Genomic patterns of introgression between hybridising birch species due to range shifts caused by climate change in the Scottish Highlands
Lead Research Organisation:
Queen Mary University of London
Department Name: Sch of Biological and Chemical Sciences
Abstract
Scientists are certain the global warming is occurring at an alarming rate, but we do not yet fully understand the effects this will have on the living world. There is good evidence that many natural species are gradually moving the ranges in which they live, to stay in environmental conditions to which they are adapted. For many species in the UK, this means moving northwards, or up mountains. One consequence of this is that some species are forced into close contact with their relatives. This arrangement can work well if they are unable to have sex together, and the two species can often coexist in the same area. But where sex is possible, things get complicated. Sexual reproduction between two species is called hybridisation, and can result in the two species merging into a single new species, or one species eliminating the other. Which of these outcomes occurs depends on many factors, including how fit the two species are relative to each other and how successful the hybrid offspring are. This project plans to investigate this in two birch tree species growing in the UK. Downy birch is common and currently expanding its range up mountains where it meets its relative, dwarf birch, which is nationally scarce. The two species can hybridise together even when they are far apart, because they are wind pollinated. They produce hybrids that grow up and hybridise with their parents. As downy birches advance up the mountains, the dwarf birches have no where left to go. We need to know how long this has been happening in the past and how quickly it is happening in the present. We can get a window on this from historical records, but these can often be patchy. Another way is to look at the DNA of the two species and look for signs of past hybridisation. Because the species hybridise so much, bits of the dwarf birch genome will be found inside the downy birch genome wherever the two species have met, even if it was a long time ago. This means that we can discover where the two species first met, and how far dwarf birch has been pushed back by downy birch. For this to work, we have to look at very many sections of DNA, all over the genomes of these two wild tree species. Until recently, this would have been impossible, but new technology lets us do this relatively easily and cheaply. We can read many parts of the DNA sequences of the two species and discover where they differ, then go back and look for these differences in areas where they have hybridised. For every tree we look at, we can find which sections of the genome are from downy birch and which are from dwarf birch. Looking more closely at that data, we can use mathematics to map which sections of the genome are moving around and which are not. In another approach to this, we can use our DNA sequence data to design sticky tags that are targeted to one species or the other. When we attach these tags to dyes, we can 'paint' the genomes of individual plants and use microscopes to look at the mixtures of the two species that they contain. Then we can look even closer, and investigate the function of genes in the sections from different species. We expect different sections of the genomes to behave in different ways, due to the genes they contain. Some sections will be so integral to a species' identity that they cannot part with them. Others will be selected by the environment and move to wherever they are needed, regardless of the species. Still others will be neutral, and drift around at random; these are the best markers of historical hybridisation and species range movements. Scientists have only just started to be able to work on the question of which parts of genomes can move freely between species, even though we have been interested in it for a long time. So this work will make an important contribution to our knowledge of how species evolve and remain separate, as well as helping us to understand how global warming will affect rare species.
People |
ORCID iD |
Richard Buggs (Principal Investigator) |
Publications
Abbott R
(2013)
Hybridization and speciation.
in Journal of evolutionary biology
Borrell JS
(2020)
Genomic assessment of local adaptation in dwarf birch to inform assisted gene flow.
in Evolutionary applications
Borrell JS
(2018)
Genetic diversity maintained among fragmented populations of a tree undergoing range contraction.
in Heredity
Buggs Richard J. A.
(2011)
Biosystematic relationships and the formation of polyploids
in TAXON
Buggs RJ
(2013)
Unravelling gene expression of complex crop genomes.
in Heredity
Buggs RJ
(2012)
Rapid, repeated, and clustered loss of duplicate genes in allopolyploid plant populations of independent origin.
in Current biology : CB
Buggs RJ
(2011)
Transcriptomic shock generates evolutionary novelty in a newly formed, natural allopolyploid plant.
in Current biology : CB
Buggs RJ
(2012)
Monkeying around with ploidy.
in Molecular ecology
Buggs RJ
(2014)
The legacy of diploid progenitors in allopolyploid gene expression patterns.
in Philosophical transactions of the Royal Society of London. Series B, Biological sciences
Buggs RJ
(2012)
Next-generation sequencing and genome evolution in allopolyploids.
in American journal of botany
Hu YN
(2019)
Population structure of Betula albosinensis and Betula platyphylla: evidence for hybridization and a cryptic lineage.
in Annals of botany
Matthews A
(2015)
250 years of hybridization between two biennial herb species without speciation.
in AoB PLANTS
Soltis D
(2012)
Polyploidy and Genome Evolution
Vallejo-Marín M
(2015)
Speciation by genome duplication: Repeated origins and genomic composition of the recently formed allopolyploid species Mimulus peregrinus.
in Evolution; international journal of organic evolution
Wang N
(2014)
Is the Atkinson discriminant function a reliable method for distinguishing between Betula pendula and B. pubescens (Betulaceae)?
in New Journal of Botany
Wang N
(2014)
Molecular footprints of the Holocene retreat of dwarf birch in Britain.
in Molecular ecology
Wang N
(2021)
Resolving phylogeny and polyploid parentage using genus-wide genome-wide sequence data from birch trees.
in Molecular phylogenetics and evolution
Wang N
(2012)
Genome sequence of dwarf birch ( Betula nana ) and cross-species RAD markers
in Molecular Ecology
Wang N
(2016)
Molecular phylogeny and genome size evolution of the genus Betula (Betulaceae).
in Annals of botany
Zohren J
(2016)
Unidirectional diploid-tetraploid introgression among British birch trees with shifting ranges shown by restriction site-associated markers.
in Molecular ecology
Description | This project has generated a draft whole genome sequence of a dwarf birch individual from Scotland, and used restriction-amplified DNA tags (RAD-tags) and microsatellites to trace patterns of introgression between hybridising birch species. This has been published in the journal Molecular Ecology, and all the data is freely available in public databases. The main data-set of the project, comprising RAD-tag data for 180 birch trees in the UK, has been published in Molecular Ecology. The micro satellite data has also been published in Molecular Ecology. This grant also led to the PhD projects of Nian Wang, James Borrell and Jasmin Zohren, with whom the PI has published work on birch population genetics and phylogenetics in Annals of Botany, and Heredity. During the course of this fellowship, the PI has also published two high impact data papers based on lab work done during his earlier postdoc position at University of Florida. A paper published in 2012 in Current Biology contains the first test in a young polyploid of the gene-dosage hypothesis for the loss/retention of duplicated genes, with the surprising finding that even in 40 generations of evolution patterns of gene loss can be predicted, and fit with patterns seen in putative ancient polyploids. Another paper published in 2011 in Current Biology showed that tissue-specific gene expression in diploid parents is relaxed upon hybridization but re-emerges in the early generations of allopolyploidy; this fits with new hypotheses about the effects of hybridisation on small-RNA-mediated regulation of gene expression. During the course of the fellowship, the PI has also published four review papers and two commentaries in academic journals. These summarise the current state of knowledge in research on plant hybridisation and polyploidy, particularly in regard to changes in the genome and transcriptome that accompany these evolutionary transitions. |
Exploitation Route | The knowledge and skills generated by this Fellowship project have applications for the conservation of birch trees in the UK (this is currently being exploited by a NERC CASE studentship). It also has applications to tree health issues, both regarding potential threats to birch trees (for example due to the bronze birch borer), and due to the general need for knowledge of tree genomics in countering tree pests and diseases generally. Trees in Britain face unprecedented threats from foreign tree diseases, and genomic research may help us to understand how trees can overcome these threats. The knowledge and expertise developed by this fellowship are currently being exploited in two ways. The PI has won a NERC CASE studentship in partnership with conservation organisations 'Trees for Life' and 'Highland Birchwoods'. This project is building on the fellowship project to apply knowledge of molecular genetics of birch to the conservation of dwarf birch, which is nationally scarce. In addition, the PI has been funded to use his expertise on tree genomics, developed via the fellowship project, to sequence the genome of the ash tree, as part of the UK's response to ash dieback. The current crisis in tree health facing the UK has highlighted a current skills shortage in the area of forest genomics; this NERC fellowship is one of the few RCUK grants to have been developing such skills prior to the crisis. |
Sectors | Environment |
URL | http://www.birchgenome.org |
Description | The project has already had a broad impact in several areas: (1) UK scientific capability. The Fellowship enhanced the UK's capability in tree genomics at a time when there was under-investment in this area. This skill area is now recognised as one of critical importance in combatting threats to tree health, such as ash dieback and the bronze birch borer. In recent months the PI has applied these skills to scientific research on ash genomics, and communicated the potential of genomics to the public, government and industry in variety of ways, including radio, newspapers and stake-holder workshops. (2) Academic community. The project has outputted major datasets of birch genomic data, including the first draft whole genome sequence of a birch species. This data has been published in a scientific paper and in public databases. The PI has also published several other papers and reviews. He has also spoken at international conferences, and organised international conferences. A paper reporting and analysing a large RAD-seq dataset has been submitted to Molecular Ecology (3) Conservationists. The PI has partnered with conservation organisations Trees for Life and Highland Birchwoods to use genomic data to enhance the conservation of dwarf birch, which is nationally scarce in the UK. He is working with Stone Lane gardens to enhance knowledge of the birch genus as a whole. (4) Public. The PI has communicated scientific findings to the public via radio, newspapers, podcasts and public conferences. (5) Silviculturalists/foresters. The PI is working closely with industry via the Future Trees Trust, of which he is a member. He has also partnered with Forest Research on ash dieback and written for "Forestry and Timber News", an industry publication. |
First Year Of Impact | 2012 |
Sector | Environment |
Impact Types | Cultural,Societal,Economic |
Description | Ash dieback genomics - Woodland study |
Amount | £75,000 (GBP) |
Funding ID | Future Proofing Plant Health |
Organisation | Department For Environment, Food And Rural Affairs (DEFRA) |
Sector | Public |
Country | United Kingdom |
Start | 08/2019 |
End | 03/2020 |
Description | Ash tree genomics: an urgent need |
Amount | £64,966 (GBP) |
Funding ID | NE/K01112X/1 |
Organisation | Natural Environment Research Council |
Sector | Public |
Country | United Kingdom |
Start | 01/2013 |
End | 01/2014 |
Description | Defra grant oak condition survey sequencing |
Amount | £126,000 (GBP) |
Funding ID | Future Proofing Plant Health TH1_21 |
Organisation | Department For Environment, Food And Rural Affairs (DEFRA) |
Sector | Public |
Country | United Kingdom |
Start | 01/2021 |
End | 03/2021 |
Description | Ecological and genomic research to optimize the conservation of dwarf birch in Scotland |
Amount | £70,000 (GBP) |
Funding ID | 1227774 |
Organisation | Natural Environment Research Council |
Sector | Public |
Country | United Kingdom |
Start | 08/2012 |
End | 12/2015 |
Description | Genome size measurements by flow cytometry for high-throughput assessment of hybridisation frequency in natural plant populations |
Amount | £15,000 (GBP) |
Funding ID | RG120345 |
Organisation | The Royal Society |
Sector | Charity/Non Profit |
Country | United Kingdom |
Start | 11/2012 |
End | 11/2013 |
Description | Genome size measurements by flow cytometry for high-throughput assessment of hybridisation frequency in natural plant populations |
Amount | £15,000 (GBP) |
Funding ID | RG120345 |
Organisation | The Royal Society |
Sector | Charity/Non Profit |
Country | United Kingdom |
Start | 11/2012 |
End | 11/2013 |
Description | Trip to foster collaboration on Betula speciation research between University of London and University of Iceland |
Amount | £700 (GBP) |
Funding ID | 3585 |
Organisation | European Commission |
Sector | Public |
Country | European Union (EU) |
Start | 07/2010 |
End | 02/2013 |
Description | Trip to foster collaboration on Betula speciation research between University of London and University of Iceland |
Amount | £700 (GBP) |
Funding ID | 3585 |
Organisation | European Commission |
Sector | Public |
Country | European Union (EU) |
Start | 07/2010 |
End | 02/2013 |
Title | RAD-tag sequence data for UK birch trees |
Description | Raw sequence and assembled RAD-tags for 15 UK birch trees |
Type Of Material | Database/Collection of data |
Year Produced | 2012 |
Provided To Others? | Yes |
Impact | None I am aware of |
URL | http://dx.doi.org/10.5061/dryad.v5gd2 |
Title | Whole genome shotgun sequence of dwarf birch (Betula nana) |
Description | Whole genome shotgun sequence of dwarf birch (Betula nana): raw Illumina reads and SOAPdenovo assembly |
Type Of Material | Database/Collection of data |
Year Produced | 2012 |
Provided To Others? | Yes |
Impact | genome available for other researchers |
URL | http://www.birchgenome.org |
Description | Partnership with Highland Birchwoods |
Organisation | Highland Birchwoods |
Country | United Kingdom |
Sector | Private |
PI Contribution | Partnership in supervising PhD student |
Collaborator Contribution | Funding, research sites, advice, applications of research |
Impact | PhD thesis of James Borrell. Various papers. |
Start Year | 2012 |
Description | Article in "Forestry and Timber News" |
Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
Part Of Official Scheme? | No |
Primary Audience | Public/other audiences |
Results and Impact | Article by Richard Buggs titled "Tree health on the agenda" in the Feb 2013 edition of industry journal "Forestry and Timber News" |
Year(s) Of Engagement Activity | 2013 |
Description | BBC News Website 11/11/12. PI's work on birch in collaboration with Stone Lane Gardens |
Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | |
Results and Impact | BBC News 11/11/12 "DNA tests for rare birch trees from Caucasus Mountains" http://www.bbc.co.uk/news/uk-england-devon-20268137 |
Year(s) Of Engagement Activity | 2012 |
Description | BBC News Website 20/11/12 Article on birch genomics results of Fellowship |
Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
Part Of Official Scheme? | No |
Primary Audience | |
Results and Impact | BBC News Website 20/11/12 Forres-based charity's effort to protect 'wee trees' http://www.bbc.co.uk/news/uk-scotland-highlands-islands-20354933 |
Year(s) Of Engagement Activity | 2012 |
Description | Babbage Podcast (The Economist) interview on tree health |
Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Public/other audiences |
Results and Impact | Babbage Podcast (The Economist) interview on tree health |
Year(s) Of Engagement Activity | 2018 |
URL | https://soundcloud.com/theeconomist/babbage-trees-take-a-bough |
Description | Darwin Day talk, Natural History Museum of Milan, 12 Feb 2012 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | |
Results and Impact | Popular level talk on plant evolution, translated into Italian Invited public lecture |
Year(s) Of Engagement Activity | 2012 |
Description | Defra TAW-SAG |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Policymakers/politicians |
Results and Impact | Richard Buggs sitting on Defra Trees and Woodlands Scientific Advisory Group |
Year(s) Of Engagement Activity | 2021,2022 |
URL | https://www.gov.uk/government/groups/trees-and-woodlands-scientific-advisory-group |
Description | Good Morning Scotland, BBC Scotland, 21/12/12 Interview on ash dieback |
Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
Part Of Official Scheme? | No |
Primary Audience | |
Results and Impact | Richard Buggs interviewed on ash dieback |
Year(s) Of Engagement Activity | 2012 |
Description | Interdepartmental Seminar, University of Helsinki |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | |
Results and Impact | Talk on PI's research, University of Helsinki, 5 June 2012, combined Plant Biology and Ecology & Evolutionary biology seminar |
Year(s) Of Engagement Activity | 2012 |
Description | Laurence Reed Show, BBC Cornwall, 21/12/12 Interview on ash dieback |
Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
Part Of Official Scheme? | No |
Primary Audience | |
Results and Impact | Richard Buggs interviewed on Laurence Reed Show, BBC Cornwall, 21/12/12 on ash dieback |
Year(s) Of Engagement Activity | 2012 |
Description | PI interviewed on Radio 4 Today Programme |
Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
Part Of Official Scheme? | No |
Primary Audience | |
Results and Impact | Today programme, BBC Radio 4, 21/12/12 Interview on ash dieback Richard Buggs was interviewed by Eddie Mair on the Radio 4 Today programme about ash dieback |
Year(s) Of Engagement Activity | 2012 |
Description | Planet Earth Online 21/12/12 "New genetics project could help save the ash tree" |
Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | |
Results and Impact | Article about PI's new research project on ash genomics |
Year(s) Of Engagement Activity | 2012 |
Description | Planet Earth Podcast, 5/2/13 Using genetics to save the ash tree |
Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
Part Of Official Scheme? | No |
Primary Audience | |
Results and Impact | Interview with Richard Buggs on Planet Earth Podcast, 5/2/13 Using genetics to save the ash tree |
Year(s) Of Engagement Activity | 2013 |
Description | Sunday Times 24/11/12 "Scientists step in to save birch" |
Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Media (as a channel to the public) |
Results and Impact | News article in Sunday Times on the results of this Fellowship project |
Year(s) Of Engagement Activity | 2012 |
URL | http://www.thesundaytimes.co.uk/sto/news/uk_news/scotland/article1168015.ece |
Description | Telegraph article |
Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | |
Results and Impact | Sunday Telegraph 9/12/12 "British woodlands need diversity from around the world" by Richard Buggs Opinion piece by Richard Buggs |
Year(s) Of Engagement Activity | 2012 |