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Cambridge NERC Doctoral Training Partnerships

Graduate Research Opportunities

Lead supervisor: Richard Durbin, Genetics

Co-supervisor: Yucheng Wang, Zoology

Brief summary: 
Study the genetic species structure and signals of adaptation in closely related willow species from present-day samples and ancient environmental DNA from the last 50k years.
Importance of the area of research concerned: 
Willows (genus Salix) are common shrubs and trees of the northern hemisphere which include multiple groups of very closely related species that have adapted to a large variety of habitats and forms from montane and arctic to temperate. Tthe unique opportunity for this project is that we have multiple time series of ancient environmental DNA (aeDNA) sequencing from sedminentary material, both from lake cores and permafrost circling the arctic, and Salix is amongst the most common eukaryotic genera in most of these samples. It is sufficiently abundant that we are able to obtain genome-wide data, allowing us to explore how species mixes and individual allele frequencies have responded to climate change over the last 50,000 years through the last glacial maximum and the holocene (indeed up to 2million years in the case of the Kap Kobenhavn samples). This will provide amongst the first and richest studies of how sets of closely related species respond genetically to severe environmental change on the timescale of tens of thousands of years.
Project summary : 
Recent genomic studies have shown that the phylogeny of Salix is complex, with both incomplete lineage sorting and evidence for past hybridisation. These conditions have recently been shown in several rapidly speciating systems to enable adaptive introgression and new species formation. We hypothesize that similar processes shape willow diversity. The student will explore the fine scale population structure of present-day species using reference genomes from the Darwin Tree of Life and other sources, and population data from present day and herbarium samples in collaboration with Royal Botanical Gardens Edinburgh. They will then analyse how changes in aeDNA allele frequencies relate to these and to known functional variation in plants. New aeDNA data from large scale studies in Iceland and elsewhere in Northern Europe will arrive during the project, enabling participation in these.
What will the student do?: 
The student will initially build a pangenome reference from available Salix reference genomes. Directly from this a new phylogeny will be built, and incomplete lineage sorting and evidence of past hybridisation will be identified (using f4 statistics and TWISST). Candidate introgressed and selected loci will be identified and correlated with functional annotation of the Salix genome and loci known known to have been under selection in other plants. Then they will map data from existing aeDNA data sets that are labelled as coming from Salicaceae and examine allele frequency changes over time and space in these, relating to the candidate present day loci under selection. After ~1 year a field trip will be taken to collect further present-day samples to follow up initial findings. There will also be opportunities to participate in ancient DNA sediment coring and processing, and data analysis in the larger scale aeDNA projects.
References - references should provide further reading about the project: 
“Late Quaternary dynamics of Arctic biota from ancient environmental genomics” Wang Y, Pedersen MW, Alsos IG, De Sanctis B, Racimo F, Prohaska A, Coissac E, Owens HL, Merkel MKF, Fernandez-Guerra A, Rouillard A, Lammers Y, Alberti A, Denoeud F, Money D, Ruter AH, McColl H, Larsen NK, Cherezova AA, Edwards ME, Fedorov GB, Haile J, Orlando L, Vinner L, Korneliussen TS, Beilman DW, Bjørk AA, Cao J, Dockter C, Esdale J, Gusarova G, Kjeldsen KK, Mangerud J, Rasic JT, Skadhauge B, Svendsen JI, Tikhonov A, Wincker P, Xing Y, Zhang Y, Froese DG, Rahbek C, Nogues DB, Holden PB, Edwards NR, Durbin R, Meltzer DJ, Kjær KH, Möller P, Willerslev E. Nature 600:86-92. doi: 10.1038/s41586-021-04016-x. (2021)
“Placing ancient DNA sequences into reference phylogenies”, Martiniano R, De Sanctis B, Hallast P, Durbin R. Mol Biol Evol. 39:msac017 doi: 10.1093/molbev/msac017. (2022)
"Phylogeny of Salix subgenus Salix s.l. (Salicaceae): delimitation, biogeography, and reticulate evolution", Jie Wu, Tommi Nyman, Dong-Chao Wang, George W Argus, Yong-Ping Yang & Jia-Hui Chen, BMC Evolutionary Biology volume 15, Article number: 31 (2015)
You can find out about applying for this project on the Department of Genetics page.