Kratochwil lab is opening in January 2021 (and recruiting!)

01/11/2020: I am immensely excited to share the news that I will join the Institute of Biotechnology at the University of Helsinki as a group leader in January 2021. I am thrilled and honoured that I will be working alongside such amazing scholars in a wonderful city and country! I will continue to work on the molecular basis of evolutionary change including cool color patterns and neuronal phenotypes in cichlid fishes and other fishes! I am looking for enthusiastic students and postdocs, who find that equally fascinating and have a background in genetics, genomics, developmental biology, evolutionary biology and/or neuroscience (incl. behavior). Official advertisement will follow in Januar, but please get in touch via email already before if you want to discuss the opportunity to join the lab!
(Photo credit: Tiia Monto)

A genomic basis for speciation in crater lake cichlids

28/10/2020: Our new study in Nature demonstrates the importance of the genetic architecture of traits under divergent selection for sympatric speciation! Neotropical Midas cichlids, where a dozen species evolved in less than 20.000 years (many in isolated crater lakes), provide a complex yet not too complex system to study the genomic changes driving and resulting from speciation. Our work suggests that simple traits (even if they behave like magic traits) are not always as conducive to speciation with gene flow as previously suggested, whereas polygenic architectures can promote rapid and stable speciation in sympatry. Very proud to have been part of this amazing collaborative effort (= getting so much done, while having fun and learning a lot) with co-first authors Andi Kautt and Alex Nater and many member from Axel Meyer Lab and the outstanding collaborators Martin Pippel and Gene Myers from Dresden.
(Photo credit: Andi Kautt)

The evolutionary history of the "stripe gene"

17/09/2020: One of the cool things about cichlids is how diverse they are. But where the genetic differences that cause this variation are coming from is often unknown. In our newest paper (published in MBE), lead by Sabine Urban we investigated where the genetic variants that cause variation in stripe patterns are coming from. She found that in one case (Lake Victoria) the causal genetic variants are much older then the species flock (with its ~500 species) and might have very much contributed to the cichlid diversity in this lake, while in another case (Lake Malawi) stripe absence/presence is driven by a likely very recent mutation!

A most remarkable case of colour change

23/07/2020: In their book "Cichlid Fishes of the Great Lakes of Africa​" (often called the "cichlid bible") Fryer and Iles described it as the “perhaps most remarkable case” of “color change reported for any cichlid”: Dominant males of the cichlid Melanochromis auratus completely switch there colours with yellow changing to black and black changing to blue, a phenomenon we investigated in a work lead by Yipeng Liang and just published in Scientific Reports. We show that the color change is caused by massive changes at all levels of biological complexity including gene expression changes as well as changes in cell organelle orientation and cell number. Interestingly the color change seems to be linked to an increased neuronal innervation and that potentially constitutes the trigger of the color change.

How brain circuitry forms using patterning genes

16/06/2020: Good things take time ... in this case it's true, the last paper of my Ph.D. thesis (and a project I started in 2008) got published in Cell reports today. Massive amounts of data and great work by Dominik Kraus and Upasana Maheshwari who lead the project. Briefly, the story shows the importance of hox genes for proper brain connectivity between two of the largest brain centres, the neocortex and the cerebellum. Hox genes hereby provide a regional identity that is important for allowing neurons to connect to the right cells. 

How color patterns form and why they look as they look

11/02/2020: Many cichlids have periodic melanic (black) patterns as stripes (horizontal) and bars (vertical). But fish would have different ways to create a dark-light-pattern: They could change the number of melanin containing dark cells (melanophores), they could increase the pigment that is produced in these cells or they could better distribute the pigment within the cells. Turns out cichlid do all of that! In work lead by Ph.D. student Yipeng Liang and published in Frontiers in Cell and Developmental Biology he used different approaches and followed their development, used histology in adults and performed gene expression analysis to show this.

Evolution by exon duplication

10/12/2020: Still influenced by the quite stunning results of our  Science paper in 2018 that showed that the same gene (agrp2) is responsible for the repeated loss and gain of stripe patterns in cichlids, we were wondering if we can find genomic explanations for the frequently repeated evolution at this genomic hotspot. In this new study published in GBE we uncover a previously unknown duplication of the last exon of agrp2. We were able to date the age of the duplication to 8-12 million years and observe surprisingly frequent changes among all African cichlid radiations including variation in presence/absence patterns and copy numbers between and even within species. As only the 5’ copy of the last exon continues to be expressed and translated, we propose that this tandem duplication might facilitate neofunctionalization or even loss-of-function of agrp2, as was already predicted by Susumu Ohno 50 years ago for gene duplication.

Thinking across levels and disciplines

11/10/2019: The first (peer-reviewed) output of our Eco-evo dynamics scientific network funded by the DFG. We investigated interaction networks across levels of biological complexity (from the perspective of our different scientific background). One intrinsic property of importance that we highlight in our "invited idea" published in Behavioural Ecology is the embedded structure of evolutionary and ecological networks. Hereby effects occurring at a given level of organization can propagate up or down to additional levels causing feedbacks that might be ignored if one does not account for this property. It is a pleasure working with you Damien, Kiyoko, Kate and PO.
The genomic basis of amelanism in a Malawi cichlid
27/05/2018: Amelanistic and albinistic morphs are among the most conspicuous pigmentation phenotypes. By genome-resequencing of the Malawi golden cichlid Melanochromis auratus we could demonstrate that a common amleanistic breed of this species is caused by the loss of the second exon of the gene oculocutaneous albinism II (oca2), also known as p(ink‐eyed dilution) gene or melanocyte‐specific transporter gene. The exon contains a highly conserved motif.  This acidic di‐leucine domain is crucial for trafficking of the Oca2 protein to melanosomes and its loss therefore likely causes the phenotype.. Oca2 has been linked to amelanistic and albinistic morphs across a wide range of vertebrates and is the most common cause of human albinism showing its conserved function. More info on the study published today in Pigment Cell and Melanoma research.
 
How stripes come and go
26/10/2018: Our latest work, published in Science today: Agouti-related peptide 2 act as molecular on/off switch facilitating the repeated evolution of stripe patterns in cichlid fishes. Our study reveals a shared genetic basis of the convergent evolution of stripe patterns across the adaptive radiations of cichlid fishes. Through a combination of several independent methods including hybrid crosses, transgenesis and CRISPR-Cas9 (the fish on the left side is an Agrp2 knockout of the normally stripeless Pundamilia nyererei) we demonstrate that recurring regulatory changes of a single gene, agrp2, have influenced the loss and gain of horizontal stripes across the three cichlid species flocks of Lakes Victoria, Malawi, and Tanganyika with their >1200 species. 
Frontiers of Science Symposium (Kyoto/Japan)
10/09/2018: Just coming back from a wonderfully intense meeting organized by the Alexander von Humboldt Foundation and  the Japan Society for the Promotion of Science. What happens if you put together 30 researchers from Japan, 30 from Germany that are working on Speciation Genomics, Molecular encryption, Astrobiology, Programmable Matter, Cosmology and Sociocultural evolution? You get very excited about these very different topics, challenge yourself to think across disciplines and find it to be an unforgettable enriching experience.
Meetings of EED (Galway/Ireland), Evolution (Montpellier/France), and DZG (Greifswald/Germany)
28/08/2018: Three fantastic conferences filled with stunning and exiting talks. Lot of new ideas for future work and collaborations. Stunning work on genomics of speciation, the genetic basis of behavior, single-cell RNA-seq during limb development, color patterns og dinosaurs, adaptive radiations on islands, CRISPR-Cas on butterflies, metabolism changes in cavefish, and cell interactions in zebrafish driving color pattern development and maintenance. I was also very glad to receive feedback for our recent work on the genetic basis of convergent color pattern evolution in cichlids. A big thank you to the organizers for these wonderful conferences.
​Symposium about "Evo-Devo of color pattern formation"
01/07/2018: At the 2018 Evolutionary Developmental Biology (EED) conference held  in Galway/Ireland I hosted a symposium addressing the mechanistic and molecular understanding of color pattern phenotypes and their evolution, a topic both central to evolutionary and developmental biology research. There is growing body of studies that demonstrate that changes in developmental processes contribute to color pattern diversification. Coloration biology is an exiting field that is interdisciplinary, integrative, uses broad methodological approaches and fascinated researchers since Darwin and Wallace. Thanks to David Parachy (University of Virginia, USA), Ricardo Mallarino (Harvard University / Princeton University, USA), Nicola Nadeau (University of Sheffield, UK) and Ingo Braasch  (University of Oregon, USA) for giving terrific talks on their exiting research on that topic. 
​More information at http://www.evodevo2018.eu/.
Transgenesis in the Midas cichlid — towards understanding gene function and regulatory evolution in an ecological model system
24/11/2017: The Midas cichlid species complex (Amphilophus spp.) is widely known among evolutionary biologists as a model system for sympatric speciation and adaptive phenotypic divergence within extremely short periods of time (a few hundred generations). For the first time in any New World cichlid, we use Tol2 transposon-mediated transgenesis in the Midas cichlid (Amphilophus citrinellus). Transgenesis is a versatile tool not only for studying regulatory elements such as promoters and enhancers, but also for testing gene function through overexpression of allelic gene variants. As such, it is an important first step in establishing the Midas cichlid as a powerful model for studying adaptive coding and non-coding changes in an ecological and evolutionary context. More information
DFG Scientific Network grant on "The role of interaction structure in eco-evolutionary dynamics"
26/07/2017​: Just had our first meeting of our newly DFG funded 'EcoEvoInteract' work group with the fantastic Carey Nadell, Damien Farine, Kate Laskowski, Kiyoko Gotanda and PO Montiglio! Very productive week developing ideas about how similar 'networks' are across biological disciplines and hierarchical levels. We aim to gain a better understanding about the role of interaction structure in eco-evolutionary dynamics. More information
​Symposium about "Integrating the genotype-phenotype map with concepts of Evo-Devo"
01/07/2017: My colleague Joost Woltering and I just organized a symposium at the  European Society for Evolutionary Developmental Biology (EED) in Uppsala this summer (July 26-29, 2016). One of the main goals of evo-devo is to understand how the functioning of ontogenetic mechanisms results in patterns of morphological evolution. Recent advances increasingly permit to understand the link between genotypes and phenotypes in more and more evolutionary and ecologically relevant model organisms. Kevin Parsons (University of Glasgow, U.K.), Michel Milinkovitch (University of Geneva, Switzerland), Haruhiko Fujiwara (University of Tokyo, Japan) and Kerstin Kaufmann  (University of Potsdam, Germany) gave talks about their exiting research on this topic. 
​More information at http://2016uppsala.evodevo.eu.
Evolution of the neural crest gene regulatory network in teleost fishes
04/11/2015: Many of the distinctive phenotypic differences found in bony fishes are largely influenced by the neural crest cell lineage, a transient population of migrating multipotent cells. Our study suggests that the molecular evolution of genes involved in the neural crest gene regulatory network matches predictions from the developmental hourglass model. Furthermore, several neural crest genes showed relaxation of purifying selection in the cichlid fishes that exhibit a wide variety of neural crest derived traits. See details in our study 'Molecular evolution of the neural crest regulatory network in ray-finned fish' published in Genome Biology and Evolution. The photo shows a close-up of the African cichlid Pundamilia (Haplochromis) nyererei from lake Victoria with its exuberant (neural-crest derived) pigmentation.
Meeting of the Society for Molecular Biology and Evolution (SMBE) in Vienna
16/07/2015: Many thanks to the organizers in Vienna for a fantastic annual meeting of the Society for Molecular Biology and Evolution SMBE from July 12th to the 16th, 2015. Really exiting talks and posters. Looking forward to the next SMBE meeting. Hopefully I can make it to  Gold Cost, Australia for SMBE 2016.

Special thanks to Alex Cagan for this nice summary of my talk about novel functional approaches to study regulatory evolution in cichlid fishes. I never thought that I would become a comic character one day ....
ChIP-seq as a novel tool to study gene ​regulation in ecological model systems such as cichlid fishes
01/07/2015: Evolutionary alterations to regulatory sequences are likely to cause adaptive phenotypic complexity, through orchestrating changes in cellular proliferation, identity and communication. For non-model organisms with adaptive key innovations, patterns of regulatory evolution have been predominantly limited to targeted sequence-based analyses. Chromatin immunoprecipitation with high-throughput sequencing (ChIP-seq) is a technology that has been primarily used in genetic model systems and is a powerful experimental tool to screen for active cis-regulatory elements. In our publication in Molecular Ecology Resources  'Mapping active promoters by ChIP-seq profiling of H3K4me3 in cichlid fish – a first step to uncover cis-regulatory elements in ecological model teleosts' we show that ChIP-seq can also be used in ecological model systems and permits genomewide functional exploration of cis-regulatory elements.
Closing the genotype-phenotype gap in non-model species
30/02/2015: The analysis of genetic and epigenetic mechanisms of the genotype-phenotypic connection has, so far, only been possible in a handful of genetic model systems. Recent technological advances, including next-generation sequencing methods and genome-editing approaches  now permit to address these fundamental questions of biology also in organisms that have been studied in their natural habitats. In a new review on 'Closing the genotype-phenotype gap : Emerging technologies for evolutionary genetics in ecological model vertebrate systems', published in BioEssays, we provide an overview of the benefits and drawbacks of these novel techniques and experimental approaches. We can anticipate that these new methods will increase the understanding of the genetic and epigenetic factors influencing adaptations and phenotypic variation in ecological settings. These new arrows in the methodological quiver of ecologist will drastically increase the understanding of the genetic basis of adaptive traits - leading to a further closing of the genotype-phenotype gap.
Larval development in the Midas cichlid: A new model for the development of species differences
26/02/2015: Central American crater lake cichlid fish of the Midas species complex (Amphilophus spp.) are a model system for sympatric speciation and fast ecological diversification. Midas cichlids have been intensively analyzed from an ecological and morphological perspective. Many ecologically relevant species-specific traits and differences arise during development. In our study in BMC Developmental Biology 'Embryonic and larval development in the Midas cichlid fish species flock (Amphilophus spp.): a new evo-devo model for the investigation of adaptive novelties and species differences' we performed a detailed descriptions of the early development of the Midas cichlid as a basis to further investigations on the ontogeny of species differences.
Epigenetic processes orchestrate brain organization
31/02/2013: As the foundation for our mind is laid, 100 billion cells are formed and appropriately connected in the brain. Despite the huge number of cells, no aspect of this process is left entirely to chance. Neurons divide, take on defined identities, migrate to the correct nodes in the network and send out their connecting axons along predefined paths to make contact with specific target neurons. The blueprint for these arrangements is encoded in the genome. However, how coordinated transcription of genes is finely tuned to achieve the precision of these processes is not yet clear. In our study  'Ezh2 orchestrates topographic tangential migration and connectivity of mouse precerebellar neurons' that has been published in Science we could show that directional migration of neurons during brain development is controlled through epigenetic processes. The migratory pattern of neurons is orchestrated through epigenetic regulation of genes within neurons and spatial signals in the environment.