Hybridization and the origin of novel taxa in Euphrasia

Lead Research Organisation: University of Edinburgh
Department Name: Sch of Biological Sciences

Abstract

Our planet has a huge number of different species, and I am striving to understand the way this diversity has formed. Recently, it has been suggested that cross-mating between species (hybridization) under natural settings, may be the first stage in producing some of these new species. This may play an important role in evolution, as unlike most species which evolve over hundreds-of-thousands or millions of years, it would be possible for a new species to form much more rapidly, in less than 100 generations. However, there are many unanswered questions about this area of evolutionary biology, such as: why does hybridization between species happen so often in some organisms and not others? And when does this produce a new species? This research will address these questions in a group of native plants where hybridization between species is common.

Eyebrights (Euphrasia) are a group of 19 species found throughout the UK. Unlike many other organisms, hybridization is common, and thought to give rise to a number of new species that are found only in the UK. One such example is the slender-heath eyebright (E. micrantha) and the common eyebright (E. officinalis), which are parents to two new species (E. rivularis and E. vigursii). To understand the way these new species have evolved, I will be collecting eyebrights from across the UK, and using state-of-the-art DNA sequencing techniques to determine the contribution of each of the parent species to the DNA of the new hybrid species. Each of these techniques will allow predictions about the outcomes of hybridization to be tested. For example, it may be predicted that one species will contribute more genes to the new species than the other. This would arise when a species produces larger flowers that are more attractive to pollinators, and so the initial hybrid will go on to mate recurrently with this large flowered species. When this occurs over many generations, most genes will come from one parent, with just a few from the other parent. By sequencing a large number of genes in the new species, as well as both the parents, we can compare the proportion coming from each of the parents.

Overall, these results will greatly help our understanding of the way new species evolve, particularly rare species that are of recent origin (in the last 10,000 years). This is of great importance to conservationists in the UK, who are trying to protect rare and endangered species. By understanding the way new eyebright species have evolved, conservation biologists can make new plans that help protect the processes involved in generating new species. This will ensure the survival of not only rare species that are currently present, but those which may evolve in the near future. Such action plans would include conserving pairs of species that hybridize and are known to produce hybrid species, as well as maintaining areas of habitat that favour hybridization.

Planned Impact

Evolutionary biologists using NGS will greatly benefit from the resources generated through this project. Protocols, bioinformatics scripts, and expertise developed will provide NGS users with new tools to address evolutionary questions in non-model organisms. As the University of Edinburgh is emerging as an international centre of excellence in the use of RAD sequencing, this project will enhance this profile by applying other genotyping-by-sequencing approaches, and associated NGS techniques, to a wider range of non-model organisms. Given the fast-pace at which these approaches are developing, and the way results can be rapidly publicised through social media outlets, this will likely make a considerable impact early in the project (within 3 years).

Results from this work will be of practical use for conservation biologists and land managers, as well as policy making agencies at the national level. An improved understanding of the evolutionary processes underlying speciation in Euphrasia will address conservation questions such as:
1) How distinct are natural populations of hybrid Euphrasia species? This will allow conservation biologists to address the best source of genetic material for supplementing declining populations.
2) Are hybrid zones actively generating novel taxa? If so, these may be considered areas of conservation priority.
3) Which areas are 'hot spots' of chloroplast genetic diversity? These sites may also be considered as areas requiring conservation measures.
These outcomes are hoped to indirectly improve quality of life of British citizens. By giving reliable information to conservation agencies, they will be able focus funds for conservation work in the most suitable way, for example by conserving the most threatened natural populations of wildflowers.

Wildlife recorders and national charities (e.g. Botanical Society of the British Isles, Botanical Society of Scotland, British Ecological Society, Plantlife) will benefit from the results and resources generated through this project. The citizen-science collection approach (see Pathways to Impact) will be an important means to engage this community, and the news articles and talks given will educate them on the importance of recording all species in the wild, not just obvious species that are easy to identify. Moreover, it is hoped that the website forum, as well as walks and workshops, will facilitate networking between wildlife records, encouraging an exchange in knowledge and expertise.

The general public (interested in plants, gardens and natural history) will benefit from science communication activities associated with the project. They will be educated in the role hybridization plays in the wild (and more generally about principles of evolutionary biology), as well as having an increased appreciation of wild plant species growing in the local area. It is hoped this will improve quality of life by encouraging people to go outside and enjoy natural areas. Similarly, school children (particularly secondary school students), will benefit from workshops and the resource pack on hybridization. It is hoped the in addition to the general outcomes of appreciating wild species, and improving education relating to evolutionary biology, they will be made aware that evolutionary research is a potential career route for those interested in understanding the natural world.

The NERC fellow would benefit from a greatly improved set of research skills. In particular, advanced training in the generation and analysis of next-generation sequencing data would represent a highly employable set of skills. This training strongly reflects themes explored in the NERC Science Theme of Biodiversity, where new sequencing approaches are used to explore the processes generating species diversity.

Publications

10 25 50

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Brown M (2021) Student Project: Horticultural protocols for experimental studies of eyebrights (Euphrasia, Orobanchaceae) in Sibbaldia: the International Journal of Botanic Garden Horticulture

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Darwin Tree Of Life Project Consortium (2022) Sequence locally, think globally: The Darwin Tree of Life Project. in Proceedings of the National Academy of Sciences of the United States of America

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Dexter KG (2017) Dispersal assembly of rain forest tree communities across the Amazon basin. in Proceedings of the National Academy of Sciences of the United States of America

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Durán-Castillo M (2022) A phylogeny of Antirrhinum reveals parallel evolution of alpine morphology. in The New phytologist

 
Description We have generated large-scale genomic data for British native eyebrights, with these data revealing the relatedness of species in this taxonomically complex group. We have found that genetic relatedness can more often be predicted by geography than species ID, suggesting a complex evolutionary history characterised by frequent hybridisation.
Exploitation Route These genomic results could be used to inform taxonomic work in this complex group and help define more meaningful species. This would in turn benefit conservation actions, which should target well-defined species.
Sectors Other

 
Description Darwin Tree of Life
Amount £141,048 (GBP)
Funding ID 218328/I/19/Z 
Organisation Wellcome Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 11/2019 
End 05/2022
 
Description NERC NBAF
Amount £5,600 (GBP)
Funding ID NBAF1031 
Organisation Natural Environment Research Council 
Sector Public
Country United Kingdom
Start 01/2017 
End 04/2017
 
Title Eyebright species maintenance (scripts and data accompanying Becher et al., Plant Communications) 
Description This gzipped TAR ball contains data and scripts related to the study on Fair Isle eyebrights by Hannes Becher, Max R. Brown, Gavin Powell, Chris Metherell, Nick J. Riddiford, and Alex D. Twyford, submitted to Plant Communications. Data: genome assembly of Euphrasia arctica, variant call files of the "tetraploid" and "conserved" sets of scaffolds, per-individual k-mer spectra, mapping depths, etc. Scripts: R scripts for the analysis of plant trait data, heterozygosity, ect.; an ipython notebook for the analysis of variant data, and a Mathematica notebook with the derivation of the formulae used to fit pop gen parameters to k-mer spectra. 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? Yes  
URL https://zenodo.org/record/3774488
 
Title Eyebright species maintenance (scripts and data accompanying Becher et al., Plant Communications) 
Description This gzipped TAR ball contains data and scripts related to the study on Fair Isle eyebrights by Hannes Becher, Max R. Brown, Gavin Powell, Chris Metherell, Nick J. Riddiford, and Alex D. Twyford, submitted to Plant Communications. Data: genome assembly of Euphrasia arctica, variant call files of the "tetraploid" and "conserved" sets of scaffolds, per-individual k-mer spectra, mapping depths, etc. Scripts: R scripts for the analysis of plant trait data, heterozygosity, ect.; an ipython notebook for the analysis of variant data, and a Mathematica notebook with the derivation of the formulae used to fit pop gen parameters to k-mer spectra. 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? Yes  
URL https://zenodo.org/record/3774489
 
Description Collaborative British native plant research with the Royal Botanic Garden Edinburgh 
Organisation Royal Botanic Garden Edinburgh (RBGE)
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution We have been collaborating in: (1) experimental studies of British native plants, (2) the use of genomics from living plant collections, (3) teaching using RBGE research collections and (4) developing genomic tools to tell plant species apart.
Collaborator Contribution Has provided essential resources including access to plant collections and care of experimental plants.
Impact https://doi.org/10.1111/nph.17752 https://doi.org/10.1098/rstb.2015.0338
Start Year 2014
 
Description Plant parasitism collaborators 
Organisation Penn State University
Country United States 
Sector Academic/University 
PI Contribution PI as part of a collaborative work group planning future research on parasitic plants. I am lead PI on the theme of 'population genomic surveys of parasitic plants'.
Collaborator Contribution Other PIs have contributed novel ideas and lead research themes.
Impact We are currently working on an ERA-CAPS grant application on parasitic plants. This research would lead to important insights into the genes underlying aggressive plant parasitism.
Start Year 2016
 
Description Plant parasitism collaborators 
Organisation University of Münster
Country Germany 
Sector Academic/University 
PI Contribution PI as part of a collaborative work group planning future research on parasitic plants. I am lead PI on the theme of 'population genomic surveys of parasitic plants'.
Collaborator Contribution Other PIs have contributed novel ideas and lead research themes.
Impact We are currently working on an ERA-CAPS grant application on parasitic plants. This research would lead to important insights into the genes underlying aggressive plant parasitism.
Start Year 2016
 
Description Plant parasitism collaborators 
Organisation Virginia Tech
Country United States 
Sector Academic/University 
PI Contribution PI as part of a collaborative work group planning future research on parasitic plants. I am lead PI on the theme of 'population genomic surveys of parasitic plants'.
Collaborator Contribution Other PIs have contributed novel ideas and lead research themes.
Impact We are currently working on an ERA-CAPS grant application on parasitic plants. This research would lead to important insights into the genes underlying aggressive plant parasitism.
Start Year 2016
 
Description Natural History Museum's Science Uncovered, Fri 25 Sept 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Presenting parasitic plants to the general public at this large scientific engagement event.
Year(s) Of Engagement Activity 2015