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Results: 5

1.
F <span style="font-variant: small-caps" class="small-caps">ig</span> . 5.—

F ig . 5.—. From: Insect Phylogenomics: Exploring the Source of Incongruence Using New Transcriptomic Data.

RADICAL analysis of nodal support. Shown are the RADICAL curves for each of the five phylogenetic hypotheses (at the top) for the complete P_matrix_g data set and the four functional subgroups based on this data set. The y axis shows the CFI and the x axis the concatenation size (number of genes).

Sabrina Simon, et al. Genome Biol Evol. 2012;4(12):1295-1309.
2.
F <span style="font-variant: small-caps" class="small-caps">ig</span> . 2.—

F ig . 2.—. From: Insect Phylogenomics: Exploring the Source of Incongruence Using New Transcriptomic Data.

RAxML topology derived from data matrix P_matrix_g (62 species, 285 genes, 79506 amino acid positions), PROTCATWAGF. Support values are derived from 1,000 bootstrap replicates. Bootstrap values are only given for nodes that lack maximum support. Stars indicate nodes for which at least 90% of data (=256 genes) have to be concatenated to recover this specific node based on the RADICAL analyses. Also shown is a barplot indicating the number of putative orthologous genes for each of the taxa in this data set. Color code: primarily wingless hexapods, gray; “palaeopteran” insects, red; polyneopteran insects, green, paraneopteran insects, purple; and holometabolan insects, pink.

Sabrina Simon, et al. Genome Biol Evol. 2012;4(12):1295-1309.
3.
F <span style="font-variant: small-caps" class="small-caps">ig</span> . 4.—

F ig . 4.—. From: Insect Phylogenomics: Exploring the Source of Incongruence Using New Transcriptomic Data.

RADICAL analysis of functional subgroups. AUC values (left column) and fixation points are provided across all total evidence nodes for the functional groups 1) cellular processes and signaling (cell = 85 genes); 2) information storage and processing (info = 80 genes); 3) metabolism (meta = 78 genes); and 4) poorly recognized (poorly = 42 genes). AUC values indicate the proportion of total concatenation space occupied by that node and the fixation point indicates the number of genes required before the node appears in all concatenation sets of that size. The star indicates the number of genes for which a node no longer occurs in any randomized concatenation set of that size or larger.

Sabrina Simon, et al. Genome Biol Evol. 2012;4(12):1295-1309.
4.
F <span style="font-variant: small-caps" class="small-caps">ig</span> . 1.—

F ig . 1.—. From: Insect Phylogenomics: Exploring the Source of Incongruence Using New Transcriptomic Data.

RAxML topology derived from data matrix M_matrix (53 species, 335 genes, 71369 amino acid positions), PROTCATWAGF model. Support values are derived from 1,000 bootstrap replicates. Bootstrap values are only given for nodes that lack maximum support. Stars indicate nodes for which at least 90% of data (=300 genes) have to be concatenated to recover this specific node based on the RADICAL analyses. Also shown is a barplot indicating the number of putative orthologous genes for each of the taxa in this data set. Color code: primarily wingless hexapods, gray; “palaeopteran” insects, red; polyneopteran insects, green, paraneopteran insects, purple; and holometabolan insects, pink.

Sabrina Simon, et al. Genome Biol Evol. 2012;4(12):1295-1309.
5.
F <span style="font-variant: small-caps" class="small-caps">ig</span> . 3.—

F ig . 3.—. From: Insect Phylogenomics: Exploring the Source of Incongruence Using New Transcriptomic Data.

RAxML topology derived from data matrix P_matrix_s (73 species, 102 genes, 24507 amino acid positions), PROTCATWAGF model. Support values are derived from 1,000 bootstrap replicates. Bootstrap values are only given for nodes that lack maximum support. Stars indicate nodes for which at least 90% of data (=92 genes) have to be concatenated to recover this specific node based on the RADICAL analyses. Also shown is a barplot indicating the number of putative orthologous genes for each of the taxa in this data set. Color code: primarily wingless hexapods, gray; “palaeopteran” insects, red; polyneopteran insects, green, paraneopteran insects, purple; and holometabolan insects, pink.

Sabrina Simon, et al. Genome Biol Evol. 2012;4(12):1295-1309.

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