Markéta Kaucká

January 06, 2025

Please refer to https://www.evolbio.mpg.de/evodevodynamics or contact Markéta Kaucká for further information on the projects after having read the recommended literature.

List of publications of the group: https://pubmed.ncbi.nlm.nih.gov/?term=kaucka+m

Please submit your application documents via our online portal.
 

Project 1. Cell type evolution

The evolution from unicellular to complex multicellular organisms required cells to diversify and acquire unique morphological and functional properties. Such cell diversification powered the emergence of novel functional and morphological traits and enabled series of evolutionary transitions that led to the enormous diversity and complexity of animals we know today. 

From an evolutionary standpoint, cell types are perceived as groups of cells that share morphological and functional features and possess specific gene expression profiles that have arisen through the evolution of a particular regulatory program. Such regulatory programs are assembled through the integration of existing molecular modules, incorporation of novel genes, and evolution of the cis-regulatory landscape. These mechanisms jointly contribute to the emergence of novel cell types and their further radiation.

The evolution of cell types has been conventionally studied by comparing the expression of a relatively small number of mostly conserved marker genes representing a cell type identity. However, a cell expresses thousands of genes, and analysing the evolution of its entire transcriptome provides more detailed insights into the cell type´s origin, and allows to dissect the homology between cell types and the evolutionary relationships

We established a novel approach to investigate the link between the evolution of protein-coding genes and the origin of cell types. We employ single-cell transcriptomics, which provides comprehensive information on the gene expression profile of cell types from any organism. We further use genomic phylostratigraphy, a method known as “gene birthdating”. The combination of the information-rich profile from single-cell transcriptomics together with the knowledge of gene origin enables us to investigate the evolutionary trends and origin of cell types´transcriptomes across the tree of life.

We are looking for a highly motivated candidate with a strong background in evolutionary and molecular biology, an appropriate methodological skillset (particularly bioinformatics; R or Python) and a proven ability to work independently on complex biological questions. Successful candidates shall have excellent problem-solving skills, a commitment to scientific excellence, and a proactive approach to learning and collaboration. A demonstrated track record of academic achievements or relevant research experience will be highly regarded. The single-cell RNA sequencing data for this project are available.

Recommended literature:

Damatac II, A. et al. Evolutionary trends in the emergence of skeletal cell types. BioRxiv (2024). https://doi.org/10.1101/2024.09.26.615131

Arendt, D. et al. The origin and evolution of cell types. Nat Rev Genet 17, 744-757 (2016). https://doi.org:10.1038/nrg.2016.127

Zeng, H. K. What is a cell type and how to define it? Cell 185, 2739-2755 (2022). https://doi.org:10.1016/j.cell.2022.06.031

Arendt, D. The evolution of cell types in animals: emerging principles from molecular studies. Nat Rev Genet 9, 868-882 (2008). https://doi.org:10.1038/nrg2416

Tarashansky, A. J. et al. Mapping single-cell atlases throughout Metazoa unravels cell type evolution. Elife 10 (2021). https://doi.org:10.7554/eLife.66747

Domazet-Loso, T., Brajkovic, J. & Tautz, D. A phylostratigraphy approach to uncover the genomic history of major adaptations in metazoan lineages. Trends Genet 23, 533-539 (2007). https://doi.org:10.1016/j.tig.2007.08.014

Domazet-Loso, T. & Tautz, D. A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns. Nature 468, 815-U107 (2010). https://doi.org:10.1038/nature09632

Achim, K. & Arendt, D. Structural evolution of cell types by step-wise assembly of cellular modules. Current Opinion in Genetics & Development 27, 102-108 (2014). https://doi.org:10.1016/j.gde.2014.05.001

Project 2. Evolution of Developmental Programs (Evolution of facial shapes)

Since the Cambrian explosion approximately 500 million years ago, vertebrates have evolved into an exceptionally diverse subphylum with unique features that enabled them to successfully inhabit most environments and niches on the planet. Across vertebrates, the body compartment that has acquired the highest degree of morphological diversity is the head and particularly the face. Today's spectrum of vertebrate facial shapes reflects evolutionary adaptations to the environment, the development of distinct feeding strategies, communication and the overall lifestyle.

The face and its shape emerge during embryonic development, a four-dimensional morphogenetic process orchestrated by conserved genes tightly regulated in time and space. Evolutionary changes result in differences in timing (heterochrony), spatial arrangements (heterotopy) or quantity (heterotopy) on multiple levels - from gene expression patterns and molecules to cell behaviour. The group Evolutionary Developmental Dynamics strives to understand the intricate process of face formation from multiple perspectives and how evolution altered developmental events to generate a broad spectrum of distinct geometries.

We integrate experimental and computational approaches and employ various vertebrate models (from mouse to shark) to investigate how evolution calibrates conserved gene expression patterns during embryogenesis to build different facial shapes. We are particularly interested in the role of non-coding sequences with regulatory functions in this complex morphogenetic process. We employ single-cell transcriptomics, single-cell ATAC sequencing, 3rd generation in situ hybridization, whole-mount imaging, genetic tracing, micro-computed tomography, bioinformatics and a battery of conventional methods of molecular, developmental and evolutionary biology.

We are looking for highly motivated candidates with a strong Evo-Devo background, an appropriate methodological skillset and a proven ability to work independently on complex biological questions. Successful candidates shall have excellent problem-solving skills, a commitment to scientific excellence, and a proactive approach to learning and collaboration. A demonstrated track record of academic achievements or relevant research experience will be highly regarded. The single-cell RNA/ATAC sequencing data for this project are available. The candidate is expected to participate in both experimental and computational approaches and work with developmental stages across species.

Recommended literature:

Attanasio C. et al. Fine Tuning of Craniofacial Morphology by Distant-Acting Developmental Enhancers. Science (2013). https://doi.org/10.1126/science.1241006

White, JD. Et al. Insights into the genetic architecture of the human face. Nature genetics (2020). https://doi.org/10.1038/s41588-020-00741-7

Kaucka, M. et al. Oriented clonal cell dynamics enables accurate growth and shaping of vertebrate cartilage. Elife 6, doi:10.7554/eLife.25902 (2017).

Kaucka, M. et al. Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. Elife 7, doi:10.7554/eLife.34465 (2018).

Murillo-Rincon, A. P. & Kaucka, M. Insights Into the Complexity of Craniofacial Development From a Cellular Perspective. Front Cell Dev Biol 8, 620735, doi:10.3389/fcell.2020.620735 (2020).

Rogers, K. W. & Schier, A. F. Morphogen gradients: from generation to interpretation. Annu Rev Cell Dev Biol 27, 377-407, doi:10.1146/annurev-cellbio-092910-154148 (2011).

Kaucka, M. Cis-regulatory landscapes in the evolution and development of the mammalian skull. Philos Trans R Soc Lond B Biol Sci 378, 20220079, doi:10.1098/rstb.2022.0079 (2023).

Marioni, J. C. & Arendt, D. How Single-Cell Genomics Is Changing Evolutionary and Developmental Biology. Annu Rev Cell Dev Biol 33, 537-553, doi:10.1146/annurev-cellbio-100616-060818 (2017).

Go to Editor View