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Antonis Rokas - Vanderbilt University. Nashville, TN, US

Antonis Rokas Antonis Rokas

Cornelius Vanderbilt Chair in Biological Sciences | Vanderbilt University

Nashville, TN, UNITED STATES

Expert on patterns of evolution, with a focus on the earliest forms of life.

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Biography

Research in Rokas' lab focuses on the study of the DNA record to gain insight into the patterns and processes of evolution. Through a combination of computational and experimental approaches, his current research aims to understand the evolution of human pregnancy, the molecular foundations of the fungal lifestyle, and the reconstruction of the tree of life. His discoveries have been reported in the world’s premier journals, receiving thousands of citations, and been recognized by many awards, including an endowed chair (2013), a Chancellor’s Award for Research (2011), an NSF CAREER award (2009) and a Searle Scholarship (2008). He serves as an Associate Editor in several journals including Evolution, Medicine & Public Health, PLoS ONE, BMC Microbiology, and G3: Genes, Genomes, Genetics.

Rokas received his undergraduate degree in Biology from the University of Crete, Greece and his PhD from Edinburgh University in Scotland. Prior to joining Vanderbilt in the summer of 2007, he was a postdoctoral fellow at the University of Wisconsin-Madison and a research scientist at the Broad Institute.

Areas of Expertise (9)

Tree of Life

Mosquito Functional Genomics

Evolution of Fungal Metabolism

Molecular Evolution

Evolutionary Development

Comparative Functional Genomics

Phylogenetics

Evolution of the Human Genome

Evolution

Education (2)

University of Edinburgh: Ph.D., Evolutionary Biology

University of Crete: B.Sc., Biology

Selected Media Appearances (8)

This Fungus Mutates. That’s Good News if You Like Cheese.

New York Times  online

2019-10-15

“You could imagine going down different flavor paths,” said Antonis Rokas, a professor of evolutionary biology at Vanderbilt University and a co-author of the study. “You could start enhancing or diminishing the mold flavor of the cheese by directing the evolutionary process.”

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A Battle Is Raging in the Tree of Life

New York Times  online

2019-08-02

“By comparing modern animals, we’re trying to infer what the ancestor was like,” said Antonis Rokas, an evolutionary biologist at Vanderbilt University. “How complex was it? What kind of genes did it have, and what kinds of traits?”

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I’m an evolutionary biologist – here’s why this ancient fungal fossil discovery is so revealing

AP News  online

2019-05-22

Biologists don’t call them “the hidden kingdom” for nothing. With an estimated 5 million species, only a mere 100,000 fungi are known to scientists. This kingdom, which includes molds, yeasts, rusts and mushrooms, receives far less attention than plants or animals. This is particularly true for fossils of fungi, most of which are discovered while hunting for more charismatic, at least to the eyes of some, plant fossils.

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An outlaw yeast thrives with genetic chaos – and could provide clues for understanding cancer growth

AP News  online

2019-05-21

“I fought the law,” the 1977 song popularized by the English punk-rock band The Clash, features catchy lyrics about the dire consequences of life as an outlaw. In human affairs, the set of rules codified in our laws helps protect individuals and maintain order in our societies. Without rules, order is lost and chaos reigns. Life’s organisms have evolved their own set of checks and balances that help fight off chaos and ensure their survival and success.

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What did the ancestor of all animals look like?

BBC News  radio

2018-11-02

The ancestor of all animals living today may have lived as long as 700 million years ago. But what did it look like? Many scientists think it would have been a single-celled organism similar to modern day microscopic organisms called ‘choanoflagellates’. Antonis Rokas, from Vanderbilt University in the United States, describes their features and explains why something like them may well have been the single-celled precursor of multi-celled animals.

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This article is more than 1 year old Evolution row ends as scientists declare sponges to be sister of all other animals

The Guardian  online

2017-11-30

Antonis Rokas, professor of biological sciences and biomedical informatics at Vanderbilt University, and who has previously published studies supporting the idea that comb jellies are the oldest sister group to all other animals, welcomed the research. “[It] is a great step in the right direction toward resolving the debate,” he said, adding that the analyses comparing the accuracy of models are insightful.

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How animals appeared on Earth: Analysis of Australian rock reveals that a flood of nutrients 650 million years ago led to a growth of algae that fed the first creatures on our planet

Daily Mail  online

2017-08-16

'The current method that scientists use in phylogenomic studies is to collect large amounts of genetic data, analyze the data, build a set of relationships and then argue that their conclusions are correct because of various improvements they have made in their analysis,' said Antonis Rokas, Cornelius Vanderbilt Professor of Biological Sciences, who devised the new approach with Vanderbilt postdoctoral scholar Xing-Xing Shen and Assistant Professor Chris Todd Hittinger from the University of Wisconsin-Madison.

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Your Most Distant Animal Relative Is Probably This Tiny Jelly

Gizmodo  online

2017-04-11

“To figure out why [these controversies persist], we specifically examined the two best-supported alternatives for a series of controversies and noted how many genes support one over the other alternative,” explained lead author Antonis Rokas in an interview with Gizmodo. “When we applied our approach to the jellies/sponges question, we found that all available data sets—eight [phylogenetic data sets] so far—favor jellies over sponges.”

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Selected Articles (5)

Unearthing fungal chemodiversity and prospects for drug discovery Current Opinion in Microbiology

Claudio Greco, Nancy P Keller, Antonis Rokas

2019

Natural products have drastically improved our lives by providing an excellent source of molecules to fight cancer, pathogens, and cardiovascular diseases that have revolutionized medicine. Fungi are prolific producers of diverse natural products and several recent advances in synthetic biology, genetics, bioinformatics, and natural product chemistry have greatly enhanced our ability to efficiently mine their genomes for the discovery of novel drugs.

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A Robust Phylogenomic Time Tree for Biotechnologically and Medically Important Fungi in the Genera Aspergillus and Penicillium mBio

Jacob L. Steenwyk, Xing-Xing Shen, Abigail L. Lind, Gustavo H. Goldman, Antonis Rokas

2019-08-27

2019

The filamentous fungal family Aspergillaceae contains >1,000 known species, mostly in the genera Aspergillus and Penicillium. Several species are used in the food, biotechnology, and drug industries (e.g., Aspergillus oryzae and Penicillium camemberti), while others are dangerous human and plant pathogens (e.g., Aspergillus fumigatus and Penicillium digitatum). To infer a robust phylogeny and pinpoint poorly resolved branches and their likely underlying contributors, we used 81 genomes spanning the diversity of Aspergillus and Penicillium to construct a 1,668-gene data matrix.

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Genome-wide analysis of Fusarium verticillioides reveals inter-kingdom contribution of horizontal gene transfer to the expansion of metabolism Fungal Genetics and Biology

Shan Gao, Scott E Gold, Jennifer H Wisecaver, Yong Zhang, Li Guo, Li-Jun Ma, Antonis Rokas, Anthony E Glenn

2019

Horizontal gene transfer (HGT) is believed to shape genomes by facilitating the rapid acquisition of adaptive traits. We hypothesized that the economically important fungus Fusarium verticillioides is an excellent candidate for investigating the potential impact of HGT on the expansion of metabolic activities given its soilborne nature and versatile lifestyle as both a symptomless endophyte as well as a maize pathogen.

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Signatures of Recent Positive Selection in Enhancers Across 41 Human Tissues G3: GENES, GENOMES, GENETICS

Jiyun M. Moon, John A. Capra, Patrick Abbot and Antonis Rokas

2019-06-18

2019

Evolutionary changes in enhancers are widely associated with variation in human traits and diseases. However, studies comprehensively quantifying levels of selection on enhancers at multiple evolutionary periods during recent human evolution and how enhancer evolution varies across human tissues are lacking.

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Extensive loss of cell-cycle and DNA repair genes in an ancient lineage of bipolar budding yeasts PLoS biology

Jacob L Steenwyk, Dana A Opulente, Jacek Kominek, Xing-Xing Shen, Xiaofan Zhou, Abigail L Labella, Noah P Bradley, Brandt F Eichman, Neža Čadež, Diego Libkind, Jeremy DeVirgilio, Amanda Beth Hulfachor, Cletus P Kurtzman, Chris Todd Hittinger, Antonis Rokas

2019

Cell-cycle checkpoints and DNA repair processes protect organisms from potentially lethal mutational damage. Compared to other budding yeasts in the subphylum Saccharomycotina, we noticed that a lineage in the genus Hanseniaspora exhibited very high evolutionary rates, low Guanine–Cytosine (GC) content, small genome sizes, and lower gene numbers. To better understand Hanseniaspora evolution, we analyzed 25 genomes, including 11 newly sequenced, representing 18/21 known species in the genus.

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