species trees
The inference of gene trees with species trees.
... gene trees and species ...gene trees based on sequence ...of species. Although the histories of genes and species are tightly linked, they are seldom identical, because genes duplicate, ...
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Polymorphism aware species trees with advanced mutation models, bootstrap and rate heterogeneity
... ten species trees with 100 leaves were randomly generated under the Yule birth model (Yule ...ten species trees is referred to as one of ten ...the species trees measured in ...
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Inferring species trees given coalescence and reticulation
... the species tree/gene tree problem As I have noted above, reticulation can be important for the evolutionary process and has implications for the performance of species tree inference methods: it should not ...
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Inferring species trees from incongruent multi-copy gene trees using the Robinson-Foulds distance
... gene trees within the model species tree using our C++ implementation of the duplication-loss model of ...gene trees, using the standard subtree transfer model of ...gene trees based on four ...
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A Maximum Pseudo-Likelihood Approach for Estimating Species Trees under the Coalescent Model
... cies trees increases to 1, and the MSE of the branch length (in coalescent units) appears to decrease to 0, indicating that MP-EST is statistically consistent in esti- mating the species trees ...
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Maximum likelihood estimation of species trees and anomaly zone detection using ranked gene trees
... test species tree inference methods in challenging regions of parameter space (Kubatko and Deg- nan, 2007; Liu and Edwards, 2009; Liu et ...gene trees has motivated many methods, the extent that they arise ...
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Locus-aware decomposition of gene trees with respect to polytomous species trees
... and species trees can be caused by locus acquisition events of any kind, including duplications and horizontal gene ...polytomic species tree, in a way that minimizes the weighted sum of the forest ...
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Synthesizing species trees from gene trees using the parameterized and graph-theoretic approaches
... large-scale species tree estimates from collections of discordant gene trees [Bininda-Emonds ...gene trees, median tree problems (also referred to as supertree problems [Bininda-Emonds (2004)]) seek ...
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Species Trees from Highly Incongruent Gene Trees in Rice
... the species tree (Degnan and Rosenberg 2006). The fact that trees built from different genes can vary has been recognized for some ...constructing species tree from incongruent gene trees was ...
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From Homologous Genes to Phylogenetic Species Trees: On Tree Representations of Binary Relations
... reconstructed species trees on the noise ...the species trees could be re- constructed correctly and 93% are reconstructed almost correct, ...Incorrect species triples thus are reduced, ...
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The Concordance of Gene Trees and Species Trees at Two Linked Loci
... of species trees on a chromosome can pro- vide information about past episodes of natural se- ...gene trees are concor- dant or discordant with the species ...the species represented by ...
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From Gene Trees to Species Trees: Algorithms for Parsimonious Reconciliation
... Cantor, Evolution of protein molecules, Mammalian Protein Metabolism (H. Carstens, and L.L.. Degnan, Inconsistency of phylogenetic estimates from concatenated data under coales[r] ...
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Phylogenetic species tree inference from gene trees despite paralogy
... Motivation Species play an important role for numerous aspects of biology ...in species trees as in ...estimated species trees based on so-called ...of species share or that are ...
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NANUQ: a method for inferring species networks from gene trees under the coalescent model
... of species trees to allow for hybridization or other lateral gene ...gene trees arising from a network can have any topology, but arise with frequencies dependent on the network structure and ...
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A survey of plant parasitic fungi occurring on selected native Namibian trees species of economic importance
... study, we had two objectives. Firstly, to investigate the cause of decline and death of Acacia species trees around Windhoek. This is in order to develop management strategies to reduce the impact of the ...
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Efficient algorithms for reconciling gene trees and species networks via duplication and loss events
... 8. Merkle D, Middendort M: Reconstruction of the cophylogenetic history of related phylogenetic trees with divergence timing information. Theory Biosci 2005, 123(4):277-299. 9. Doyon JP, Scornavacca C, Gorbunov ...
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Species-specific responses to forest soil inoculum in planted trees in an abandoned agricultural field
... effect of adding live compared to sterilized soil; (2) a positive effect of adding yellow birch soil 12.. compared to red oak soil (although there were no significant be[r] ...
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Isolation and molecular characterization of Cryptococcus species isolated from pigeon nests and Eucalyptus trees
... Cryptococcus uzbekistanensis is a non-capsulated yeast that was first isolated from a desert soil sample from near Bukhara, Uzbekistan, in 1999 by Chernov et al. Afterwards, Fonseca et al. identified that this ...
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Comparative biogeography of New Zealand trees: species richness, height, leaf traits and range sizes
... of trees (215 species ≥6 m in ...more species at a quadrat scale of ...small trees (≤15 m in height) and we argue that it is a legacy of allopatric speciation and radiation during the late ...
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From Prosodic Trees to Syntactic Trees
... Since the Mesoretic annotation is supposed to mark the structure of every verse unambiguously, we expect to parse every verse successfully with exactly one tree assigned to it, given that (1) the annotation is perfectly ...
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