Faculty Appointments
Professor of Biological Sciences
Cornelius Vanderbilt Chair in Biological SciencesCornelius Vanderbilt Chair in Biological SciencesAssociate Professor of Biomedical InformaticsAssociate Professor of Biomedical Informatics
Education
Ph.D., Evolutionary Biology, University of Edinburgh, Edinburgh, United KingdomB.Sc., Biology, University of Crete, Rethymnon, Greece
Office Address
20450 Biological Sciences
VU Station B, 35-1634
Nashville, TN 37235, USA
TN
VU Station B, 35-1634
Nashville, TN 37235, USA
TN
Research Description
The shape of a bird’s beak or a whale’s flipper contains information not only about the organ’s function but also about its history. Similarly, information stored in DNA includes not only instructions about a cell’s function or the transformation of an egg into an embryo, but also a record, imperfect to be sure, of the organism’s biological past, and its history of change and adaptation. Far from the prevailing notion of the genome as a “blueprint”, the DNA of any organism more likely resembles a continually edited palimpsest, assembled over 3.5 billion years, whose sequence of letters contains important clues to major organism features that are largely yet to be deciphered.
In the Rokas lab, we study the DNA record to gain insight into the patterns and processes of evolution as well as to understand the evolution of the eukaryotic genome. We do so using both computational and experimental approaches to address three major questions:
I. How did human pregnancy evolve?
II. What are the molecular foundations of the fungal lifestyle?
III. How can we elucidate the tree of life?
We are working with several different lineages that span the diversity of the tree of life, but predominantly on mammals, fungi, insects and plants. Because, many of the approaches we employ to study these themes are novel and unfamiliar to biologists in general, we also investigate their utility for understanding the function and evolution of the genomes of non-model organisms and lineages.
In the Rokas lab, we study the DNA record to gain insight into the patterns and processes of evolution as well as to understand the evolution of the eukaryotic genome. We do so using both computational and experimental approaches to address three major questions:
I. How did human pregnancy evolve?
II. What are the molecular foundations of the fungal lifestyle?
III. How can we elucidate the tree of life?
We are working with several different lineages that span the diversity of the tree of life, but predominantly on mammals, fungi, insects and plants. Because, many of the approaches we employ to study these themes are novel and unfamiliar to biologists in general, we also investigate their utility for understanding the function and evolution of the genomes of non-model organisms and lineages.
Research Keywords
Evolutionary Biology, Computational Biology, Microbiology, Chemical Biology, Medical Mycology, Evolutionary Genomics, Pregnancy, Fungi, Mammals, Metabolism
Publications
Rokas A. The Origin and Early Evolution of Fungi: Challenges, Inferences, and Principles. Annu Rev Cell Dev Biol [print-electronic]. 2026 Jun 6/9/2026; PMID: 42263716, PMCID: PMC13285959, DOI: 10.1146/annurev-cellbio-111524-045246, ISSN: 1530-8995.
Danis T, Lin D, Caetano DS, Funston GF, Rokas A. Gestation length both shapes and is shaped by other life history traits in terrestrial eutherian mammals. Evol Lett. 2025 Dec; 9(6): 628-36. PMID: 41357153, PMCID: PMC12676461, PII: qraf028, DOI: 10.1093/evlett/qraf028, ISSN: 2056-3744.
Riedling OL, David KT, Rokas A. Global patterns of diversity and distribution in Aspergillus fungi are driven by human and environmental influences. Curr Biol [print-electronic]. 2025 Sep 9/22/2025; 35(18): 4453-4466.e3-4466.e3. PMID: 40848724, PMCID: PMC13181834, PII: S0960-9822(25)01026-7, DOI: 10.1016/j.cub.2025.07.081, ISSN: 1879-0445.
David KT, Schraiber JG, Crandall JG, Labella AL, Opulente DA, Harrison MC, Wolters JF, Zhou X, Shen XX, Groenewald M, Hittinger CT, Pennell M, Rokas A. Convergent expansions of keystone gene families drive metabolic innovation in Saccharomycotina yeasts. Proc Natl Acad Sci U S A [print-electronic]. 2025 Jun 6/10/2025; 122(23): e2500165122. PMID: 40460114, PMCID: PMC12167968, DOI: 10.1073/pnas.2500165122, ISSN: 1091-6490.
Sauters TJC, Rokas A. Patterns and mechanisms of fungal genome plasticity. Curr Biol. 2025 Jun 6/9/2025; 35(11): R527-R544-R544. PMID: 40494309, PMCID: PMC12161452, PII: S0960-9822(25)00432-4, DOI: 10.1016/j.cub.2025.04.003, ISSN: 1879-0445.
Harrison MC, Ubbelohde EJ, LaBella AL, Opulente DA, Wolters JF, Zhou X, Shen XX, Groenewald M, Hittinger CT, Rokas A. Machine learning enables identification of an alternative yeast galactose utilization pathway. Proc Natl Acad Sci U S A [print-electronic]. 2024 Apr 4/30/2024; 121(18): e2315314121. PMID: 38669185, PMCID: PMC11067038, DOI: 10.1073/pnas.2315314121, ISSN: 1091-6490.
Opulente DA, LaBella AL, Harrison MC, Wolters JF, Liu C, Li Y, Kominek J, Steenwyk JL, Stoneman HR, VanDenAvond J, Miller CR, Langdon QK, Silva M, Gonçalves C, Ubbelohde EJ, Li Y, Buh KV, Jarzyna M, Haase MAB, Rosa CA, CCadež N, Libkind D, DeVirgilio JH, Hulfachor AB, Kurtzman CP, Sampaio JP, Gonçalves P, Zhou X, Shen XX, Groenewald M, Rokas A, Hittinger CT. Genomic factors shape carbon and nitrogen metabolic niche breadth across Saccharomycotina yeasts. Science [print-electronic]. 2024 Apr 4/26/2024; 384(6694): eadj4503. PMID: 38662846, PMCID: PMC11298794, DOI: 10.1126/science.adj4503, ISSN: 1095-9203.
Steenwyk JL, Li Y, Zhou X, Shen XX, Rokas A. Incongruence in the phylogenomics era. Nat Rev Genet [print-electronic]. 2023 Dec; 24(12): 834-50. PMID: 37369847, PMCID: PMC11499941, PII: 10.1038/s41576-023-00620-x, DOI: 10.1038/s41576-023-00620-x, ISSN: 1471-0064.
Rokas A. Evolution of the human pathogenic lifestyle in fungi. Nat Microbiol [print-electronic]. 2022 May; 7(5): 607-19. PMID: 35508719, PMCID: PMC9097544, PII: 10.1038/s41564-022-01112-0, DOI: 10.1038/s41564-022-01112-0, ISSN: 2058-5276.
Danis T, Lin D, Caetano DS, Funston GF, Rokas A. Gestation length both shapes and is shaped by other life history traits in terrestrial eutherian mammals. Evol Lett. 2025 Dec; 9(6): 628-36. PMID: 41357153, PMCID: PMC12676461, PII: qraf028, DOI: 10.1093/evlett/qraf028, ISSN: 2056-3744.
Riedling OL, David KT, Rokas A. Global patterns of diversity and distribution in Aspergillus fungi are driven by human and environmental influences. Curr Biol [print-electronic]. 2025 Sep 9/22/2025; 35(18): 4453-4466.e3-4466.e3. PMID: 40848724, PMCID: PMC13181834, PII: S0960-9822(25)01026-7, DOI: 10.1016/j.cub.2025.07.081, ISSN: 1879-0445.
David KT, Schraiber JG, Crandall JG, Labella AL, Opulente DA, Harrison MC, Wolters JF, Zhou X, Shen XX, Groenewald M, Hittinger CT, Pennell M, Rokas A. Convergent expansions of keystone gene families drive metabolic innovation in Saccharomycotina yeasts. Proc Natl Acad Sci U S A [print-electronic]. 2025 Jun 6/10/2025; 122(23): e2500165122. PMID: 40460114, PMCID: PMC12167968, DOI: 10.1073/pnas.2500165122, ISSN: 1091-6490.
Sauters TJC, Rokas A. Patterns and mechanisms of fungal genome plasticity. Curr Biol. 2025 Jun 6/9/2025; 35(11): R527-R544-R544. PMID: 40494309, PMCID: PMC12161452, PII: S0960-9822(25)00432-4, DOI: 10.1016/j.cub.2025.04.003, ISSN: 1879-0445.
Harrison MC, Ubbelohde EJ, LaBella AL, Opulente DA, Wolters JF, Zhou X, Shen XX, Groenewald M, Hittinger CT, Rokas A. Machine learning enables identification of an alternative yeast galactose utilization pathway. Proc Natl Acad Sci U S A [print-electronic]. 2024 Apr 4/30/2024; 121(18): e2315314121. PMID: 38669185, PMCID: PMC11067038, DOI: 10.1073/pnas.2315314121, ISSN: 1091-6490.
Opulente DA, LaBella AL, Harrison MC, Wolters JF, Liu C, Li Y, Kominek J, Steenwyk JL, Stoneman HR, VanDenAvond J, Miller CR, Langdon QK, Silva M, Gonçalves C, Ubbelohde EJ, Li Y, Buh KV, Jarzyna M, Haase MAB, Rosa CA, CCadež N, Libkind D, DeVirgilio JH, Hulfachor AB, Kurtzman CP, Sampaio JP, Gonçalves P, Zhou X, Shen XX, Groenewald M, Rokas A, Hittinger CT. Genomic factors shape carbon and nitrogen metabolic niche breadth across Saccharomycotina yeasts. Science [print-electronic]. 2024 Apr 4/26/2024; 384(6694): eadj4503. PMID: 38662846, PMCID: PMC11298794, DOI: 10.1126/science.adj4503, ISSN: 1095-9203.
Steenwyk JL, Li Y, Zhou X, Shen XX, Rokas A. Incongruence in the phylogenomics era. Nat Rev Genet [print-electronic]. 2023 Dec; 24(12): 834-50. PMID: 37369847, PMCID: PMC11499941, PII: 10.1038/s41576-023-00620-x, DOI: 10.1038/s41576-023-00620-x, ISSN: 1471-0064.
Rokas A. Evolution of the human pathogenic lifestyle in fungi. Nat Microbiol [print-electronic]. 2022 May; 7(5): 607-19. PMID: 35508719, PMCID: PMC9097544, PII: 10.1038/s41564-022-01112-0, DOI: 10.1038/s41564-022-01112-0, ISSN: 2058-5276.