COS PhD Program
The Foulkes group investigates how constant exposure to darkness has affected phenotypic variation of behavior in unrelated cavefish species. Worldwide, around 100 cave-dwelling fish species have been described, and all share a striking set of so-called “troglomorphic” phenotypes, including complete eye loss, lack of pigmentation, and absence of scales. The mechanisms responsible for the evolution of these traits are still poorly understood. Working with the cavefish Phreatichthys andruzzii, a fish from beneath the somalian desert and isolated from the day-night cycle for over 2 million years, the Foulkes group recently revealed another striking consequence of life in perpetual darkness: the loss of a normal circadian clock. By comparing P.andruzzii with other species of cavefish, the Foulkes group focuses on the genetic network underlying temporally patterned behavior and will address how it independently and in different species has adapted to a nearly identical environmental stimulus.
The Guse group analyzes the molecular basis of coral symbiosis and its role in environmental adaptation. Reef-building corals are strictly dependent on a functional symbiosis with dinoflagellates (genus Symbiodinium) that reside in the gastrodermal host cells and contribute to host nutrition by transferring photosynthetic products to the host. The genus Symbiodinium contains hundreds of types, but the corals associate specifically with certain types of symbionts and not others. Different symbiont-host associations have been hypothesized to contribute to the ability to thrive under and adapt to different environmental conditions. Using a marine sea anemone Aiptasia pallida as a model for coral symbiosis, the lab will identify and functionally analyze key-players of symbiosis at the cellular level and complement these laboratory findings with comparative experiments with coral larvae collected in the field.
The freshwater cnidarian Hydra exhibits an archetypal gastrula-shaped body plan. During gastrulation, the site of the embryonic blastopore develops into the polyp’s mouth. This mouth forms a robust signaling center that regulates the animal’s body shape by being a source for Wnt signaling proteins that form a gradient of activity along the oral-aboral body axis in the embryo and adult polyp. The five distinct species of European Hydra, although all similar in morphology, exhibit distinct differences in their body shape and size, as well as in the mode of gastrulation. So far both, the molecular mechanisms of gastrulation and the role of Wnt genes in various Hydra species are completely unknown. The Holstein and Özbek groups have sequenced the genomes of several Hydra species in collaboration with Rob Steele (UC Irvine), and will use this information to investigate the role of the regulatory network of Wnt genes in different Hydra species with an emphasis on embryogenesis and Wnt gradient shape.
Germlines are organs or cell populations that produce gametes such as the egg and the sperm cell. They contain, and faithfully transmit, the parental genetic information to the offspring upon sexual reproduction. The Johnston Group investigate aspects of germline evolution using plant model systems Physcomitrella patens (moss) and Arabidopsis thaliana (thale cress) that represent Paleozoic and Cenozoic era, respectively. In most multicellular organisms, separation of the germline from the soma is a crucial developmental phase, which is governed by complex cell differentiation processes and reprogramming events. This developmental switch across evolutionary boundaries represents a key “macro-evolution” step, presumably in response to increasing light and dry environments. By comparing germline and soma development in A.thaliana and P.patens, this project aims to unravel the contribution of the Retinoblastoma (RB) pathway in this evolutionary transition.
The Koch group investigates the genetic basis of phenotypic variation that allows plant populations to adapt to environmental changes. Higher plants very often hybridize, and polyploidization (genome doubling) is a common process followed by rapid genome downsizing and secondary diploidization. This evolutionary path allows the rapid introgression from traits and characters from one gene pool into another, which facilitates rapid adaptation to environmental change. Focusing on the genus Arabidopsis within the alpine flora, a hybrid zone between A. lyrata X A. arenosa serves as example of habitat differentiation. A 900 km2 introgression zone between these two species has been recently identified in the Austrian eastern Forealps (Wachau region), and is now used to study evolution, adaptation and speciation “in action”.
The Lemke group uses gastrulation as a genetically tractable model of morphogenesis to address the molecular principles contributing to the evolution of novel form. Specifically, the group studies selected fly species in the insect order Diptera (origin: 250 million years ago), within which Drosophila melanogaster serves as genetically dissected reference organism. On the one hand, work in the lab focuses on gross, qualitative morphogenetic differences between D.melanogaster and distantly related flies (midges: 250 mya; scuttle flies: 150 mya), which are analyzed by complementing classical histochemical analyses with confocal and light sheet microscopy. To test whether the genetic players identified for such major morphological leaps are likewise responsible for subtle and quantitative morphogenetic adaptation on smaller evolutionary scales, the lab is employing comparisons within the genus Drosophila (50 mya).
The Lohmann group uses larval feeding in the fruit fly Drosophila melanogaster as a genetically tractable model to study development, wiring, and activity of a neural behavioral network at the mechanistic level. Feeding is the most dominant behavior of D.melanogaster larvae (80% of life time), it is quantifiable, the associated neural activity can be measured, development of the neuronal circuitry can be traced back to embryogenesis, and gene function can be specifically and selectively tested by RNAi knock-down in the nervous system. Recent work in the Lohmann group has shown that the group 4 Hox gene Deformed (Dfd) is critical to establish the motor unit critical for animal feeding. Current questions focus on putative changes in the Dfd regulatory network and how these resulted in the adaptation of feeding behavior to nutrients and consistency of different food sources within flies. The putatively conserved role of group 4 Hox genes in establishing feeding-related motor patterns throughout the animal kingdom is addressed together with the Holstein group by analyzing the contribution of Hox and ParaHox genes to the primitive feeding movements of cnidarians.
The Maizel group investigates the cellular and molecular basis of developmental plasticity in the model plant species Arabidopsis thaliana. Specifically, the Maizel group uses development of the root system, in particular the formation of the lateral roots as a model system to study the genetic basis of developmental plasticity. Lateral root are constantly formed by the mobilization of a few founder cells that start to proliferate and organise themselves into a new organ which grows out of the main root. The Maizel group has recently pioneered, in collaboration with the group of EHK Stelzer (Frankfurt) the use of light sheet-based fluorescence microscopy to study the morphodynamics of lateral root formation. This technique achieves a minimally invasive, multi-color, 4D imaging at organ, cellular and sub-cellular scales, and, combined with segmentation and tracking methodology, allows for a quantitative analysis of morphogenesis and growth. This technique is ideally suited to systematically identify and quantify phenotypic variation during plant organ formation and its contribution to phenotypic novelty within and between species.