Adaptation Genomics

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


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. (in press) 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

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 the focus of much of my current research.

Variation in mutation rate

Mutations are the ultimate source of genetic variation, and mutation rate can vary temporally and spatially. One of my current projects is investigating how mutation rate is influenced by stress 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 Click here to read more.

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. Click here to read more.

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.