In order to identify the closest outgroup to the Cape Verde populations, we sequenced the genomes of 78 Africans (mainly from the Moroccan Atlas Mountains) including herbarium specimen from locations where seeds were not available (South Africa and Algeria). In addition, to identify potential outgroup populations, we sequenced 48 individuals from the Canary Islands and 14 individuals from Madeira. By comparison to samples from Cvi-0 we have now identified a set of closest relatives and are using these as our outgroup individuals for crosses and phenotyping.
An unexpected bonus also came out of this work. We were surprised to find that the samples we sequenced from Africa all clustered far from the well-studied Eurasian populations and that they best represent the origin of the A. thaliana species, relative to all other sampled and sequenced individuals. We published these results in PNAS last year (Durvasula et. al., PNAS 2017).
As I mentioned above, we also sequenced Madeirans and Canary Islands populations. The Madeiran population appeared to diverge long ago (~80-90 kya) and turned out to be useful for making additional inferences about population history in Eurasia. Briefly, this population serves as a banked ancestor of the now-admixed Iberian relict population. Having this ‘parent’ population allowed us to gain new insights into the history of admixture and timing of population expansions in Eurasia. Another surprising result in this paper was that we found evidence for positive natural selection via a selective sweep for the ancestral haplotype of a well-studied inversion polymorphism on Chromosome 1. This was surprising because in Eurasia it is the derived haplotype that shows evidence of a sweep. We have been in discussions with a group that is following this result up to examine the pattern in more detail. Our study of Madeiran population history is published in Molecular Biology and Evolution, (Fulgione et al., MBE 2017).
In both studies we find surprising consistency between major climatic shifts and the timing of inferred migrations and population splits. We wrote a perspective describing these patterns and relating our work to other recent work in A. thaliana population history (Fulgione and Hancock, New Phytologist 2018). More recently, we annotated structural variation using short-read sequencing data in a worldwide data set and conducted analyses to identify regions of the genome that were especially prone to or resistant to structural variation. We found that defense response genes were prone to contain structural variation and showed evidence that balancing selection was operating on these.
We have submitted two papers for publication that deal specifically with adaptation within the Cape Verde Islands (CVI) and are writing up several others. The first of the submitted papers releases the genetic data for the project and is the first description of the island population history. This paper shows that the CVI populations are as distinct as new species, that they adapted through multivariate changes involving several traits, and that an important early step in adaptation was convergent loss of function in two major flowering time genes (FRI and FLC). In the second paper, we show evidence for a two-step adaptive walk that rewired nutrient transport.
References
Tergemina, E., et al., A two-step adaptive walk rewires nutrient transport in a novel edaphic environment, in review.
Fulgione, A.*, Neto, C.*, et al., Parallel reduction in flowering time from new mutations enabled evolutionary rescue in colonizing Arabidopsis lineages, accepted Nature Communications, * represents multiple first authors.
Göktay, M., Fulgione, A., Hancock, A.M. A new catalogue of structural variants in A. thaliana lines from Africa, Eurasia and North America reveals a signature of balancing selection at defense response genes, Molecular Biology and Evolution 2021, doi:10.1093/molbev/msaa309.
Durvasula, A.*, Fulgione, A.*, et al., African genomes illuminate the early history of Arabidopsis thaliana, Proceedings of the National Academy of Sciences 2017, 114(20), 5213-5218.
Fulgione, A., Koornneef, M., Roux, F., Hermisson, J., Hancock, AM., Madeiran Arabidopsis thaliana Reveals Ancient Long-Range Colonization and Clarifies Demography in Eurasia, Molecular Biology and Evolution 2018, 35, 564–574.
Fulgione, A., Hancock, AM., Archaic lineages broaden our view on the history of Arabidopsis thaliana, New Phytologist 2018, Jun 4. Doi: 10.1111/nph. 15244.
