Data from: Contrasting the effects of natural selection, genetic drift and gene flow on urban evolution in white clover (Trifolium repens)
Johnson, Marc T.J., University of Toronto
Prashad, Cindy M., University of Toronto
Lavoignat, Mélanie, Agrosup Dijon
Saini, Hargurdeep S., University of Canberra
Published Jul 18, 2018 on Dryad.
Cite this dataset
Johnson, Marc T.J.; Prashad, Cindy M.; Lavoignat, Mélanie; Saini, Hargurdeep S. (2018). Data from: Contrasting the effects of natural selection, genetic drift and gene flow on urban evolution in white clover (Trifolium repens) [Dataset]. Dryad. https://doi.org/10.5061/dryad.2dq7pf3
Urbanization is a global phenomenon with profound effects on the ecology and evolution of organisms. We examined the relative roles of natural selection, genetic drift and gene flow in influencing the evolution of white clover (Trifolium repens), which thrives in urban and rural areas. Trifolium repens exhibits a Mendelian polymorphism for the production of hydrogen cyanide (HCN), a potent antiherbivore defence. We quantified the relative frequency of HCN in 490 populations sampled along urban-rural transects in 20 cities. We also characterized genetic variation within 120 populations in eight cities using 16 microsatellite loci. HCN frequency increased by 0.6% for every km from an urban centre, and the strength of this relationship did not significantly vary between cities. Populations did not exhibit changes in genetic diversity with increasing urbanization, indicating that genetic drift is unlikely to explain urban-rural clines in HCN frequency. Populations frequently exhibited isolation-by-distance and extensive gene flow along most urban-rural transects, with the exception of a single city that exhibited genetic differentiation between urban and rural populations. Our results show that urbanization repeatedly drives parallel evolution of an ecologically important trait across many cities that vary in size, and this evolution is best explained by urban-rural gradients in natural selection.
Frequency of cyanogenesis within populations across 20 cities
Mean values per city used in analyses. Intercept and slope refer to OLS regressions of cyanogenesis VS standardized distance
Gene diversity statistics used in population genetic analyses. R file is "R_8citiesSummary_gen div_2017.12.24"
R file used for genetic diversity analyses based on microsatts
Allele calls at 16 microwatt loci for each individual used in DAPC analyses. Note the labels for the rows is in the file pops_genind_2018.1.27
Individual levels labels formatted for hierarchical subsetting of data
R script for DAPC analyses. Two files are used; older files included in the scripts are not included.
R script for redundancy analyses
These scripts were used to test for isolation by distance and the effect of urbanization on genetic differentiation while controlling for IBD. There are a lot of individual files that go into these analyses. Available upon request to Marc Johnson (Marc.email@example.com).
R file of all analyses done on population level stats of cyanogenesis. The R file also contains scripts performed on city_meanvals data (city mean values)