Antonis Rokas, Ph.D.

Professor

antonis.rokas@vanderbilt.edu

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Faculty Appointments
Professor of Biological Sciences Cornelius Vanderbilt Chair in Biological SciencesAssociate 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
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.
Research Keywords
Phylogenomics, Evolutionary Functional Genomics, Evolution of Fungal Metabolism, Evolution of Human Pregnancy, Tree of Life
Publications
Zhao L, Zhou X, Rokas A, Cone RD. Functional variants of the melanocortin-4 receptor associated with the Odontoceti and Mysticeti suborders of cetaceans. Sci Rep. 2017 Jul 7/18/2017; 7(1): 5684. PMID: 28720755, PMCID: PMC5515947, PII: 10.1038/s41598-017-05962-1, DOI: 10.1038/s41598-017-05962-1, ISSN: 2045-2322.

Steenwyk J, Rokas A. Extensive Copy Number Variation in Fermentation-Related Genes Among Saccharomyces cerevisiae Wine Strains. G3 (Bethesda). 2017 May 5/5/2017; 7(5): 1475-85. PMID: 28292787, PMCID: PMC5427499, PII: g3.117.040105, DOI: 10.1534/g3.117.040105, ISSN: 2160-1836.

Wisecaver JH, Borowsky AT, Tzin V, Jander G, Kliebenstein DJ, Rokas A. A Global Coexpression Network Approach for Connecting Genes to Specialized Metabolic Pathways in Plants. Plant Cell [print-electronic]. 2017 May; 29(5): 944-59. PMID: 28408660, PMCID: PMC5466033, PII: tpc.17.00009, DOI: 10.1105/tpc.17.00009, ISSN: 1532-298X.

Shen XX, Hittinger CT, Rokas A. Contentious relationships in phylogenomic studies can be driven by a handful of genes. Nat Ecol Evol. 2017 Apr 4/10/2017; 1(5): 126. PMID: 28812701, PII: s41559-017-0126, DOI: 10.1038/s41559-017-0126, ISSN: 2397-334X.

Abbot P, Rokas A. Mammalian pregnancy. Curr. Biol. 2017 Feb 2/20/2017; 27(4): R127-R128. PMID: 28222284, PII: S0960-9822(16)31272-6, DOI: 10.1016/j.cub.2016.10.046, ISSN: 1879-0445.

Ortiz JF, Rokas A. CTDGFinder: A Novel Homology-Based Algorithm for Identifying Closely Spaced Clusters of Tandemly Duplicated Genes. Mol. Biol. Evol [print-electronic]. 2017 Jan; 34(1): 215-29. PMID: 28007975, PII: msw227, DOI: 10.1093/molbev/msw227, ISSN: 1537-1719.

Lind AL, Smith TD, Saterlee T, Calvo AM, Rokas A. Regulation of Secondary Metabolism by the Velvet Complex Is Temperature-Responsive in Aspergillus. G3 (Bethesda). 2016 Dec 12/7/2016; 6(12): 4023-33. PMID: 27694115, PMCID: PMC5144971, PII: g3.116.033084, DOI: 10.1534/g3.116.033084, ISSN: 2160-1836.

Shen XX, Zhou X, Kominek J, Kurtzman CP, Hittinger CT, Rokas A. Reconstructing the Backbone of the Saccharomycotina Yeast Phylogeny Using Genome-Scale Data. G3 (Bethesda). 2016 Dec 12/7/2016; 6(12): 3927-39. PMID: 27672114, PMCID: PMC5144963, PII: g3.116.034744, DOI: 10.1534/g3.116.034744, ISSN: 2160-1836.

Zhou X, Peris D, Kominek J, Kurtzman CP, Hittinger CT, Rokas A. In silico Whole Genome Sequencer & Analyzer (iWGS): A Computational Pipeline to Guide the Design and Analysis of de novo Genome Sequencing Studies. G3 (Bethesda) [print-electronic]. 2016 Sep 9/16/2016; PMID: 27638685, PMCID: PMC5100864, PII: g3.116.034249, DOI: 10.1534/g3.116.034249, ISSN: 2160-1836.

Shen XX, Salichos L, Rokas A. A Genome-Scale Investigation of How Sequence, Function, and Tree-Based Gene Properties Influence Phylogenetic Inference. Genome Biol Evol. 2016 Sep 9/2/2016; 8(8): 2565-80. PMID: 27492233, PMCID: PMC5010910, PII: evw179, DOI: 10.1093/gbe/evw179, ISSN: 1759-6653.

Wisecaver JH, Alexander WG, King SB, Hittinger CT, Rokas A. Dynamic Evolution of Nitric Oxide Detoxifying Flavohemoglobins, a Family of Single-Protein Metabolic Modules in Bacteria and Eukaryotes. Mol. Biol. Evol [print-electronic]. 2016 Aug; 33(8): 1979-87. PMID: 27189567, PII: msw073, DOI: 10.1093/molbev/msw073, ISSN: 1537-1719.

Kobert K, Salichos L, Rokas A, Stamatakis A. Computing the Internode Certainty and Related Measures from Partial Gene Trees. Mol. Biol. Evol [print-electronic]. 2016 Jun; 33(6): 1606-17. PMID: 26915959, PMCID: PMC4868120, PII: msw040, DOI: 10.1093/molbev/msw040, ISSN: 1537-1719.

Eidem HR, Rinker DC, Ackerman WE, Buhimschi IA, Buhimschi CS, Dunn-Fletcher C, Kallapur SG, Pavlicev M, Muglia LJ, Abbot P, Rokas A. Comparing human and macaque placental transcriptomes to disentangle preterm birth pathology from gestational age effects. Placenta [print-electronic]. 2016 May; 41: 74-82. PMID: 27208410, PII: S0143-4004(16)30043-1, DOI: 10.1016/j.placenta.2016.03.006, ISSN: 1532-3102.

Alexander WG, Wisecaver JH, Rokas A, Hittinger CT. Horizontally acquired genes in early-diverging pathogenic fungi enable the use of host nucleosides and nucleotides. Proc. Natl. Acad. Sci. U.S.A [print-electronic]. 2016 Apr 4/12/2016; 113(15): 4116-21. PMID: 27035945, PMCID: PMC4839431, PII: 1517242113, DOI: 10.1073/pnas.1517242113, ISSN: 1091-6490.

Kim M, Cooper BA, Venkat R, Phillips JB, Eidem HR, Hirbo J, Nutakki S, Williams SM, Muglia LJ, Capra JA, Petren K, Abbot P, Rokas A, McGary KL. GEneSTATION 1.0: a synthetic resource of diverse evolutionary and functional genomic data for studying the evolution of pregnancy-associated tissues and phenotypes. Nucleic Acids Res [print-electronic]. 2016 Jan 1/4/2016; 44(D1): D908-16. PMID: 26567549, PMCID: PMC4702823, PII: gkv1137, DOI: 10.1093/nar/gkv1137, ISSN: 1362-4962.

Rokas A, Soltis PS. Editorial overview: Genomes and evolution: "Seq-ing" answers in life's genomes [editorial]. Curr. Opin. Genet. Dev [print-electronic]. 2015 Dec; 35: iv-vi. PMID: 26684354, PII: S0959-437X(15)00128-8, DOI: 10.1016/j.gde.2015.11.005, ISSN: 1879-0380.

Hittinger CT, Rokas A, Bai FY, Boekhout T, Gonçalves P, Jeffries TW, Kominek J, Lachance MA, Libkind D, Rosa CA, Sampaio JP, Kurtzman CP. Genomics and the making of yeast biodiversity. Curr. Opin. Genet. Dev [print-electronic]. 2015 Dec; 35: 100-9. PMID: 26649756, PMCID: PMC4771062, PII: S0959-437X(15)00108-2, DOI: 10.1016/j.gde.2015.10.008, ISSN: 1879-0380.

Wang Y, Zhou X, Yang D, Rokas A. A Genome-Scale Investigation of Incongruence in Culicidae Mosquitoes [letter]. Genome Biol Evol. 2015 Nov 11/25/2015; 7(12): 3463-71. PMID: 26608059, PMCID: PMC4700963, PII: evv235, DOI: 10.1093/gbe/evv235, ISSN: 1759-6653.

Phillips JB, Abbot P, Rokas A. Is preterm birth a human-specific syndrome?. Evol Med Public Health. 2015 Jun 6/14/2015; 2015(1): 136-48. PMID: 26077822, PMCID: PMC4493222, PII: eov010, DOI: 10.1093/emph/eov010.

Eidem HR, Ackerman WE, McGary KL, Abbot P, Rokas A. Gestational tissue transcriptomics in term and preterm human pregnancies: a systematic review and meta-analysis. BMC Med Genomics. 2015 Jun 6/5/2015; 8: 27. PMID: 26044726, PMCID: PMC4456776, PII: 10.1186/s12920-015-0099-8, DOI: 10.1186/s12920-015-0099-8, ISSN: 1755-8794.

Eidem HR, McGary KL, Rokas A. Shared Selective Pressures on Fungal and Human Metabolic Pathways Lead to Divergent yet Analogous Genetic Responses. Mol. Biol. Evol [print-electronic]. 2015 Jun; 32(6): 1449-55. PMID: 25681382, PII: msv034, DOI: 10.1093/molbev/msv034, ISSN: 1537-1719.

Lind AL, Wisecaver JH, Smith TD, Feng X, Calvo AM, Rokas A. Examining the evolution of the regulatory circuit controlling secondary metabolism and development in the fungal genus Aspergillus. PLoS Genet. 2015 Mar; 11(3): e1005096. PMID: 25786130, PMCID: PMC4364702, PII: PGENETICS-D-14-03141, DOI: 10.1371/journal.pgen.1005096, ISSN: 1553-7404.

Hirbo J, Eidem H, Rokas A, Abbot P. Integrating Diverse Types of Genomic Data to Identify Genes that Underlie Adverse Pregnancy Phenotypes. PLoS ONE. 2015; 10(12): e0144155. PMID: 26641094, PMCID: PMC4671692, PII: PONE-D-15-37377, DOI: 10.1371/journal.pone.0144155, ISSN: 1932-6203.

Wisecaver JH, Rokas A. Fungal metabolic gene clusters-caravans traveling across genomes and environments. Front Microbiol. 2015; 6: 161. PMID: 25784900, PMCID: PMC4347624, DOI: 10.3389/fmicb.2015.00161.

Wisecaver JH, Slot JC, Rokas A. The evolution of fungal metabolic pathways. PLoS Genet. 2014 Dec; 10(12): e1004816. PMID: 25474404, PMCID: PMC4256263, PII: PGENETICS-D-14-01830, DOI: 10.1371/journal.pgen.1004816, ISSN: 1553-7404.

Salichos L, Stamatakis A, Rokas A. Novel information theory-based measures for quantifying incongruence among phylogenetic trees. Mol. Biol. Evol [print-electronic]. 2014 May; 31(5): 1261-71. PMID: 24509691, PII: msu061, DOI: 10.1093/molbev/msu061, ISSN: 1537-1719.

Zhou X, Rokas A. Prevention, diagnosis and treatment of high-throughput sequencing data pathologies. Mol. Ecol [print-electronic]. 2014 Apr; 23(7): 1679-700. PMID: 24471475, DOI: 10.1111/mec.12680, ISSN: 1365-294X.

Soria PS, McGary KL, Rokas A. Functional divergence for every paralog. Mol. Biol. Evol [print-electronic]. 2014 Apr; 31(4): 984-92. PMID: 24451325, PII: msu050, DOI: 10.1093/molbev/msu050, ISSN: 1537-1719.

McGary KL, Slot JC, Rokas A. Physical linkage of metabolic genes in fungi is an adaptation against the accumulation of toxic intermediate compounds. Proc. Natl. Acad. Sci. U.S.A [print-electronic]. 2013 Jul 7/9/2013; 110(28): 11481-6. PMID: 23798424, PMCID: PMC3710872, PII: 1304461110, DOI: 10.1073/pnas.1304461110, ISSN: 1091-6490.

Salichos L, Rokas A. Inferring ancient divergences requires genes with strong phylogenetic signals. Nature [print-electronic]. 2013 May 5/16/2013; 497(7449): 327-31. PMID: 23657258, PII: nature12130, DOI: 10.1038/nature12130, ISSN: 1476-4687.

Rinker DC, Pitts RJ, Zhou X, Suh E, Rokas A, Zwiebel LJ. Blood meal-induced changes to antennal transcriptome profiles reveal shifts in odor sensitivities in Anopheles gambiae. Proc. Natl. Acad. Sci. U.S.A [print-electronic]. 2013 May 5/14/2013; 110(20): 8260-5. PMID: 23630291, PMCID: PMC3657813, PII: 1302562110, DOI: 10.1073/pnas.1302562110, ISSN: 1091-6490.

Gibbons JG, Rokas A. The function and evolution of the Aspergillus genome. Trends Microbiol [print-electronic]. 2013 Jan; 21(1): 14-22. PMID: 23084572, PMCID: PMC3534798, PII: S0966-842X(12)00175-8, DOI: 10.1016/j.tim.2012.09.005, ISSN: 1878-4380.

Gibbons JG, Salichos L, Slot JC, Rinker DC, McGary KL, King JG, Klich MA, Tabb DL, McDonald WH, Rokas A. The evolutionary imprint of domestication on genome variation and function of the filamentous fungus Aspergillus oryzae. Curr. Biol [print-electronic]. 2012 Aug 8/7/2012; 22(15): 1403-9. PMID: 22795693, PMCID: PMC3416971, PII: S0960-9822(12)00586-6, DOI: 10.1016/j.cub.2012.05.033, ISSN: 1879-0445.

Gibbons JG, Beauvais A, Beau R, McGary KL, Latgé JP, Rokas A. Global transcriptome changes underlying colony growth in the opportunistic human pathogen Aspergillus fumigatus. Eukaryotic Cell [print-electronic]. 2012 Jan; 11(1): 68-78. PMID: 21724936, PMCID: PMC3255943, PII: EC.05102-11, DOI: 10.1128/EC.05102-11, ISSN: 1535-9786.

Slot JC, Rokas A. Horizontal transfer of a large and highly toxic secondary metabolic gene cluster between fungi. Curr. Biol [print-electronic]. 2011 Jan 1/25/2011; 21(2): 134-9. PMID: 21194949, PII: S0960-9822(10)01651-9, DOI: 10.1016/j.cub.2010.12.020, ISSN: 1879-0445.

Slot JC, Rokas A. Multiple GAL pathway gene clusters evolved independently and by different mechanisms in fungi. Proc. Natl. Acad. Sci. U.S.A [print-electronic]. 2010 Jun 6/1/2010; 107(22): 10136-41. PMID: 20479238, PMCID: PMC2890473, PII: 0914418107, DOI: 10.1073/pnas.0914418107, ISSN: 1091-6490.

Hittinger CT, Gonçalves P, Sampaio JP, Dover J, Johnston M, Rokas A. Remarkably ancient balanced polymorphisms in a multi-locus gene network. Nature [print-electronic]. 2010 Mar 3/4/2010; 464(7285): 54-8. PMID: 20164837, PMCID: PMC2834422, PII: nature08791, DOI: 10.1038/nature08791, ISSN: 1476-4687.

Hittinger CT, Johnston M, Tossberg JT, Rokas A. Leveraging skewed transcript abundance by RNA-Seq to increase the genomic depth of the tree of life. Proc. Natl. Acad. Sci. U.S.A [print-electronic]. 2010 Jan 1/26/2010; 107(4): 1476-81. PMID: 20080632, PMCID: PMC2824393, PII: 0910449107, DOI: 10.1073/pnas.0910449107, ISSN: 1091-6490.

Gibbons JG, Janson EM, Hittinger CT, Johnston M, Abbot P, Rokas A. Benchmarking next-generation transcriptome sequencing for functional and evolutionary genomics. Mol. Biol. Evol [print-electronic]. 2009 Dec; 26(12): 2731-44. PMID: 19706727, PII: msp188, DOI: 10.1093/molbev/msp188, ISSN: 1537-1719.

Rokas A, Abbot P. Harnessing genomics for evolutionary insights. Trends Ecol. Evol. (Amst.) [print-electronic]. 2009 Apr; 24(4): 192-200. PMID: 19201503, PII: S0169-5347(09)00027-5, DOI: 10.1016/j.tree.2008.11.004, ISSN: 0169-5347.

Rokas A. The origins of multicellularity and the early history of the genetic toolkit for animal development. Annu. Rev. Genet. 2008; 42: 235-51. PMID: 18983257, DOI: 10.1146/annurev.genet.42.110807.091513, ISSN: 0066-4197.

Rokas, A, Carroll, SB. Bushes in the Tree of Life. PLoS Biology. 2006; 11((11)): e352.

Prudhomme, B, Gompel, N, Rokas, A, Kassner, VA, Williams, TM, Yeh, SD, True, JR, Carroll, SB. Repeated morphological evolution through cis-regulatory changes in a pleiotropic gene. Nature. 2006; ((440)): 1050-3.

Rokas, A, Krueger, D, Carroll, SB. Animal evolution and the molecular signature of radiations compressed in time. Science. 2005; ((310)): 1933-8.

Hittinger, CT, Rokas, A, Carroll, SB. Parallel inactivation of multiple GAL pathway genes and ecological diversification in yeasts. Proc. Natl. Acad. Sci. USA. 2004; ((101)): 14144-9.

Rokas, A*, Williams, BL*, King, N, Carroll, SB. Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature. 2003; ((425)): 798-804.

Rokas, A, Holland, PWH. Rare genomic changes as a tool for phylogenetics. Trends Ecol. Evol.. 2000; ((15)): 454-9.

Averof, M, Rokas, A, Wolfe, KH, Sharp, PM. Evidence for a high frequency of simultaneous double-nucleotide substitutions. Science. 2000; ((287)): 1283-6.