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Investigating woody transitions in Brassicaceae

Investigating massive convergent evolutionary shifts towards secondary woodiness within Brassicaceae: a molecular phylogenetic approach 

Supervisors
Dr. Frederic Lens, Dr. Rutger Vos, Dr. Frank Stokvis

Contact
frederic.lens@naturalis.nl, rutger.vos@naturalis.nl, frank.stokvis@naturalis.nl

Period & duration
Ca. 6 months

Study & level
MSc-students

Background and context

The family Brassicaceae includes about 3700 species of which most of them are small herbs, such as Arabidiopsis thaliana. Together with colleagues from Germany and the US, we compiled a list of over 400 woody Brassicaceae species, which are scattered in at least 70 different clades based on published molecular phylogenies. All these woody species are derived from herbaceous relatives, a remarkable phenomenon known as secondary or derived woodiness. To have a more realistic estimation of shifts towards secondary woodiness within the family, the DNA barcode lab of Naturalis has sequenced many of the missing woody species. With the original sequences, we assume that the number of shifts will probably extend to over 100, emphasizing massive convergent evolutionary shifts towards wood formation in a single family and making Brassicaceae one of the top five families with secondarily woody species.

A glimpse of the variation of non-related secondarily woody Brassicaceae

Fig. 1: A glimpse of the variation of non-related secondarily woody Brassicaceae native to the Canary Islands [1], ranging from small to large shrubs. A: Parolinia intermedia. B: Erysimum scoparium. C: Lobularia canariensis. D: Descurainia bourgeauana

A complementary MSc project at the university of Osnabruck is dealing with a niche modelling study that assesses whether the woody species have a different ‘niche’ compared to the herbaceous ones; this provides us with some clues why Brassicaceae have become woody throughout evolution. This information can also be linked to ongoing work on drought stress experiments in stems of secondarily woody and herbaceous species (part of Larissa Chacon’s PhD thesis), and to the ongoing genomic and transcriptomic analyses of woody stems in Arabidopsis [2] and Brassica (part of Nicolas Davin’s PhD thesis).

Objectives & goals 

This MSc project will contribute to a high-impact paper focusing on massive convergent shifts towards secondary woodiness in Brassicaceae. Most of the substantial sequencing work has been finalised by the DNA barcode lab. After aligning original with published sequences, a selection of sequences from crucial species that failed will be tried again in this MSc project based on the DNA extractions. The resulting aligned datasets will be used to reconstruct improved phylogenies for all the targeted subgroups (see approach). If possible, also dated molecular phylogenies will be produced for some of the selected groups to investigate in which paleoclimate woodiness has evolved (link with complementary niche modelling study).

Methods, tasks and approach

Since a family-wide phylogeny in Brassicaceae does not reveal enough resolution, we are targeting 17 Brassicaceae subgroups with woody and herbaceous species. The selection of molecular markers is based on the markers used in published phylogenies for the same subgroups. To give you a rough idea about the molecular dataset that is generated by the DNA barcode lab of Naturalis: the nuclear marker ITS has been sequenced for over 200 species belonging to 12 groups, the chloroplast markers trnL-F and ndhF are sequenced for over 100 species and 85 species, respectively, and nine other markers are sequenced for a limited number of species. Success rate of sequencing differs between markers and groups, so an additional sequencing effort is desired.

Requirements
Experience with the software package Geneious is recommended, as well as some background in performing evolutionary reconstruction analyses (Bayesian, Maximum Likelihood).

References

Lens F, Davin N, Smets E, del Arco M. 2013. Insular woodiness on the Canary Islands: a remarkable case study of parallel evolution. Int J Plant Sci 174: 992-1013. [2] Davin N, Hefer CA, Edger PP, Mizrachi E, Schuetz M, Smets E, Myburg AA, Douglas CJ, Schranz ME, Lens F. 2016. Functional network analysis of genes differentially expressed during xylogenesis in soc1ful woody Arabidopsis plants. The Plant Journal 86: 376-390.