June 2018: Front row, Duan Tianlin, Maria Guerrina, Eva Hodková. Second row: Chen Jun, Martin Lascoux, Sylvain Glémin. Third row: Nathalie Zeballos, Chen Chen, Luis Leal, Marion Orsucci, Dmytro Kryvokhyzha, Bogoljub Trickovic. Last row: Pascal Milesi
I am a professor of population genetics at the Evolutionary Biology Centre, Uppsala University. Over a period of five years (2009-2014) I have shared my time between Uppsala and Shanghai where I worked at the Chinese Academy of Sciences (PICB, together with Li Haipeng) and at Fudan University (together with David Waxman).
I primarily work on plant species, and more specifically on forest trees (spruces, birches, larches, poplars) and weeds (Capsella bursa-pastoris and its relatives). I have been working on an array of issues revolving around the interaction of the different evolutionary forces, in particular the interplay between demography and selection in shaping genetic diversity. Lately I have been especially interested in question related to the genetic basis of local adaptation. When addressing evolutionary questions we are using an array of techniques, including genomics, growth chamber experiments and field experiments. Although not a theoretical population geneticist myself I have been collaborating closely with some of them over the years.
I’m a research director at the French CNRS and currently visiting researcher at EBC. My works concern theoretical population genetics and evolutionary genomics. I use population genetics modeling and sequence data analyses approaches, mainly in plant species. My current research topics are:
– The evolution of mating systems and their genomic consequences
– The evolution of GC content in plants and the role of GC-biased gene conversion
– The genetic and genomic of plant domestication
– The consequences of life-history traits on molecular evolution
I have a strong interest in population genetics and molecular evolution.
The last years I have been working on local adaptation in Norway spruce. We collected population samples from parallele latitudinal clines in Scandinavia, in Russia (along Ob river and Yenisei river). We focused on photoperiodic genes and studied the clinal variation in allele frequency, in gene expression, and in bud-set. Studies on these three clines tell us that convergent evolution could involve the same group of genes and possibly even the same mutations.
I am also interested in siRNA expression and its regulatory roles in spruce. Conifer trees have a very different expression pattern of siRNA compared to angiosperm species on the dominant role of 21nt siRNA. This could be related to the “NBS-LRR” gene family, which is one of the largest gene families in spruce and is thought to play an important role in resistant functions.
I did all my studies at the University of Montpellier (South of France) where I obtained a MSc degree in evolutionary biology and ecology. Then, I graduated at the institute for evolutionary biology of Montpellier (ISEM). I studied mosquitoes’ resistance to insecticides, and more specifically the influence of its genomic architecture (mainly gene duplications) on adaptation in relation to environmental variation.
At Uppsala University, I continue to investigate genotype-phenotype relationships in relation to environment but this time at the genomic scale. I am currently involved in four projects. The first project aims to understand what shapes the hybrid zone between P. abies and P. obovata along a longitudinal gradient across the Ural Mountains by investigating local adaptation pattern while correcting for population structure. The goal of the second project –which is part of the Gentree European project — aims to investigate how evolutionary history and local adaptation shaped the genomic variation of seven tree species at the European scale. The objective of the last one is to characterize the genomic variation of the material used to create the P. abies breeding program in Sweden, and use the latter as a common garden experiment to link genotype to phenotype in relation to the ancestral environment from which the trees originate.
Finally, I’m investigating, through a simulation approach, our ability to detect loci underlying quantitative traits leading to phenotypic trade-offs across contrasted environments.
During my PhD, I worked on host specialization and reproductive isolation in moths species. I have developed a great interest for the study of the role of specialization as a driver in the formation of new species. The aim of my work was to combine (1) experimental approaches (using life history traits measurement) and (2) molecular analyses (especially gene expression, RNA-seq approach) to understand the biological factors associated to adaptation and speciation and to reconstruct the evolutionary history of populations.
Now as a postdoc, my aims are twofold. First, I continue in the same direction, i.e. I retain a multi-scale approach to detect the presence of selection on quantitative traits (leaf color, rosette size, height plant, number of flowers, etc …) and on expression in 10 species of “Lineage I” of Brassicaceae. Second, I have started to test if the competitive ability of different Capsella bursa-pastoris accessions depends on the density of competitors and if there exist any differences between populations from different geographic areas. The aim is to test whether the loss of genetic diversity and the accumulation of deleterious mutation are associated with a higher sensitivity to competition.
The information will soon be available
I obtained my MSc degree doing Erasmus Mundus Master Programme in Evolutionary Biology (MEME). I have always been fascinated by hybridization and polyploidy, so almost all my projects deal with these phenomena. I studied diploid-polyploid complexes of spined loaches (Cobitis), incipient hybrid speciation of invasive sculpins (Cottus), and speciation with gene flow in Heliconius butterflies. Currently as my PhD project, I investigate genomic and phenotypic changes associated with polyploidy and hybrid origin in the allotetraploid weed Capsella bursa-pastoris. I analyze both RNA-Seq and whole genome DNA sequencing data and use the information on variation in major phenotypic traits such as flowering time. Defended in March 2018.
After working on the population demographic history of Picea schrenkiana during my Master at Lanzhou University, I continue to study spruce species, but I now mainly focus on the population genetic structure and local adaptation of boreal spruce species. Intraspecific latitudinal clines in genotypes and phenotypes are widely interpreted as basic evidence for natural selection and adaptation to local environment. Two parallel latitudinal clines in gene expression and allele frequency have been detected in Norway spruce (Picea abies) and Siberian spruce (Picea obovata). However, the coverage of high latitude populations was insufficient in the previous study of Picea obovata. So we added samples from populations higher higher latitudes, to test for clinal variation.
I study at the Department of Mathematics (CIM) where my main supervisor is Ingemar Kaj. My PhD project is “Stochastic Methods in Evolutionary Biology” and it is also co-supervised by Martin Lascoux.
The project revolves around the fact that the fundamental evolutionary forces in nature, such as reproduction, mutation, selection, etc. are regulated by random mechanisms which act over millions of years, and the signatures of these mechanisms are visible today as statistical patterns of variation in genome data. The scientific aims include study of various measures of deviation from neutral evolution with three research directions: 1) The role of non-synonymous and synonymous differences as a signature of selection in gene sequence evolution. 2) The study of random genetic drift occurring in finite structured populations. 3) Research around the genetic architecture of complex traits.
Luis is currently studying Nordic birch populations in order to map their adaptive response in the face of global climate change. Over 50 different birch species can be found along the Eurasian continent, often living in sympatry, their evolutionary histories interwoven by common selective forces and recurrent hybridization and introgression events. We will be looking into three birch species present in Sweden – silver, downy, and dwarf – and use genomic data collected along a latitudinal cline to investigate the roles played by hybridization, selection, and population demographic history in shaping local adaptation.
Before joining Martin’s group, Luis worked with Niclas Backström at the Department of Ecology and Genetics, Uppsala University, where he used gene expression profiling to identify genes and pathways underpinning diapause regulation in wood-white butterflies.
Text & picture to come soon
Sandra Petrone, 2015. Do mating system and ploidy level affect the sensitivity to competition in Capsella species?
Xuyue Yang, 2016. The effect of mating system, ploidy level and range expansion on the sensitivity to competition in Capsella species
Mimmi Eriksson, 2017 (at Göteborg University): Characterizing the genetic load in Capsella bursa-pastoris across its range.
Tianlin Duan, 2018. How independently can the two genomes of an allotetraploid species evolve? The case of the shepherd’s purse (C. bursa-pastoris)
Visiting and project students:
Ning Weixuan: University of Oulu, June-July 2016.
Johanna Girodolle: 2d year student at SupAgro, Montpellier France, Sept 2016-Dec 2016.
Clémence Monot: 2d year student at ENSAIA, Nancy France, March 2017-June 2017.
Tianlin Duan: Project student, Uppsala University, March 2017-July 2017.
Margaux Jullien: PhD student, Université de Montpellier, France, Sept 2017-December 2017.
Eva Hodková: PhD student, Czech University of Life Sciences Prague, Czech Republic, April 2018-September 2018.
Johanna Hansen: Project student, Uppsala University, March 2018-July 2018
Chen Chen: Project student, Uppsala University, April 2018-August 2018
Bogoljub Trickovic: MEME student, Montepllier, March 2018-July 2018
Nathalie Zeballos: 2d year student at SupAgro, Montpellier France, May 2018-August 2018.
Jianquan Liu, Sichuan University
Vladimir Semerikov, Russian Academy of Sciences, Ekaterinburg
Giovanni G Vendramin, CNR, Florence
Amandine Cornille, Postdoc, currently CR2 at CNRS, Paris.
Michael Stocks, PhD student, currently postdoc at University of Sheffield
Thomas Källman, PhD student and postdoc, currently bioinformatician at BILS, Uppsala University
Karl Holm, PhD student and postdoc, currently Lecturer at the Independent Learning Centre, The Chinese University of Hong Kong , Hong Kong.
Sofia Hemmilä, PhD student, currently course coordinator at Uppsala University
Tanja Slotte, PhD student, currently Associate Professor at Stockholm University
Padraic Corcoran, MsC, currently postdoc at University of Sheffield.
Per Sjödin, PhD student, currently Researcher in Mattias Jakobsson’s group at EBC
Johan Fogelqvist, PhD student, currently Researcher at the Swedish University of Agricultural Sciences
Marita Kruskopf-Österberg, PhD student, currently Manager at INC Research, Uppsala.
Lars Berg, PhD student
Anna Palmé, PhD student and postdoc, currently Senior Scientist at Nordic Genetic Resource Centre (NordGen)
Hanna Larsson, PhD student, currently teacher in Uppsala
Vladimir Semerikov, Postdoc, currently researcher, Russian Academy of Sciences, Yekaterinburg, Russia
Alf Ceplitis, Postdoc, currently oat breeder with Lanmtmännen, Sweden
Laura Parducci, Postdoc, currently Assistant professor Uppsala University
Niclas Gyllenstrand, Postdoc, currently Lab head, Museum of Natural History, Stockholm
Myriam Heuertz,Postdoc, currently Chargé de recherches, INRA-Bordeaux, France
Susanne Gustafsson, Postdoc, currently at Swedish University of Agricultural Sciences
Ma Xiao-Fei, Postdoc, currently PI, Chinese Academy of Sciences, Lanzhou, PRC
Yoshiaki Tsuda, Postdoc, currently Assistant Professor, Sugadaira Montane Research Center University of Tsukuba, Japan