Dr Ludovic Dutoit, Our People, Department of Zoology

Teaching

I am also an organiser of data analysis workshops such as:

Research Interests

We have a range of research interests within evolutionary genomics. We are using population genomic, transcriptomic and eDNA to approach research questions in Ecology and Evolution. We have specific interests in understanding genomic signatures of sexual conflict, the speciation process, and the evolutionary forces shaping genomic variation both in a fundamental context and within the realm of conservation biology.

Prospective Students

I am always happy to discuss research opportunities with prospective students. I have a wide range of projects available, ranging from summer projects to PhD.

Publications

Ni, S., McCulloch, G. A., Kroos, G. C., King, T. M., Dutoit, L., Foster, B. J., Hema, K., Jandt, J. M., Peng, M., Dearden, P. K., & Waters, J. M. (2024). Human-driven evolution of color in a stonefly mimic. Science, 386(6270), 453-458. doi: 10.1126/science.ado5331 Journal - Research Article

Vaux, F., Parvizi, E., Duffy, G. A., Dutoit, L., Craw, D., Waters, J. M., & Fraser, C. I. (2024). First genomic snapshots of recolonising lineages following a devastating earthquake. Ecography. Advance online publication. doi: 10.1111/ecog.07117 Journal - Research Article

Ara, M. G., McCulloch, G. A., Dutoit, L., Wallis, G. P., & Ingram, T. (2024). Genomics reveals repeated landlocking of diadromous fish on an isolated island. Ecology & Evolution, 14, e10987. doi: 10.1002/ece3.10987 Journal - Research Article

Verry, A. J. F., Mas-Carrió, E., Gibb, G. C., Dutoit, L., Robertson, B. C., Waters, J. M., & Rawlence, N. J. (2024). Ancient mitochondrial genomes unveil the origins and evolutionary history of New Zealand's enigmatic takahē and moho. Molecular Ecology, 33, e17227. doi: 10.1111/mec.17227 Journal - Research Article

Clark, A. C., Edison, R., Esvelt, K., Kamau, S., Dutoit, L., Champer, J., … Alexander, A., & Gemmell, N. J. (2024). A framework for identifying fertility gene targets for mammalian pest control. Molecular Ecology Resources, 24(2), e13901. doi: 10.1111/1755-0998.13901 Journal - Research Article

2024

Journal - Research Article

2023

Journal - Research Article

Waters, J. M., Campbell, C. S. M., & Dutoit, L. (2023). Fish biogeography and hybridization: Do contemporary distributions predict introgression history? Evolution, 77(11), 2409-2419. doi: 10.1093/evolut/qpad147

van Galen, L. G., Orlovich, D. A., Lord, J. M., Nilsen, A. R., Dutoit, L., & Larcombe, M. J. (2023). Correlated evolution in an ectomycorrhizal host-symbiont system. New Phytologist. Advance online publication. doi: 10.1111/nph.18802

Dufresnes, C., Dutoit, L., Brelsford, A., Goldstein-Witsenburg, F., Clément, L., López-Baucells, A., … Goudet, J. (2023). Inferring genetic structure when there is little: Population genetics versus genomics of the threatened bat Miniopterus schreibersii across Europe. Scientific Reports, 13(1), 1523. doi: 10.1038/s41598-023-27988-4

Grosser, S., Dutoit, L., Foster, Y., Robertson, F., Fidler, A. E., Martini, D., Knapp, M., & Robertson, B. C. (2023). Genomic evidence of a functional RH2 opsin in New Zealand parrots and implications for pest control. New Zealand Journal of Zoology, 50(2), 341-349. doi: 10.1080/03014223.2022.2053554

Journal - Research Other

Dutoit, L., Mitchell, K. J., Dussex, N., Kemper, C. M., Larsson, P., Dalén, L., Rawlence, N. J., & Marx, F. G. (2023). Convergent evolution of skim feeding in baleen whales [Note]. Marine Mammal Science. Advance online publication. doi: 10.1111/mms.13047

Dutoit, L., & McCulloch, G. A. (2023). Fun in facets: A flexible new tool for population genomics in R. Molecular Ecology Resources. Advance online publication. doi: 10.1111/1755-0998.13773

Vaux, F., Dutoit, L., Fraser, C. I., & Waters, J. M. (2023). Genotyping-by-sequencing for biogeography. Journal of Biogeography, 50, 262-281. doi: 10.1111/jbi.14516

Conference Contribution - Published proceedings: Abstract

Johnson, S., Thomas, L., Dutoit, L., Trewick, S., & McCulloch, G. (2023). Population genomics of an iconic stag beetle. Proceedings of the 71st Entomological Society of New Zealand (ESNZ) Conference. (pp. 58). Retrieved from https://ento.org.nz/

McCulloch, G., Dutoit, L., Davis, A., Waters, J. M., & King, T. M. (2023). Isolation by rock stack? Genomics reveals metapopulation dynamics of alpine wētā. Proceedings of the 71st Entomological Society of New Zealand (ESNZ) Conference. (pp. 56). Retrieved from https://ento.org.nz/

Conference Contribution - Verbal presentation and other Conference outputs

Alvarez-Costes, S., Baker, C. S., Constantine, R., Carroll, E., Dutoit, L., Ferreira, S., … Gemmell, N., Gillum, J., … Rayment, W., … Urban, L., & Alexander, A. (2023, August). Reference genomes, genome-wide heterozygosity, and historical demography of Hector's (Cephalorhynchus hectori hectori) and Māui (Cephalorhynchus hectori maui) dolphins. Verbal presentation at the Queenstown Molecular Biology (QMB) Genomics Satellite, Queenstown, New Zealand.

2022

Journal - Research Article

McCulloch, G. A., Foster, B. J., Dutoit, L., & Waters, J. M. (2022). Repeated alpine flight loss within the widespread New Zealand stonefly Nesoperla fulvescens hare (Plecoptera: Gripopterygidae). Insect Systematics & Diversity, 6(6), 1. doi: 10.1093/isd/ixac027

Campbell, C. S. M., Dutoit, L., King, T. M., Craw, D., Burridge, C. P., Wallis, G. P., & Waters, J. M. (2022). Genome-wide analysis resolves the radiation of New Zealand's freshwater Galaxias vulgaris complex and reveals a candidate species obscured by mitochondrial capture. Diversity & Distributions, 28, 2255-2267. doi: 10.1111/ddi.13629

Ragsdale, A., Ortega-Recalde, O., Dutoit, L., Besson, A. A., Chia, J. H. Z., King, T., Nakagawa, S., Hickey, A., Gemmell, N. J., Hore, T., & Johnson, S. L. (2022). Paternal hypoxia exposure primes offspring for increased hypoxia resistance. BMC Biology, 20, 185. doi: 10.1186/s12915-022-01389-x

Fraser, C. I., Dutoit, L., Morrison, A. K., Pardo, L. M., Smith, S. D. A., Pearman, W. S., Parvizi, E., Waters, J., & Macaya, E. C. (2022). Southern hemisphere coasts are biologically connected by frequent, long-distance rafting events. Current Biology, 32, 3154-3160. doi: 10.1016/j.cub.2022.05.035

McCulloch, G. A., Dutoit, L., Craw, D., Kroos, G. C., & Waters, J. M. (2022). Genomics reveals exceptional phylogenetic diversity within a narrow-range flightless insect. Insect Systematics & Diversity, 6(2), 5. doi: 10.1093/isd/ixac009

Rawlence, N. J., Salis, A. T., Spencer, H. G., Waters, J. M., Scarsbrook, L., Mitchell, K. J., … Dutoit, L., King, T. M., … Kennedy, M. (2022). Rapid radiation of Southern Ocean shags in response to receding sea ice. Journal of Biogeography, 49, 942-953. doi: 10.1111/jbi.14360

Babio, L., Lokman, P. M., Damsteegt, E. L., & Dutoit, L. (2022). Are cell junctions implicated in the regulation of vitellogenin uptake? Insights from an RNAseq-based study in eel, Anguilla australis. Cells, 11, 550. doi: 10.3390/cells11030550

Perry, B. J., Mohammadi Darestani, M., Ara, M. G., Hoste, A., Jandt, J. M., Dutoit, L., … Ingram, T., & Geoghegan, J. L. (2022). Viromes of freshwater fish with lacustrine and diadromous life histories differ in composition. Viruses, 14(2), 257. doi: 10.3390/v14020257

Parvizi, E., Dutoit, L., Fraser, C. I., Craw, D., & Waters, J. M. (2022). Concordant phylogeographic responses to large-scale coastal disturbance in intertidal macroalgae and their epibiota. Molecular Ecology, 31, 646-657. doi: 10.1111/mec.16245

Conference Contribution - Published proceedings: Abstract

Stubbs, A., Dutoit, L., Foster, Y., Grosser, S., Jenkinson, T., McKinlay, B., Robertson, F., … Robertson, B. (2022). A genomics approach to kea (Nestor notabilis) conservation management. Proceedings of the 11th Australasian Ornithological Conference. 41. Retrieved from https://aocauckland.blogs.auckland.ac.nz/

Prystupa, S., Dutoit, L., Foster, Y., Grosser, S., Robertson, F., Stubbs, A., … Robertson, B. (2022). Did the rodent eradication program impact the genetic health of an endemic bird species? A genomic investigation of the Lord Howe currawong. Proceedings of the 11th Australasian Ornithological Conference. 38. Retrieved from https://aocauckland.blogs.auckland.ac.nz/

Dutoit, L., Nadachowska-Brzyska, K., Smeds, L., Kardos, M., Gustafsson, L., & Ellegren, H. (2022). Estimating contemporary effective population size in an island population of collared flycatchers (Ficedula albicollis). Proceedings of the 11th Australasian Ornithological Conference. 48. Retrieved from https://aocauckland.blogs.auckland.ac.nz/

Conference Contribution - Verbal presentation and other Conference outputs

van Galen, L., Orlovich, D., Lord, J., Bohorquez, J., Nilsen, A., Summerfield, T., Dutoit, L., & Larcombe, M. (2022, May). Environment and host effects on New Zealand Nothofagus ectomycorrhizal fungal communities. Verbal presentation at the Fungal Network of New Zealand 35th New Zealand 'Virtual' Fungal Foray including the 20th Mycology Colloquium, [Online].

2021

Journal - Research Article

McCulloch, G. A., Guhlin, J., Dutoit, L., Harrop, T. W. R., Dearden, P. K., & Waters, J. M. (2021). Genomic signatures of parallel alpine adaptation in recently-evolved flightless insects. Molecular Ecology, 30, 6677-6686. doi: 10.1111/mec.16204

Foster, Y., Dutoit, L., Grosser, S., Dussex, N., Foster, B. J., Dodds, K. G., … Robertson, F., … Robertson, B. C. (2021). Genomic signatures of inbreeding in a critically endangered parrot, the kākāpō. Genes Genomes Genetics, 11(11), jkab307. doi: 10.1093/g3journal/jkab307

Nadachowska-Brzyska, K., Dutoit, L., Smeds, L., Kardos, M., Gustafsson, L., & Ellegren, H. (2021). Genomic inference of contemporary effective population size in a large island population of collared flycatchers (Ficedula albicollis). Molecular Ecology, 30, 3965-3973. doi: 10.1111/mec.16025

McCulloch, G. A., Foster, B. J., Dutoit, L., Harrop, T. W. R., Guhlin, J., Dearden, P. K., & Waters, J. M. (2021). Genomics reveals widespread ecological speciation in flightless insects. Systematic Biology, 70(5), 863-876. doi: 10.1093/sysbio/syaa094

McCulloch, G. A., Madeira, P. T., Makinson, J. R., Dutoit, L., Blair, Z., Walter, G. H., … Purcell, M. F. (2021). Phylogenomics resolves the invasion history of Acacia auriculiformis in Florida. Journal of Biogeography, 48, 453-464. doi: 10.1111/jbi.14013

Conference Contribution - Published proceedings: Abstract

Eda, A. R. A., Centeno, F., Bishop, P., Godfrey, S., Dutoit, L., Rand, C., Easton, L., & Stanton, J. (2021). Evaluation of DNA extraction kits for examining skin microbial composition of New Zealand native frog. Proceedings of the University of Otago Student Research Symposium: Te Wānaka Rakahau: Ākoka. (pp. 26). [Abstract]

Stubbs, A., Dutoit, L., Foster, Y., Robertson, F., Van Stijn, T., & Robertson, B. (2021). Genetics to inform conservation management of kea (Nestor notabilis) in New Zealand. Proceedings of the University of Otago Student Research Symposium: Te Wānaka Rakahau: Ākoka. (pp. 58). [Abstract]

Cadzow, M., Dutoit, L., Senanayake, D., Bixley, M., & Faya, N. (2021). Otago bioinformatics spring school. Proceedings of the eResearch NZ Conference. (pp. 18-19). Retrieved from https://www.eresearchnz2021.org.nz

Conference Contribution - Verbal presentation and other Conference outputs

Nadachowska-Brzyska, K., Dutoit, L., Smeds, L., Kardos, M., Gustafsson, L., & Ellegren, H. (2021, June). Estimating contemporary effective population size in an island population of collared flycatchers (Ficedula albicollis). Verbal presentation at the Virtual Evolution Conference, [Online].

2020

Journal - Research Article

Mugal, C. F., Wang, M., Backström, N., Wheatcroft, D., Ålund, M., Sémon, N., … Dutoit, L., … Ellegren, H. (2020). Tissue-specific patterns of regulatory changes underlying gene expression differences among Ficedula flycatchers and their naturally occurring F₁ hybrids. Genome Research, 31(12), 1727-1739. doi: 10.1101/gr.254508.119

Ruzicka, F., Dutoit, L., Czuppon, P., Jordan, C. Y., Li, X.-Y., Olito, C., … Connallon, T. (2020). The search for sexually antagonistic genes: Practical insights from studies of local adaptation and statistical genomics. Evolution Letters, 4(5), 398-415. doi: 10.1002/evl3.192

Young, M. J., Dutoit, L., Robertson, F., van Heezik, Y., Seddon, P. J., & Robertson, B. C. (2020). Species in the faeces: DNA metabarcoding as a method to determine the diet of the endangered yellow-eyed penguin. Wildlife Research, 47(6), 509-522. doi: 10.1071/wr19246

Parvizi, E., Fraser, C. I., Dutoit, L., Craw, D., & Waters, J. M. (2020). The genomic footprint of coastal earthquake uplift. Proceedings of the Royal Society of London: Series B, 287, 20200712. doi: 10.1098/rspb.2020.0712

Ingram, T., Dutoit, L., Mikheev, P., Khan, S., & Schallenberg, M. (2020). Phenotypic, ecological and genomic variation in common bully (Gobiomorphus cotidianus) populations along depth gradients in New Zealand's Southern Great Lakes. Canadian Journal of Fisheries & Aquatic Sciences, 77(10), 1678-1687. doi: 10.1139/cjfas-2020-0015

Padovan, A., Chick, R. C., Cole, V. J., Dutoit, L., Hutchings, P. A., Jack, C., & Fraser, C. I. (2020). Genomic analyses suggest strong population connectivity over large spatial scales of the commercially important baitworm, Australonuphis teres (Onuphidae). Marine & Freshwater Research, 71(11), 1549-1556. doi: 10.1071/MF20044

Donald, K. M., McCulloch, G. A., Dutoit, L., & Spencer, H. G. (2020). Population structure of the New Zealand whelk, Cominella glandiformis (Gastropoda: Buccinidae), suggests sporadic dispersal of a direct developer. Biological Journal of the Linnean Society, 130, 49-60. doi: 10.1093/biolinnean/blaa033

Peters, J. C., Waters, J. M., Dutoit, L., & Fraser, C. I. (2020). SNP analyses reveal a diverse pool of potential colonists to earthquake-uplifted coastlines. Molecular Ecology, 29, 149-159. doi: 10.1111/mec.15303

Journal - Research Other

Alexander, A., & Dutoit, L. (2020). Roe deer on ice: Selection despite limited effective population size through the Pleistocene. Molecular Ecology, 29, 2765-2767. doi: 10.1111/mec.15511

Conference Contribution - Published proceedings: Abstract

Dutoit, L. (2020). Sexual conflict in a shared genome [Invited]. Proceedings of the Genetics Otago (GO) Zoom Symposium. Retrieved from https://blogs.otago.ac.nz/go/2020-3/

Ragsdale, A. K., Dutoit, L., Besson, A. A., King, T., Gemmell, N. J., Hore, T., & Johnson, S. L. (2020). Paternal hypoxia exposure primes offspring for increased hypoxia resistance. Integrative & Comparative Biology, 60(Suppl. 1), (pp. E192). doi: 10.1093/icb/icaa006

2019

Journal - Research Article

Cole, T. L., Dutoit, L., Dussex, N., Hart, T., Alexander, A., Younger, J. L., … Ellenberg, U., … Mattern, T., … Waters, J. M. (2019). Receding ice drove parallel expansions in Southern Ocean penguins. PNAS, 116(52), 26690-26696. doi: 10.1073/pnas.1904048116

Rexer-Huber, K., Veale, A. J., Catry, P., Cherel, Y., Dutoit, L., Foster, Y., … Waters, J., & Robertson, B. C. (2019). Genomics detects population structure within and between ocean basins in a circumpolar seabird: The white-chinned petrel. Molecular Ecology, 28, 4552-4572. doi: 10.1111/mec.15248

McCulloch, G. A., Foster, B. J., Dutoit, L., Ingram, T., Hay, E., Veale, A. J., Dearden, P. K., & Waters, J. M. (2019). Ecological gradients drive insect wing loss and speciation: The role of the alpine treeline. Molecular Ecology, 28, 3141-3150. doi: 10.1111/mec.15114

Conference Contribution - Published proceedings: Abstract

Ragsdale, A., Dutoit, L., Besson, A., King, T., Gemmell, N., Hore, T., & Johnson, S. (2019). Paternal hypoxia exposure primes offspring for increased hypoxia resistance. Proceedings of the 16th Asian Conference on Transcription. (pp. 48-49). Retrieved from http://act2019.p.events4you.currinda.com/days/2019-12-02/

Cole, T., Dutoit, L., Dussex, N., Hart, T., Alexander, A., Frugone, M. J., … Ellenberg, U., … Mattern, T., … Waters, J. (2019). Receding ice drove rapid expansions in eight Southern Ocean penguins. Proceedings of the Genetics Society of Australasia (GSA) Conference. Retrieved from https://event.crowdcompass.com/gsa2019

Ragsdale, A., Dutoit, L., Chia, J., Gemmell, N., & Johnson, S. (2019). It's in your head: How echoes of the past shape future progeny. Proceedings of the Genetics Society of Australasia (GSA) Conference. Retrieved from https://event.crowdcompass.com/gsa2019

Foster, Y. A. L., Dutoit, L., & Robertson, B. C. (2019). Genomic architecture of inbreeding in all living adults of the critically endangered kākāpō parrot (Strigops habroptilus). Proceedings of the Genetics Society of Australasia (GSA) Conference. Retrieved from https://event.crowdcompass.com/gsa2019

Young, M. J., Robertson, F., Dutoit, L., Mattern, T., Seddon, P. J., Robertson, B. C., & van Heezik, Y. (2019). Evidence for declining diet quality of mainland yellow-eyed penguins (Megadyptes antipodes): Is this their final dive? Proceedings of the 10th International Penguin Conference (IPC10). (pp. 73). Retrieved from https://www.penguin-conference.com

Cole, T. L., Dutoit, L., Dussex, N., Hart, T., Alexander, A., Frugone, M. J., … Ellenberg, U., … Mattern, T., … Waters, J. M. (2019). Contrasting demographic histories between widespread and endemic penguin taxa. Proceedings of the 10th International Penguin Conference (IPC10). (pp. 39-40). Retrieved from https://www.penguin-conference.com

2018

Journal - Research Article

Dutoit, L., Mugal, C. F., Bolívar, P., Wang, M., Nadachowska-Brzyska, K., Smeds, L., … Ellegren, H. (2018). Sex‐biased gene expression, sexual antagonism and levels of genetic diversity in the collared flycatcher (Ficedula albicollis) genome. Molecular Ecology, 27(18), 3572-3581. doi: 10.1111/mec.14789

Bolívar, P., Mugal, C. F., Rossi, M., Nater, A., Wang, M., Dutoit, L., & Ellegren, H. (2018). Biased inference of selection due to GC-biased gene conversion and the rate of protein evolution in flycatchers when accounting for it. Molecular Biology & Evolution, 35(10), 2475-2486. doi: 10.1093/molbev/msy149

Connallon, T., Olito, C., Dutoit, L., Papoli, H., Ruzicka, F., & Yong, L. (2018). Local adaptation and the evolution of inversions on sex chromosomes and autosomes. Philosophical Transactions of the Royal Society B, 373(1757), 20170423. doi: 10.1098/rstb.2017.0423

2017

Journal - Research Article

Dutoit, L., Burri, R., Nater, A., Mugal, C. F., & Ellegren, H. (2017). Genomic distribution and estimation of nucleotide diversity in natural populations: Perspectives from the collared flycatcher (Ficedula albicollis) genome. Molecular Ecology Resources, 17(4), 586-597. doi: 10.1111/1755-0998.12602

Dutoit, L., Vijay, N., Mugal, C. F., Bossu, C. M., Burri, R., Wolf, J., & Ellegren, H. (2017). Covariation in levels of nucleotide diversity in homologous regions of the avian genome long after completion of lineage sorting. Proceedings of the Royal Society B, 284(1849), 20162756. doi: 10.1098/rspb.2016.2756

Conference Contribution - Verbal presentation and other Conference outputs

Dutoit, L., Vijay, N., Mugal, C. F., Bossu, C. M., Burri, R., Wolf, J., & Ellegren, H. (2017, January). Co-variation in levels of nucleotide diversity in homologous regions of the avian genome long after completion of lineage sorting. Verbal presentation at the 50th Population Genetics Group Annual Meeting (PopGroup 50), Cambridge, UK.

Awarded Doctoral Degree

Dutoit, L. (2017). Determinants of genomic diversity in the collared flycatcher (Ficedula albicollis) (PhD). Uppsala University, Uppsala, Sweden. Retrieved from http://uu.diva-portal.org/smash/record.jsf?pid=diva2%3A1150692&dswid=7366

2016

Journal - Research Article

Uebbing, S., Künstner, A., Mäkinen, H., Backström, N., Bolivar, P., Burri, R., Dutoit, L., … Ellegren, H. (2016). Divergence in gene expression within and between two closely related flycatcher species. Molecular Ecology, 25(9), 2015-2028. doi: 10.1111/mec.13596

Conference Contribution - Published proceedings: Abstract

Dutoit, L. (2016). Co-variation in levels of nucleotide diversity in the avian genome long after completion of lineage sorting. Proceedings of the 22nd European Annual Meeting for PhD Students in Evolutionary Biology (EMPSEB 22). (pp. 37). Retrieved from https://empseb22dotorg.wordpress.com

2015

Journal - Research Article

Witsenburg, F., Clément, L., López-Baucells, A., Palmeirim, J., Pavlinić, I., Scaravelli, D., … Dutoit, L., … Christe, P. (2015). How a haemosporidian parasite of bats gets around: The genetic structure of a parasite, vector and host compared. Molecular Ecology, 24(4), 926-940. doi: 10.1111/mec.13071

Burri, R., Nater, A., Kawakami, T., Mugal, C. F., Olason, P. I., Smeds, L., … Dutoit, L., … Ellegren, H. (2015). Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum of Ficedula flycatchers. Genome Research, 25(11), 1656-1665. doi: 10.1101/gr.196485.115

Conference Contribution - Poster Presentation (not in published proceedings)

Dutoit, L. (2015, June). Guidelines for samping of genetic diversity based on whole-genome re-sequencing data from collared flycatchers (Ficedula albicollis). Poster session presented at the Evolution, Guarujá, Brazil.

Conference Contribution - Verbal presentation and other Conference outputs

Dutoit, L. (2015, September). Conservation of the genetic diversity landscape across two distantly related passerine species. Verbal presentation at the 21st European Annual Meeting for PhD Students in Evolutionary Biology (EMPSEB 21), Stirling, UK.

2014

Conference Contribution - Poster Presentation (not in published proceedings)

Dutoit, L., Vijay, N., Kawakami, T., Burri, R., Wolf, J., & Ellegren, H. (2014, January). Conservation of local levels of genetic diversity between two distantly related bird species. Poster session presented at the 47th Population Genetics Group Annual Meeting (PopGroup 47), Bath, UK.