Lab Members

Tom Stewart, Postdoc
Oliver Griffith, Postdoc
Eric Erkenbrack, Postdoc
Arun Chavan, Graduate Student
Cong Liang, Graudate Student
Jamie Maziarz, Research Associate
Stella Protopapas, Research Assistant
Tessa Adler, Undergraduate
Elaine Kosowsky, Lab Assistant
Amy Mulholland, Senior Administrative Assistant

The Boss

Gunter Wagner

MK_181113_75 jpg

My research program aims at understanding the evolution of complex characters. This problem has many dimensions, including the question how complex characters can evolve by random mutation and selection (i.e. evolvability, the evolution of evolvability, the role of modularity etc), the biological nature of character identity (homology) and the genetic mechanisms for the origin of novel characters. Most of the effort in my lab focuses on the evolution of the gene regulatory network underlying the origin of a novel cell type, the endometrial stromal cells of placental mammals. This research led us towards an investigation of the role of transcription factor protein evolution in particular the origin of novel protein-protein interactions. The second focus is the developmental basis of avian digit identity. Ever since the discovery that birds are dinosaurs we face the problem whether avian wing digits are 1,2, 3, or 2, 3, 4. All these empirical research problems bring with them a host of conceptual and theoretical problems that I also like to address, such as the nature of character individuation, the structure of the homology concept and the role of measurement theory in formulating evolutionary models.

Contact Information

Yale University Department of Ecology & Evoultionary Biology
165 Prospect Street, Osborn Memorial Lab 327A, New Haven, CT 06520
850 West Campus Drive, Integrated Science & Technology Center, 108, West Haven, CT 06516
Phone Number: (203) 737-3091
e-mail address: gunter.wagner[at]


Tom Stewart


I am interested in explaining patterns of biological diversity. My research focuses on vertebrate appendages—their origin and diversification—and attempts to integrate genetic and generic models of development. In particular, I am studying how digit identity is established and how it evolves by employing in vitro and in vivo experimental approaches.

Yale University Department of Ecology & Evolutionary Biology
850 West Campus Drive, Integrated Science & Technology Center, 107, West Haven, CT 06516
e-mail address: tom.stewart[at]

Oliver Griffith


My research aims to identify the mechanisms that underpin the evolution of complex phenotypes, such as placentation. My research program integrates genomics, developmental biology, and ecophysiology to understand the mechanism that give rise to the selectable variation that has resulted in the evolution of complex traits.


At Yale I aim to identify the genetic basis for placental functions in lizards, and to identify how the placenta impacts the ecophysiology of lizards in a changing climate. In particular I will show whether placentae can facilitate reproductive plasticity in lizards, identify the genetic basis of this plasticity, and identify if placental plasticity offers a fitness advantage in the warmer, less predictable environments predicted by climate models.


Yale University Department of Ecology & Evolutionary Biology
850 West Campus Drive, Integrated Science & Technology Center, 107, West Haven, CT 06516
e-mail address: oliver.griffith[at]


Eric Erkenbrack

Eric Erkenbrack

Gene regulatory networks (GRNs) are assemblages of regulatory genes that cross-regulate each other via protein-protein interactions and cis-regulatory control of transcription encoded in the genome. DNA linkages and post-transcriptional/translational interactions of regulatory genes direct cell-fate decisions in developmental systems. I am interested in how these systems are wired, how they give rise to differentiated cell types and ultimately how they evolve. In the Wagner Lab, I approach these systems-level problems by studying mammalian pregnancy. To better understand how GRNs are wired and the molecular mechanisms driving cell fate decisions, I study the terminal differentiation of decidual cells from their progenitor cell type, endometrial stromal fibroblasts, in the human uterus. We aim to construct a predictive GRN that provides a causal explanation of this cellular differentiation event. Studying mammalian pregnancy also allows us to approach the conceptual problem of how GRNs and cell types evolve. We approach these biological problems comparatively by studying pregnancy in diverse mammalian systems. Importantly, we are studying pregnancy in a marsupial mammal, an outgroup of placental mammals and a system which lacks the terminal differentiation event of endometrial stromal fibroblasts into decidual stromal cells. By comparing and interrogating development of cell types and GRNs in diverse mammalian taxa, we hope to get at the fundamental features of the important concepts of regulatory and developmental evolution.

Graduate Students

Arun Chavan


With an interest in understanding the mechanistic basis of evolutionary innovations, I am studying decidual cells, a novel cell-type that originated in the placental mammal lineage. I use functional genomic tools such as transcriptomics and ATAC-seq to uncover the gene regulatory evolution associated with its origin. More general questions about evolution of placental mammal pregnancy naturally follow from this topic, and have led me into studying placental histology and hormonal regulation of pregnancy in basal placental mammals. Engaging in themselves, these questions also help us understand the context in which decidual cells originated.

Yale University Department of Ecology & Evolutionary Biology
850 West Campus Drive, Integrated Science & Technology Center, 107, West Haven, CT 06516
e-mail address: arun.chavan[at]

Cong Liang

Cong Liang

I’m interested in using mathematical models to illustrate cell type evolutionary principles. Currently, I’m working on a model of the correlated cell type transcriptome evolution in the same species. We observed in the lab that transcriptomic data from various cell types of different species clustering more frequently by species type rather than by homologous cell types. This leads to a hypothesis that cell types have different levels of individuality to each other. I’m using a stochastic model of transcriptome evolution to explain this phenomenon.

Yale University Department of Ecology & Evolutionary Biology
850 West Campus Drive, Integrated Science & Technology Center, 107, West Haven, CT 06516
e-mail address: cong.liang[at]


Stella Protopapas


I am a recent graduate from Smith College and have started working with the Wagner lab analyzing what proteins are present, and where, in the cervix of the opossum throughout gestation using immunohistochemistry. The results of this project will also be compared to the results of transcriptomic data and RNAseq data to produce a more complete picture of gestation in marsupials in comparison to eutherians.

Research Associates
Jamie Maziarz
Yale University Department of Ecology & Evolutionary Biology
850 West Campus Drive, Integrated Science & Technology Center, 107, West Haven, CT 06516
e-mail address: jamie.maziarz[at]

Lab Assistants

Elaine Kosowsky


Yale University Department of Ecology & Evolutionary Biology
850 West Campus Drive, Integrated Science & Technology Center, 107, West Haven, CT 06516
e-mail address: elaine.kosowsky[at]


Amy Mulholland


Yale University, West Campus – Systems Biology Institute
850 West Campus Drive, Integrated Science & Technology Center, 106, West Haven, CT 06516
e-mail address: amy.mulholland[at]

Former graduate students
Andreas Wagner (91-95), Department for Biochemistry, University of Zürich, Switzerland

Bruce Rannala (91-96), Univ. of Alberta, Canada

Bernhard Misof(91-97), Zoologisches Forschungsinstitut und Museum Alexander König, Bonn, Germany

Martin Baatz(91-97), Definiens Imaging GmbH, Germany

Manfred Laubichler(91-97), School of Life Sciences, Arizona State University, AZ

Christian Pazmandi (91-00), University of Innsbruck, Austria

Jason Mezey(95-00), Department of Biological Statistics and Computational Biology, Cornell University, NY

Homayoun Bagheri(95-01), Institute of Zoology, University of Zurich, Switzerland

Ashley Carter (97-02), California State University Long Beach, CA

Maxim Shpak (97-03), University of Texas at Auston, TX

Casey W. Dunn (00-05), Department of Ecology and Evolutionary Biology, Brown University, RI

Jutta Roth (01-05), National Institute for Medical Research, Division of Developmental Biology, UK

Geffrey Stopper(02-06), Sacred Heart University, Fairfield, CT

Deena Emera, (-12), Yale University School of Medicine, Department of Genetics.

Mary Rorick, (-12), Department of Ecology and Evolutionary Biology, University of Michigan.

Jacob Musser, (-15) EMBL Heidelberg, Germany

Koryu Kin, (-15) Cell and Developmental Biology, University of Dundee, UK

Yeonwoo Park, (Undergrad -15), Yale Medical School


Former postdocs

Kalle Rytkonen, University of Turku

Peter Krall (93-97), private company

Maria-Jose Blanco (93-95), Madrid, Spain

Rafaelle Callabretta (97-98), CNRS, Rome, Italy

Gavin Naylor (96-97), The School of Computational Science and Information Technology, Florida State University, FL

Thomas Hansen (98-99), University of Oslo, Norway

Xue Liangy (99-00), Ningbo University, PR China

Elena Kramer (99-00), Harvard University, MA

Chi-hua Chiu (97-01), Department of Genetics and Anthropology, Rutgers University, NJ

August Hämmerli (03-04)

Hans Larsson (01-02), Department of Biology, McGill University, Montreal, Quebec, Canada

Tiana Kohlsdorf (04-06), Departamento de Biologia, FFCLRP, Universidade de Sao Paulo, Brazil

Matthew Brandley (08-10), University of Sydney Postdoctoral Fellow, School of Biological Sciences.

Rebecca Young Brim (-12), University of Texas at Austin, Visiting Scientist.

Vincent Lynch (-12), Department of Genetics, University of Chicago, Assistant Professor.

Kathryn Brayer (-12), Cancer Research, University of New Mexico, Post-Doc.

Zhe Wang (-12), East China Normal University, Shanghai.

Mauris Nnamani (-15), Seres Theraputics, Boston MA


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