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<p><b>Additional
file 1.</b>
Final alignments (files with .aln.fasta extension) and phylogenetic
trees (files with fastree.newick extension) for all the protein
families analyzed in the study. Additionally, in case of three
protein families: AIF, OMI and caspase/metacaspase the subfolders
were created, containing the key subtrees (files in nexml format
generated with Dendroscope).</p>
<p><br>
</p>
<p><b>Additional
file 2</b><b>.</b>
Additional BLASTP results and taxonomy reports conducted
to confirm the key results in case of the three protein families:
AIF, caspase/metacaspase and htra.
BLASTP results and taxonomy reports were obtained with NCBI WWW with
two strategies: by selecting only a few eukaryotic proteomes (for the
species from Table S2 in Supplementary Methods) as a search database
(see file eukaryotic_strategy.pdf) and by extending selected
proteomes from the first search strategy with all bacterial and
archeal proteomes (see file extended_strategy.pdf). Please see
README.md for more details regarding information for given specific
file.
</p>
<p><br>
</p>
<p><b>Additional
file 3. </b>Mega
sessions for consensus phylogenetic trees calculated for arbitrarily
chosen metacaspases and caspases, OMI/HTRA proteases and AIFs.
Separate sessions files are available for calculations based on MLE
(maximum likelihood estimation), NJ (neighbor-joining) and ME
(minimal evolution).</p>
<p><br>
</p>
<p><b>Additional
Figure S1.</b>
Competition assay between <i>ndi1</i><i>Δ
</i>and
wild-type Saccharomyces cerevisiae BY4741 strains under anaerobic
conditions.</p>
<p><br>
</p>
<p><b>Additional
Figure S2.</b>
Growth curves for all tested in this study yeast strains cultivated
in prolonged cultures in aerobic (A) or anaerobic (B) conditions. The
values of mean and standard deviation from duplicate experiments are
shown for each time point.</p>
<p><br>
</p>
<p><b>Additional
Figure S3. </b>Yeast
strains used in the experimental evolution are unable to grow on
medium supplemented with non-fermentable carbon source. Cells grown
on glucose-containing (A) and glycerol-containing (B) solid medium.
Single colonies were streaked on the appropriate plate and incubated
at 28⁰C for 3 days. Wild-type strain shows robust growth on both
media, whereas mutant strains grow only on glucose-containing plate.<br>
<br>
</p
