TY - GEN
T1 - The trees in the peaks
AU - Sankoff, David
AU - Zheng, Chunfang
AU - Lyons, Eric
AU - Tang, Haibao
N1 - Funding Information:
Research supported in part by grants from the Natural Sciences and Engineering Research Council of Canada (NSERC). DS holds the Canada Research Chair in Mathematical Genomics.
Publisher Copyright:
© Springer International Publishing Switzerland 2016.
PY - 2016
Y1 - 2016
N2 - We suggest a gene-tree/species-tree approach to speciation and whole genome duplication (WGD) to resolve the occurrence of these events in phylogenetic analysis. We propose a more principled way of estimating the parameters of gene divergence and fractionation than the standard mixture of normals analysis. We formulate an algorithm for resolving data on local peaks in the distributions of duplicate gene similarities for a number of related genomes. Illustrating with a comprehensive analysis of WGD-origin duplicate gene data from six members of the family Brassicaceae, we discuss the effects of variable evolutionary rates and data degradation due to fractionation. We introduce the notion of peak tree, as a template for all gene trees evolving by speciation, WGD and fractionation.
AB - We suggest a gene-tree/species-tree approach to speciation and whole genome duplication (WGD) to resolve the occurrence of these events in phylogenetic analysis. We propose a more principled way of estimating the parameters of gene divergence and fractionation than the standard mixture of normals analysis. We formulate an algorithm for resolving data on local peaks in the distributions of duplicate gene similarities for a number of related genomes. Illustrating with a comprehensive analysis of WGD-origin duplicate gene data from six members of the family Brassicaceae, we discuss the effects of variable evolutionary rates and data degradation due to fractionation. We introduce the notion of peak tree, as a template for all gene trees evolving by speciation, WGD and fractionation.
KW - Algorithms
KW - Brassicaceae
KW - Gene tree
KW - Mixture of distributions
KW - Species tree
KW - Whole genome duplication
UR - http://www.scopus.com/inward/record.url?scp=84979088371&partnerID=8YFLogxK
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U2 - 10.1007/978-3-319-38827-4_1
DO - 10.1007/978-3-319-38827-4_1
M3 - Conference contribution
AN - SCOPUS:84979088371
SN - 9783319388267
T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
SP - 3
EP - 14
BT - Algorithms for Computational Biology - 3rd International Conference, AlCoB 2016, Proceedings
A2 - Vega-Rodríguez, Miguel A.
A2 - Santander-Jiménez, Sergio
A2 - Botón-Fernández, María
A2 - Martín-Vide, Carlos
PB - Springer-Verlag
T2 - 3rd International Conference on Algorithms for Computational Biology, AlCoB 2016
Y2 - 21 June 2016 through 22 June 2016
ER -