THE PHADNISTAS

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Nitin Phadnis

Assistant Professor

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Spencer Koury

Postdoctoral Researcher

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Jim Baldwin-Brown

Postdoctoral Researcher

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Shelley Reich

Graduate Student

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Chelsea Gosney

Graduate Student 

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Thomas King

Graduate Student 

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Josh Seoane

Lab Aide

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Aubrey Hawks

Undergraduate Researcher

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Jackson Bladen

Undergraduate Researcher

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Michelle White

Undergraduate Researcher

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Zach Bowser

Undergraduate Researcher

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Lab Mascot

 

Lab Alumni

Postdocs

Kimberly Frizzell, Ph.D.

Undergraduates

Alyssa Black

Josina Goodman

Scientist at ARUP Laboratories

Grad Students

Nora Brown

Alysha Scheeler

Lane Mulvey

Ping Guo

Amanda Jones

Stephanie VanBeuge

Nichole Johnson

Evin Padhi

Kobe Ikegami

Graduate student at Cornell University

Chris Leonard

Junior Scientist at Tempus

High School Students

Frances Willberg

Maria Reyes

Scientist at Recursion Pharmaceuticals

Graduate student in Clark Lab

Rotation Students

Research Technicians

Randee Young

Graduate Student at University of California, San Diego

Clay Carey

Rachel Cosby

Rufino Rodriguez

Samantha Hill

Rodrigo Costa

Lincoln Gay

Thomas Carter

Chris Large

Graduate Student at University of Washington

Thomas King

David Almanzar

Krystle Osby

Deeptha Vasudevan

Jessica Vincent

WHAT WE STUDY

The Molecular Basis of Speciation

Speciation, the process by which one species splits into two, involves the evolution of reproductive isolating barriers such as the sterility or inviability of hybrids between previously interbreeding populations. Even in his masterpiece “On The Origin of Species”, Darwin could find no satisfactory solution to the apparent paradox of why natural selection would tolerate the onset of genetic barriers such as hybrid sterility and inviability that diminish the prospect  of successful reproduction and, therefore, termed this problem the "mystery of mysteries".

 

The key to uncovering the molecular and evolutionary basis of speciation involves the identification of genes that cause hybrid sterility and inviability then find the molecular mechanisms of hybrid dysfunction from these genes. However, identification of genes that drive speciation represents an indispensable and rate limiting step even in the post-genomic era. Despite decades of intense efforts, very few such genes have been identified. Thus, we know even less about the evolutionary forces and the molecular developmental pathways that are disrupted in hybrids. Our lab specializes in identifying hybrid sterility and inviability genes in a variety of Drosophila species, such as the D. melanogasterD. pseudoobscura and D. bipectinata groups of species. Current projects also involve developing genomics strategies to rapidly identify hybrid sterility and inviability genes and using cell biological approaches to understand the molecular basis of speciation.

Intra-Genomic Evolutionary Conflict

Genomes, instead of being static entities, are dynamic collectives of genes that are in evolutionary conflict with each other. For example, segregation distorters are selfish genetic elements that subvert the mechanisms of meiosis to over-represent themselves in gametes, thus gaining a massive evolutionary advantage. Segregation distorters enjoy their evolutionary advantage even when they impose a fitness cost on the individual carrying the distorter alleles, and thus represent a class of selfish elements. These fitness costs provide selection pressure for the evolution of genes that can suppress segregation distortion. However, successful suppression of distortion in turn puts back selection pressure on the distorter genes to evolve resistance to suppression. This continuing evolutionary arms race between segregation distorter genes and their suppressors can lead to the rapid evolution of the genes involved in this conflict.

These enigmatic selfish elements – which work by violating Mendel’s Laws – are ubiquitous in nature and are a potent evolutionary force in influencing the structures of genomes. Yet, almost nothing is known about their genic basis or molecular mechanism. We are interested in understanding how these elements subvert meiosis. These studies help us understand the evolutionary genetics of such conflicts and also shed light on the inner workings of the meiotic machinery. We are currently studying the molecular basis of segregation distortion in D. pseudoobscura Bogota-USAhybrids, and the SR system in D. pseudoobscura. Current projects also involve studying segregation distortion in very young species pairs where genetic conflict may have driven the evolution of hybrid sterility between species.

Causes and Effects of Positive Selection

Advances in whole-genome sequencing technologies and population genetic methods to detect selection in genome-wide studies have revealed several classes of genes that evolve rapidly under positive selection. While detecting signatures of selection at genomic locations has become easier, a detailed understanding of the evolutionary causes and the functional consequences of the rapid divergence of genes is still missing. Comparative genomics has revealed rapid evolution driven by positive selection in interesting classes of genes, e.g. genes involved in meiosis, nuclear transport, dosage compensation, RNA interference, etc., and we are interested in understanding the causes of rapid evolution at these genes, and the consequences of functional divergence.

 

While traditional approaches attempt the mapping of interesting phenotypes to genes, we instead use a reverse approach. While individual genes co-evolve with the internal genomic environment of their own species to maintain their function, there is no guarantee that these genes will function in the context of the genome of another species. We are interested in the functional analyses of genes that have evolved rapid sequence divergence under positive selection between D. melanogaster and its closest sister species D. simulans.  Molecular analyses of non-complementing genes and the phenotypes revealed during inter-species swaps provide an exciting window into understanding the causes of positive selection at these genes and into uncovering the divergence of molecular functions of genes that evolve rapidly between species.

 
 

PUBLICATIONS

Jacob C Cooper, Ping Guo, Jackson Bladen, Nitin Phadnis 2019 A triple-hybrid cross reveals a new hybrid incompatibility locus between D. melanogaster and D. sechellia. bioRxiv 590588

 

EVOLUTION COMMUNITY

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UCEGG

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Shapiro Lab

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Clark Lab

Utah Center for Evolution, Genetics, and Genomics

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Elde Lab

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Kardon Lab

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Yandell Lab

OUR COMMUNITY

At the University of Utah we have numerous resources and programs to help our students succeed.

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The Bioscience Ph.D program at the University of Utah facilitates the entry and training of Ph.D students through a range of disciplines in the biological sciences. It serves as a source of intellectual diversity for both students and the labs they work in. The Program coordinates activities such as student recruiting and admissions, academic advising, career development,  curriculum, and social events.

The newly minted School of Biological Sciences offers opportunities to learn, work, and collaborate across levels of biological organization and styles of research. Faculty research interests span the complete spectrum of biological phenomena and disciplines, from biochemistry to global environmental change.

The University of Utah has a proud tradition in research in genetics, which has by the Training Program in Genetics, funded by the National Institutes of Health for more than thirty years. The Training Program in Genetics and students trained by this program contributed to landmark discoveries in genetics, including discovery of restriction fragment length polymorphisms, development of a genetic linkage map in humans, and methods for targeted gene disruption in vertebrates.

At the University of Utah, we have leading researchers working in diverse areas of developmental biology and using a wide array of model organisms (bacteria, yeast, C. elegans, Drosophila, mammals, Xenopus, chick, zebrafish and Arabidopsis). These scientists are brought together by the Developmental Biology Interest Group (DBIG).

 

CONTACT US

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Location

Our lab is in the Biology building on the University of Utah Main Campus, Room 212

Email

Phone

Lab: (801) 587-3916

Office: (801) 585-0493

Address

Department of Biology, University of Utah

257 South 1400 East

Salt Lake City, UT 84112