Phylogenetic tree
The present analysis was performed on the phylogeny published by
Kurtzman and Robnett (2003). Although there has been new and more
complete developments for Saccharomycotina (Shen et al., 2018, Salichos
& Rokas, 2013), these phylogenies does not contain the number of
measured species compiled here. Also, the phylogeny does not change much
excepting for some tips involving the Saccharomyces genus
(S. paradoxus and S. cerevisiae appear as sister species
in Kurtzman & Robnett, 2003). In any event, we re-analyzed the data
using Shen et al. (2018) phylogeny, for which we could compile a
combination of 24 species and traits, and results were similar to what
is reported here. Since the original Kurtzman and Robnett’s phylogeny
was not available in digital format, we recompiled it using the
descriptions of the original paper (Kurtzman & Robnett, 2003), and the
instructions that the first author kindly provided. This phylogeny was
obtained using four nuclear genes (large subunit rRNA, small subunit
SSU, ITS-5.8S and translation elongation factor-1α) and two
mitochondrial genes (mitochondrial SS rRNA and COXII) (Kurtzman &
Robnett, 2003). We downloaded the sequences reported by the author to
obtain the phylogenetic relatedness among species using the maximum
likelihood (ML) function included in the software MEGA v6 (Tamura et
al., 2013). ML was used with the defaults provided as well as with the
gamma distribution, using similar set parameter Kurtzman and Robnett
(2003) phylogeny. The bootstrap was performed with 1000 replicates. We
employed same method reported for Kurtzman & Robnett (2003) to obtain
same topology using concatenated genes. We time-calibrated the phylogeny
using three different historical events: the loss of the respiratory
complex I, which is dated to 150 millions of years ago (MYA;
(Marcet-Houben et al., 2009), the horizontal transfer of the URA1 gene,
which according to (Dujon, 2010) occurred 125 MYA and the WGD, which
according to (Wolfe & Shields, 1997) occurred 100 MYA (Fig. 1A). The
calibration was performed with the chronopl command in ape (Paradis,
2012).
Traits were compiled from the values published by Hagman et al. (2013)
[the complete dataset is provided in Table A1], and pruned to make
them suitable for the comparative analysis, respecting branch lengths
and species representation in the phylogeny. This is pruning is a common
practice in phylogenetic comparative methods whenever trait values are
compiled from literature and not necessarily are represented in the
phylogenetic tree. In our case, pruning unavoidably reduced the sample
size from 50 original strains, to 31 species with trait values.
According to Cressler et al. (2015, pp 959), OU methods have relatively
good performance in model discrimination even with sample sizes as small
as 20 species, as long as the sample is representative of the biological
diversity of the group (Cressler et al., 2015). This is our case, as we
used a wide variety of Crabtree positive and negative species (see Fig
1). When two trait values were available for a single species, we took
trait averages. We averaged strain values for Candida glabrata(two strains), Eremothecium corylii (two strains), E.
sinecaudum (two strains), Kazachstania lodderae (two strains),Kluyveromyces lactis (two strains), Kluyveromyces
marxcianus (four strains), Lachancea kluyveri (two strains),Saccharomyces cerevisiae (two strains), Saccharomyces
pastorianus (two strains), Tetrapisispora iriomotensis (two
strains), Torulaspora franciscae (two strains).