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Using highly conserved low—copy nuclear genes to reconstruct well-resolved phylogenies of animals,fungi,plants and highly divergent eukaryotes

David Geiser  
【摘要】:正A comprehensive and reliable eukaryotic tree of life is important for many aspects of biological studies from comparative developmental and physiological analyses to translational medicine and agriculture.Both gene-rich and taxon-rich approaches are effective strategies to improve phylogenetic accuracy and are greatly facilitated by marker genes that are universally distributed,well conserved and orthologous across eukaryotes.We have identified over 900 genes useful for phylogenomic studies and show that these genes can robustly resolve the eukaryotic phylogeny,even for difficult deep eukaryotic relationships.In addition,we demonstrate that a smaller subset(~30) of these genes could resolve controversial relationships among widely divergent taxa and at various depths in the eukaryotic tree of life, providing strong support for difficult relationships such as the monophyly and branching order of some eukaryotic supergroups.Within supergroups,these marker genes resulted in fungal phylogenies that are congruent with previous phylogenies,with Microsporidia as sister to fungi.In animals,we found high supports for both deep level branching patterns such as the monophyly of Protostomia and Ecdysozoa,and specific hypotheses for rooting the placental mammals.These genes could be obtained from both plants and fungi through PCR with degenerate primers,and facilitated construction of highly supported phylogenies with resolved relationships among angiosperms.Among the well-supported angiosperm relationships are well-known major groups such as monophyly of eudicots,monocots,magnoliids,and many ordinal clades, as well as the placement of Amborellales,Nymphaeales,and Austrobaileyales as successive sister groups of other flowering plants.The sequence comparison among angiosperms indicates that these genes contain more informative sites than the commonly used chloroplast genes,and that closely related species still show sequence divergence in some coding regions and in introns.They are excellent for both gene-rich and taxon-rich analyses and facilitate a more complete understanding of the eukaryotic tree of life at different levels of divergence.

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