage of characters is over 60% of the full-length alignment. (B) Tree topology constructed with 77 taxa (i.e., two Malawimonas excluded) from the saved 16,000 trees after discarding first 8,000 cycles as burn-in (maxdiff = 0.083). CCTH is the abbreviation of Cryptophyta, Centrohelida, Telonemia, and Haptophyta. Additional statistical support values for the main nodes in the tree marked by capital letters in boxes are listed in table 1.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3351787&req=5

fig3: Phylogenomic position of Collodictyon inferred from 124 genes under the CAT mixture model in PhyloBayes v3.2. Branches that received 1.00 PP are marked by filled circles. The branch length of Entamoeba is shortened by 50% to save space. (A) Tree topology constructed with 79 taxa from the saved 18,000 trees after discarding the first 6,000 cycles as burn-in (maxdiff = 0.137). Missing data for each taxon is shown as a color barplot (left bar: missing number of genes; right bar: missing percentage of characters). Bars marked by “*” indicate the missing percentage of characters is over 60% of the full-length alignment. (B) Tree topology constructed with 77 taxa (i.e., two Malawimonas excluded) from the saved 16,000 trees after discarding first 8,000 cycles as burn-in (maxdiff = 0.083). CCTH is the abbreviation of Cryptophyta, Centrohelida, Telonemia, and Haptophyta. Additional statistical support values for the main nodes in the tree marked by capital letters in boxes are listed in table 1.

Mentions: Because our 18S and 18S + 28S rDNA trees suggested that Collodictyon might have diverged very early in eukaryote evolution and that these two genes alone were not sufficient to infer ancient relationships, we sought to increase the phylogenetic signal by constructing an alignment of 124 protein-coding genes and 79 taxa. Phylogenomic trees inferred with both Bayesian and ML methods consistently recovered most eukaryote supergroups as in recent studies (Rodriguez-Ezpeleta et al. 2007; Burki et al. 2009; Hampl et al. 2009), generally with high statistical support (table 1). Differing from published phylogenies (Burki et al. 2009; Minge et al. 2009), the Bayesian inference (fig. 3A) did not recover Breviata as sister to Amoebozoa and Telonema did not branch within CCTH, but these were instead placed as a sister to Opisthokonta (0.75 PP) and SAR (0.91 PP). Of much interest, our analyses showed that Collodictyon branched outside any of the major lineages (fig. 3A and supplementary fig. S1A, Supplementary Material online), more specifically at the bifurcation of the so-called “unikonts” (Amoebozoa and Opisthokonta) and “bikonts” (Archaeplastida, SAR, Excavata, CCTH; the terms unikonts and bikonts are used here for simplicity and do not refer to their original description; Stechmann and Cavalier-Smith 2002; Roger and Simpson 2009). Although Collodictyon did not fall within any of the supergroups, an affinity to another enigmatic genus Malawimonas was recovered with 0.79 PP and 86% BP.


Collodictyon--an ancient lineage in the tree of eukaryotes.

Zhao S, Burki F, Bråte J, Keeling PJ, Klaveness D, Shalchian-Tabrizi K - Mol. Biol. Evol. (2012)

Phylogenomic position of Collodictyon inferred from 124 genes under the CAT mixture model in PhyloBayes v3.2. Branches that received 1.00 PP are marked by filled circles. The branch length of Entamoeba is shortened by 50% to save space. (A) Tree topology constructed with 79 taxa from the saved 18,000 trees after discarding the first 6,000 cycles as burn-in (maxdiff = 0.137). Missing data for each taxon is shown as a color barplot (left bar: missing number of genes; right bar: missing percentage of characters). Bars marked by “*” indicate the missing percentage of characters is over 60% of the full-length alignment. (B) Tree topology constructed with 77 taxa (i.e., two Malawimonas excluded) from the saved 16,000 trees after discarding first 8,000 cycles as burn-in (maxdiff = 0.083). CCTH is the abbreviation of Cryptophyta, Centrohelida, Telonemia, and Haptophyta. Additional statistical support values for the main nodes in the tree marked by capital letters in boxes are listed in table 1.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3351787&req=5

fig3: Phylogenomic position of Collodictyon inferred from 124 genes under the CAT mixture model in PhyloBayes v3.2. Branches that received 1.00 PP are marked by filled circles. The branch length of Entamoeba is shortened by 50% to save space. (A) Tree topology constructed with 79 taxa from the saved 18,000 trees after discarding the first 6,000 cycles as burn-in (maxdiff = 0.137). Missing data for each taxon is shown as a color barplot (left bar: missing number of genes; right bar: missing percentage of characters). Bars marked by “*” indicate the missing percentage of characters is over 60% of the full-length alignment. (B) Tree topology constructed with 77 taxa (i.e., two Malawimonas excluded) from the saved 16,000 trees after discarding first 8,000 cycles as burn-in (maxdiff = 0.083). CCTH is the abbreviation of Cryptophyta, Centrohelida, Telonemia, and Haptophyta. Additional statistical support values for the main nodes in the tree marked by capital letters in boxes are listed in table 1.
Mentions: Because our 18S and 18S + 28S rDNA trees suggested that Collodictyon might have diverged very early in eukaryote evolution and that these two genes alone were not sufficient to infer ancient relationships, we sought to increase the phylogenetic signal by constructing an alignment of 124 protein-coding genes and 79 taxa. Phylogenomic trees inferred with both Bayesian and ML methods consistently recovered most eukaryote supergroups as in recent studies (Rodriguez-Ezpeleta et al. 2007; Burki et al. 2009; Hampl et al. 2009), generally with high statistical support (table 1). Differing from published phylogenies (Burki et al. 2009; Minge et al. 2009), the Bayesian inference (fig. 3A) did not recover Breviata as sister to Amoebozoa and Telonema did not branch within CCTH, but these were instead placed as a sister to Opisthokonta (0.75 PP) and SAR (0.91 PP). Of much interest, our analyses showed that Collodictyon branched outside any of the major lineages (fig. 3A and supplementary fig. S1A, Supplementary Material online), more specifically at the bifurcation of the so-called “unikonts” (Amoebozoa and Opisthokonta) and “bikonts” (Archaeplastida, SAR, Excavata, CCTH; the terms unikonts and bikonts are used here for simplicity and do not refer to their original description; Stechmann and Cavalier-Smith 2002; Roger and Simpson 2009). Although Collodictyon did not fall within any of the supergroups, an affinity to another enigmatic genus Malawimonas was recovered with 0.79 PP and 86% BP.

Bottom Line: Collodictyon shares cellular characteristics with Excavata and Amoebozoa, such as ventral feeding groove supported by microtubular structures and the ability to form thin and broad pseudopods.These may therefore be ancient morphological features among eukaryotes.Overall, this shows that Collodictyon is a key lineage to understand early eukaryote evolution.

View Article: PubMed Central - PubMed

Affiliation: Microbial Evolution Research Group, Department of Biology, University of Oslo, Oslo, Norway.

ABSTRACT
The current consensus for the eukaryote tree of life consists of several large assemblages (supergroups) that are hypothesized to describe the existing diversity. Phylogenomic analyses have shed light on the evolutionary relationships within and between supergroups as well as placed newly sequenced enigmatic species close to known lineages. Yet, a few eukaryote species remain of unknown origin and could represent key evolutionary forms for inferring ancient genomic and cellular characteristics of eukaryotes. Here, we investigate the evolutionary origin of the poorly studied protist Collodictyon (subphylum Diphyllatia) by sequencing a cDNA library as well as the 18S and 28S ribosomal DNA (rDNA) genes. Phylogenomic trees inferred from 124 genes placed Collodictyon close to the bifurcation of the "unikont" and "bikont" groups, either alone or as sister to the potentially contentious excavate Malawimonas. Phylogenies based on rDNA genes confirmed that Collodictyon is closely related to another genus, Diphylleia, and revealed a very low diversity in environmental DNA samples. The early and distinct origin of Collodictyon suggests that it constitutes a new lineage in the global eukaryote phylogeny. Collodictyon shares cellular characteristics with Excavata and Amoebozoa, such as ventral feeding groove supported by microtubular structures and the ability to form thin and broad pseudopods. These may therefore be ancient morphological features among eukaryotes. Overall, this shows that Collodictyon is a key lineage to understand early eukaryote evolution.

Show MeSH