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Reconciliation of Gene and Species Trees [PDF]
BioMed Research International, 2014 The first part of the paper briefly overviews the problem of gene and species trees reconciliation with the focus on defining and algorithmic construction of the evolutionary scenario. Basic ideas are discussed for the aspects of mapping definitions, costs of the mapping and evolutionary scenario, imposing time scales on a scenario, incorporating ...
Rusin, L. Y. +3 more
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Simulating trees with millions of species [PDF]
Bioinformatics, 2020 Abstract Motivation The birth-death (BD) model constitutes the theoretical backbone of most phylogenetic tools for reconstructing speciation/extinction dynamics over time. Performing simulations of reconstructed trees (linking extant taxa) under the BD model in backward time, conditioned on the number
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Gene Trees in Species Trees [PDF]
Systematic Biology, 1997 Exploration of the relationship between gene trees and their containing species trees leads to consideration of how to reconstruct species trees from gene trees and of the concept of phylogeny as a cloud of gene histories. When gene copies are sampled from various species, the gene tree relating these copies might disagree with the species phylogeny ...
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RECONCILIATION WITH NON-BINARY SPECIES TREES [PDF]
Computational Systems Bioinformatics, 2007 Reconciliation extracts information from the topological incongruence between gene and species trees to infer duplications and losses in the history of a gene family. The inferred duplication-loss histories provide valuable information for a broad range of biological applications, including ortholog identification, estimating gene duplication times ...
Benjamin Vernot +3 more
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Species-specific water use by forest tree species: From the tree to the stand [PDF]
Agricultural Water Management, 2012 Peer ...
Aranda García, Ismael +3 more
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Estimating Species Trees from Unrooted Gene Trees [PDF]
Systematic Biology, 2011 In this study, we develop a distance method for inferring unrooted species trees from a collection of unrooted gene trees. The species tree is estimated by the neighbor joining (NJ) tree built from a distance matrix in which the distance between two species is defined as the average number of internodes between two species across gene trees, that is ...
Liu, Liang, Yu, Lili
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Gene tree correction for reconciliation and species tree inference [PDF]
Algorithms for Molecular Biology, 2012 Reconciliation is the commonly used method for inferring the evolutionary scenario for a gene family. It consists in "embedding" inferred gene trees into a known species tree, revealing the evolution of the gene family by duplications and losses. When a species tree is not known, a natural algorithmic problem is to infer a species tree from a set of ...
Swenson Krister M +2 more
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Frontiers in Genetics, 2022 Dalbergia odorifera is a rare and precious rosewood specie, whose wood is a very high-quality material for valuable furniture and carving crafts. However, limited information is available about the process of wood formation in D. odorifera.
Wenxiu Zhao +10 more
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Light-related variation in sapling architecture of three shade-tolerant tree species of the Mexican rain forest [PDF]
, 2008 The crown architecture of three shade-tolerant tree species (two subcanopy and one mid-canopy) was analyzed in relation to the light regime of the forest understorey.
Bongers, F +5 more
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Gene tree species tree reconciliation with gene conversion [PDF]
Journal of Mathematical Biology, 2019 Gene tree/species tree reconciliation is a recent decisive progress in phylo-genetic methods, accounting for the possible differences between gene histories and species histories. Reconciliation consists in explaining these differences by gene-scale events such as duplication, loss, transfer, which translates mathematically into a mapping between gene ...
Hasic, Damir, Tannier, Eric
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