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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.

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Changes in bootstrap support for key nodes in the inferred trees as fast-evolving sites were removed. Site rates were estimated from an alignment without two Malawimonas and Collodictyon species (76 taxa). Sites were then removed in 5% increments from alignments consisting of (A) 79 taxa (including Collodictyon and Malawimonas) and (B) 77 taxa (including Collodictyon). ML Bootstrap values (BP) for Collodictyon + Malawimonas, unikonts, bikonts, and Opisthokonta (used as a reference) were calculated under the PROTCATLGF model in RAxML v7.2.6. BP values shaded by gray rectangles are listed in table 1 and supplementary figure S6 (Supplementary Material online).
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fig4: Changes in bootstrap support for key nodes in the inferred trees as fast-evolving sites were removed. Site rates were estimated from an alignment without two Malawimonas and Collodictyon species (76 taxa). Sites were then removed in 5% increments from alignments consisting of (A) 79 taxa (including Collodictyon and Malawimonas) and (B) 77 taxa (including Collodictyon). ML Bootstrap values (BP) for Collodictyon + Malawimonas, unikonts, bikonts, and Opisthokonta (used as a reference) were calculated under the PROTCATLGF model in RAxML v7.2.6. BP values shaded by gray rectangles are listed in table 1 and supplementary figure S6 (Supplementary Material online).

Mentions: To further investigate the evolutionary origin of Collodictyon, we attempted to increase the phylogenetic versus nonphylogenetic signal ratio by removing the fastest evolving sites, which have been shown to bear the highest degree of homoplasy (Brinkmann and Philippe 1999). Because our analyses suggested that Collodictyon is excluded from the known eukaryote supergroups, we successively monitored the statistical support for unikonts and bikonts. Most notably, the bootstrap support for unikonts increased as the fastest evolving sites were removed, reaching a peak value of 96% after removing 20% of sites (table 1 and fig. 4B), whereas the bikonts remained highly supported (BP > 95%) during this experiment. Moreover, a Bayesian phylogeny constructed with the alignment removing the 20% fastest evolving sites showed strong evidence for excluding Collodictyon from unikonts (PP = 1.00; CAT-BP = 93%) or bikonts (PP = 1.00; CAT-BP = 100%) (fig. 5 and table 1). Cross-validation test showed that the CAT model fits our data better than the LG model with a score averaged over 10 replicates of 2451.36 ± 132.9 (all replicates favored the “CAT” model). The global phylogeny inferred from the CAT model should be favored, although both models recovered the same position of Collodictyon (fig. 5B and supplementary fig. S6B, Supplementary Material online). Hence, after the removal of the noisiest positions in our alignment, Collodictyon was robustly placed close to the bifurcation of unikonts and bikonts.


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)

Changes in bootstrap support for key nodes in the inferred trees as fast-evolving sites were removed. Site rates were estimated from an alignment without two Malawimonas and Collodictyon species (76 taxa). Sites were then removed in 5% increments from alignments consisting of (A) 79 taxa (including Collodictyon and Malawimonas) and (B) 77 taxa (including Collodictyon). ML Bootstrap values (BP) for Collodictyon + Malawimonas, unikonts, bikonts, and Opisthokonta (used as a reference) were calculated under the PROTCATLGF model in RAxML v7.2.6. BP values shaded by gray rectangles are listed in table 1 and supplementary figure S6 (Supplementary Material online).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

fig4: Changes in bootstrap support for key nodes in the inferred trees as fast-evolving sites were removed. Site rates were estimated from an alignment without two Malawimonas and Collodictyon species (76 taxa). Sites were then removed in 5% increments from alignments consisting of (A) 79 taxa (including Collodictyon and Malawimonas) and (B) 77 taxa (including Collodictyon). ML Bootstrap values (BP) for Collodictyon + Malawimonas, unikonts, bikonts, and Opisthokonta (used as a reference) were calculated under the PROTCATLGF model in RAxML v7.2.6. BP values shaded by gray rectangles are listed in table 1 and supplementary figure S6 (Supplementary Material online).
Mentions: To further investigate the evolutionary origin of Collodictyon, we attempted to increase the phylogenetic versus nonphylogenetic signal ratio by removing the fastest evolving sites, which have been shown to bear the highest degree of homoplasy (Brinkmann and Philippe 1999). Because our analyses suggested that Collodictyon is excluded from the known eukaryote supergroups, we successively monitored the statistical support for unikonts and bikonts. Most notably, the bootstrap support for unikonts increased as the fastest evolving sites were removed, reaching a peak value of 96% after removing 20% of sites (table 1 and fig. 4B), whereas the bikonts remained highly supported (BP > 95%) during this experiment. Moreover, a Bayesian phylogeny constructed with the alignment removing the 20% fastest evolving sites showed strong evidence for excluding Collodictyon from unikonts (PP = 1.00; CAT-BP = 93%) or bikonts (PP = 1.00; CAT-BP = 100%) (fig. 5 and table 1). Cross-validation test showed that the CAT model fits our data better than the LG model with a score averaged over 10 replicates of 2451.36 ± 132.9 (all replicates favored the “CAT” model). The global phylogeny inferred from the CAT model should be favored, although both models recovered the same position of Collodictyon (fig. 5B and supplementary fig. S6B, Supplementary Material online). Hence, after the removal of the noisiest positions in our alignment, Collodictyon was robustly placed close to the bifurcation of unikonts and bikonts.

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