43 research outputs found

    Kulmuni et al_ Supplementary Data set S1

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    CSP sequences from whole genome sequencing (WSG) projects AEVX01, ADTU01, AEAB01, AEAC01, ADOQ01, ADIH01 and AEAQ01 of the ants Acromyrmex echinatior, Atta cephalotes, Camponotus floridanus, Harpegnathos saltator, Linepithema humile, Pogonomyrmex barbatus and Solenopsis invicta, respectively

    Details of the <i>Solenopsis invicta</i> odorant binding proteins.

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    <p>*This single Sanger read appears to be partially unspliced and frameshifted.</p><p>**The total number of 454 reads contributing to this SiOBP3/<i>Gp-9</i> contig is unclear, because it strangely assembled in several different non-overlapping contigs.</p><p>The columns are: Gene – number we are assigning; cDNA – length of cDNA in base pairs, excluding polyA tail; TotAA – conceptual precursor protein length including signal sequence; MatAA – mature secreted protein length excluding signal sequence according to PSORTII; 454 – number of 454 reads contributing to contig; Sanger – number of Sanger reads contributing to contig; C – number of conserved cysteines; PolyA – presence of single or multiple poly-adenylation sites.</p

    Results of the selection analyses for the best alignment method (PRANK), and two others (CLUSTAL and MUSCLE) and the MAP dataset of <i>Solenopsis</i>.

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    <p>Given are the log-likelihoods of the null hypotheses (H<sub>0</sub>), which assume no selection, and alternative hypotheses (H<sub>a</sub>), which allow for positive selection. Likelihood-ratio tests (LRT) of positive selection are conducted to compare the two hypotheses. Levels of significance are 3.84 at 5% and 6.63 at 1% for the site model and 3.84 at 5% and 5.99 at 1% for the branch and branch-site models, following the χ<sub>1</sub><sup>2</sup> distribution to guide against violations of model assumptions. Statistically significant LRTs for positive selection are indicated by italics and *** for p≪0.01. Note that inference of positive selection greatly depends on the alignment method used.</p

    consensus-bb

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    Consensus DNA sequence of 403 protein coding genes in the SB variant of the fire ant social chromosome supergene

    Details of the multiple sequence alignment (MSA) methods used and maximum likelihood phylogenies estimated from them.

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    <p>We define the core length as the number of character positions from the first to the last of the characteristic cysteine residues (C1–C6) of the OBPs. The log-likelihoods (LnL), parsimony informative characters, tree size, and average approximate likelihood-ratio tests (aLRT) are derived from the ML analyses. Robinson-Foulds tree distances (RF distance) are calculated by comparing the ant and bee MAP trees to the ML trees derived under the other MSA methods. Best scores of the MSAs compared to the BAli-Phy MAP are in highlighted in bold italics.</p

    Maximum a-posteriori (MAP) phylogeny and alignment of the <i>Solenopsis invicta</i> (SiOBP) odorant binding proteins.

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    <p>A. The <i>S. invicta</i> MAP phylogeny. The branch in grey is collapsed in the 50% consensus tree. Branch support is posterior probabilities derived from 3241 samples taken after the burn-in was discarded. Even though the node support in the conserved ortholog clade is relatively poor, the exact same topology of the orthologs was recovered in the honey bee MAP tree (not shown), suggesting that the branching pattern is accurate. B. The <i>S. invicta</i> MAP-AU plot. The quality of the alignment is indicated through a heat map. Red (warm colors) indicates areas of high quality alignment, blue (cold colors) signifies areas of low certainty. Note that there are considerable high quality alignment blocks in the N-terminal signal peptide and the C-terminal protein tail.</p

    consensus-lb.cds

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    Consensus amino acid sequence of 403 protein-coding genes in the Sb variant of the fire ant Solenopsis invicta social chromosome supergene

    Maximum likelihood phylogenies of the fire ant OBPs (SiOBPs) and honey bee OBPs (AmOBPs).

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    <p>The phylogenies are based on the two best alignments (top: MUSCLE, bottom: PRANK). All trees are midpoint rooted in the absence of a suitable outgroup. Branch support is SH-like aLRT derived from PhyML analyses.</p

    Genotypes of B and b haploid males.

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    Filtered VCF file with variants called from whole-genome sequences of 16 Solenopsis invicta haploid males with Cortex. 8 samples have the Gp-9B genotype (f1_B to f7_B, gdo10), 8 samples have the Gp-9b genotype (f1b to f7b, gdo10)
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