1 Supplementary Figures

Transcription

1 Supplementary Figures D. simulans (dsim) D. sechellia (dsec) D. melanogaster (dmel) S. cerevisiae (scer) S. paradoxus (spar) S. mikatae (smik) S. bayanus (sbay) S. castellii (scas) C. glabrata (cgla) K. waltii (kwal) A. gossypii (agos) K. lactis (klac) D. yakuba (dyak) D. erecta (dere) D. ananassae (dana) D. pseudoobscura (dpse) D. persimils (dper) D. willistoni (dwil) D. mojavensis (dmoj) D. virilis (dvir) D. grimshawi (dgri) ~ million years ~ million years. Figure S: Species names, abbreviations, and phylogeny

2 Name T T T T T T T T T9 T T T T T T Topology ((((((dere,dyak),dmel),dana),dpse),dwil),((dmoj,dvir),dgri)) ((((((dere,dmel),dyak),dana),dpse),dwil),((dmoj,dvir),dgri)) ((((((dere,dyak),dmel),dana),dpse),dwil),((dgri,dvir),dmoj)) ((((((dmel,dyak),dere),dana),dpse),dwil),((dmoj,dvir),dgri)) ((((((dere,dmel),dyak),dana),dpse),dwil),((dgri,dvir),dmoj)) ((((((dere,dyak),dmel),dana),dpse),dwil),((dgri,dmoj),dvir)) ((((((dmel,dyak),dere),dana),dpse),dwil),((dgri,dvir),dmoj)) ((((((dere,dyak),dmel),dana),dwil),dpse),((dmoj,dvir),dgri)) (((((dere,dyak),dmel),dana),(dpse,dwil)),((dmoj,dvir),dgri)) ((((((dere,dmel),dyak),dana),dpse),dwil),((dgri,dmoj),dvir)) (((((dere,dyak),dmel),dana),(dpse,dwil)),((dgri,dvir),dmoj)) ((((((dere,dmel),dyak),dana),dwil),dpse),((dmoj,dvir),dgri)) ((((((dmel,dyak),dere),dana),dpse),dwil),((dgri,dmoj),dvir)) ((((((dere,dyak),dmel),dana),dwil),dpse),((dgri,dvir),dmoj)) (((((dere,dmel),dyak),dana),(dpse,dwil)),((dmoj,dvir),dgri)) Figure Sa: Naming scheme for ortholog gene-trees for 9 fly species. Ordered by ML frequency. SPIDIR SPIDIR (D=.) SPIDIR (D=.) PHYML BIONJ MrBayes DNAPARS T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.9%) T (.%) T (9.%) T (.%) T (.%) T (.9%) T (.%) T (.%) T (.%) T (.9%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.9%) T (.%) T (.%) T (.9%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.9%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.9%) T (.%) T9 (.%) T (.%) T (.%) T (.%) T (.%) T (.9%) T (.%) T (.%) T9 (.9%) T9 (.%) T (.%) T (.%) T9 (.%) T (.%) T (.%) T (.%) T (.%) T9 (.%) T9 (.%) T (.%) T9 (.%) T (.9%) T (.%) T (.%) T (.%) T (.%) T (.9%) T (.%) Figure Sb: Most frequently constructed ortholog gene-trees for 9 fly species. Different methods reconstruct the same topologies at similar frequencies.

3 Name T T T T T T T T T9 T T T T T T Topology (((((((dsec,dsim),dmel),(dere,dyak)),dana),(dper,dpse)),dwil),((dmoj,dvir),dgri)) ((((((((dsec,dsim),dmel),dere),dyak),dana),(dper,dpse)),dwil),((dmoj,dvir),dgri)) (((((((dsec,dsim),dmel),(dere,dyak)),dana),(dper,dpse)),dwil),((dgri,dvir),dmoj)) ((((((((dsec,dsim),dmel),dyak),dere),dana),(dper,dpse)),dwil),((dmoj,dvir),dgri)) ((((((((dsec,dsim),dmel),dere),dyak),dana),(dper,dpse)),dwil),((dgri,dvir),dmoj)) (((((((dsec,dsim),dmel),(dere,dyak)),dana),(dper,dpse)),dwil),((dgri,dmoj),dvir)) ((((((((dsec,dsim),dmel),dyak),dere),dana),(dper,dpse)),dwil),((dgri,dvir),dmoj)) (((((((dsec,dsim),dmel),(dere,dyak)),dana),dwil),(dper,dpse)),((dmoj,dvir),dgri)) ((((((dsec,dsim),dmel),(dere,dyak)),dana),((dper,dpse),dwil)),((dmoj,dvir),dgri)) ((((((((dsec,dsim),dmel),dere),dyak),dana),(dper,dpse)),dwil),((dgri,dmoj),dvir)) (((((((dmel,dsim),dsec),(dere,dyak)),dana),(dper,dpse)),dwil),((dmoj,dvir),dgri)) (((((((dere,dyak),(dsec,dsim)),dmel),dana),(dper,dpse)),dwil),((dmoj,dvir),dgri)) (((((((dmel,dsec),dsim),(dere,dyak)),dana),(dper,dpse)),dwil),((dmoj,dvir),dgri)) (((((((dsec,dsim),dmel),dere),dyak),dana),((dper,dpse),dwil)),((dmoj,dvir),dgri)) ((((((((dsec,dsim),dmel),dere),dyak),dana),dwil),(dper,dpse)),((dmoj,dvir),dgri)) Figure Sa: Naming scheme for ortholog gene-trees for fly species. Ordered by ML frequency. SPIDIR PHYML BIONJ MrBayes DNAPARS T (.%) T (.9%) T (.9%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (9.%) T (.%) T (.%) T (.%) T (.9%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.9%) T (.9%) T (.%) T (.%) T (.%) T (.9%) T (.%) T (.%) T (.%) T (.9%) T (.%) T (.%) T (.%) T (.%) T (.%) T9 (.%) T (.%) T9 (.%) T9 (.%) T9 (.%) T (.%) T9 (.%) T (.%) T (.%) T (.%) T (.%) T (.%) Figure Sb: Most frequently constructed ortholog gene-trees for fly species. Different methods reconstruct the same topologies at similar frequencies. SPIDIR PHYML BIONJ MrBayes DNAPARS T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T9 (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T9 (.%) T9 (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T9 (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T9 (.%) Figure Sc: Most frequent gene-trees for simulated fly orthologs ( species). Simulated trees have similar errors at nearly the same relative frequencies as those found in real fly gene-trees.

4 PHYML MrBayes BIONJ Occurrence T T T (.%) T T T 9 (.%) T T T 9 (.%) T T T (.%) T T T (.%) T T T 9 (.%) T T T (.%) T T T 9 (.%) T T T (.%) T T T (.%) T T T (.9%) T T T (.%) T T T (.%) T T T (.%) T T T (.%) T T T (.%) T9 T9 T9 (.%) T T T (.%) T T T (.%) T T T (.%) Figure Sd: Most frequently constructed ortholog gene-trees for fly species. When methods are aquired to agree, reconstruction frequency for each topology decreases.

5 Name T T T T T T T T T T T T T T T T T9 T T T Topology ((((((spar,yeast),smik),sbay),scas),cgla),((agos,kwal),klac)) ((((((spar,yeast),smik),sbay),scas),cgla),((agos,klac),kwal)) (((((spar,yeast),smik),sbay),(cgla,scas)),((agos,kwal),klac)) ((((((spar,yeast),smik),sbay),cgla),scas),((agos,kwal),klac)) (((((spar,yeast),smik),sbay),(cgla,scas)),((agos,klac),kwal)) ((((((spar,yeast),smik),sbay),cgla),scas),((agos,klac),kwal)) ((((((spar,yeast),smik),sbay),scas),klac),((agos,kwal),cgla)) ((((((spar,yeast),smik),sbay),scas),cgla),((klac,kwal),agos)) (((((((spar,yeast),smik),sbay),scas),klac),kwal),(agos,cgla)) ((((((spar,yeast),smik),sbay),scas),(agos,kwal)),(cgla,klac)) (((((spar,yeast),smik),sbay),(cgla,scas)),((klac,kwal),agos)) ((((((spar,yeast),sbay),smik),scas),cgla),((agos,klac),kwal)) ((((((smik,yeast),spar),sbay),scas),cgla),((agos,kwal),klac)) ((((((spar,yeast),sbay),smik),cgla),scas),((agos,kwal),klac)) ((((((spar,yeast),smik),sbay),scas),(agos,klac)),(cgla,kwal)) (((((spar,yeast),smik),sbay),(klac,scas)),((agos,kwal),cgla)) ((((((spar,yeast),smik),sbay),scas),(klac,kwal)),(agos,cgla)) (((((spar,yeast),smik),sbay),(agos,kwal)),((klac,scas),cgla)) (((((spar,yeast),smik),sbay),klac),((agos,kwal),(cgla,scas))) (((((spar,yeast),smik),sbay),(agos,kwal)),((cgla,klac),scas)) Figure Sa: Naming scheme for ortholog gene-trees for 9 fungi species. Ordered by ML frequency. SPIDIR SPIDIR (D=.) SPIDIR (D=.) PHYML BIONJ MrBayes DNAPARS T (.%) T (.%) T (.%) T (.%) T (9.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.9%) T (9.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (9.%) T (.%) T (.9%) T (.%) T9 (.9%) T (.%) T (.%) T (.%) T (.9%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T9 (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T9 (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.9%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.9%) T (.%) T9 (.%) T (.%) T (.%) T (.9%) T (.%) T (.%) T (.%) T (.%) T (.%) T9 (.%) T (.9%) T9 (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.9%) T (.9%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.9%) T (.9%) T (.%) T (.%) T9 (.%) T (.%) T9 (.%) T (.%) T9 (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T9 (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T (.%) T9 (.%) T (.%) T (.%) T9 (.%) T (.%) T (.%) T (.%) T (.%) T9 (.%) Figure Sb: Most frequently constructed gene-tree topologies on 9 syntenic fungi orthologs. Topologies are numbered by their frequency across all methods.

6 Effect of gene length on reconstruction avg RF error.... spidir spidir-d. spidir-d. phyml bionj mrbayes parsimony bionj (ds) phyml (pep) bionj (pep) mrbayes (pep) parsimony (pep)..... gene length percentile Figure S: Robinson Foulds (RF) error correlates with sequence length for the 9 fly species. Acuracy improvements made by SPIDIR are also apparent for partial tree correctness (RF error). RF error is calculated as the fraction of internal branches that incorrectly bi-partition the leaves.

7 9 Fly orthologs Effect of percent identity on reconstruction 9 Fungal orthologs Effect of percent identity on reconstruction reconstruction accuracy.... SPIDIR (D=.) SPIDIR (D=.) SPIDIR SPIDIR SPIDIR (D=.) SPIDIR (D=.) PHYML BIONJ MrBayes Parsimony BIONJ(dS) PHYML(pep) BIONJ(pep) MrBayes (pep) Parsimony (pep) reconstruction accuracy.... SPIDIR (D=.) SPIDIR (D=..) SPIDIR SPIDIR SPIDIR (D=.) SPIDIR (D=.) PHYML BIONJ MrBayes Parsimony BIONJ (ds) PHYML (pep) BIONJ (pep) MrBayes (pep) Parsimony (pep) percent identity.... percent identity Figure S: Effect of mutation rate (nucleotide percent identity) on phylogenetic reconstruction accuracy. Reconstruction accuracy drops for both fast and slow evolving genes. Peptide alignments perform worse overall and saturate near. nucleotide percent identity, where most mutations are likely to beonly in the wobble codon position. Neighbor Joining on silent mutations (ds) increases slightly for slower evolving genes.

8 9 fly species (exclude dsec, dsim, dper) branch mean st dev st dev/mean dmel... dyak.9.. dere...9 dana..9. dpse.9.. dwil...9 dvir... dmoj.9..9 dgri fly species branch mean st dev st dev/mean dsim...9 dsec... dmel.9.. dyak... dere... dana... dpse... dper... dwil... dmoj...9 dvir.9.. dgri Figure S: Species-specific rates for the 9 and fly tree. Branches lengths are drawn with the mean species-specific rate. Thick line segments represent one standard deviation of the species-specific rate. Substitutions/site are relative, such that the branch lengths of each tree sums to one. The st dev/mean for each branch measures the tightness of its rate distribution.

9 dmel absolute branch lengths (a=.99, b=., Pval=.e-) dsim absolute branch lengths (a=.9, b=.9, Pval=9.9e-) dsec absolute branch lengths (a=., b=., Pval=.e-) dere absolute branch lengths (a=., b=., Pval=.e-) dyak absolute branch lengths (a=., b=9.9, Pval=.e-) dana absolute branch lengths (a=., b=., Pval=.e-) dpse absolute branch lengths (a=.9, b=., Pval=.e+) dper absolute branch lengths (a=., b=., Pval=.e+) dwil absolute branch lengths (a=., b=., Pval=.9e-) dmoj absolute branch lengths (a=., b=., Pval=.9e-) dvir absolute branch lengths (a=.9, b=., Pval=.e-) dgri absolute branch lengths (a=., b=., Pval=.e-) absolute branch lengths (a=.9, b=.9, Pval=.e-) absolute branch lengths (a=.99, b=., Pval=.e-) absolute branch lengths (a=., b=., Pval=.e-) absolute branch lengths (a=.9, b=.9, Pval=.e-) absolute branch lengths (a=., b=.9, Pval=.e-) absolute branch lengths (a=.9, b=., Pval=.e-) absolute branch lengths (a=., b=., Pval=.9e-) 9 absolute branch lengths (a=.9, b=., Pval=.e-) absolute branch lengths (a=.9, b=.9, Pval=.e-) absolute branch lengths (a=., b=9.9, Pval=.e-) Figure S: Branch length distributions fitted by gamma for every branch in the fly tree. out of absolute branch lengths significantly (p >.) fits the gamma distribution by Kolmogorov- Smirnov test (using middle 9% of lengths). Remaining branch lengths are closely approximated by gamma distribution. 9

10 dmel relative branch lengths (mean=.9, sdev=., pval=.9e-) dsim relative branch lengths (mean=., sdev=., pval=.e-) dsec relative branch lengths (mean=., sdev=., pval=.9e-) dere relative branch lengths (mean=., sdev=., pval=.9e-) rel rel rel rel dyak relative branch lengths (mean=., sdev=., pval=.e-) dana relative branch lengths (mean=., sdev=., pval=.9e-) dpse relative branch lengths (mean=.9, sdev=., pval=.e+) dper relative branch lengths (mean=., sdev=., pval=.e+) rel rel rel rel dwil relative branch lengths (mean=., sdev=., pval=.e-) dmoj relative branch lengths (mean=., sdev=., pval=.e-) dvir relative branch lengths (mean=., sdev=., pval=.9e-) dgri relative branch lengths (mean=., sdev=., pval=.9e-) rel rel rel rel relative branch lengths (mean=., sdev=.9, pval=.e-) relative branch lengths (mean=.9, sdev=.9, pval=.e-) relative branch lengths (mean=., sdev=.9, pval=.e-) relative branch lengths (mean=., sdev=., pval=9.9e-) rel rel rel rel relative branch lengths (mean=., sdev=., pval=.e-) relative branch lengths (mean=., sdev=.9, pval=.e-) relative branch lengths (mean=., sdev=., pval=.e-9) 9 relative branch lengths (mean=.9, sdev=., pval=.e-) rel rel rel rel relative branch lengths (mean=., sdev=.9, pval=.e-) relative branch lengths (mean=., sdev=., pval=.e-) rel rel Figure S9: Normalized length distributions fitted by normal for every branch in the fly tree. 9 out of relative branch lengths significantly (p >.) fits the normal distribution by Kolmogorov- Smirnov test (using middle 9% of lengths). Remaining branch lengths are closely approximated by normal distribution.

11 branch mean st dev st dev / mean scer..9. spar.9.. smik... sbay..9.9 scas.9.9. cgla... agos.99.. kwal.9.. klac Figure S: Species-specific rates for the 9 fungi tree. Branches lengths are drawn with the mean species-specific rate. Thick line segments represent one standard deviation of the species-specific rate. Substitutions/site are relative, such that the branch lengths of each tree sums to one. The st dev/mean for each branch measures the tightness of its rate distribution.

12 yeast absolute branch lengths (a=.9, b=9.99, Pval=.e-) spar absolute branch lengths (a=., b=9., Pval=.999e-) smik absolute branch lengths (a=.9, b=.9, Pval=.9e-) sbay absolute branch lengths (a=., b=., Pval=.e-) scas absolute branch lengths (a=., b=9., Pval=9.e-) cgla absolute branch lengths (a=., b=., Pval=.e-) klac absolute branch lengths (a=., b=., Pval=.e-) kwal absolute branch lengths (a=.9, b=9., Pval=.e-) agos absolute branch lengths (a=., b=., Pval=.9e-) absolute branch lengths (a=., b=., Pval=.e-) absolute branch lengths (a=.9, b=., Pval=.e-) absolute branch lengths (a=.9, b=., Pval=.9e-) absolute branch lengths (a=., b=., Pval=.e-) absolute branch lengths (a=9., b=., Pval=.e-) absolute branch lengths (a=., b=., Pval=.e-) absolute branch lengths (a=.9, b=9., Pval=.e-) Figure S: Branch length distributions fitted by gamma for every branch in the fungal tree. out of absolute branch lengths significantly (p >.) fits the gamma distribution by Kolmogorov- Smirnov test (using middle 9% of lengths).

13 yeast relative branch lengths (mean=., sdev=., pval=.9e-) spar relative branch lengths (mean=.9, sdev=., pval=.e-) smik relative branch lengths (mean=., sdev=., pval=.e-) sbay relative branch lengths (mean=., sdev=.9, pval=.9e-) rel rel rel rel scas relative branch lengths (mean=.9, sdev=., pval=.e-) cgla relative branch lengths (mean=., sdev=., pval=.e-) klac relative branch lengths (mean=., sdev=.9, pval=.e-) kwal relative branch lengths (mean=.9, sdev=., pval=.e-) rel rel rel rel agos relative branch lengths (mean=.99, sdev=., pval=.9e-) relative branch lengths (mean=., sdev=., pval=.9e-) relative branch lengths (mean=., sdev=., pval=.e-) relative branch lengths (mean=., sdev=.9, pval=.e-) rel rel rel rel relative branch lengths (mean=., sdev=., pval=.e-) relative branch lengths (mean=., sdev=., pval=9.e-) relative branch lengths (mean=., sdev=., pval=.e-) relative branch lengths (mean=., sdev=., pval=.e-) rel rel rel rel Figure S: Normalized length distributions fitted by normal for every branch in the fungal tree. out of relative branch lengths significantly (p >.) fits the normal distribution by Kolmogorov-Smirnov test (using middle 9% of lengths).

14 yeast spar smik sbay scas cgla klac kwal agos yeast spar smik sbay scas cgla klac kwal agos yeast spar smik sbay scas cgla klac kwal agos Absolution branch length correlations yeast spar smik sbay scas cgla klac kwal agos Relative branch length correlations.. -. Figure S: Absolute (left) and relative (right) branch length correlations within the fungal tree. Ancerstral species are numbered as shown.

15 gene tree counts 9% of gene trees Correlation with average gene tree Figure S: Histogram of gene tree branch length correlations between species tree branch lengths and fly ortholog gene trees. 9% of gene trees have a correlation greater than. with the species tree, indicating gene trees are highly correlated with each other.

16 fly branch variances fly branch means.... variance... mean dvir dpse dere dmoj dyak dwil dsec dgri dmel dper dsim dana. > gene length > gene length Figure S: Variances of species-specific rates decrease with increasing sequence length, indicating that the variance of a species-specific distribution is partly due to distance estimation error (left). Speciesspecific means are not affected by sequence length (right). Mean and variance were calculated for relative branch lengths of fly gene trees binned by gene length into four bins (<,,, > ).

17 TAB] DATASET : Beta Hemoglobin Orthologs Method Topology chosen Ratio Result Topology Topology SPIDIR likelihood Topology. Correct.9.9 Max likelihood Topology 9.9 Wrong Neighbor Joining Topology. Wrong Parsimony Topology. Wrong Species Expected Topology Topology Likelihood branch Length Stdev Branch Abs length Rel length Likelihood Branch Abs length Rel length Likelihood comparison mouse.9. d... y.... rat.. c... x human.. e.... hmr+human.9.99 w... dog.. v..9.. dog+hmr.. a+f..99. mr.. b.9... hmr+mr.. z.9.9. Family rate alpha=. beta=.99 rate=..9 rate=... Total.9.9. DATASET : Alpha and Beta Hemoglobin Paralogs Method Topology chosen Ratio Result Topology Topology SPIDIR likelihood Topology. Correct. 9. Max likelihood Topology.E+ Correct Neighbor Joining Topology Correct. 99. Parsimony Topology. Correct 9.. Species Expected Topology Topology Likelihood branch Length Stdev Branch Abs length Rel length Likelihood Branch Abs length Rel length Likelihood comparison mouse.9. d... y....9 rat.. c...9 x.... human.. e.... hmr+human.9.99 w...9 dog.. v.... dog+hmr.. a+f... mr.. b.... hmr+mr.. z... Family rate alpha=. beta=.99 rate=.9. rate= Total. 9.. Figure S: (Dataset ) Evaluation of two topologies (Figure b, e) for four hemoglobinbeta orthologs by three phylogenetic methods and SPIDIR. Due to long branch attraction, each method finds the incorrect Topology as more likeliy. In constrast, SPIDIR uses learned branch length distributions (Expected) to compute the likelihood of each branch and concludes that Topology is -fold more likely. (Dataset ) Evaluation of two topologies (Figure b, e) for two hemoglobin-beta orthologs (mouse and rat) and two hemoglobin-alpha orthologs (human and dog). Since these genes are related by an ancestral duplication that is well before the mammalian speciation, the branch lengths support the topology T with a -fold likelihood ratio.

18 branch bootstrap corresponds to branch accuracy on fly orthologous alignments. accuracy (fraction conguent to species tree)... bootstrap Figure S: Branch bootstrap values from reconstructing fly ortholog trees plotted against probability of branch being correct. Probability of correctness for a branch with bootstrap X was estimated by percentage of correct branches with bootstraps within X / to X + /.

19 a comparison of accuracy for each go term. spidir accuracy phyml accuracy b GO Term p-value SPIDIR PHYML total oocyte microtubule cytoskeleton polarization.9 (.%) (.%) mrna cleavage and polyadenylation specificity factor complex. (.%) (.%) establishment and/or maintenance of cytoskeleton polarity. (.%) (.%) establishment and/or maintenance of microtubule cytoskeleton polarity. (.%) (.%) oocyte microtubule cytoskeleton organization. (.%) (.%) mannosyl-oligosaccharide mannosidase activity. (.%) (.%) mannosidase activity.9 (.%) (.%) antifungal humoral response (sensu Protostomia).9 (.%) (.%) endoribonuclease activity. (.%) (.%) structural constituent of peritrophic membrane (sensu Insecta). (.%) (.%) RAB small monomeric GTPase activity. (.%) (.%) SH/SH adaptor protein activity. (.%) (.%) carboxylesterase activity. (.%) (.%) transmembrane receptor protein tyrosine kinase docking protein activity. (.%) (.%) transmembrane receptor protein tyrosine kinase signaling protein activity. (.%) (.%) Figure S: (a) Accuracy comparison of SPIDIR vs PHYML for each GO term. Each tree was associated with each GO term of the D. melanogaster gene. (b) GO terms for which SPIDIR most significantly under performs PHYML. P-values are computed using the hypergeometric test. P-values above have not been corrected for multiple-testing. Doing so would decrease significance even further. No GO term performs significantly worse (p >.) for SPIDIR than for PHYML. 9

20 klac to scer (mu=.9, sigma=.) (mu=., sigma=.) klac to spar (mu=.9, sigma=.) (mu=., sigma=.) klac to smik (mu=.9, sigma=.) (mu=.9, sigma=.) klac to sbay (mu=.9, sigma=.) (mu=., sigma=.) klac to scas (mu=.9, sigma=.) (mu=.9, sigma=.) klac to cgla (mu=., sigma=.) (mu=., sigma=.) Figure S9: Branch distributions of trees with duplication approximated by normal. For each of the gene families in our WGD dataset, we identified the distance between one pre-duplication species, K. lactis, and two ohnologs in a post-duplication species. These distances were normalized by the estimated family rate for each gene tree. The histogram of branch lengths is plotted against the normal expected by the model (sum of several independent normals).