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 group. 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 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 major project we are currently undertaking is on improving the 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(ish)-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 the 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 even without a reference genome. It has been possible thanks to a number of colleagues across Europe, from Scotland and Portugal through Serbia to Lithuania, who provided samples from across the range of both species.
Genetics and energetics in Apodemus mice
The second project, currently being developed by Rohan Raval in collaboration with Drs Karol Zub and Jan Boratyński at the Mammal Research Institute of the Polish Academy of Sciences (MRI PAS) in Białowieża, Poland, will attempt to characterise the patterns of metabolic rates in a single population of A flavicolis continually sampled for multiple seasons. The project would involve genotyping and pedigree analysis of a large, wild population of mice and lab-based measures of basal metabolic rates (BMR) and torpor. Our goal is to measure heritability of BMR in the wild throughout multiple seasons as well as population variation of and gene activity in torpor.
Seventy years of genetic variation in a population of Apodemus flavicolis in Białowieża forest
Due its wide range and large population size, Apodemus has been a popular ecological model organism since a long time before the advent of modern sequencing methods. Many museums and field stations have amassed collections of Apodemus samples, which are a large and largely untapped resource of genetic history of these species. The challenge in accessing this information is degradation of DNA, making it difficult to obtain a set of orthologous loci from multiple individuals. We have recently been funded by NERC NBAF to develop and/or modify existing DNA pull-down methods to extract orthologous loci from even highly degraded DNA and use it in RAD-seq genotyping. On this project, we are collaborating with MRI PAS, thanks to whom we have access to an extensive collection of Apodemus samples dating back to the second World War and with prof. Nadir Alvarez from the Natural History Museum of Geneva in Switzerland, who previously developed RAD-seq pull-down techniques to be used in insects and plants. We hope that these methods will enable spatial and temporal comparisons of genetic diversity in Apodemus as well.
We expect that all the fundamental work described above will inform and direct our further high-resolution studies on adaptations, the main interest of BrykLab.
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. They 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 Dr Karol Zub at MRI PAS and Dr José Melo-Ferreira at the Research Centre in Biodiversity and Genetic Resources at the University of Porto on elucidating the molecular and evolutionary forced underlying the seasonal colour change.
We have started from Sanger–sequencing a host of putative candidate genes affecting coat colour in order to exclude a possibility of stable coding-sequence polymorphism affecting coat colour change (this part of the project is also one of the final year research projects we offer to students at Huddersfield) and we hope to move towards genome-wide investigations in the near future.
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 Frank Yinnguan Chan and Marek Kucka from the Friedrich Miescher Laboratory of the Max Planck Society in Tübingen, Germany (sequencing, library preparation)
Dr Karol Zub and Dr Jan Boratyński from the Mammal Research Institute of the Polish Academy of Sciences (MRI PAS) in Białowieża, Poland (Apodemus and Mustela samples, energetics, ecology)
Dr Jose Melo-Ferreira from the Research Centre in Biodiversity and Genetic Resources at the University of Porto, Portugal (Mustela coat colouration)
Many others, who provided samples and/or expertise on Apodemus phylogeography, sample preparation and/or data analysis, especially: Dr Jochan Michaux, Dr Allan McDevitt, Dr Jeremy Herman, Dr Vladimir Jovanovic.