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8 results for “gene genealogies”
Simulated genomes from manuscript "On the Genes, Genealogies and Geographies of Quebec"
<p>Tree sequences of simulated whole genomes of 1.4M present day individuals with at least four grandparents linked to the BALSAC French-Canadian pedigree.<br> <br> Although the tree sequences have been censored to remove personal identifying information, we have included temporal (decade) and spatial (latitude and longitude) information for the 1.4M samples and their ~2M genealogically recoded genetic ancestors.</p>
FIGURE 1 in A multiple gene genealogy reveals the phylogenetic placement of Iodosphaeria tongrenensis sp. nov. in Iodosphaeriaceae (Xylariales)
FIGURE 1. MP tree based on dataset of LSU, ITS and SSU sequences. Bootstrap support values for maximum parsimony (MP) greater than 50% are given above the nodes. The strains numbers are given after the species names. The tree is rooted to Botryosphaeria ribis. All sequences from type strains are shown in bold face.
FIGURE 2 in A multiple gene genealogy reveals the phylogenetic placement of Iodosphaeria tongrenensis sp. nov. in Iodosphaeriaceae (Xylariales)
FIGURE 2. Iodosphaeria tongrenensis (holotype). A. Herbarium material. B, C. Ascomata on the surface of host. D. Section of ascoma. E. Peridium. F,G. Ascus apical apparatus (stained in Melzer´s reagent). H–J. Mature asci with ascospores. K. Ceratosporium -like conidia. L–O. Ascospores (N, O stained in India ink). Scale bars: B=1 mm, C=300 μm, D=50 μm, E=10 μm, F, G=5 μm, H–K=10 μm, L–O=5 μm.
FIGURE 3 in A multiple gene genealogy reveals phylogenetic placement of Rhopalostroma lekae
FIGURE 3. Rhopalostroma lekae in OA after 2 weeks (MFLUCC 13-0123). A: Averse showing melanized pigments and central mycelia. B: Reverse side of culture. C: Development of stromatal primordia in the culture. D: Melanized mycelia at the centre. E–G: Conidiophores from simple to more complex structure. H–J: Development of conidia and conidiogenesis cells. K: Conidia. Bars: c–d 1mm; e–k 50 µm.
FIGURE 2 in A multiple gene genealogy reveals phylogenetic placement of Rhopalostroma lekae
FIGURE 2. Rhopalostroma lekae (MFLU 13-0440). A: Habit on bark. B: Separated mature stromata. C: Stromata with dark purplish pigments in head part. D: Longitudinal section of stroma showing perithecial alignment in the periphery of stroma. E: Cross section of the stroma (head) showing perithecia. F and G: Mature ascus in water. H: Ascus in Melzer's reagent, Note the lack of an apical apparatus. I: KOH extractable pigments of stroma (left-head, right–stipe). J–l: Mature ascospores in water. Bars: a–b 5 mm; c–d 1 mm; e 2 mm; f–l 10 µm.
FIGURE 4 in A multiple gene genealogy reveals phylogenetic placement of Rhopalostroma lekae
FIGURE 4. Stromatal HPLC-UV profiles of major metabolites in Rhopalostroma lekae.
FIGURE 1 in A multiple gene genealogy reveals phylogenetic placement of Rhopalostroma lekae
FIGURE 1. The phylogram inferred from likelihood analysis of family Xylariaceae using ITS-LSU-RPB2 sequences. Strain/culture numbers are given following the taxon names; Type specimens and ex/epi-type strains are highlighted in bold. The bootstrap support values from likelihood analysis>50% from 1000 RAxML replicates are shown above the branches. The tree is rooted with Diatrype disciformis (out group).
Gene genealogy interrogation advances resolution of recalcitrant phylogenies
<p>Addressing phylogenetic problems using complex genomic datasets usually proceeds either via concatenation of all gene sequences into a supermatrix for model-based analysis or by estimation of individual gene genealogies to produce a summary tree under the coalescent. No approach is without shortcomings, as concatenation can amplify undesired biases and coalescent approaches can be sensitive to gene tree estimation error. Here, we present a method to account for gene tree error in genome-wide datasets by individually interrogating gene fragments in a statistical framework using topology tests. We apply this method to resolve controversial relationships within the largest freshwater fish radiation using newly generated exon-wide data (1051 loci) for 225 species. While both concatenation and coalescent methods reveal substantial incongruence, our novel approach resolves the interrelationships of major lineages with high confidence. We investigate the utility of our method by reanalysing published datasets for other emblematic groups proven recalcitrant to phylogenetic resolution. </p>
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