Current Research

Fungal Plant Pathogen Genetics & Genomics

Past Research

Adapation Genomics

I have a long standing interest in understanding how organisms cope with the challenges they face and how this drives phenotypic and genome evolution. Recent advances in genomic techniques are providing great insights into understanding adaptation and phenotypic evolution and speciation.

Stapley J, Reger J, Feulner, PGD, Smadja C, Galindo J, Ekblom R, Bennison C, Ball A, Beckerman AP and Slate J. (2010) Adaptation Genomics: the next generation, Trends in Ecology and Evolution 25:705-712 (pdf).

Kokko H, Chaturvedi A, Croll D, Fischer MC, Karrenberg S, Kerr B, Rolshausen G and Stapley J. (2017) Can evolution supply what ecology demands? Trends in Ecology and Evolution 32: 187-197.

Rodríguez-Verdugo A, Buckley J and Stapley J. (2017) Genomic basis of eco-evolutionary dynamics (Meeting Review) Molecular Ecology 26:1456-1464.

Mutation and recombination, the genomic engines of adaptation.

Adaptation is determined by two fundamental parameters; mutation, that generates heritable genetic variation, and recombination, that determines the efficacy of selection to fix beneficial adaptive alleles. These parameters influence the genomic context of an adaptive allele and the adaptive potential of a population or species. How these evolutionary parameters evolve is a long-standing question in evolutionary biology and a focus of my research.

Variation in mutation rate

Mutations are the ultimate source of genetic variation, and mutation rate can vary temporally and spatially. One of my recent projects studied how stress influenced mutation rate in Arabidopsis. The other is investigating how Transposable elements (TEs) are involved in adaptation and how these may contribute to the success of invasive species.

Stapley J, Santure, AW and Dennis, SR (2015) Transposable elements as agents of rapid adaptation may explain the genetic paradox of invasive species. Molecular Ecology 22: 2241-2252

Variation in recombination rate

Recombination is a process where DNA is chopped and then swapped between parental chromosomes, it happens during meiosis, and it occurs in nearly all living organisms. The swapping of DNA from each parent creates novel combinations of genetic variants and helps species adapt and respond to changing environments and cope with pathogens and parasites. The recombination frequency and position has an enormous influence on many aspects of biology. Too few or too many recombination events can cause infertility, human diseases including cancer, and influence how well populations cope with a changing environment. Considering these impacts, we expect that the number of recombination events and their position in the genome should be tightly controlled and highly conserved. Yet, what we observe is an enormous amount of variation in the number of recombination events, between species, populations and individuals, and variation in where recombination occurs in the genome. Although, there has been exciting new advances in identifying the genes that govern recombination, explaining why this variation exists is a major challenge in biology.

Stapley J, Feulner PGD, Johnston SE, Santure AW, Smadja CM (2017) Variation in recombination frequency and distribution across Eukaryotes: patterns and processes. Philosophical Transactions of the Royal Society B: Biological Sciences 372.

Colour trait evolution and genetics

Ultraviolet signalling in flat lizards, Platysaurus broadleyi

Male competition is a driving force in the evolution and exaggeration of male traits and colourful male badges are a striking example of this. Ultraviolet (UV) colour badges are an interesting example of colourful signals that while invisible to us are used extensively in a range of other taxa. We investigated how UV signals were used during male contests in the Augrabies flat lizard. Click here to read more

Stapley J and Whiting MJ. (2006) UV signals fighting ability in a lizard. Biology Letters 2: 169-172.

Avian genome evolution

Genetic linkage map of the zebra finch genome

The Zebra finch is a model species in evolutionary biology and neurobiology. A limitation to identifying genes underlying variation in traits has been a lack of genomic resources in this species. To help address this problem and complement the zebra finch genome sequence we developed a first generation linkage map for the zebra finch using SNPs. The linkage map provided much insight into the evolution of avian genomes.

Stapley J, Birkhead TR, Burke T and Slate J. (2008) A linkage map of the zebra finch Taeniopygia guttata provides new insight into avian genome evolution. Genetics 179:651-667

Patterns of linkage disequilibrium and recombination across the zebra finch genome

The pattern of linkage disequilibrium across the genome provides valuable insight into the distribution of recombination events, and also has important implications for gene mapping studies. Using the genetic linkage map and the recently completed whole genome sequence I analysed the genome-wide pattern of linkage disequilibrium (LD) and recombination rate in the zebra finch. The analysis revealed unusual patterns of LD and interesting differences between the macro- and microchromosomes.

Stapley J, Birkhead TR, Burke T and Slate J. (2008) A linkage map of the zebra finch Taeniopygia guttata provides new insight into avian genome evolution. Genetics 179:651-667.

Teaching, mentoring and outreach

Undergraduate Teaching

Population and Quantitative Genetics (701-1413-00), ETH Zürich

Training and Workshops

Physalia Course: Adaptation genomics Dec 2019

Lead NERC Biomolecular Analysis Facility Training Workshop in Population Genomics at the University of Liverpool, and I was a teaching assistant on an Advanced Statistics in R course at University of Sheffield and the R Boot Camp in Zagreb, Croatia.

Career Development, Networking and Equality events

Equal Opportunity Event: Let’s Redress the Leaky Pipeline, which was funded by European Society of Evolutionary Biology Equal Opportunities Initiative.

Rants ‘n Raves: Networking and Communication Event;  Lets Get Visible – developing a professional digital profile; How to Give a Great Lecture and Postdoc Away Day.

Mentoring

I participated in the University of Sheffield Thesis Mentoring Program, developed by the wonderful Dr Kay Guccione. I was recognised as an outstanding mentor two years in a row. To see my student’s feedback click here, go to Nov 2014 and May 2015 and search Stapley. I have also been a co-supervisor and unofficial supervisor of postgraduate students (masters/honours/4th year and PhD) at University of Sheffield and supervisor of Interns at Smithsonian Tropical Research Institute.

Outreach

I was awarded a Widening Participation Grant from the University of Sheffield to develop an outreach activity on ultraviolet signalling that could be used in Secondary Schools. I  also developed and run activities for visitors of Discovery Night at the University of Sheffield (2014, 2015).