The megadiverse genus
Phylogenetic studies of
- NSF-PAR ID:
- 10233380
- Author(s) / Creator(s):
- ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; more »
- Publisher / Repository:
- Wiley-Blackwell
- Date Published:
- Journal Name:
- Journal of Systematics and Evolution
- Volume:
- 59
- Issue:
- 4
- ISSN:
- 1674-4918
- Page Range / eLocation ID:
- p. 726-762
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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The subphylum Saccharomycotina is a lineage in the fungal phylum Ascomycota that exhibits levels of genomic diversity similar to those of plants and animals. The Saccharomycotina consist of more than 1 200 known species currently divided into 16 families, one order, and one class. Species in this subphylum are ecologically and metabolically diverse and include important opportunistic human pathogens, as well as species important in biotechnological applications. Many traits of biotechnological interest are found in closely related species and often restricted to single phylogenetic clades. However, the biotechnological potential of most yeast species remains unexplored. Although the subphylum Saccharomycotina has much higher rates of genome sequence evolution than its sister subphylum, Pezizomycotina , it contains only one class compared to the 16 classes in Pezizomycotina . The third subphylum of Ascomycota , the Taphrinomycotina , consists of six classes and has approximately 10 times fewer species than the Saccharomycotina . These data indicate that the current classification of all these yeasts into a single class and a single order is an underappreciation of their diversity. Our previous genome-scale phylogenetic analyses showed that the Saccharomycotina contains 12 major and robustly supported phylogenetic clades; seven of these are current families ( Lipomycetaceae , Trigonopsidaceae , Alloascoideaceae , Pichiaceae , Phaffomycetaceae , Saccharomycodaceae , and Saccharomycetaceae ), one comprises two current families ( Dipodascaceae and Trichomonascaceae ), one represents the genus Sporopachydermia , and three represent lineages that differ in their translation of the CUG codon (CUG-Ala, CUG-Ser1, and CUG-Ser2). Using these analyses in combination with relative evolutionary divergence and genome content analyses, we propose an updated classification for the Saccharomycotina , including seven classes and 12 orders that can be diagnosed by genome content. This updated classification is consistent with the high levels of genomic diversity within this subphylum and is necessary to make the higher rank classification of the Saccharomycotina more comparable to that of other fungi, as well as to communicate efficiently on lineages that are not yet formally named.more » « less
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DNA ‐sequence‐based phylogenetic hypothesis of species relationships in the coca family (Erythroxylaceae) and presents its implications for the intrageneric taxonomy and neotropical biogeography ofErythroxylum . We also identify the closest wild relatives and evolutionary relationships of the cultivated coca taxa.Methods We focused our phylogenomic inference on the largest taxonomic section in the genus
Erythroxylum (Archerythroxylum O.E.Schulz) using concatenation and gene tree reconciliation methods from hybridization‐based target capture of 427 genes.Key Results We show that neotropical
Erythroxylum are monophyletic within the paleotropical lineages, yetArcherythroxylum and all of the other taxonomic sections from which we sampled multiple species lack monophyly. We mapped phytogeographic states onto the tree and found some concordance between these regions and clades. The wild speciesE. gracilipes andE. cataractarum are most closely related to the cultivatedE. coca andE. novogranatense , but relationships within this “coca” clade remain equivocal.Conclusions Our results point to the difficulty of morphology‐based intrageneric classification in this clade and highlight the importance of integrative taxonomy in future systematic revisions. We can confidently identify
E. gracilipes andE. cataractarum as the closest wild relatives of the coca taxa, but understanding the domestication history of this crop will require more thorough phylogeographic analysis.
