Dr Luke Dunning
School of Biosciences
Senior Research Fellow
- Profile
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- NERC Independent Research Fellow, University of Sheffield, UK (2020‒present)
- Postdoctoral Research Associate, University of Sheffield, UK (2015‒2020)
- Postdoctoral Research Associate, Imperial College London, UK (2013‒2014)
- PhD, University of Auckland, NZ (2014)
- MRes in Biosciences, Cardiff University, UK (2008)
- BSc in Ecology and Environmental Management, Cardiff University, UK (2007)
- Research interests
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I am an evolutionary biologist interested in understanding how organisms adapt to novel environments by combining cutting-edge genomic techniques, ecological analyses and experimental approaches. Most of my research focuses on rapid adaptation in the grass family, the most economically and ecologically important group of plants.
- The evolutionary consequences of lateral gene transfer in grasses.
Our previous work has shown that lateral gene transfer (LGT) is prevalent in grasses where it is responsible for spreading functional genes of adaptive significance between species. We are building on this work to understand the ecological drivers, evolutionary implications and the mechanisms behind these transfers. - Pan-genome variation and local adaptation in grasses.
Not all individuals within an species have the same set of genes, and this gene content variation is likely to have important consequences for environmental adaptation. We are currently investigating the evolutionary forces resulting in this mosaic pattern of gene presence, and trying to understand how this variation is distributed at different biological levels. - Adapting to life on the beach
Dune grasses have convergently evolved to tolerate an ecologically stressful cocktail of drought, salinity, high winds and burial under moving sand. They are also key ecosystem engineers that stabilise and maintain the sand dunes, the most at-risk habitat in Europe. We use genomic techniques and experimental approaches to understand how coastal beach grasses survive in an environment where the sands are literally shifting around them, and how these adaptive traits have evolved over time. In collaboration with coastal ecologists and coastal engineers, we also aim to determine how genetic variation with a plant can translate to whole landscape changes
- The evolutionary consequences of lateral gene transfer in grasses.
- Publications
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Show: Featured publications All publications
Featured publications
Journal articles
- Origin and evolution of the bread wheat D genome. Nature.
- Identifying genomic regions associated with C4 photosynthetic activity and leaf anatomy in Alloteropsis semialata. New Phytologist. View this article in WRRO
- Lateral gene transfer generates accessory genes that accumulate at different rates within a grass lineage. New Phytologist. View this article in WRRO
- Hybridisation and chloroplast capture between distinct Themeda triandra lineages in Australia. Molecular Ecology.
- Widespread lateral gene transfer among grasses. New Phytologist. View this article in WRRO
- Lateral gene transfer acts as an evolutionary shortcut to efficient C4 biochemistry. Molecular Biology and Evolution, 37(11), 3094-3104. View this article in WRRO
- Lateral transfers of large DNA fragments spread functional genes among grasses. Proceedings of the National Academy of Sciences, 116(10), 4416-4425. View this article in WRRO
All publications
Journal articles
- Plastic responses to past environments shape adaptation to novel selection pressures. Proceedings of the National Academy of Sciences, 122(5).
- Origin and evolution of the bread wheat D genome. Nature.
- Identifying genomic regions associated with C4 photosynthetic activity and leaf anatomy in Alloteropsis semialata. New Phytologist. View this article in WRRO
- Lateral gene transfer generates accessory genes that accumulate at different rates within a grass lineage. New Phytologist. View this article in WRRO
- Leaf anatomy explains the strength of C4 activity within the grass species Alloteropsis semialata. Plant, Cell and Environment.
- Genetic assimilation of ancestral plasticity during parallel adaptation to zinc contamination in Silene uniflora. Nature Ecology and Evolution.
- Hybridisation and chloroplast capture between distinct Themeda triandra lineages in Australia. Molecular Ecology.
- Inferring the genome-wide history of grasses. Molecular Plant.
- Upregulation of C4 characteristics does not consistently improve photosynthetic performance in intraspecific hybrids of a grass. Plant, Cell & Environment. View this article in WRRO
- Rapid parallel adaptation to anthropogenic heavy metal pollution. Molecular Biology and Evolution. View this article in WRRO
- Widespread lateral gene transfer among grasses. New Phytologist. View this article in WRRO
- Complex evolutionary history of two ecologically significant grass genera, Themeda and Heteropogon (Poaceae: Panicoideae: Andropogoneae). Botanical Journal of the Linnean Society.
- Contrasted histories of organelle and nuclear genomes underlying physiological diversification in a grass species. Proceedings of the Royal Society B: Biological Sciences, 287(1938). View this article in WRRO
- Lateral gene transfer acts as an evolutionary shortcut to efficient C4 biochemistry. Molecular Biology and Evolution, 37(11), 3094-3104. View this article in WRRO
- Reticulate evolution, lateral gene transfer, and innovation in plants. American Journal of Botany, 107(4), 541-544.
- Population-specific selection on standing variation generated by lateral gene transfers in a grass. Current Biology, 29. View this article in WRRO
- Ecological speciation in sympatric palms : 3. Genetic map reveals genomic islands underlying species divergence in Howea. Evolution, 73(9), 1986-1995.
- Key changes in gene expression identified for different stages of C4 evolution in Alloteropsis semialata.. Journal of Experimental Botany. View this article in WRRO
- Phylogenomics using low‐depth whole genome sequencing: a case study with the olive tribe. Molecular Ecology Resources. View this article in WRRO
- Lateral transfers of large DNA fragments spread functional genes among grasses. Proceedings of the National Academy of Sciences, 116(10), 4416-4425. View this article in WRRO
- C4 anatomy can evolve via a single developmental change. Ecology Letters, 22(2), 302-312. View this article in WRRO
- Contrasting phylogeographic structures between freshwater lycopods and angiosperms in the British Isles. Botany Letters, 165(3-4), 476-486. View this article in WRRO
- Gene duplication and dosage effects during the early emergence of C4 photosynthesis in the grass genus Alloteropsis. Journal of Experimental Botany, 69(8), 1967-1980. View this article in WRRO
- Highly Expressed Genes Are Preferentially Co-Opted for C4 Photosynthesis. Molecular Biology and Evolution, 35(1), 94-106. View this article in WRRO
- The recent and rapid spread of Themeda triandra. Botany Letters, 164(4), 327-337. View this article in WRRO
- Introgression and repeated co-option facilitated the recurrent emergence of C4 photosynthesis among close relatives.. Evolution, 71(6), 1541-1555. View this article in WRRO
- Genome biogeography reveals the intraspecific spread of adaptive mutations for a complex trait. Molecular Ecology, 25(24), 6107-6123. View this article in WRRO
- Substitutions in the Glycogenin-1 Gene Are Associated with the Evolution of Endothermy in Sharks and Tunas. Genome Biology and Evolution, 8(9), 3011-3021. View this article in WRRO
- Ecological speciation in sympatric palms: 1. Gene expression, selection and pleiotropy. Journal of Evolutionary Biology. View this article in WRRO
- Ecological speciation in sympatric palms: 2. Pre- and post-zygotic isolation. Journal of Evolutionary Biology. View this article in WRRO
- Evidence of positive selection associated with placental loss in tiger sharks. BMC Evolutionary Biology, 16(1). View this article in WRRO
- Parallel molecular routes to cold adaptation in eight genera of New Zealand stick insects. Scientific Reports, 5(13965). View this article in WRRO
- The Genome of the “Great Speciator” Provides Insights into Bird Diversification. Genome Biology and Evolution, 7(9), 2680-2691. View this article in WRRO
- Evaluation of genetic isolation within an island flora reveals unusually widespread local adaptation and supports sympatric speciation. Philosophical Transactions of the Royal Society B: Biological Sciences, 369(1648). View this article in WRRO
- Divergent transcriptional responses to low temperature among populations of alpine and lowland species of New Zealand stick insects (Micrarchus). Molecular Ecology, 23(11), 2712-2726.
- Overwintering in New Zealand stick insects. New Zealand Entomologist, 37(1), 35-44.
- Positive selection in glycolysis among Australasian stick insects. BMC Evolutionary Biology, 13(1). View this article in WRRO
- Identification of cold-responsive genes in a New Zealand alpine stick insect using RNA-Seq. Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, 8(1), 24-31.
- Using functional traits and phylogenetic trees to examine the assembly of tropical tree communities. Journal of Ecology, 100(3), 690-701.
- A nuclear phylogenomic tree of grasses (Poaceae) recovers current classification despite gene tree incongruence. New Phytologist.
- A new species of Vallisneria L. for Western Australia and recircumscription of V. triptera S.W.L.Jacobs & K.Frank. Telopea, 27.
- C4 photosynthesis provided an immediate demographic advantage to populations of the grass Alloteropsis semialata. New Phytologist.
- Morphological and genetic evidence suggest gene flow among native and naturalized mint species. American Journal of Botany.
- Alloteropsis semialata as a study system for C4 evolution in grasses. Annals of Botany.
- Extrachromosomal circular DNA as a vehicle to gene transfer in plants. Plant Physiology.
- The mechanisms underpinning lateral gene transfer between grasses. PLANTS, PEOPLE, PLANET.
- C4 trees have broader niches than their close C3 relatives. Journal of Experimental Botany.
- Low dispersal and ploidy differences in a grass maintain photosynthetic diversity despite gene flow and habitat overlap. Molecular Ecology.
- Broad-scale amplification of matK for DNA barcoding plants, a technical note. Botanical Journal of the Linnean Society, 164(1), 1-9.
Chapters
- Population Genomics Advances and Opportunities in Conservation of Kiwi (Apteryx spp.), Population Genomics Springer International Publishing
Preprints
- Gene turnover and contingency facilitated the repeated evolution of C4photosynthesis in grasses, Cold Spring Harbor Laboratory.
- Dietary restriction is evolutionary conserved on the phenotypic and mechanistic level, Cold Spring Harbor Laboratory.
- Chromosome-scale genome assembly and linkage map forSilene uniflorareveal the recombination landscape in a rapidly evolving plant species, Cold Spring Harbor Laboratory.
- Nuclear phylogenomics of grasses (Poaceae) supports current classification and reveals repeated reticulation, Cold Spring Harbor Laboratory.
- Plastic responses to past environments shape adaptation to novel selection pressures, Cold Spring Harbor Laboratory.
- Identifying leaf anatomy and metabolic regulators that underpin C4photosynthesis inAlloteropsis semialata, Cold Spring Harbor Laboratory.
- Origin and evolution of the bread wheat D genome, Cold Spring Harbor Laboratory.
- Variation in the rate lateral gene transfers accumulate in a grass lineage, Cold Spring Harbor Laboratory.
- Inter-specific gene flow following the naturalization of a cultivated mint promotes the formation of a coalescent complex, Authorea.
- Genetic assimilation of ancestral plasticity during parallel adaptation, Cold Spring Harbor Laboratory.
- Hybridisation and chloroplast capture between ancient Themeda triandra ecotypes in Australia, Cold Spring Harbor Laboratory.
- Upregulation of C4 characteristics does not consistently improve photosynthetic performance in intraspecific hybrids of a grass, Cold Spring Harbor Laboratory.
- Low dispersal and recurrent polyploidization in a grass maintain photosynthetic diversity despite gene flow and habitat overlap, Authorea, Inc..
- Rapid Parallel Adaptation to Anthropogenic Heavy Metal Pollution, Cold Spring Harbor Laboratory.
- Origin and evolution of the bread wheat D genome. Nature.
- Research group
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Postdoctoral Research Associates:
- Dr Lara Pereira
- Dr Emma Curran
- Dr William Brightly (NSF fellow - Co-supervised)
Technicians:- Dr Emily Bailes
PhD Students:- Catherine Collins
- George Hirons-Alecrim
- Noah Bourne
- Emily Baker
- Ghadah Fhaid (Co-supervised)
- Violette Pepper (Co-supervised)
- Rafaela Stagiopoulou (Co-supervised)
Masters Students:
- Harvey Jeffrey (MBiolSci)