45 research outputs found

    Ground-dove BEAST tree file

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    Maximum clade credibility tree and divergence time estimates from BEAST

    Ground-dove Garli tree file

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    Maximum likelihood tree file from two searches of 500 bootstrap replicates in GARLI

    AT contents of atp8 genes.

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    Computed from entire gene sequences, different codon sets, and fourfold degenerate sites. (XLSX)</p

    AT contents of cob genes.

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    Computed from entire gene sequences, different codon sets, and fourfold degenerate sites. (XLSX)</p

    Phylogenetic signal of the mitogenome state of Amblycera (fragmented versus single-chromosome).

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    Blue is values of D under simulation using Browning motion. Red is values of D under simulation with random phylogenetic structure. Black vertical line indicates value of D over actual tree (D = 0.281), P of E(D) under Brownian motion model = 0.177, P of E(D) under no phylogenetic structure model = 0.001. (TIF)</p

    Pairs of Amblycera selected for comparison of gene rearrangements.

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    Circles at the tips indicate mitogenome structure (single-chromosome versus fragmented), and samples compared within a pair connected with blue line. Codes at the nodes indicate ancestral genomes, as in S20 and S21 Tables. Both topology and branch lengths preserved from the nuclear concatenated tree. (TIF)</p

    AT contents of cox2 genes.

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    Computed from entire gene sequences, different codon sets, and fourfold degenerate sites. (XLSX)</p

    Bayesian credible set of configurations showing changes in fragmentation rate in mitogenomes of Amblycera.

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    Circles at the branches indicate rate shift events included in nine most probable reconstructions, numbers above the plots indicate posterior probabilities. Overall reconstructed rate on each branch shown with color from low rate (dark blue) to high rate (red) as indicated by the scale bar in Fig 4. (TIF)</p

    Percent AT content of different partitions of single-chromosome and fragmented amblyceran mitogenomes.

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    Categories indicate values for entire sequences, coding regions, different codon positions, and fourfold degenerate sites. Centerline–median; box limit–upper and lower quartiles; whiskers—interquartile range. The black dotted line shows the average percent AT content for insect mitogenomes available on NCBI GenBank (76.0%). (TIF)</p

    Dated phylogenomic tree with ancestral state reconstruction of mitogenome evolution in Amblycera under irreversible model.

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    Circles at the tips indicate mitogenome structure (single-chromosome versus fragmented). Pie charts at the nodes show the frequency distribution of reconstructed ancestral state after 1000 simulations of stochastic character mapping using an irreversible fragmentation model (USR). Time scale at bottom in millions of years ago (Mya).</p
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