Marvin Choquet » Members
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- Identification and distribution of Calanus species in the northern hemisphere, using molecular tools
- Mitochondrial genome and phylogeography of Calanus species
- Population genomics of Calanus finmarchicus, glacialis and hyperboreus
- Target capture enrichment protocols for gene capture on Calanus species
- Phenology, vertical distribution and dynamics of Calanus species in boreal areas of sympatry
- Hybridization and species boundaries within the Calanus genus
- Whole genome sequencing of Calanus finmarchicus and glacialis.
I am interested in combining molecular and ecological approaches together to bring answers to evolutionary questions on zooplankton organisms, including keystone copepods and pteropods. Also, I am interested in experimenting the new technologies related to sequencing on non-model organisms. With my team, we have developed a specific protocol of a genome reduction method that enables reaching the genetic information stored in Calanus spp. DNA. This protocol is useful to understand the underlying dynamics of the current and past distribution of Calanus species (in that case), and has also proven useful in other organisms (such as pteropods). One of the long-term project I am currently very interested in is to sequence the whole genome of Calanus finmarchicus and glacialis, which are particularly large genomes. As there are new technologies and new protocols coming up regularly in this fast-evolving field of research, I have started combining different cutting-edge techniques to experiment them on a challenging large genome such as Calanus species. The goal is to find THE approach that will be feasible to sequence a large and complex genome from very little DNA (Calanus are small) of a non-model organism. Once available, doing comparative genomics on Calanus species genomes will help understand the ecological success of these key species in the ocean and shed light on why they need such a large genome.
Combining Ecological and Molecular Approaches to redefine the baseline knowledge of the genus Calanus in the North Atlantic and the Arctic Oceans.
Start date: September 2014
End date: December 2017
Galice Hoarau (Nord University, Bodø)
Prof. Janne Søreide (UNiS, Svalbard)
PhD thesis abstract:
Species of the genus Calanus dominate the zooplankton biomass in the North Atlantic and Arctic Ocean where they play a key role both as grazers and as prey for many commercially important species. Calanus species are frequently used as climate indicators due to their distinct environmental preferences. The overall goal of this thesis was to use currently existing molecular tools and to develop new ones in order to address critical ecological and evolutionary questions related to the genus Calanus in the North Atlantic and in the Arctic Ocean.
Species identification remains a challenge within the genus, especially between C. finmarchicus and C. glacialis. We used a set of nuclear molecular markers to accurately identify Calanus to species level to redefine their respective distributions. Molecular species identification revealed much wider and overlapping distributions than previously known for all four Calanus species inhabiting the North Atlantic and Arctic regions, questioning both the validity of previous morphological ID and the presumed ongoing range shifts forced by climate change. Furthermore, microsatellites data suggested that C. glacialis is more resident in the fjords compared to C. finmarchicus.
An assessment of the commonly used morphological ID criteria was conducted with the help of the molecular tools. None of the prosome length, the red pigmentation in antennules and in genital somite, nor the shape of the gnathobase and the structure of the fifth pair of swimming legs were 100% reliable for species identification. So far only DNA can reliably discriminate between species, although some of the morphological traits can be more useful in some regions than other. Misidentification is thus likely to be widespread.
In two Nordland fjords, C. finmarchicus, C. glacialis, C. helgolandicus and C. hyperboreus were co-occurring during winter-spring. Both C. finmarchicus and C. glacialis adult females and males were present simultaneously in the fjords, potentially allowing for hybridization. However, hybridization is not likely to occur as no hybrid were found in the fjords and neither among >4400 individuals from the 83 distinct locations sampled in the North Atlantic and the Arctic Ocean.
In zooplankton, global lack of genomic resources available has hampered the development of population genomics approaches. Sequencing genomes, mitogenomes and transcriptomes is now critical. Thus, the mitogenome of C. glacialis was sequenced and annotated. Furthermore, using sequence capture enrichment, a set of ca. 100k SNPs was developed for C. finmarchicus and C. glacialis. These resources will be crucial to assess the connectivity between populations and species.
Overall, this thesis substantially advances our understanding of the Calanus species complex and dynamics in the North Atlantic and Arctic Oceans. The inclusions of molecular tools enabled us to fill important knowledge gaps regarding these key species. The new genomic resources developed will open the way to many new studies, to better understand the impact of climate change in Calanus at population, species and ecosystem level.
- M. Choquet, G. Burckard, S. Skreslet, G. Hoarau, J. Søreide. No evidence for hybridization between Calanus finmarchicus and C. glacialis in a subarctic area of sympatry. Limnology & Oceanography. 2020. (https://doi.org/10.1002/lno.11583)
- M. Choquet. Customize and get the most out of your reduced-representation sequencing experiment with the new simulation software RADinitio. Perspective in News & Views in Molecular Ecology Resources. 2020. (https://doi.org/10.1111/1755-0998.13218)
- L. Q. Choo – T. M. P. Bal, M. Choquet, I. Smolina, P. Ramos-Silva, F. Marlétaz, M. Kopp, G. Hoarau, K. T. C. A. Peijnenburg. Novel genomic resources for shelled pteropods: a draft genome and target capture probes for Limacina bulimoides, tested for cross-species relevance. BMC Genomics. 2020. (https://doi.org/10.1186/s12864-019-6372-z)
- E. Skottene, A. M. Tarrant, A. J. Olsen, D. Altin, M.-A. Østensen, B. H. Hansen, M. Choquet, B. M. Jenssen, R. E. Olsen. The β-oxidation pathway is downregulated during diapause termination in Calanus copepods. Nature: Scientific Reports. 2019. (https://doi.org/10.1038/s41598-019-53032-5)
- E. Skottene, A. M. Tarrant, A. J. Olsen, D. Altin, B. H. Hansen, M. Choquet, R. E. Olsen, B. M. Jenssen. A crude awakening: Effects of crude oil on lipid metabolism in calanoid copepods terminating diapause. The Biological Bulletin. 2019. (https://doi.org/10.1086/705234)
- Boavida J. R. – Becheler R., M. Choquet, N. Franck, M. Taviani, J.-F. Bourillet, A. L. Meistertzheim, A. Grehan, A. Savini, S. Arnaud-Haond. Out of the Mediterranean? Post-glacial colonization pathways varied among cold-water coral species. Journal of Biogeography. 2019.
- Choquet M. – Smolina I., A. K. S. Dhanasiri, L. Blanco-Bercial, M. Kopp, A. Jueterbock, A. Y. M. Sundaram, G. Hoarau. Towards population genomics in non-model species with large genomes; a case study of the marine zooplankton Calanus finmarchicus. The Royal Society Open Science Journal. 2019.
- Basedow S. L., D. McKee, I. Lefering, A. Gislason, M. Daase, E. Trudnowska, E. S. Egeland, M. Choquet, S. Falk-Petersen. Remote sensing of zooplankton swarms. Nature: Scientific Reports. 2019.
- Daase M., K. Kosobokova, K. S. Last, J. H. Cohen, M. Choquet, M. Hatlebakk, J. E. Søreide. New insights into the biology of Calanus spp. (Copepoda) males in the Arctic. Marine Ecology Progress Series. 2018.
- Choquet, K. Kosobokova, S. Kwasniewski, M. Hatlebakk, A. K. S. Dhanasiri, W. Melle, C. Svensen, J. E. Søreide, G. Hoarau. Can morphology reliably distinguish between the copepods Calanus finmarchicus and C. glacialis, or is DNA the only way? Limnology & Oceanography: Methods. 2018.
- Bucklin, K. DiVito, I. Smolina, M. Choquet, J. M. Questel, G. Hoarau, R. J. O’Neill. Population Genomics of Marine Zooplankton – Chapter 19 in: Population Genomics: Marine Organisms. Book, Springer. 2018.
- Choquet, M. Hatlebakk, A. K. S. Dhanasiri, K. Kosobokova, I. Smolina, J. E. Søreide, C. Svensen, W. Melle, S. Kwasniewski, K. Eiane, M. Daase, V. Tverberg, S. Skreslet, A. Bucklin, G. Hoarau. Genetics redraws pelagic biogeography of Calanus. Biology Letters. 2017.
- Choquet, H. J. Alves Monteiro, J. Bengtsson-Palme & G. Hoarau. The complete mitochondrial genome of the copepod Calanus glacialis. Mitochondrial DNA Part B, 2:2, 506-507. 2017.