Convergent Evolution of Intron Structures Figure 5. Phylogenetic distribution of BP-AG distance across hemiascomicetous yeasts. For each species, the distribution represents the fraction of introns with a certain distance to the AG from base -50 (most left) to base -1 (most right, terminal G). Grey background highlights relative lack of constraint BP-AG distance, and broken lines show the lineages that likely experienced the evolution of BP-AG distance constraint. doi:10.1371/journal.pgen.1000148.g005 comparisons is surprising and intriguing. To further test whether the observed stronger intron consensus sequence signal in intron- poor organisms could truly reflect retained greater boundary strengths from ancestor, we further divided the orthologous set into those introns shared with a more closely related intron-poor species (Y. lipolytica for A. fumigatus; C. parvum for T. gondii) and those shared only with distantly related species. Whereas the former could conceivably retain some specific ancestral signal due to lack of change, the second set represent divergences dating back upwards of a billion years ago to early eukaryotic evolution, seemingly precluding similarities in trends across individual intron boundary strengths representing lack of sequence change since Table 4. Intron signal features. A. fumigatus S. pombe A. thaliana H. sapiens T. gondii Intron subset All introns Orthologous All introns Orthologous All introns Orthologous All introns Orthologous All introns Orthologous All All Cons. to Ylip Not Cons. to Ylip Cons. to Ylip Not Cons. to Ylip All Cons. to Cpar Not Cons. to Cpar 25 18267 183 171 12 4722 125 107 18 134535 128 197835 157 27085 86 61 2.3 2.8 * 2.8 3.6 3.9 3.7 3.9 3.3 1.5 1.9 2.3 3.2 * 2.5 2.9 * 2.8 3.8 Introns studied 59ss strength (bits) % of introns containing most common branch point motif for given number of degenerate sites 0 1 2 3 10.97% (actgac) 17.96% (ctgacw) 29.99% (ctracw) 43.18% (ctrayw) 18.58% (actgac) * 28.42% (ctgacw) 41.53% (ctracw) 56.83% (ctrayw) 19.30% (actgac) 33.33% (ctgaca) 21.61% (actaac) 22.40% (actaac) 21.50% (actaac) 27.78% (actaac) 8.23% (tctgat) 14.06% (ctgatt) 7.90% (ctgacc) 8.70% (ctgact) 4.54% (tctgac) 6.98% (ctgatg) 4.92% (actaac) 28.07% (actrac) 50.00% (ctraca) 35.26% (actaay) 33.60% (actaay) 31.78% (actaay) 44.44% (actaay) 14.95% (tctrat) 23.44% (ctratt) 40.94% (ctracw) 56.73% (ctrayw) 58.33% (ctraya) 75.00% (ctraym) 50.46% (wctaay) 56.22% (wctray) 53.60% (ctaayw) 61.60% (ctrayw) 54.21% (ctaayw) 62.62% (ctrayw) 50.00% (wctaay) 55.56% (wctray) 23.36% (wctrat) 30.47% (ctraty) 30.99% (wctray) 38.28% (ctrayw) 14.06% (ctgacy) 22.80% (ctgayy) 34.32% (ctrayw) 16.15% (ctgayt) 8.45% (tctgay) 28.57% (tctray) 14.06% (ctgayk) 11.63% (ctgayg) 17.44% (ctrayg) 9.84% (actaay) 14.75% (ctrayg) 40.99% (wctray) 17.75% (ctrayk) 24.42% (ctrayk) 21.31% (ctrayk) 32.00% (ctrays) 12.00% (tctgac) 24.00% (ctgayg) 28.00% (ctgayr) *Indicates that the subset of orthologous introns is statistically significantly different at the P,0.05 level from all introns. For branch points, only 0-fold degeneracy was tested. doi:10.1371/journal.pgen.1000148.t004 PLoS Genetics | www.plosgenetics.org 8 August 2008 | Volume 4 | Issue 8 | e1000148