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Gene Trees, Species Trees, and Species Networks - Rice University
horizontal gene transfer, the species phylogeny may not be a tree; instead, .... the MRCA of taxa B and C is a sister taxon of both A and D, since it is the ..... species (organismal) tree, and Ξ is a set of HGT edges whose addition to T results.
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Gene Trees, Species Trees, and Species Networks
izontal gene transfer (HGT)—transfer of genetic material across the ... not violate the tree model of organismal evolutionary relationships; rather, the incon- .... b g c . G a. G b. G c. (e). Figure 1.1 (a) Gene tree that agrees with the species tree. ... (b ). (c). (d). Figure 1.2 (a) The tree of the gene whose evolution is shown in Figure ...
[ 40_(42)Nakhleh_NakhlehRuthsInnan.pdf - Read/Download File

From Gene to Organismal Phylogeny: Reconciled Trees and the
Gene trees need not faithfully reflect species trees for a ... sorting, and horizontal transfer. ... (a,b) and (c,d) are paralogous, in which case the explanation of ...
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From Gene to Organismal Phylogeny: Reconciled Trees and the
ship between gene trees and species trees may be more complex ... sorting, and horizontal transfer. ... gene clades (a,b) and (c,d) are paralogous, in which case.
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1 Gene trees and species trees The lines of organismal descent that
(genes, organisms, populations, species) do we wish to study? And, what .... At one extreme, meiotically independent nucleotide position, for. A. D. B. E. C. F. A. C. B. D ... the three possible trees: A and B sister, B and C sister, or A and C sister . Thus, if we ..... called horizontal gene transfer), introgression, and lineage fusion .
[ GeneTreesSpeciesTrees.pdf - Read/Download File

estimating species trees using multiple-allele dna sequence data
conflicts among individual gene trees, or because the species from which multiple alleles ... We use the following abbreviations: D: Sequence data; G: a vector ... and one copy from species C. The shaded areas in A and B repre- ..... 2006), transfer of genes in the yeast strains investigated is ..... From gene to organismal phy-.
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Coalescent methods for estimating phylogenetic trees - Harvard
Jun 6, 2009 ... Liang Liu a, Lili Yu b, Laura Kubatko c, Dennis K. Pearl c, Scott V. Edwards a,* ... distinction between gene trees and species trees has come to the fore of .... phylogeny of species include deep coalescence, horizontal transfer, and gene ... the model described above for multilocus sequences D, gene trees.
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How reticulated are species? - Mallet Group - Harvard University
In microbes, lateral gene transfer is the dominant process that spoils ... affect all parts of the tree of life, not just the recent species at the tips. Our .... allowed us to trace the organismal history ..... Figure 2. Phylogenetic discordance B/D mimicry region of Heliconius genomes. ..... Boschetti C, Carr A, Crisp A, Eyres I, et al. 2012.
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Accurate gene-tree reconstruction by learning gene- and species
zontal gene transfer, gene conversions, ... (D) Gene duplication and loss events are inferred by reconciling a gene tree to a species tree, ... (C) Percentage of gene trees congruent to the species phylogeny correlates with gene length, regardless of ... (B) Gene-specific rates of 5154 fly orthologs ...... From gene to organismal.
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Accurate gene-tree reconstruction by learning gene- and species
Matthew D. Rasmussen. 1 ... gene trees to the known phylogeny relating the species (Figure 1d), in a process ... Therefore, in absence of horizontal gene transfer, gene ..... proposed gene-tree topology T, branch lengths b are estimated from the ..... S. castellii, and C. glabrata ohnologs from the Yeast Gene Order Browser ...
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velasco gene trees final - Philsci-Archive
organismal pedigrees with their corresponding Tree as well as gene .... transfer, a subset of genes is passed from one organism to another without this involving .... statement like 'half of the genes in species A-D show a D(C(B,A)) topology but.
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Trees within trees: Phylogeny and historical associations - CiteSeerX
... biogeography, coevolution, gene trees, molecular evolution, horizontal transfer ... between gene and organismal phylogeny, and the macroevolutionary ... between gene and species trees is a more recent development1,3. ..... c d. (b) duplication sorting events reconciled tree. 1. 2. 3. 4 a b c d. (2). (3). (4) missing genes. (c) ...
[ trees_within_trees.pdf - Read/Download File

When we estimate organismal phylogenies with a particular molecular ... been called the gene tree-species tree problem (e.g., 8,9,10) where gene tree refers to ... by (a) a horizontal transfer of the gene, (b) ancestral lineage sorting, and (c) ... a b a b. R. D. I. O. Pacific Symposium on Biocomputing 6:571-582 (2001) ...
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Keywords: Apicomplexa, incongruence, gene tree, species tree
Sep 26, 2008 ... support the species tree and a total of 48 different gene tree topologies are observed. ... inference of organismal phylogeny (Delsuc, Brinkmann, and Philippe ..... species tree can be explained by a single lateral gene transfer event. ..... Minimum bootstrap cutoff (%). Robust b. Intermediate c. Sensitive d. 0.
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Confounding Factors in HGT Detection - Derek Ruths
organisms via horizontal gene transfer (HGT) (Doolittle et al., 2003; Ochman et al. , 2000). .... Gene tree that disagrees with the species tree due to HGT from C to B (a) and ... with a single HGT event from X to Y . (b) The underlying organismal ( species) ..... Figure 5 shows two trees ST and GT where jNj D 3Д; i.e., the two trees ...
[ recombcg06-jcb.pdf - Read/Download File

Full Text (PDF)
Jun 22, 2010 ... the phylogenies of orthologous genes in Escherichia, Salmonella, and Citrobacter, or ... recombination | species | Tree of Life | population structure | incomplete .... ability to discern otherwise robust organismal relationships. Here, .... and D). Support for (A and C) or rejection of (B and D) alternative clades is.
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Assessing Approaches for Inferring Species Trees - CLAS Users
Dec 23, 2014 ... deep coalescence (Deep-c) costs, the NJst distance method, the MulRF ... species sampling, gene tree error, and duplication and loss rates on the ... recombination, or lateral gene transfer (LGT; Maddison. 1997). ... 2011a,b), and even LGTs (Whidden ..... taxa in the model species tree and the D/L rate used.
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Bacteria, Sex, and Systematics - Laura Franklin-Hall
phylogenies of different organismal parts, I argue there are no particular ... genes have different histories, and species cease to be monophyletic, vi- ... trees. They conjecture that gene transfers occurred whenever they find disagreement ..... were of interest, organisms A, B, and C would form a species, while D would not be.
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Download PDF - Springer
Accurate Detection of Horizontal Gene Transfer ... tection entails comparing the topology of a gene tree to that of the species tree, ... D. (a). (b). (c). Fig. 1. (a) A phylogenetic network with a single HGT edge from X to Y , ancestors ...... [16] Lerat, E., Daubin, V., Moran, N.A.: From gene trees to organismal phylogeny in prokary-.
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Gene tree discordance, phylogenetic inference and the multispecies
Mar 21, 2009 ... (c) A gene tree in a species tree, obtained by ignoring individuals ... (a) HGT: a lineage jumps from the population ancestral to A and B to the population .... gene transfer (HGT) between species [38] and recombina- tion [27,39 ... (c,d) For six and seven taxa, the most probable gene tree is an AGT. For each ...
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