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Open Access Highly Accessed Research article

The evolution of Dscam genes across the arthropods

Sophie AO Armitage1*, Rebecca Y Freiburg1, Joachim Kurtz1 and Ignacio G Bravo12

Author Affiliations

1 Institute for Evolution and Biodiversity, University of Münster, Hüfferstrasse 1, 48149 Münster, Germany

2 Unit of Infections and Cancer, Catalan Institute of Oncology (ICO), Gran Via de L' Hospitalet, 199, 08907 L'Hospitalet de Llobregat, Barcelona, Spain

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BMC Evolutionary Biology 2012, 12:53  doi:10.1186/1471-2148-12-53

Published: 13 April 2012

Additional files

Additional file 1:

An overview of the workflow followed for the HMM construction and use, and for the gene predictions.

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Additional file 2:

Supplementary methods.

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Additional file 3:

Genbank (NCBI) accession numbers for the known and putative Dscam-hv and Dscam-like genes used in the overall phylogenies.

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Additional fie 4:

Information regarding the HMMs for the Dscam-like gene search. Including the HMM identities, the lengths of each of the HMMs in amino acids, and the HMM amino acid start position relative to the D. melanogaster Dscam2 sequence (total length 2,040 aa).

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Additional file 5:

Dscam-like HMM.

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Additional file 6:

Putative Dscam-like orthologs/co-orthologs and the number of Hidden Markov Models positively identified for each ortholog/co-ortholog. Grey boxes indicate an HMM hit with an e-value ≤ 0.001. White boxes indicate an e-value greater than 0.001 or no match. The identities of the Dscam-like genes were assigned according to the phylogenetic tree in Figure 3.

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Additional file 7:

D. mojavensis HMM results. Results for the Dscam-like HMMs built from A. mellifera, D. melanogaster and T. castaneum and run against the translated D. mojavensis genome. For a total of five 'matching' HMMs and above we found only four hits in the genome (i.e. four genes: one Dscam-hv and three Dscam-like), which had HMMs with significant hits in the correct order. The conservative cut-off value, which was subsequently used when searching other species for Dscam-like genes, is shown as a dashed line, i.e. a minimum of six HMMs had to match the sequence in the correct order and all with an e-value below 0.001.

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Additional file 8:

Arthropod HMM results. Number of hits for the Dscam-like HMMs built from A. mellifera, D. melanogaster, D. mojavensis and T. castaneum and run against the translated genomes of A. gambiae, A. mellifera, A. pisum, B. mori, D. pulex, I. scapularis, P. humanus humanus and T. castaneum. The cut-off value is shown as a dashed line.

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Additional file 9:

Dscam-hv HMM.

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Additional file 10:

Ig2 HMM.

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Additional file 11:

Ig3 HMM.

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Additional file 12:

Ig7 HMM.

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Additional file 13:

E-value distribution among putative hypervariable exons found across all arthropod species using our HMMs. The vertical dashed line marks the cut-off e-value of 0.0001.

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Additional file 14:

Amino acid alignment of putative Dscam gene family members. The complete protein alignment of 44 sequences was created using MUSCLE. All Ig2, Ig3 and Ig7 orthologous regions were removed from the alignment. The resulting alignment was shortened using Gblocks.

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Additional file 15:

Tests of alternative tree topologies. The "best" tree (top; Additional files 22 & 23) was tested against alternative hypotheses for the relationships between different Dscam clades by constructing alternative topologies (bottom two trees) and performing the Shimodaira-Hasegawa test. Neither of the two alternative topologies was significantly worse than the "best" tree at the 1% level.

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Additional file 16:

Nucleotide alignment of all arthropod Ig2 variants.

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Additional file 17:

Nucleotide alignment of all arthropod Ig3 variants.

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Additional file 18:

Nucleotide alignment of all arthropod Ig7 variants.

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Additional file 19:

Nucleotide alignment of all D. melanogaster and D. mojavensis Ig2 variants.

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Additional file 20:

Nucleotide alignment of all D. melanogaster and D. mojavensis Ig3 variants.

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Additional file 21:

Nucleotide alignment of all D. melanogaster and D. mojavensis Ig7 variants.

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Additional file 22:

Maximum likelihood (RAxML) phylogeny of the Dscam/DSCAM gene family, resulting in the best tree (Additional files 15 and 23). Bootstrap values (out of 100) are shown at the nodes. The vertical bars to the right are the same as in Figures 3 and 4 and follow the taxa colour codes in Figure 2. The scale bar represents 0.2 substitutions per site.

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Additional file 23:

Bayesian (PhyloBayes) phylogeny of the Dscam/DSCAM gene family, resulting in the best tree (Additional file 15 & Additional file 22). Posterior probabilities are shown at the nodes. The vertical bars to the right are the same as in Figures 3 and 4 and follow the taxa colour codes in Figure 2. The scale bar represents 0.4 substitutions per site.

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Additional file 24:

Bayesian (PhyloBayes, relaxed clock) dated phylogeny of the Dscam/DSCAM gene family. 95% confidence intervals for divergence times (millions of years) are shown next to the key nodes. The x-axis shows the time scale in millions of years. The topology follows that of the original best tree (see Additional file 15, 22 and Additional file 23). Nodes used for fossil calibrations are shown with a grey circle, for details see materials and methods. The vertical bars follow the bar colours of taxa written in black in Figure 2.

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Additional file 25:

Bayesian (PhyloBayes) phylogeny of all hypervariable Ig2 variants across the arthropods. A putative Ixodes scapularis Ig2 sequence is the outgroup. Bootstrap values are shown at the nodes. The scale bar represents 0.4 substitutions per site.

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Additional file 26:

Maxiumum likelihood (RAxML) phylogeny of all hypervariable Ig2 variants across the arthropods. A putative Ixodes scapularis Ig2 sequence is the outgroup. Bootstrap values are shown at the nodes. The scale bar represents 0.3 substitutions per site.

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Additional file 27:

Maximum likelihood (RAxML) phylogeny of hypervariable Ig2 variants (exon 4) from Drosophila melanogaster and D. mojavensis. A putative Ixodes scapularis Ig2 sequence is the outgroup. Bootstrap values are shown at the nodes. The scale bar represents 0.3 substitutions per site.

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Additional file 28:

Bayesian (PhyloBayes) phylogeny of all hypervariable Ig3 variants across the arthropods. A putative Ixodes scapularis Ig3 sequence is the outgroup. Bootstrap values are shown at the nodes. The scale bar represents 0.3 substitutions per site.

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Additional file 29:

Maxiumum likelihood (RAxML) phylogeny of all hypervariable Ig3 variants across the arthropods. A putative Ixodes scapularis Ig3 sequence is the outgroup. Bootstrap values are shown at the nodes. The scale bar represents 0.4 substitutions per site.

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Additional file 30:

Bayesian (PhyloBayes) phylogeny of all hypervariable Ig7 variants across the arthropods. A putative Ixodes scapularis Ig7 sequence is the outgroup. Bootstrap values are shown at the nodes. The scale bar represents 0.5 substitutions per site.

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Additional file 31:

Maxiumum likelihood (RAxML) phylogeny of all Ig7 variants across the arthropods. A putative Ixodes scapularis Ig7 sequence is the outgroup. Bootstrap values are shown at the nodes. The scale bar represents 0.6 substitutions per site.

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Additional file 32:

Bayesian (PhyloBayes) phylogeny of hypervariable Ig 3 variants (exon 6) from Drosophila melanogaster and D. mojavensis. A putative Ixodes scapularis Ig3 sequence is the outgroup. Bootstrap values are shown at the nodes. The scale bar represents 1 substitution per site.

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Additional file 33:

Maximum likelihood (RAxML) phylogeny of hypervariable Ig3 variants (exon 6) from Drosophila melanogaster and D. mojavensis. A putative Ixodes scapularis Ig3 sequence is the outgroup. Bootstrap values are shown at the nodes. The scale bar represents 0.6 substitutions per site.

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Additional file 34:

Bayesian (PhyloBayes) phylogeny of hypervariable Ig7 variants (exon 9) from Drosophila melanogaster and D. mojavensis. A putative Ixodes scapularis Ig7 sequence is the outgroup. Bootstrap values are shown at the nodes. The scale bar represents 2 substitutions per site.

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Additional file 35:

Maximum likelihood (RAxML) phylogeny of hypervariable Ig7 variants (exon 9) from Drosophila melanogaster and D. mojavensis. A putative Ixodes scapularis Ig7 sequence is the outgroup. Bootstrap values are shown at the nodes. The scale bar represents 0.3 substitutions per site.

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