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Quest for Orthologs Entails Quest for Tree of Life: In Search of the Gene Stream.

Boeckmann B, Marcet-Houben M, Rees JA, Forslund K, Huerta-Cepas J, Muffato M, Yilmaz P, Xenarios I, Bork P, Lewis SE, Gabaldón T, Quest for Orthologs Species Tree Working Gro - Genome Biol Evol (2015)

Bottom Line: Topological differences are observed not only at deep speciation events, but also within younger clades, such as Hominidae, Rodentia, Laurasiatheria, or rosids.The evolutionary relationships of 27 archaea and bacteria are highly inconsistent.The largest concordant species tree includes 77 of the QfO reference organisms at the most.

View Article: PubMed Central - PubMed

Affiliation: Swiss-Prot, Swiss Institute of Bioinformatics, Geneva, Switzerland brigitte.boeckmann@isb-sib.ch.

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Related in: MedlinePlus

Overview of critical spots in reconstructed species phylogenies. For lack of space, all species trees were pruned to include only species which illustrate yet unresolved phylogenies and contradicting topologies. Color codes: Light green = topologies supporting the consensus tree (fig. 3); dark green = topologies supporting the consensus tree with significant support; red = topologies differ from the consensus tree; dark red = topologies with significant support differ from the consensus tree; light gray = unresolved and/or unknown topologies.
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evv121-F2: Overview of critical spots in reconstructed species phylogenies. For lack of space, all species trees were pruned to include only species which illustrate yet unresolved phylogenies and contradicting topologies. Color codes: Light green = topologies supporting the consensus tree (fig. 3); dark green = topologies supporting the consensus tree with significant support; red = topologies differ from the consensus tree; dark red = topologies with significant support differ from the consensus tree; light gray = unresolved and/or unknown topologies.

Mentions: In eukaryotes, 67% (80/119) of the internal nodes of a rooted binary tree are congruent, 79% (94/119) are congruent or compatible (multifurcating), and alternative phylogenies are suggested for 21% (25/119) of the internal nodes. Various reasons can be given for the topological differences within the eukaryotic clade. Tree reconstruction artifacts are frequently explained by the lack of a phylogenetic signal or the failing to discriminate a phylogenetic signal from noise. The former is commonly observed in closely related species, species which diverged in a short interval from a common lineage (short common branch length) or in genes under strong structural and functional constraints, thus evolving at a low rate and lacking shared traits. When homoplasy prevails synapomorphy in genes of fast-evolving species, taxa tend to be grouped by mistake—an artifact known as LBA (Schulmeister 2004). For the 147 QfO reference organisms, such knowledge can, for instance, help explain topological incongruence observed for discrete representatives of invertebrate clades sampled along the human lineage as well as for species which diverged early from major clades such as ecdysozoans. Differing phylogenies are not only observed at deep nodes, but also at recent speciation events (figs. 2 and 3A). The phylogeny of Homininae is an example: The topology is unresolved in the NCBI classification, and a monophyletic origin of chimp and gorilla is suggested by sToL. Opentree implemented a resolved but differing species history—human being more closely related to chimp than to gorilla—based on relevant published phylogenies. One of the underlying studies is a recent phylogenetic analysis of complete mitochondrial primate genomes that provides significant support for a common ancestor of human and chimp after the divergence of gorilla, which is in agreement with many other clade-specific analyses (Pozzi et al. 2014). Within the mammalian branch, we note two further clades with contradicting phylogenies: Glires and Laurasiatheria. Within the first group, the rodents Cavia porcellus and Spermophilus tridecemlineatus show an interchanged divergence order, and each of the two topologies is suggested by two of the four species trees that include the relevant QfO reference organisms. Tree-HC provides significant branch support for a monophyletic origin of Murinae and C. porcellus, and Opentree has implemented supporting results for the same topology. For Laurasiatheria, none of the species trees suggest the same phylogeny. For the same clades, incongruence is also observed in various published phylogenies, thus indicating that phylogenetic signals which are derived from the different data sets are ambiguous.Fig. 2.—


Quest for Orthologs Entails Quest for Tree of Life: In Search of the Gene Stream.

Boeckmann B, Marcet-Houben M, Rees JA, Forslund K, Huerta-Cepas J, Muffato M, Yilmaz P, Xenarios I, Bork P, Lewis SE, Gabaldón T, Quest for Orthologs Species Tree Working Gro - Genome Biol Evol (2015)

Overview of critical spots in reconstructed species phylogenies. For lack of space, all species trees were pruned to include only species which illustrate yet unresolved phylogenies and contradicting topologies. Color codes: Light green = topologies supporting the consensus tree (fig. 3); dark green = topologies supporting the consensus tree with significant support; red = topologies differ from the consensus tree; dark red = topologies with significant support differ from the consensus tree; light gray = unresolved and/or unknown topologies.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4524488&req=5

evv121-F2: Overview of critical spots in reconstructed species phylogenies. For lack of space, all species trees were pruned to include only species which illustrate yet unresolved phylogenies and contradicting topologies. Color codes: Light green = topologies supporting the consensus tree (fig. 3); dark green = topologies supporting the consensus tree with significant support; red = topologies differ from the consensus tree; dark red = topologies with significant support differ from the consensus tree; light gray = unresolved and/or unknown topologies.
Mentions: In eukaryotes, 67% (80/119) of the internal nodes of a rooted binary tree are congruent, 79% (94/119) are congruent or compatible (multifurcating), and alternative phylogenies are suggested for 21% (25/119) of the internal nodes. Various reasons can be given for the topological differences within the eukaryotic clade. Tree reconstruction artifacts are frequently explained by the lack of a phylogenetic signal or the failing to discriminate a phylogenetic signal from noise. The former is commonly observed in closely related species, species which diverged in a short interval from a common lineage (short common branch length) or in genes under strong structural and functional constraints, thus evolving at a low rate and lacking shared traits. When homoplasy prevails synapomorphy in genes of fast-evolving species, taxa tend to be grouped by mistake—an artifact known as LBA (Schulmeister 2004). For the 147 QfO reference organisms, such knowledge can, for instance, help explain topological incongruence observed for discrete representatives of invertebrate clades sampled along the human lineage as well as for species which diverged early from major clades such as ecdysozoans. Differing phylogenies are not only observed at deep nodes, but also at recent speciation events (figs. 2 and 3A). The phylogeny of Homininae is an example: The topology is unresolved in the NCBI classification, and a monophyletic origin of chimp and gorilla is suggested by sToL. Opentree implemented a resolved but differing species history—human being more closely related to chimp than to gorilla—based on relevant published phylogenies. One of the underlying studies is a recent phylogenetic analysis of complete mitochondrial primate genomes that provides significant support for a common ancestor of human and chimp after the divergence of gorilla, which is in agreement with many other clade-specific analyses (Pozzi et al. 2014). Within the mammalian branch, we note two further clades with contradicting phylogenies: Glires and Laurasiatheria. Within the first group, the rodents Cavia porcellus and Spermophilus tridecemlineatus show an interchanged divergence order, and each of the two topologies is suggested by two of the four species trees that include the relevant QfO reference organisms. Tree-HC provides significant branch support for a monophyletic origin of Murinae and C. porcellus, and Opentree has implemented supporting results for the same topology. For Laurasiatheria, none of the species trees suggest the same phylogeny. For the same clades, incongruence is also observed in various published phylogenies, thus indicating that phylogenetic signals which are derived from the different data sets are ambiguous.Fig. 2.—

Bottom Line: Topological differences are observed not only at deep speciation events, but also within younger clades, such as Hominidae, Rodentia, Laurasiatheria, or rosids.The evolutionary relationships of 27 archaea and bacteria are highly inconsistent.The largest concordant species tree includes 77 of the QfO reference organisms at the most.

View Article: PubMed Central - PubMed

Affiliation: Swiss-Prot, Swiss Institute of Bioinformatics, Geneva, Switzerland brigitte.boeckmann@isb-sib.ch.

Show MeSH
Related in: MedlinePlus