Using herbarium specimens to elucidate the evolutionary genomics of plant invasion

Using herbarium specimens to elucidate the evolutionary genomics of plant invasion

Photo: Laurene LecaudeyIn herbaria, a vast amount of plant species from different time periods and locations are preserved. Due to improvements in DNA extraction, sequencing and analysis, it is now possible to obtain genomes from historic herbarium samples.

Especially the analysis of invasive plant species offers to help elucidate fundamental evolutionary questions e.g. if the same genes are affected by adaptation to similar environments and what type of mutation (de novo or standing variation) contribute most to adaptation in the introduced range(s).

In this project, modern and historic herbarium samples of the annual weed common ragweed (Ambrosia artemisiifolia) will be obtained. Ragweed is native to North America and became invasive upon introduction to Europe. It is now established on all continents except Antarctica. Genomic data will be used to infer population genetic structure in the native and the introduced range, changes in the structure and allele frequencies over time and to identify genomic regions putatively under selection. Therefore, low-depth sequencing data will be mapped against a draft reference genome for A. artemisiifolia, genotype likelihoods will be inferred using ANGSD, and population genetic structure will be estimated. To identify genomic regions putatively under selection, an outlier analysis based on the genomic distribution of Wright’s fixation index FST will be used. We expect to find repeated patterns of local adaptation and a higher frequency of adaptation from standing variation compared to de novo mutations in the introduced range. Moreover, we expect to find that large-effect alleles will contribute more to adaptation in the introduced range


Contacts

Contacts

PhD Candidate: Vanessa Carina Bieker

Supervisors:

Project status: Ongoing

Project status: Ongoing

Project period: 02.2017 - 01.2021