Lab Members

Xinghong Ma, Visiting Faculty
Eric Erkenbrack, Postdoc
Anasuya Dighe, Postdoc

Daniel Stadtmauer, Graduate Student
Pranav Kantroo, Graduate Student

Jamie Maziarz, Research Associate

Rachel Bobo, Undergraduate Researcher

Irene Pak, Undergraduate Researcher
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]

Visiting Faculty

Xinghong Ma

I’m a Visiting Fellow in the Department of Ecology and Evolutionary Biology at Yale. I am from Northeast Agricultural University, China, where I am a professor at the College of Life Science. The long-term goal of my research is to combine genetic, cellular, and molecular approaches to improve understanding of the mechanisms governing embryo implantation and uterine decidualization during mammalian pregnancy. Ubiquitin-mediated protein modification plays an important role in most, if not all, eukaryotic cellular processes. Using genetically engineered mice we are now exploring the roles of ubiquitin pathway in mouse pregnancy. I am also interested in studies of the evolution of the molecular mechanisms of implantation.


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.

Anasuya Dighe

I am intrigued by the relation between sequence and structure of biomolecules that elegantly orchestrates complex physiological processes in all life forms. As a computational biologist, my doctoral work at Indian Institute of Science, Bangalore (India) explored the structure of biomolecules. I analyzed the three dimensional organization of proteins from a mathematical perspective by applying concepts of network biology to study the dissemination of information through structure of signaling proteins.

As a post-doctoral associate in the Wagner lab, I am interested in exploring the other aspect i.e. sequence. Among mammals, the degree of placental invasion correlates with vulnerability to malignancy. My research aims to explore this link from an evolutionary standpoint. Specifically, I am interested in performing mathematical analyses on sequence data contained in the transcriptomes of endometrial stromal fibroblasts (ESFs) and skin fibroblasts (SFs) from diverse species in order to elucidate evolutionary determinants governing invasiveness.


Graduate Students

Daniel Stadtmauer

[entry under construction]

Pranav Kantroo

Drawing the parallels between seemingly unrelated phenomena and appreciating their linkages has been an integral part of my learning experience as a graduate student. This style of learning has molded my research interests — I have gravitated towards areas that draw from each other in search of recurrent motifs. For this reason I am interested in studying the general overarching principles behind how biological systems process information to give rise to complexity, by developing mathematical models and simulations.



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

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]


Yujie Zou, Wuhan University, China

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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