Figure_3

Alignment in MEGA format used to generate the phylogenetic tree in Figure

Additional_file_6

Alignment in MEGA format used to generate the phylogenetic tree in Additional File

Figure_2_and_additional_file_6_alignment

Raw clustalW alignment for the trees in Figure 3 and Additional File

Figure_1

Alignment in MEGA format used to generate the phylogenetic tree in Figure

Figure_1_alignment

Raw clustalW alignment for the tree in Figure

Intron Lengths Can Be Used as a Molecular Clock

<p><i>y</i>-axis, magnitude of the Spearman correlation coefficient for the five <i>Drosophila</i> distributions shown in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0020015#pcbi-0020015-g008" target="_blank">Figure 8</a>. <i>x</i>-axis, time (millions of years) since last common ancestor based on protein similarities as calculated in [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0020015#pcbi-0020015-b030" target="_blank">30</a>]. Black bars above and below each data point denote observed variance in the data and were obtained by randomly resampling 1,000 orthologous intron pairs 100 times. Best-fitting curve (shown in black) y = −0.0057x + 0.9266; R² = 0.9875.</p

D. melanogaster Intron Lengths Are Highly Correlated with Their Inferred D. pseudoobscura Orthologs; D. melanogaster Paralogous Introns Show No Such Correlation

<p>(A) <i>x</i>-axis, length (log₁₀) of annotated D. melanogaster introns; <i>y</i>-axis, length (log₁₀) of their inferred orthologs in the D. pseudoobscura genome. Red circles indicate those introns containing a transposon in <i>D. melanogaster;</i> blue circles indicate those introns containing a transposon in <i>D. pseudoobscura;</i> gold circles indicate introns without identifiable transposons in either species. Spearman correlation coefficient: 0.637; <i>p</i> < 0.001.</p> <p>(B) Intron lengths of paralogs having the same intron–exon structure as judged by the positions of their splice junctions relative to the protein alignments of their reciprocal best-hit best HSPs. <i>x</i>-axis, length (log₁₀) of introns in an annotated D. melanogaster gene; <i>y</i>-axis, length (log₁₀) of corresponding paralogous introns. Spearman correlation coefficient: 0.448; <i>p</i> < 0.001.</p

Global Overview of Gene Structure in Six Annotated Animal Genomes

<p>(A) Intron length. Annotated intron length (log₁₀) is plotted on the <i>x</i>-axis; the frequency at which introns of that length occur in an organism's genome is plotted on the <i>y</i>-axis.</p> <p>(B) Exon length. <i>x</i>-axis, coding-exon length in nucleotides; <i>y</i>-axis, frequency.</p> <p>(C) Intron density. A transcript's intron density is equal to its number of coding introns divided by the length of the protein it encodes. <i>y</i>-axis, frequency of annotated transcripts with a particular intron density. <i>x</i>-axis, intron density binned in increments of 0.5 introns/100 amino acid (see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0020015#s4" target="_blank">Materials and Methods</a>). Deuterostomes are shown in shades of blue; protostomes in shades of red.</p

Neighbor-Joining Trees Summarizing Proteome-Wide Trends in Protein Similarity and Genome-Wide Trends in Intron–Exon Structural Similarity

<p>Proteome-wide trends in protein similarity (A), and genome-wide trends in intron–exon structural similarity (B). Numbers beneath tree nodes are bootstrap values.</p

Lengths of Orthologous Introns within a Quartet Are More Correlated than Those of Paralogous Introns

<p>(A) Quartet orthologous intron pairs. <i>x</i>-axis, length (log₁₀) of introns in human members of each quartet; <i>y</i>-axis, length (log₁₀) of corresponding orthologous introns in the mouse member of the same quartet. Spearman correlation coefficient: 0.903; <i>p</i> < 0.001.</p> <p>(B) Paralogous introns. <i>x</i>-axis, length (log₁₀) of introns in human members of each quartet; <i>y</i>-axis, length (log₁₀) of corresponding paralogous introns in the other human member of the same quartet. Spearman correlation coefficient: 0.140; <i>p</i> < 0.001. The mouse distributions are essentially identical to their human counterparts.</p