The Tree versus the Forest: The Fungal Tree of Life and the Topological Diversity within the Yeast Phylome
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{"title"=>"The Tree versus the forest: The fungal tree of life and the topological diversity within the yeast phylome", "type"=>"journal", "authors"=>[{"first_name"=>"Marina", "last_name"=>"Marcet-Houben", "scopus_author_id"=>"27267797400"}, {"first_name"=>"Toni", "last_name"=>"Gabaldón", "scopus_author_id"=>"57188954266"}], "year"=>2009, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "isbn"=>"1932-6203", "pmid"=>"19190756", "scopus"=>"2-s2.0-84857229990", "doi"=>"10.1371/journal.pone.0004357", "sgr"=>"84857229990", "pui"=>"618783990"}, "id"=>"3de54a61-955f-31a7-a3c7-d27a1fe822b9", "abstract"=>"A recurrent topic in phylogenomics is the combination of various sequence alignments to reconstruct a tree that describes the evolutionary relationships within a group of species. However, such approach has been criticized for not being able to properly represent the topological diversity found among gene trees. To evaluate the representativeness of species trees based on concatenated alignments, we reconstruct several fungal species trees and compare them with the complete collection of phylogenies of genes encoded in the Saccharomyces cerevisiae genome. We found that, despite high levels of among-gene topological variation, the species trees do represent widely supported phylogenetic relationships. Most topological discrepancies between gene and species trees are concentrated in certain conflicting nodes. We propose to map such information on the species tree so that it accounts for the levels of congruence across the genome. We identified the lack of sufficient accuracy of current alignment and phylogenetic methods as an important source for the topological diversity encountered among gene trees. Finally, we discuss the implications of the high levels of topological variation for phylogeny-based orthology prediction strategies.", "link"=>"http://www.mendeley.com/research/tree-versus-forest-fungal-tree-life-topological-diversity-within-yeast-phylome", "reader_count"=>110, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>7, "Student > Doctoral Student"=>1, "Researcher"=>36, "Student > Ph. D. Student"=>39, "Student > Postgraduate"=>5, "Student > Master"=>12, "Student > Bachelor"=>5, "Lecturer"=>2, "Professor"=>3}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>7, "Student > Doctoral Student"=>1, "Researcher"=>36, "Student > Ph. D. Student"=>39, "Student > Postgraduate"=>5, "Student > Master"=>12, "Student > Bachelor"=>5, "Lecturer"=>2, "Professor"=>3}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Engineering"=>2, "Environmental Science"=>3, "Biochemistry, Genetics and Molecular Biology"=>16, "Mathematics"=>1, "Agricultural and Biological Sciences"=>78, "Medicine and Dentistry"=>2, "Philosophy"=>1, "Chemistry"=>1, "Computer Science"=>2, "Immunology and Microbiology"=>2}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>2}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Chemistry"=>{"Chemistry"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>78}, "Computer Science"=>{"Computer Science"=>2}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>16}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>2}, "Environmental Science"=>{"Environmental Science"=>3}, "Philosophy"=>{"Philosophy"=>1}}, "reader_count_by_country"=>{"United States"=>7, "United Kingdom"=>3, "Spain"=>6, "Canada"=>1, "Netherlands"=>1, "Korea (South)"=>1, "Denmark"=>1, "Poland"=>1, "Brazil"=>1, "Mexico"=>1, "Uganda"=>1, "South Africa"=>1, "France"=>1, "Chile"=>1, "Germany"=>4}, "group_count"=>3}

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  • {"files"=>["https://ndownloader.figshare.com/files/449484", "https://ndownloader.figshare.com/files/449535", "https://ndownloader.figshare.com/files/449574", "https://ndownloader.figshare.com/files/449611", "https://ndownloader.figshare.com/files/449659", "https://ndownloader.figshare.com/files/449769", "https://ndownloader.figshare.com/files/449818", "https://ndownloader.figshare.com/files/449861", "https://ndownloader.figshare.com/files/449943", "https://ndownloader.figshare.com/files/449985"], "description"=>"<div><p>A recurrent topic in phylogenomics is the combination of various sequence alignments to reconstruct a tree that describes the evolutionary relationships within a group of species. However, such approach has been criticized for not being able to properly represent the topological diversity found among gene trees. To evaluate the representativeness of species trees based on concatenated alignments, we reconstruct several fungal species trees and compare them with the complete collection of phylogenies of genes encoded in the <em>Saccharomyces cerevisiae</em> genome. We found that, despite high levels of among-gene topological variation, the species trees do represent widely supported phylogenetic relationships. Most topological discrepancies between gene and species trees are concentrated in certain conflicting nodes. We propose to map such information on the species tree so that it accounts for the levels of congruence across the genome. We identified the lack of sufficient accuracy of current alignment and phylogenetic methods as an important source for the topological diversity encountered among gene trees. Finally, we discuss the implications of the high levels of topological variation for phylogeny-based orthology prediction strategies.</p></div>", "links"=>[], "tags"=>["fungal", "topological", "yeast", "phylome"], "article_id"=>148600, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Marina Marcet-Houben", "Toni Gabaldón"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0004357.s001", "https://dx.doi.org/10.1371/journal.pone.0004357.s002", "https://dx.doi.org/10.1371/journal.pone.0004357.s003", "https://dx.doi.org/10.1371/journal.pone.0004357.s004", "https://dx.doi.org/10.1371/journal.pone.0004357.s005", "https://dx.doi.org/10.1371/journal.pone.0004357.s006", "https://dx.doi.org/10.1371/journal.pone.0004357.s007", "https://dx.doi.org/10.1371/journal.pone.0004357.s008", "https://dx.doi.org/10.1371/journal.pone.0004357.s009", "https://dx.doi.org/10.1371/journal.pone.0004357.s010"], "stats"=>{"downloads"=>58, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/The_Tree_versus_the_Forest_The_Fungal_Tree_of_Life_and_the_Topological_Diversity_within_the_Yeast_Phylome/148600", "title"=>"The Tree versus the Forest: The Fungal Tree of Life and the Topological Diversity within the Yeast Phylome", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2009-02-03 02:23:20"}
  • {"files"=>["https://ndownloader.figshare.com/files/909316"], "description"=>"<p>A) Phylogenetic tree representing the evolutionary relationships among the 60 fungal species considered in the study, as resulting from the ML analysis of the concatenated alignment of 69 widespread proteins. Numbers on the nodes indicate two different types of support values. The first number indicates the phylome support for that node, that is, the percentage of trees in the phylome that support the specific arrangement of the three or four groups of species defined by its daughter nodes (see B). An asterisk next to this number indicates that the topology obtained by the species tree is not the most common among the trees in the phylome. Whenever there is a second number (in bold), this indicates the bootstrap support when this is lower than 100. Partitions that do not have this second number have a bootstrap support of 100. Branches with dashed lines indicate evolutionary relationships that are supported by less than 50% of the trees in the phylome. B) Schematic representation of the two types of support values for the different nodes in the tree. X indicates the phylome support for the specific topology indicated by that node. Two types of nodes do exist attending to the number of partitions delimited by their daughter nodes. A first class of nodes (top), delimit relative topologies of three partitions (A, B and C), whereas a second class (bottom) delimit four partitions (A, B, C and D). Phylome support values indicate the percentage of trees that show exactly the relative grouping of the three or four groups delimited by the node. This percentage is expressed over the fraction of trees that contain at least one species from each of the partitions considered. The second number (Y) indicates the bootstrap support for the partition delimited by that node, but does not provide specific support for the specific arrangement of the sub-partitions within that partition. C) Correlation between the fungal species tree topologies recovered by the individual trees included in the concatenated alignment (Y axis) and all the trees in the phylome (X axis). In both cases the fraction of trees that are compatible with a given topology, as computed with the topology scanning algorithm, is represented.</p>", "links"=>[], "tags"=>["fungal"], "article_id"=>579776, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Marina Marcet-Houben", "Toni Gabaldón"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0004357.g001", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_Fungal_species_tree_/579776", "title"=>"The Fungal species tree.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-02-03 02:42:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/909418"], "description"=>"<p>The synteny based and manually curated orthology predictions available at YGOB database <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0004357#pone.0004357-Byrne1\" target=\"_blank\">[18]</a> is taken as a golden set to compute the number of true positives (TP), false positives (FP) and false negatives (FN) yielded by each method. For each method, the sensitivity S = TP/(TP+FN) and the positive predictive value P = TP/(TP+FP) are computed.</p>", "links"=>[], "tags"=>["orthology", "inference"], "article_id"=>579877, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Marina Marcet-Houben", "Toni Gabaldón"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0004357.g002", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_different_orthology_inference_algorithms_/579877", "title"=>"Comparison of different orthology inference algorithms.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-02-03 02:44:37"}

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