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From event-labeled gene trees to species trees

Maribel Hernandez-Rosales, Marc Hellmuth, Nicolas Wieseke, Katharina T Huber, Vincent Moulton, Peter F Stadler
2012 BMC Bioinformatics  
Conclusions: The knowledge of event labels in a gene tree strongly constrains the possible species tree and, for a given species tree, also the possible reconciliation maps.  ...  Simulated data shows that the event-labeled gene trees convey a large amount of information on underlying species trees, even for a large percentage of losses.  ...  We discussed here the properties of reconciliation maps μ from a gene tree T along with an event labelling map t and a gene to species assignment map σ to a species tree S.  ... 
doi:10.1186/1471-2105-13-s19-s6 fatcat:2zo2nx677zf67jw2ecjjezsj5a

From event labeled gene trees to species trees [article]

Maribel Hernandez-Rosales, Marc Hellmuth, Nicolas Wieseke, Katharina T. Huber, Vincent Moulton, Peter F. Stadler
2017 arXiv   pre-print
Conclusions: The knowledge of event labels in a gene tree strongly constrains the possible species tree and, for a given species tree, also the possible reconciliation maps.  ...  Simulated data shows that the event-labeled gene trees convey a large amount of information on underlying species trees, even for a large percentage of losses.  ...  We discussed here the properties of reconciliation maps µ from a gene tree T along with an event labelling map t and a gene to species assignment map σ to a species tree S and show that (T,t) event labeled  ... 
arXiv:1705.04190v1 fatcat:t4ghynm7uvcm3gxzrfw6kbltni

Gene-Tree Reconciliation with MUL-Trees to Resolve Polyploidy Events

W. C. Thomas Gregg, S. Hussain Ather, Matthew W. Hahn
2017 Systematic Biology  
Here, we have adapted an algorithm for topologybased gene-tree reconciliation to work with multi-labeled trees (MUL-trees).  ...  This means that common methods for estimating the parental lineages of allopolyploidy events are not accurate, and can lead to incorrect inferences about the number of gene duplications and losses.  ...  Reconciliation with a gene tree from an allopolyploid lineage. a) A representative gene tree is shown, with every homolog labeled, including the two homoeologs from allopolyploid species B.  ... 
doi:10.1093/sysbio/syx044 pmid:28419377 fatcat:72xws34ehrh4pdsmfjlnnir57q

Gene-tree reconciliation with MUL-trees to resolve polyploidy events [article]

Gregg W.C. Thomas, S. Hussain Ather, Matthew W. Hahn
2016 bioRxiv   pre-print
Here, we have adapted an algorithm for topology-based gene-tree reconciliation to work with multi-labeled trees (MUL-trees).  ...  This means that common methods for estimating the parental lineages of allopolyploidy events are not accurate, and can lead to incorrect inferences about the number of gene duplications and losses.  ...  These tips map to species A and 189 B, respectively, and the first node in the singly-labeled species tree (going from tips to root) that 190 .  ... 
doi:10.1101/058149 fatcat:4tgprlzc6vewxlbbmgdhiov3vq

Gene Family Evolution by Duplication, Speciation, and Loss

Cedric Chauve, Jean-Philippe Doyon, Nadia El-Mabrouk
2008 Journal of Computational Biology  
First, given a gene tree for a gene family, can the evolutionary history of this family be explained with only speciation and duplication events? Such gene trees are called DS-trees.  ...  We then study a natural extension of this problem: what is the minimum number of gene losses involved in an evolutionary history leading to an observed gene tree or set of gene trees?  ...  Acknowledgments This work was supported by grants from NSERC to Cedric Chauve and Nadia El-Mabrouk and from Simon Fraser University to Cedric Chauve.  ... 
doi:10.1089/cmb.2008.0054 pmid:18781833 fatcat:26v2lhpawrcjzndbe3xlnmux4q

Forbidden Time Travel: Characterization of Time-Consistent Tree Reconciliation Maps

Nikolai Nojgaard, Manuela Geiß, Daniel Merkle, Peter F. Stadler, Nicolas Wieseke, Marc Hellmuth, Marc Herbstritt
2017 Workshop on Algorithms in Bioinformatics  
The aim is then to find a mapping of the gene tree T into the species tree S and, at least implicitly, an event-labeling on the vertices of the gene tree T .  ...  The applications we envision for the theory developed, here, however assume that the gene tree and its event labels are inferred from (sequence) data, i.e., (T ; t, σ) is restricted to those labeled trees  ... 
doi:10.4230/lipics.wabi.2017.17 dblp:conf/wabi/NojgaardGMSWH17 fatcat:3uuyptwf7bboba4j3gjgkl5zya

Biologically feasible gene trees, reconciliation maps and informative triples

Marc Hellmuth
2017 Algorithms for Molecular Biology  
The history of gene families-which are equivalent to event-labeled gene trees-can be reconstructed from empirically estimated evolutionary event-relations containing pairs of orthologous, paralogous or  ...  We provide a polynomial-time algorithm to decide whether there is a species tree for a given event-labeled gene tree, and in the positive case, to construct the species tree and the respective (restricted  ...  Acknowledgements I would like to thank Nikolai Nøjgaard and Nicolas Wieseke for all the outstanding and fruitful discussions!  ... 
doi:10.1186/s13015-017-0114-z pmid:28861118 pmcid:PMC5576477 fatcat:xsigcfjvyjddzob3jtd4uh7chy

Construction of Gene and Species Trees from Sequence Data incl. Orthologs, Paralogs, and Xenologs [article]

Marc Hellmuth, Nicolas Wieseke
2016 arXiv   pre-print
However, existing methods that rely only on 1:1 orthologs to infer species trees are strongly restricted to a small set of allowed genes that provide information about the species tree.  ...  In this work, we introduce a novel method to compute species phylogenies based on sequence data including orthologs, paralogs or even xenologs.  ...  From Sequence Data to Species Trees In this section, we provide the main steps in order to infer event-labeled gene trees and species trees from respective estimated event-relations.  ... 
arXiv:1602.08268v1 fatcat:o6vwgxfcyfdifef6j5gfxkag5i

Biologically Feasible Gene Trees, Reconciliation Maps and Informative Triples [article]

Marc Hellmuth
2017 arXiv   pre-print
The history of gene families - which are equivalent to event-labeled gene trees - can be reconstructed from empirically estimated evolutionary event-relations containing pairs of orthologous, paralogous  ...  We provide a polynomial-time algorithm to decide whether there is a species tree for a given event-labeled gene tree, and in the positive case, to construct the species tree and the respective (restricted  ...  These algorithms require as input an event-labeled gene tree and species tree.  ... 
arXiv:1701.07689v4 fatcat:lj3ls6mdofgbnjkqtum45mvkpe

Predicting the Evolution of Syntenies—An Algorithmic Review

Nadia El-Mabrouk
2021 Algorithms  
Although the reconciliation approach between a gene tree and a species tree addresses the problem of inferring such events for single-gene families, little effort has been dedicated to the generalization  ...  However, syntenies also evolve through other events modifying their content in genes, such as duplications, losses or horizontal gene transfers, i.e., the movement of genes from one species to another.  ...  Figure 6 . 6 (1) Two gene trees (red and blue) and a species tree S. Leaves of the gene trees are labeled according to the genome the corresponding gene belongs to.  ... 
doi:10.3390/a14050152 fatcat:cqnfgv3st5a3dipcje7dcnk6wm

Effect of Incomplete Lineage Sorting on Tree-Reconciliation-Based Inference of Gene Duplication [chapter]

Yu Zheng, Louxin Zhang
2013 Lecture Notes in Computer Science  
We quantify the effect of ILS on gene duplication inference in a species tree in terms of the expected number of false duplication events inferred from reconciling a random gene tree, which occurs with  ...  In the tree reconciliation approach to infer the duplication history of a gene family, the gene (family) tree is compared to the corresponding species tree.  ...  ACKNOWLEDGMENTS The authors would like to thank the anonymous reviewers for their valuable comments on the first version of this work.  ... 
doi:10.1007/978-3-642-38036-5_26 fatcat:l2r7urkaindobmpfj3lx2g7ux4

A Characterization of the Set of Species Trees that Produce Anomalous Ranked Gene Trees

James H. Degnan, Noah A. Rosenberg, Tanja Stadler
2012 IEEE/ACM Transactions on Computational Biology & Bioinformatics  
Here, we fully characterize the set of unranked species tree topologies that give rise to ARGTs, showing that this set contains all species tree topologies with five or more taxa, with the exceptions of  ...  inference of species trees.  ...  ACKNOWLEDGMENTS This work was supported by grants from the New Zealand Marsden Fund and the Burroughs Wellcome Fund, and by the US National Science Foundation (NSF) grant DBI-1146722.  ... 
doi:10.1109/tcbb.2012.110 pmid:22868677 fatcat:rz73c7gd45bfvksy3elqmw3w7y

Effect of Incomplete Lineage Sorting On Tree-Reconciliation-Based Inference of Gene Duplication

Yu Zheng, Louxin Zhang
2014 IEEE/ACM Transactions on Computational Biology & Bioinformatics  
We quantify the effect of ILS on gene duplication inference in a species tree in terms of the expected number of false duplication events inferred from reconciling a random gene tree, which occurs with  ...  In the tree reconciliation approach to infer the duplication history of a gene family, the gene (family) tree is compared to the corresponding species tree.  ...  ACKNOWLEDGMENTS The authors would like to thank the anonymous reviewers for their valuable comments on the first version of this work.  ... 
doi:10.1109/tcbb.2013.2297913 pmid:26356016 fatcat:yizpxvhi7vbmdcd2asqabfx5k4

On the Multiple Gene Duplication Problem [chapter]

Michael Fellows, Michael Hallett, Ulrike Stege
1998 Lecture Notes in Computer Science  
Multiple Gene Duplication asks to nd the species tree S which requires the fewest numb e r o f m ultiple gene duplication events to be postulated in order to explain a set of gene trees G1; G 2 ; : : :  ...  explain in an evolutionarily meaningful way how the gene trees could have arisen with respect to the species tree.  ...  Previous models for rectifying gene trees with species trees considered a duplication event to e ect one gene at a time.  ... 
doi:10.1007/3-540-49381-6_37 fatcat:etcra64zezfolgrf37xp32sllm

Identifying the Rooted Species Tree from the Distribution of Unrooted Gene Trees under the Coalescent [article]

Elizabeth S. Allman, James H. Degnan, John A. Rhodes
2010 arXiv   pre-print
The length of any pendent branch leading to a leaf of the species tree is also identifiable for any species from which more than one gene is sampled.  ...  This multispecies coalescent model provides a framework for phylogeneticists to infer species trees from gene trees using maximum likelihood or Bayesian approaches.  ...  We also thank two anonymous reviewers, one of whom suggested the extension to nonbinary trees.  ... 
arXiv:0912.4472v2 fatcat:wonlwqkrkbgy3lxbu3szlqlsu4
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