The topology of the cladogram has been estimated conservatively from previous analyses using genome [12,23] or multi-locus sequence data [27,36]. Major clades [36] are color-coded (clade names are shown in Figure 2). Only one reference genome per species is included with preference given to the highest quality and/or most widely used reference genome. Only publicly available genome assemblies are included. Interspecies hybrids are discussed in the text but are not shown here. WGD, whole genome duplication; recent work has shown that the WGD was caused by an allopolyploidization event that occurred between an early member of the Zygosaccharomyces/Torulaspora clade and an early member of the Kluyveromyces/Lachancea/Eremothecium clade, thus making this part of the phylogeny a network, rather than a tree [73]. CTG clade, yeasts using an alternate codon table where CTG encodes serine, instead of leucine. JGI, genomes publicly available on MycoCosm at http://genome.jgi-psf.org/programs/fungi/index.jsf, which are subject to the usage terms of the DOE Joint Genome Institute until formal publication. GB1, GenBank Accession CCBQ000000000; GB2, Genbank Accession JPPO00000000; GB3, GenBank Accession AEOI00000000; GB4, GenBank Accession LCTY00000000.