Gene tree
Reconciliation and local gene tree rearrangement can be of mutual profit
... phylogenetic tree or phylogeny is a tree depicting evo- lutionary relationships among biological entities that are believed to have a common ...A gene family is a group of genes descending from a ...
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Isometric gene tree reconciliation revisited
... species tree is rooted, but the gene tree is ...species tree can be rooted by including an outgroup, finding an appropriate outgroup for a multi-gene family, which may harbor ancient ...
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Gene tree parsimony for incomplete gene trees: addressing true biological loss
... a gene tree gt and a species tree ST, two formu- lations for the number of losses have been ...Dup- tree [4], two popular methods for “solving” GTP), we will show that this can be incorrect ...
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A polynomial time algorithm for calculating the probability of a ranked gene tree given a species tree
... species tree, and assuming the gene tree evolved under the multi-species coalescent [1], the most probable gene tree topology can have a different topology from that of the species ...a ...
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Gene tree correction for reconciliation and species tree inference
... a gene tree as indicating potentially misplaced genes, we developed a polynomial-time algorithm for inferring the minimum number of leaf-removals required to transform a gene tree into an ...
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OrthoFinder: phylogenetic orthology inference for comparative genomics
... the tree is employed, rather than the iterative search and rearrange- ment employed by DLCpar, the post-order traversal en- ables more parsimonious interpretations of child clades below a node to be identified ...
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Accuracy of phylogeny reconstruction methods combining overlapping gene data sets
... as gene-specific substitution para- ...model tree but to the original result obtained with that very method (Figure ...true gene trees, that means, if reconstruction error is not the main cause that ...
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Inferring species trees from incongruent multi-copy gene trees using the Robinson-Foulds distance
... of gene trees can be divided into two broad categories: non-parametric methods based on gene tree parsimony (GTP), and parametric methods that use like- lihood ...discordant gene trees and try ...
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Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria)
... underlying gene-tree heterogeneity created by deep coales- cence events, which might lead to statistical inconsistency of concatenation-based methods in the anomaly zone ...species tree reconstructed ...
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S18 family of mitochondrial ribosomal proteins: evolutionary history and Gly132 polymorphism in colon carcinoma
... S18 gene evolved without any gene duplications or losses (see above), its eukaryotes homologs underwent a couple of gene duplications and losses upon the evolution within eukaryotic species ...MAP ...
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Evolutionary history of bacteriophages with double-stranded DNA genomes
... family tree T sf is a tree inferred from alignment of protein sequences that belong to a ...This tree has n leaves that are labeled by the set of n bacteriophages, where n is much less than the total ...
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Identification, prevalence and pathogenicity of Colletotrichum species causing anthracnose of Capsicum annuum in Asia
... ApMat gene for some reference strains, it was difficult to provide a good support for placement of some species such as ...gs tree (Fig. 3). Individual gene trees of ITS, act, tub2, chs-1 loci (data ...
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Challenges in Species Tree Estimation Under the Multispecies Coalescent Model
... the gene tree topology, resulting in information ...in gene tree reconstruction due to the finite number of sites at each locus (called the mutation variance by Huang and Knowles ...that ...
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Molecular evolution of the small subunit of ribulose bisphosphate carboxylase: nucleotide substitution and gene conversion.
... Correlation between the gene tree and the species tree: As with ribosomal gene families, the inability to observe ancient lineages of SSU genes within gene families b[r] ...
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Isolation and nucleotide variation of COBRA gene in a tropical timber tree Neolamarckia cadamba
... the gene can be determined (Stukenbrock and Mcdonald, 2007; Berglund et ...COBRA gene in the deposition of cellulose microfibrils is crucial in the development of secondary cell ...COBRA gene and ...
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Updating the evolutionary history of Carnivora (Mammalia): a new species-level supertree complete with divergence time estimates
... reference tree under the optimal model of evolution in a ML fra- mework to establish the heights of each node relative to some ancestral and/or daughter ...each gene in the data set, with the final date ...
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ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses
... marker gene that can be aligned across distant taxonomic lineages to build a “ foundation ” phylogenetic ...marker gene that allows for higher taxonomic resolution are aligned within groups of closely ...
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Coordinating the IUCN Red List of North American tree species: A special session at the USFS gene conservation of tree species workshop
... native tree species, based on a globally standardized system, would enable an objective and systematic prioritization of species for future conservation action and enable stakeholders from a wide range of sectors ...
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Bioinformatics Analysis of NprR NprX Quorum Sensing System of Bacillus thuringiensis Isolates from the Papaloapan Region, Oaxaca Mexico
... The phylogenetic tree based on nprR gene nucleotide sequence built on 29 strains isolated and 32 strains of B. cereus group from the literature (Figure 4, Electronic Supplementary Material Table S3) show a ...
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Hyphal wall protein 1 gene: A potential marker for the identification of different Candida species and phylogenetic analysis
... Currently, only few genetic markers have been reported for the specific identification of C. parapsilosis complex. Some of the markers introduced in different studies include the SADH [14], RPS0 [23], mitochondrial ...
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