Gene trees
The Concordance of Gene Trees and Species Trees at Two Linked Loci
... species trees on a chromosome can pro- vide information about past episodes of natural se- ...which gene trees are concor- dant or discordant with the species ...the gene tree with the species ...
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OCTAL: Optimal Completion of gene trees in polynomial time
... estimated gene tree, and so implicitly assumes that the gene tree is accurate; since estimated gene trees have some error, another approach would allow the low sup- port branches in ...
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Non-parametric correction of estimated gene trees using TRACTION
... Because gene trees often have low accuracy, a natural problem is to try to improve gene tree estimation using an estimated or known species ...estimated gene trees with respect to a ...
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Gene tree parsimony for incomplete gene trees: addressing true biological loss
... is gene tree esti- mation error, which is likely to occur with most biologi- cal datasets (see discussion in ...estimated gene trees and species trees are highly accurate, so that every ...
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Biologically feasible gene trees, reconciliation maps and informative triples
... event-labeled gene trees (T ; t, σ ) for which a species tree exists can be character- ized by a set of species triples S (T ; t, σ ) that is easily con- structed from a subset of triples displayed in ...a ...
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Inferring species trees from incongruent multi-copy gene trees using the Robinson-Foulds distance
... the gene trees within the model species tree using our C++ implementation of the duplication-loss model of ...evolved gene trees, using the standard subtree transfer model of ...used ...
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The link between orthology relations and gene trees: a correction perspective
... a gene tree with a species tree, many tree‑free methods are also available (usually based on sequence ...and gene trees has been formally considered from the per‑ spective of reconstructing ...
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NANUQ: a method for inferring species networks from gene trees under the coalescent model
... Several recent works [9, 10] have taken a Bayesian approach to inference of species networks from genetic sequence data, to obtain a joint posterior on both spe- cies networks and gene trees. As attractive ...
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Locus-aware decomposition of gene trees with respect to polytomous species trees
... between gene and species trees can be caused by locus acquisition events of any kind, including duplications and horizontal gene ...binary gene tree into a forest of subtrees that can be ...
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Cubic time algorithms of amalgamating gene trees and building evolutionary scenarios
... searching for an “average” graph of a given set of graphs. In the phylogenetic context, that will describe the desired supertree. Such graph will globally minimize the total sum of differences between each reconciled ...
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Of woods and webs: possible alternatives to the tree of life for studying genomic fluidity in E. coli
... of gene trees that con- tained mobile genetic elements (> 0 #natives when MGE are the natives), that were exclusively found in patho- genic hosts (p-score = 0 for when PATH are natives), and that ...
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Lineage specific rediploidization is a mechanism to explain time lags between genome duplication and evolutionary diversification
... of gene trees sampled among those available from the sequence capture data was done to maximize the overall representation of each salmon chromosome, with a higher sampling effort per- formed in putative ...
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Phylogenomics of the olive tree (Olea europaea) reveals the relative contribution of ancient allo- and autopolyploidization events
... of gene evolutionary histories, has helped to uncover an- cient polyploidization (paleoploidization) events [12, 24 – ...in gene trees and their frequencies, with the expected topologies resulting ...
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ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses
... phylogenetic trees using multiple genetic ...marker gene that can be aligned across distant taxonomic lineages to build a “ foundation ” phylogenetic ...marker gene that allows for higher taxonomic ...
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Chromosome evolution at the origin of the ancestral vertebrate genome
... To enable comparisons between the pre-1R vertebrate ancestor genome reconstruction and extant species, we assigned genes to each of the 17 pre-1R chromo- somes. Among Amniota genes, only ohnologs could be confidently ...
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Inversion Monophyly in African Anopheline Malaria Vectors
... In Drosophila the monophyly of inversions has been confirmed by the fact that DNA sequences within the breakpoints of inversions produce gene trees identical to those dedu[r] ...
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Accuracy of phylogeny reconstruction methods combining overlapping gene data sets
... ML trees, one with HKY + Γ and one with GTR + Γ , results in the same tree topology but different branch lengths (HKY tree in Figure ...rooted gene trees, we root each tree artificially with a taxon ...
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Evaluating, Accelerating and Extending the Multispecies Coalescent Model of Evolution
... inferred gene trees from each locus without accounting for their uncertain- ties, and employ nonparametric criteria such as ...in gene tree topologies is typically low, so using fixed gene ...
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A polynomial time algorithm for calculating the probability of a ranked gene tree given a species tree
... ranked gene trees efficiently may also be of interest in the context of computing probabilities of unranked gene trees, partic- ularly because no polynomial time algorithm has been found for ...
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Where Do I Come From? Using Student’s Mitochondrial DNA to Teach About Phylogeny, Molecular Clocks, and Population Genetics
... Furthermore gene genealogies often have the complicating factor of ancestral polymorphism (which could lead to conflicting gene trees) and introgression (as observed be- tween humans and Neanderthals ...
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