Publications

In Press

Grass Phylogeny Working Group III. A nuclear phylogenomic tree of grasses (Poaceae) recovers current classification despite gene tree incongruence New Phytologist view paper

2024

Cavalet-Giorsa E, González-Muñoz A, Athiyannan N, Holden S, Salhi A, Gardener C, Quiroz-Chávez J, Rustamova SM, Elkot AE, Patpour M, Rasheed A, Mao L, Lagudah ES, Periyannan SK, Sharon A, Himmelbach A, Reif JC, Knauft M, Mascher M, Stein N, Chayut N, Ghosh S, Perovic D, Putra A, Perera AB, Hu C-Y, Yu G, Ahmed HI, Laquai KD, Rivera LF, Chen R, Wang Y, Gao X, Liu S, Raupp WJ, Olson EL, Lee J-Y, Chhuneja P, Kaur S, Zhang P, Park RF, Ding Y, Liu D-C, Li W, Nasyrova FY, Dvorak J, Abbasi M, Li M, Kumar N, Meyer WB, Boshoff WHP, Steffenson BJ, Matny O, Sharma PK, Tiwari VK, Grewal S, Pozniak C, Chawla HS, Ens J, Dunning LT, Kolmer JA, Lazo GR, Xu S, Gu Y, Xu X, Uauy C, Abrouk M, Bougouffa S, Brar GS, Wulff BBH, Krattinger SG. Origin and evolution of the bread wheat D genome. Nature, 633: 848-855 view paper  

Alenazi AS, Pereira L, Christin P-A, Osborne CP, Dunning LT. Identifying genomic regions associated with C4 photosynthetic activity and leaf anatomy in Alloteropsis semialata. New Phytologist, 243:1698-1710 view paper

Jobson RW, Dunning LT. A new species of Vallisneria L. for Western Australia and recircumscription of V. triptera SWL Jacobs & K. Frank. Telopea, 27: 27–38 view paper

Sotelo G, Gamboa S, Dunning LT, Christin P-A, Varela S. C4 photosynthesis provided an immediate demographic advantage to populations of the grass Alloteropsis semialata. New Phytologist, 242: 774-785 view paper

Olofsson JK, Tyler T, Dunning LT, Hjertson M, Rühling Å, Hansen AJ. Morphological and genetic evidence suggest gene flow among native and naturalized mint species. American Journal of Botany, 111: e16280 view paper 

2023

Raimondeau P, Bianconi M E, Pereira L, Parisod C, Christin P-A, Dunning L T. Lateral gene transfer generates accessory genes that accumulate at different rates within a grass lineage. New Phytologist, 240: 2072-2084 view paper

Pereira L, Bianconi M E, Osborne C P, Christin P-A, Dunning L T. Alloteropsis semialata as a study system for C4 evolution in grasses. Annals of Botany, 132: 356-382 view paper

Pereira L, Dunning L T. Extrachromosomal circular DNA as a vehicle to gene transfer in plants. Plant Physiology, 193: 172-173. view paper

Alenazi A S, Bianconi M E, Middlemiss E, Milenkovic V, Curran E V, Sotelo G, Lundgren M R, Nyirenda F, Pereira L, Christin P A, Dunning L T. Leaf anatomy explains the strength of C4 activity within the grass species Alloteropsis semialata. Plant, Cell & Environment, 46: 2310:2322. view paper

Pereira L, Christin P A, Dunning L T. The mechanisms underpinning lateral gene transfer between grasses. Plants, People, Planet, 5: 672-682. View paper 

Wood D P, Holmberg J A, Osborne O G, Helmstetter A J, Dunning L T, Ellison A R, Smith R J, Lighten J, Papadopulos A S. Genetic assimilation of ancestral plasticity during parallel adaptation to zinc contamination in Silene uniflora. Nature Ecology & Evolution, 7: 414-23. view paper

2022

Dunning L T, Olofsson J K, Papadopulos A S T, Hibdige S G S, Hidalgo O, Leitch I J, Baleeiro P C, Ntshangase S, Barker N, Jobson R W. Hybridisation and chloroplast capture between distinct Themeda triandra lineages in Australia. Molecular Ecology, 31: 5846-5860. View paper     

Bianconi, M E, Christin, P A, & Dunning, L T. Inferring the genome-wide history of grasses. Molecular Plant, 15: 591-592. View paper 

Young, S N, Dunning, L T, Liu, H, Stevens, C J, Lundgren, M R. C4 trees have a broader niche than their close C3 relatives. Journal of Experimental Botany, 73: 3189-3204. View paper

Bianconi, M E, Sotelo, G, Curran, E V, Milenkovic, V, Samaritani, E, Dunning, L T, Bertolino, L T, Osborne, C P, Christin, P A. Upregulation of C4 characteristics does not consistently improve photosynthetic performance in intraspecific hybrids of a grass. Plant, Cell & Environment, 45: 1398-1411. View paper

2021

Hibdige, S G, Raimondeau, P, Christin, P A, Dunning, L T. Widespread lateral gene transfer among grasses. New Phytologist, 230: 2474–2486. View paper

Papadopulos, A S, Helmstetter, A J, Osborne, O G, Comeault, A A, Wood, D P, Straw, E A, Mason, L D, Fay, M F, Parker, J, Dunning, L T, Foote, A D. Rapid parallel adaptation to anthropogenic heavy metal pollution. Molecular Biology and Evolution, 38: 3724–3736. View paper

Arthan, W, Dunning, L T, Besnard, G, Manzi, S, Kellogg, E A, McKain, M R, Hackel, Lehmann, C E R, Mitchley, J, Vorontsova, M S. Complex evolutionary history of two ecologically significant grass genera, Themeda and Heteropogon (Poaceae: Panicoideae: Andropogoneae). Botanical Journal of the Linnean Society, 196: 437–455. View paper

Olofsson, J K, Curran, E V, Nyirenda, F, Bianconi, M E, Dunning, L T, Milenkovic, V, Sotelo, G, Hidalgo, O, Powell, R F, Lundgren, M R, Leitch, I J, Nosil, P, Osborne, C P, Christin, P A. Low dispersal and ploidy differences in a grass maintain photosynthetic diversity despite gene flow and habitat overlap. Molecular Ecology, 30: 2116–2130. View paper

2020

Dunning, L T, Christin, P A. Reticulate evolution, lateral gene transfer, and innovation in plants. American Journal of Botany, 107: 541–4. View paper

Phansopa, C, Dunning, L T, Reid, J D, Christin, PA. Lateral gene transfer acts as an evolutionary shortcut to efficient C4 biochemistry. Molecular Biology and Evolution, 37: 3094–3104. View paper

Bianconi, M, Dunning, L T, Curran, E V, Hidalgo, O, Powell, R F, Mian, S, Leitch, I J, Lundgren, M, Manzi, S, Vorontsova, M, Besnard, G, Osborne, C P, Olofsson, J K, Christin, P A. Contrasted histories of organelle and nuclear genomes underlying physiological diversification in a grass species. Proceedings of the Royal Society B, 28720201960. View paper

2019

Dunning, L T, Olofsson, J K, Parisod, C, Choudhury, R R, Moreno-Villena, J J, Yang, Y, Dionora, J, Quick, W P, Park, M, Bennetzen, J L, Besnard, G, Nosil, P, Osborne, C P, Christin, P A. Lateral transfers of large DNA fragments spread functional genes among grasses. Proceedings of the National Academy of Sciences of the United States of America, 116: 4416–4425. View paper

​Dunning, L T, Moreno-Villena, J J, Lundgren, M R, Dionora, J, Salazar, P, Adams, C, Nyirenda, F, Olofsson, J K, Mapaura, A, Grundy, I M, Kayombo, C J, Dunning, L A, Kentatchime, F, Ariyarathne, M, Yakandawala, D, Besnard, G, Quick, W P, Bräutigam, A, Osborne, C P, Christin, P-A. Key changes in gene expression identified for different stages of C4 evolution in Alloteropsis semialata. Journal of Experimental Botany, 70: 3255–3268. View paper

​Lundgren, M R, Dunning, L T, Olofsson, J K, Moreno-Villena, J J, Bouvier, J W, Sage, T, Khoshravesh, R, Sultmanis, S, Stata, M, Ripley, B S, Vorontsova, M S, Besnard, G, Adams, C, Cuff, N, Mapaura, A, Bianconi, M, Long, C M, Christin, P-A, Osborne, C P. C4 anatomy can evolve via a single developmental change. Ecology Letters, 22: 302–312. View paper

Olofsson, J K, Dunning, L T, Lundgren, M R, Barton, H J, Thompson, J, Cuff, N, Ariyarathne, M, Yankandawala, D, Zeng, K, Osborne, C P, Nosil, P, Christin, P A. Standing variation generated by lateral gene transfer contributes to local adaptation in a grass. Current Biology, 29: 3921–3927. View paper

Olofsson, J K, Cantera, I, Van de Paer, C, Hong-Wa, C, Zedane, L, Dunning, L T, Alberti, A, Christin, P-A, Besnard, G. Phylogenomics using low-depth whole genome sequencing: A case study with the olive tribe. Molecular Ecology Resources, 19: 877–892. View paper

​Papadopulos, A S T, Igea, I, Dunning, L T, Osborne, O G, Quan, X, Pellicer, J, Turnbull, C, Hutton, I, Naker, W J, Butlin, R K, Savolainen. Ecological speciation in sympatric palms: 3. Genetic map reveals genomic islands underlying species divergence in Howea. Evolution, 73: 1986–1995. View paper

2018

Wood, D P, Olofsson, J K, McKenzie, S W, Dunning, L T. Contrasting phylogeographic structures between freshwater lycopods and angiosperms in the British Isles. Botany Letters, 165: 476–486. View paper

​Bianconi, M E, Dunning, L T, Moreno-Villena, J J, Osborne, C P, Christin, P A. Gene duplication and dosage effects during the early emergence of C4 photosynthesis. Journal of Experimental Botany, 9: 1967–1980. View paper

​Moreno-Villena, J J, Dunning, L T, Osborne, C P, Christin, P A. Highly expressed genes are preferentially co-opted for C4 photosynthesis. Molecular Biology and Evolution, 35: 94–106. View paper

2017

Dunning, L T, Lundgren, M R, Moreno-Villena, J J*, Namaganda, M, Edwards, E J, Nosil, P, Osborne, C P, Christin, P A. Introgression and repeated co-option facilitated the recurrent emergence of C4 photosynthesis among close relatives. Evolution, 71: 1541–1555. View paper

​Dunning, L T, Liabot, A L, Olofsson, J K, Smith, E K, Vorontsova, M S, Besnard, G, Simpson, K J, Lundgren, M R, Addicott, E, Handasyde, T, Gallagher, R V, Chu, Y, Pennington, R T, Christin, P A, Lehmann, C E R. The recent and rapid spread of Themeda triandra. Botany Letters, 164: 327–337. View paper

2016

Dunning, L T, Hipperson, H, Baker, W J, Butlin, R K, Devaux, C, Hutton, I, Igea, J, Papadopulos, A S T, Quan, X, Smadja, C M, Turnbull, C G N, Savolainen, V. Ecological speciation in sympatric palms: 1. Gene expression, selection and pleiotropy. Journal of Evolutionary Biology, 29: 1472–1487. View paper

​Hipperson, H, Dunning, L T, Baker, W J, Butlin, R K, Hutton, I, Papadopulos, A S T, Smadja, C M, Wilson, T C, Devaux, C, Savolainen, V. Ecological speciation in sympatric palms: 2. Pre and post-zygotic isolation. Journal of Evolutionary Biology, 29: 2143–2156. View paper

​Olofsson, J K, Bianconi, M, Besnard, G, Dunning, L T, Lundgren, M R, Holota, H, Vorontsova, M S, Hidalgo, O, Leitch, I J, Nosil, P, Osborne, C P, Christin, P A. Genome biogeography reveals the intraspecific spread of adaptive mutations for a complex trait. Molecular Ecology, 25: 6107–23. View paper

​Swift, D G, Dunning, L T, Jgea, J, Brooks, E J, Jones, C S, Noble, L R, Ciezarek, A, Humble, E, Savolainen, V. Evidence of positive selection associated with placental loss in tiger sharks. BMC Evolutionary Biology, 16:1. View paper

​Ciezarek, A G, Dunning, L T, Jones, C S, Noble, L R, Humble, E, Stefanni, S S, Savolainen, V. Substitutions in the glycogenin-1 gene are associated with the evolution of endothermy in sharks and tunas. Genome Biology and Evolution, 8: 3011–21. View paper

2015

Dennis, A B, Dunning, L T, Sinclair, B J, Buckley, T R. Parallel molecular routes to cold adaptation in eight genera of New Zealand stick insects. Scientific Reports, 5: 13965. View paper

​Cornetti, L, Valente, L M, Dunning, L T, Quan, X, Black, R A, Herbert, O, Savolainen, V. The genome of the “great speciator” provides insights into bird diversification. Genome Biology and Evolution, 7: 2680–2691. View paper

2014

Dunning, L T, Dennis, A B, Sinclair, B J, Newcomb, R D, Buckley, T R. Divergent transcriptional responses to low temperature among populations of alpine and lowland species of New Zealand stick insects (Micrarchus). Molecular Ecology, 23: 2712–2726. View paper

​Papadopulos, A S T, Kaye, M, Devaux, C, Hipperson, H, Lighten, J, Dunning, L T, Hutton, I, Baker, W, Butlin, R K, Savolainen, V. 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: 20130342. View paper

2013

Dunning, L T, Dennis, A B, Thomson, G, Sinclair, B J, Newcomb, R D, Buckley, T R. Positive selection in glycolysis among Australasian stick insects. BMC Evolutionary Biology, 13: 215. View paper

​Dunning, L T, Dennis, A B, Park, D, Sinclair, B J, Newcomb, R D, Buckley, T R. 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: 24–31. View paper​

Dennis, A B, Dunning, L T, Dennis, C J, Sinclair, B J, Buckley, T R. Overwintering in New Zealand stick insects. New Zealand Entomologist, 37: 35–44. View paper

2012

Baraloto, C, Hardy, O J, Paine, C E, Dexter, K G, Cruaud, C, Dunning, L T, Gonzalez, M A, Molino, J F, Sabatier, D, Savolainen, V, Chave, J. Using functional traits and phylogenetic trees to examine the assembly of tropical tree communities. Journal of Ecology, 100: 690–701. View paper

2010

Dunning, L T, Savolainen, V. Broad‐scale amplification of matK for DNA barcoding plants, a technical note. Botanical Journal of the Linnaean Society, 164: 1–9. View paper

Book chapters

Ramstad, K M, Dunning, L T (2020) Population genomics advances and opportunities in conservation of kiwi (Apteryx spp.). In: Population genomics. Springer, Cham. View chapter

Popular science

Raimondeau, Pereira, Dunning (2023) Wild plants may edit their genomes in the same way we make GM crops – and it could be crucial to evolution. The Conversation. View article

Dunning, L T (2021) Natural GM: How plants and animals steal genes from other species to accelerate evolution. The Conversation. View article

Dunning, L T (2017) How the horse can help solve one of evolution’s biggest questions. The Conversation. View article

Dunning, L T (2017) Octopuses can defy their own genetic instructions – and it’s slowed down their evolution. The Conversation. View article