On wood and yellow-necked mice
Rodents from the genus Apodemus are the most common mammals of the Paleoarctic region and the main interest of our research. They occupy environments as different as Spain and Siberia, contribute to spread of human diseases like Lyme borreliosis and tick-borne encephalitis and are a rich target for evolutionary studies. However, they are very underdeveloped in terms of their genomic and genetic resources. Our long-term goal is therefore to help establish Apodemus as a full–blown model organism and utilise its generalist ecology for studies of evolution in the wild.
Phylogeography of Apodemus mice
The first project we are undertaking is improving the existing European phylogeography of the two species, Apodemus flavicolis (yellow-necked mouse, also confusingly called wood mouse in Polish) and Apodemus sylvaticus (wood mouse). The goal is to collect and describe large-scale (n > 350 samples) data on genetic diversity and connectivity of the species and help answer some of the mysteries of recolonisation of Europe by small mammals following last glaciation. The project is helmed by Maria Luisa Martin Cerezo and utilises restriction-site-associated DNA sequencing (RAD-seq) to obtain whole-genome, high-density genotypes without a reference genome.
Genetics and energetics in Apodemus mice
Seventy years of genetic variation in a population of Apodemus flavicolis in Białowieża forest
, we have access to contemporary samples of Apodemus from around Poland, as well as to an extensive collection of samples dating back to the second World War that enable spatial and temporal comparisons of genetic diversity. We aim to employ RAD–seq to develop a set of whole-genome genetic markers in Apodemus and use them to conduct several comparisons of genetic variation and population structure in A. flavicolis and A. sylvaticus. This fundamental work will inform and direct further high-resolution studies on adaptations, sympatric speciation or host-pathogen interactions, among others.
Seasonal coat colour change in Mustela nivalis weasels
There are two subspecies of least weasels in north–eastern Poland. Mustela nivalis nivalis and Mustela nivalis vulgaris live in relative sympatry (M. n. vulgaris is a recent invader from the south) and are similarly-looking during most of the year. However, when the days start to get shorter, the coat of the M. n. nivalis changes to completely white, providing it with camouflage and increased survival on snow cover, whereas the coat of the M. n. vulgaris stays a similar shade of brown during the entire year.
We are collaborating with This is a (relatively) more straightforward project than the Apodemus, as the putatively adaptive phenotype is known. With our collaborators at MRI PAS, we aim to investigate both the molecular mechanisms responsible for the seasonal coat colour change (a phenomenon studied much less than the permanent colour patterns in mammals), as well as genomic signatures of selection around those coat colour loci. We also hope to elucidate potential hybridisation between the two subspecies, again thanks to genome–wide SNP markers.
Development of HE and A–level experimental teaching resources in synthetic biology
Synthetic biology has enjoyed an explosive growth and a dramatic rise in prominence in the last decade, but the branch of synthetic biology that focuses on standardisation of DNA parts and thorough characterisation of genetic circuits still appears to be somewhat less than what it should be (with the fantastic exception of the International Genetically Engineered Machines competition). There is still a lack of well–characterised and tested sets of parts that allow for introducing synthetic biology concepts and techniques to secondary schools.
National Centre for Biotechnology Education at the University of Reading have been working on a Wellcome Trust–funded project to develop experimental resources in synthetic biology for the A-level education, following our previous work on the UNIGEMS project. While I am no longer formally a part of the Wellcome project, we are collaborating with NCBE on the development and refinement of the protocols to assemble and manipulate plasmid DNA sequences in E. coli without specialised equipment such as PCR machines or chemically–competent cells.
This project is being finalised by Alexandra Siddall; our goal is to have a complete set of plasmids with various DNA parts assembled, quantitatively characterised and deposited at http://www.addgene.org/Jaroslaw_Bryk/.
Rabbit’s Friends and Relations
Our research would not be possible without these fantastic collaborators:
Dr Karol Zub from the Mammal Research Institute of the Polish Academy of Sciences (MRI PAS) in Białowieża, Poland (Apodemus and Mustela samples, energetics, ecology)
Dr Frank Yinnguan Chan from the Friedrich Miescher Laboratory of the Max Planck Society in Tübingen, Germany (sequencing and library preparation)
Dr Steve Patterson from the [University of Liverpool], UK (Apodemus 10x genomics sequencing and genome annotation)
Dr John Schollar from the National Centre for Biotechnology Education at the [University of Reading], UK (synthetic biology, education)
Dr Cheryl Reynolds from University of Huddersfield (education)
Many others who provided samples and/or expertise on Apodemus phylogeography, sample preparation or data analysis, in particular: Jochan Michaux, Allan McDevitt, Jeremy Herman, Vladimir Jovanovic, Marek Kucka.