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A comparative phylogenetic approach for dating whole genome duplication events

B. A. Chapman, J. E. Bowers, S. R. Schulze, A. H. Paterson
2004 Bioinformatics  
Results: We describe a large-scale approach to estimate the timing of duplication events in a phylogenetic context.  ...  Motivation: Whole genome duplications have played a major role in determining the structure of eukaryotic genomes.  ...  Estill for valuable comments on the manuscript, and J. Kissinger and E. Kraemer for suggestions on the techniques. B.C. is supported by a Howard Hughes predoctoral fellowship.  ... 
doi:10.1093/bioinformatics/bth022 pmid:14734308 fatcat:y2qeodb65fauphnq5rpxf2d3ma

Tetraodon genome confirms Takifugu findings: most fish are ancient polyploids

Yves Van de Peer
2004 Genome Biology  
Ray-finned fish underwent a whole-genome duplication some 350 million years ago that might explain their evolutionary success.  ...  An evolutionary hypothesis suggested by studies of the genome of the tiger pufferfish Takifugu rubripes has now been confirmed by comparison with the genome of a close relative, the spotted green pufferfish  ...  Second, by using a comparative approach in which they compared the Tetraodon genome with that of human, which has not undergone the genome-duplication event (Figure 1 ), Jaillon et al.  ... 
doi:10.1186/gb-2004-5-12-250 pmid:15575976 pmcid:PMC545788 fatcat:ogxg65eudnawtmflznthjd2nye

From 2R to 3R: evidence for a fish-specific genome duplication (FSGD)

Axel Meyer, Yves Van de Peer
2005 Bioessays  
(23) A similar estimate for the FSGD was obtained by Christoffels et al. (33) who followed a similar approach when analyzing the whole Takifugu genome.  ...  point for the dating of gene duplication events.  ... 
doi:10.1002/bies.20293 pmid:16108068 fatcat:u2qq5isx7vhvlfqi4wt6gpdfta

Assigning duplication events to relative temporal scales in genome-wide studies

J. Huerta-Cepas, T. Gabaldon
2010 Bioinformatics  
We conclude that the topology-based approach is more appropriate for assigning duplications to temporal scales when analyses need to include ancient events, and that the study of recent duplications may  ...  of a reliable set of gene pairs duplicated in a single event.  ...  ACKNOWLEDGEMENT The authors wish to thank Leonardo Arbiza for providing interesting comments to this work.  ... 
doi:10.1093/bioinformatics/btq609 pmid:21075746 fatcat:is5zggvik5c7jfxlyysa2ojaai

Major events in the genome evolution of vertebrates: Paranome age and size differ considerably between ray-finned fishes and land vertebrates

K. Vandepoele, W. De Vos, J. S. Taylor, A. Meyer, Y. Van de Peer
2004 Proceedings of the National Academy of Sciences of the United States of America  
In addition, analysis of >150 block duplications in the Fugu genome clearly supports a fish-specific genome duplication (Ϸ320 million years ago) that coincided with the vast radiation of most modern ray-finned  ...  Both relative and absolute dating of the complete predicted set of protein-coding genes suggest that initial genome duplications, estimated to have occurred at least 600 million years ago, shaped the genome  ...  K.V. and W.D.V. thank the Vlaams Instituut voor de Bevordering van het Wetenschappelijk-Technologisch Onderzoek in de Industrie for a predoctoral fellowship.  ... 
doi:10.1073/pnas.0307968100 pmid:14757817 pmcid:PMC341801 fatcat:s3246e5lujcorhaunnwc33qdnq

Turning the clock back on ancient genome duplication

Cathal Seoighe
2003 Current Opinion in Genetics and Development  
before the most recent duplication event.  ...  Recent contributions have gone on to refine date estimates for these duplications and, in the case of Arabidopsis, to infer additional, more ancient, rounds of duplication by reconstructing gene order  ...  Acknowledgements I am grateful to Victoria Nembaware and Chris Gehring for critical comments and suggestions.  ... 
doi:10.1016/j.gde.2003.10.005 pmid:14638327 fatcat:byfexllewza2derh54ok3rwudq

Extending the Reach of Phylogenetic Inference [chapter]

Bernard M. E. Moret
2013 Lecture Notes in Computer Science  
Comparing the complete genomes of vertebrates is a daunting problem.  ...  The new approaches include an extension of the time-tested and universally used comparative method, as well as applications of phylogenetic approaches to genomic transcripts and cell types, objects not  ...  Combining large-scale duplication events with rearrangements events, for instance, appears crucial to the understanding of genomic evolution, but remains poorly solved to date, even though researchers  ... 
doi:10.1007/978-3-642-40453-5_1 fatcat:ilmiouqtdnbzlodqtzumcnsywi

Plants with double genomes might have had a better chance to survive the Cretaceous-Tertiary extinction event

J. A. Fawcett, S. Maere, Y. Van de Peer
2009 Proceedings of the National Academy of Sciences of the United States of America  
Starting from paralogous genes lying in duplicated segments or identified in large expressed sequence tag collections, we dated these youngest duplication events through penalized likelihood phylogenetic  ...  Most flowering plants have been shown to be ancient polyploids that have undergone one or more whole genome duplications early in their evolution.  ...  Here, we investigated the timing of these younger genome duplication events in plants by using phylogenetic approaches.  ... 
doi:10.1073/pnas.0900906106 pmid:19325131 pmcid:PMC2667025 fatcat:jjdimpxcmfcynkvho7vic34rru

The flowering world: a tale of duplications

Yves Van de Peer, Jeffrey A. Fawcett, Sebastian Proost, Lieven Sterck, Klaas Vandepoele
2009 Trends in Plant Science  
Acknowledgements We thank the Bioinformatics and Evolutionary Genomics team, as well as Riccardo Velasco and Francesco Salamini for discussions. Steven Maere is acknowledged for technical help.  ...  S.P. is indebted to the Institute for the Promotion of Innovation by Science and Technology in Flanders (IWT). K.V. is a postdoctoral fellow of the Fund for Scientific Research Flanders (FWO).  ...  so, in whole-genome duplications (WGDs).  ... 
doi:10.1016/j.tplants.2009.09.001 pmid:19818673 fatcat:sjepb6vidvbgbjgh3pbe636tiq

Constraining the timing of whole genome duplication in plant evolutionary history

James W. Clark, Philip C. J. Donoghue
2017 Proceedings of the Royal Society of London. Biological Sciences  
We apply this approach to dating the two major genome duplication events shared by all seed plants (z) and flowering plants (1) , estimating the seed plant WGD event at 399-381 Ma, and the angiosperm WGD  ...  Whole genome duplication (WGD) has occurred in many lineages within the tree of life and is invariably invoked as causal to evolutionary innovation, increased diversity, and extinction resistance.  ...  We thank members of the Bristol Palaeobiology Research Group for discussion and two anonymous reviewers for their comments and improvements to the manuscript.  ... 
doi:10.1098/rspb.2017.0912 pmid:28679730 pmcid:PMC5524505 fatcat:p44xupq5gzcijowq4nfrhfaqcq

MAXIMUM LIKELIHOOD PHYLOGENETIC RECONSTRUCTION FROM HIGH-RESOLUTION WHOLE-GENOME DATA AND A TREE OF 68 EUKARYOTES

YU LIN, FEI HU, JIJUN TANG, BERNARD M. E. MORET
2012 Biocomputing 2013  
We describe a maximum likelihood (ML) approach for phylogenetic analysis that takes into account genome rearrangements as well as duplications, insertions, and losses.  ...  Comparative genomics, evolutionary biology, and cancer research all require tools to elucidate the mechanisms, history, and consequences of those evolutionary events, while phylogenetics could use whole-genome  ...  Results for a dataset of high-resolution eukaryotic genomes Conclusion In spite of many compelling reasons for using whole-genome data in phylogenetic reconstruction, practice to date has continued to  ... 
doi:10.1142/9789814447973_0028 fatcat:m2ffeprzf5c4nbcojuw2z5opii

Genome duplication and multiple evolutionary origins of complex migratory behavior in Salmonidae

Markos A. Alexandrou, Brian A. Swartz, Nicholas J. Matzke, Todd H. Oakley
2013 Molecular Phylogenetics and Evolution  
Our study represents the first attempt to estimate the absolute timing of a complex behavioral trait in relation to a genome duplication event.  ...  Multiple rounds of whole genome duplication have repeatedly marked the evolution of vertebrates, and correlate strongly with morphological innovation.  ...  Acknowledgements We acknowledge support from the Center for Scientific Com-  ... 
doi:10.1016/j.ympev.2013.07.026 pmid:23933489 fatcat:3zhuecqfnzex5gobv7noxh2nyq

Surviving the K-T mass extinction: New perspectives of polyploidization in angiosperms

D. E. Soltis, J. G. Burleigh
2009 Proceedings of the National Academy of Sciences of the United States of America  
(11) take a novel approach to date ancient polyploidy that combines phylogenetic comparisons and methods for dating duplications that do not assume a constant rate of molecular evolution (16) .  ...  350 million years are the result of whole genome duplications (WGDs) (9) .  ... 
doi:10.1073/pnas.0901994106 pmid:19336584 pmcid:PMC2667080 fatcat:zq2nxnpwiva37hqkeqr4fzscum

PLAZA: A Comparative Genomics Resource to Study Gene and Genome Evolution in Plants

S. Proost, M. Van Bel, L. Sterck, K. Billiau, T. Van Parys, Y. Van de Peer, K. Vandepoele
2009 The Plant Cell  
Precomputed data sets cover homologous gene families, multiple sequence alignments, phylogenetic trees, intra-species whole-genome dotplots and genomic colinearity between species.  ...  Here, we describe PLAZA, an online platform for plant comparative genomics (http://bioinformatics.psb.ugent.be/plaza/).  ...  because out-paralogs (homologs from duplication events pre-dating speciation) will not be grouped.  ... 
doi:10.1105/tpc.109.071506 pmid:20040540 pmcid:PMC2814516 fatcat:aojc3qdqnjgq3lwwivu67zixdy

Detection and Phylogenetic Assessment of Conserved Synteny Derived from Whole Genome Duplications [chapter]

Shigehiro Kuraku, Axel Meyer
2012 Msphere  
Identification of intragenomic conservation of gene compositions in multiple chromosomal segments led to evidence of whole genome (WGDs) duplications.  ...  The process by which WGDs have been maintained and decayed provides us with clues for understanding how the genome evolves.  ...  Whether a new duplicate arose in a small-scale event (for example, tandem duplication) or large-scale event (for example, WGD), the fate of the new duplicate largely depends on the pattern in functional  ... 
doi:10.1007/978-1-61779-582-4_14 pmid:22407717 fatcat:hmce4j5hjrctroj76vig6broge
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