A genome-scale phylogeny of the kingdom Fungi

Li, Yuanning; Steenwyk, Jacob L.; Chang, Ying; Wang, Yan; James, Timothy Y.; Stajich, Jason E.; Spatafora, Joseph W.; Groenewald, Marizeth; Dunn, Casey W.; Hittinger, Chris Todd; Shen, Xing-Xing; Rokas, Antonis

doi:10.1016/j.cub.2021.01.074

A genome-scale phylogeny of the kingdom Fungi

Journal Article · Wed Feb 17 23:00:00 EST 2021 · Current Biology

DOI:https://doi.org/10.1016/j.cub.2021.01.074· OSTI ID:1804876

^[1]; ^[2]; Chang, Ying ^[3]; ^[4]; ^[5]; ^[6]; Spatafora, Joseph W. ^[3]; Groenewald, Marizeth ^[7]; Dunn, Casey W. ^[8]; ^[9]; Shen, Xing-Xing ^[10]; Rokas, Antonis ^[2]

Vanderbilt Univ., Nashville, TN (United States); Vanderbilt University Department of Biological Sciences,
Vanderbilt Univ., Nashville, TN (United States)
Oregon State Univ., Corvallis, OR (United States)
Univ. of California, Riverside, CA (United States); Univ. of Toronto, ON (Canada)
Univ. of Michigan, Ann Arbor, MI (United States)
Univ. of California, Riverside, CA (United States)
Westerdijk Fungal Biodiversity Inst., Utrecht (The Netherlands)
Yale Univ., New Haven, CT (United States)
Univ. of Wisconsin, Madison, WI (United States)
Zhejiang Univ., Hangzhou (China)

Phylogenomic studies using genome-scale amounts of data have greatly improved understanding of the tree of life. Despite the diversity, ecological significance, and biomedical and industrial importance of fungi, evolutionary relationships among several major lineages remain poorly resolved, especially those near the base of the fungal phylogeny. To examine poorly resolved relationships and assess progress toward a genome-scale phylogeny of the fungal kingdom, we compiled a phylogenomic data matrix of 290 genes from the genomes of 1,644 species that includes representatives from most major fungal lineages. We also compiled 11 data matrices by subsampling genes or taxa from the full data matrix based on filtering criteria previously shown to improve phylogenomic inference. Analyses of these 12 data matrices using concatenation- and coalescent-based approaches yielded a robust phylogeny of the fungal kingdom, in which ~85% of internal branches were congruent across data matrices and approaches used. We found support for several historically poorly resolved relationships as well as evidence for polytomies likely stemming from episodes of ancient diversification. By examining the relative evolutionary divergence of taxonomic groups of equivalent rank, we found that fungal taxonomy is broadly aligned with both genome sequence divergence and divergence time but also identified lineages where current taxonomic circumscription does not reflect their levels of evolutionary divergence. Finally, our results provide a robust phylogenomic framework to explore the tempo and mode of fungal evolution and offer directions for future fungal phylogenetic and taxonomic studies.

View Accepted Manuscript (DOE)

Research Organization:: Great Lakes Bioenergy Research Center, Madison, WI (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: SC0018409

OSTI ID:: 1804876

Journal Information:: Current Biology, Journal Name: Current Biology Journal Issue: 8 Vol. 31; ISSN 0960-9822

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
Phylogenomics
ancient diversification
coalescence
concatenation
phylogenetic signal
polytomy test
relative evolutionary divergence
taxonomy
zygomycetes

A genome-scale phylogeny of the kingdom Fungi

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