Issue 4 (May 2020) of New Phytologist comprises a dedicated section devoted to Oak Genomics. This was a timely initiative by Christophe Plomion and Francis Martin as it came 2 years after the publication of the Quercus robur genome (Plomion et al., 2018). This special issue is introduced by and editorial of Christophe and Francis and comprises in total 10 papers, among which 7 were co-autored by scientists of our group at BIOGECO, working on Q. robur and Q. petraea (see below). There are mainly outcomes of recent research projects as GENOAK and TREEPEACE dealing with microevolution. Among other highlights, this issue provides the most complete phylogenetic reconstruction of the genus Quercus (Hipp et al., 1198-1212) and shows for the first time how introgression between oak species fostered adaptation to new environments (Leroy et al., 1171-1182).
Bartholomé J, Brachi B, Marçais B, Mougou-Hamdame,... et al. 2020. The genetics of exapted resistance to two exotic pathogens in pedunculate oak. New Phytologist 226 : 1088-1103 (pdf)
Cannon CH, Petit RJ 2020. The oak synganeom: more than the sum of its parts. New Phytologist 226 : 978-983 (pdf)
Hipp AL, Manos PS, Hahn M, Avishai M,.. et al. 2020. The genomic landscape of the global oak phylogeny. New Phytologist 226 : 1198-1212 (pdf)
Kremer A, Hipp AL 2020. Oaks : an evolutionary success story. New Phytologist 226 : 987-1011 (pdf)
Leroy T, Louvet JM, Lalanne C, Le Provost G, Labadie K, Aury JM, Delzon S, Plomion C, Kremer A 2020. Adaptive introgression as a driver of local adaptation to climate in European white oaks. New Phytologist 226 : 1171-1182 (pdf)
Leroy T, Rougemont Q, Dupouey JL, Bodénès C, Lalanne C, Belser C, Labadie K, Le Provost G, Aury JM, Kremer A, Plomion C 2020. Massive postglacial gene flow between European white oaks uncovered genes underlying species barriers. New Phytologist 226 : 1183-1197 (pdf)
Leroy T, Plomion C, Kremer A 2020. Oak tree symbolism in the light of genomics. New Phytologist 226 :1012-1017 (pdf)
Planetary intermixing is the subject of debate. The various migrations that they cover are a fundamental feature of societies and living environments, throughout history; but their apparent contemporary acceleration arouses strong and often hostile reactions. This book starts from several intuitions: the intellectually fruitful initiative of exploring human, plant and animal migrations at the same time. The need to take stock of these mixes, to put the arguments that are exchanged in depth and the interest of drawing the parallel between the different migrations. An ultimately in doing so, to delineate the space for an intellectual and political accepted construction of planetary intermixing.
Patrick Moquay & Véronique Mure (coordonnateurs)
Brassages planétaires. Jardiner le monde avec Gilles Clément
Hermann éditeurs. 266 pages. ISBN 979 1 0370 0357 7
Kremer A. Brassages génétiques, diversité et adaptation. p. 105-111
Clément G., Coccia E., Kremer A., Tassin J., Thiery S. Migrer, une condition d’existence du vivant. p.249-251
What forests will we leave to future generations? Will they be able to meet all the expectations that our societies hope for? Will they be able to meet these external demands while ensuring their own sustainability? These are the recurring questions that are frequently raised in the fora, both scientific and citizen. Whatever their origin, these questions reflect the interest that humans have today in forests, and the challenges that they represent in the ecological and economic balances of our societies. "Cultivated forests", "plantation forests", "industrial forests", "natural forests", all these qualifiers frequently attributed to the current forests of Aquitaine reflect the more or less strong imprint of man in their use, if not their exploitation. They also show how diverse forests have become. The singular "forest" no longer has any reason for being and this diversification already suggests new forms that the future and its uncertainties could create. At their own pace, past and present, forests are in motion and their changes are now becoming noticeable at our own time scales. Understanding its speed and mechanisms to predict their future evolution becomes a question and a challenge of research. The biological obstacles often invoked in research on trees and forests become assets here. It is this trajectory between forests of the past, present forests and forests of tomorrow that is reconstructed in this book through that of research carried out for the last 50 years in the Nouvelle Aquitaine Region.
Arbez M, Carnus JM, Kremer A (ed.) 2017. Forêts d'hier et de demain. 50 ans de recherche en Aquitaine. Presses Universitaires de Bordeaux, LGPA Editions. 250 pages
Presses Universitaires de Bordeaux
33607 Pessac Cedex
It all started in 2006, when twenty five universities and research institutes from fifteen European countries joined forces to set up EVOLTREE as a Network of Excellence. EVOLTREE aimed to link four major disciplines Ecology, Genetics, Genomics, and Evolution to address global issues faced by European forests, such as environmental changes and the erosion of biodiversity. Funded by the European Union within the 6th framework programme, it spent the next four years developing and setting up the necessary experimental and monitoring infrastructures and physical and electronic resources upon which long term research could be built. Now self-funding (based on financial contributions from some partners and "in-kind" contributions from others in the form of running relevant scientific training courses), EVOLTREE was integrated into the European Forest Instuitute (EFI) network.
This book contains a selection of 10 articles from the 165 listed on the Web of Science which have been funded by EVOLTREE. It also describes the main physical and electronic infrastructures and other resources and initiatives, from which the forest genetics research community, in particular the network's present members can benefit.
Kremer A, Hayes S, Gonzalez-Martinez SC (eds) 2016 Evolution of trees and communities: Ten years of the Evoltree Network. GP editions-Bordeaux, 192 pages
69 Route d'Arcachon 33612 Cstas France
At the start of the 2010s, the Aquitaine Region asked the scientific community to make a review on the current state of knowledge on the impact of climate change in the Region. More than 370 researchers contributed to this synthesis, which resulted in the publication of two successive volumes in 2013 and 2018. The first volume emphasizes the known impacts and their effects, while the second addresses mainly the measures that can be taken to adapt to climate change. The structure in both volumes considers first general issues and concerns raised by climate change then provides up to date knowledge of the impacts in different sectors (agriculture, mountains, sea, atmosphere ..).
I was part of the editorial board of both volumes and author and coordinator of a chapter in each volume regarding the impact in the forestry sector.
Chapter on forests in the 2013 volume (p 126-156)
After recalling the ecological and economic importance of forests in Aquitaine, this chapter reviews the already visible effects of global change on forests. The steadily increase of growth, the earlier time of bud burst and the migration of some species are the most visible effects of the environmental changes underway. These trends are predicted to be maintained even if productivity trends could show geographic variation over the coming decades. Climate change will increase the exposure of forests to phytosanitary and physical risks (fires, drought), and to the emergence of new pathogens. Adaptive management policies are envisaged with the aim of improving the resilience of forest stands, or strengthening the mechanisms for adapting species to environmental change. Forests also offer opportunities to mitigate the effects of climate change, which reside in their capacity to store carbon in soils and biomass and replace fossil carbon in forest products used in various other sectors (energy, construction..)
Chapter on forest in the 2018 Volume (p 226-247)
This chapter questions what will be the forests of tomorrow in Nouvelle Aquitaine in the context of climate change, and the expectations of public authorities and forest owners: What species will populate our forests? Can we expect major changes in their composition? How can human action accompany this transition in composition? It emphasizes anthropogenic actions to maintain and renew indigenous species, and it questions the past and future introduction of exotic species to anticipate the adaptive demands imposed by climate change. In a second part, the policies recommended by the European Union and France in the forest-wood domain are dealt with, with regard to their adaptation to climate change and their role in its mitigation. Finally, this second part also discusses the expectations of private forest owners in the face of climate change, following a survey carried out among them on this subject.
Le Treut H. et coll. 2013 Les impacts du changement climatique en Aquitaine. Presses Universitaires de Bordeaux, LGPA éditions, 370 pages. ISBN: 978-2-86781-874-5
Le Treut H. et coll. 2018 Anticiper les changements climatiques en Nouvelle Aquitaine pour agir dans les territoires.Editions Région Nouvelle-Aquitaine.486 pages. ISBN: 978-2-9564516-0-0
Oak is the ultimate Gascon tree. Chantal Armagnac and Jean-Bernard Laffitte, lead us from the Pyrenean foothills to the Atlantic dunes to the corridor of the Garonne, to illustrate hom oak coming from Spain has conquered Gascony. In addition to the archival documents drawn from the libraries of forester friends, Chantal Armagnac has collected precious testimonies from many trades, loggers, carpenters, boatmen, naturalists, herdsmen, coopers to highlight the close links woven between oaks and humans communities for millennia.
I contributed to this adventure by writing the preface to the book. I venture there to an unusual comparison of the evolutionary trajectories of man and oak, by asking myself about their strategies which contributed to their success on our planet. Given the accounts of Chantal Armagnac and the history of the two species, one could undoubtedly conclude that man has gained more from being a partner of oak, than an oak from being a partner of man. Future times may be more difficult for the oaks, and the opportunities should not fail to express our appreciation to the oaks.
Chantal Armagnac, Jean-Bernard Laffitte
Le chêne arbre, arbre roi de Gascogne
Editions « Le vert en l’air », 160 pages
The editors of this book attempted to synthesize some of the major uses of molecular markers in natural resource management in a volume targeted not only at scientists but also at individual actively making conservation and management decisions. They organized a conference in October 2008 at the John S Wright Forestry Center (Purdue University, Indiana, USA) to which the authors of the book were invited.
I made a review on the historical and contemporary dynamics of genetic differentiation in European oaks, where fossil and genetic data have been assembled across their entire continental distribution.Assembling lessons from phylogeography, paleobotany, and simulations, we conclude that long-lived tree species have responded quite rapidly to environmental change, despite their low evolutionary rate at the gene level Indeed, and as suggested by theoretical investigations, the tempo of differentiation is driven by the standing level of genetic diversity and gene flow. In comparison to earlier studies that highlighted these features of trees, this review shows the mechanisms by which the interaction between gene flow and local selection pressures accelerates the rate of differentiation, by building up favorable allelic associations among genes contributing to fitness-related traits. Intergenic allelic associations are the cause of the rapid differentiation, and they explain the coexistence of strong phenotypic differentiation in trees (as assessed in provenance tests) and extensive gene flow. It is likely that these mechanisms were actually favored during the repeated interglacial–glacial periods allowing widespread tree species to colonize and adapt to new suited environments. How these mechanisms are acting during ongoing climatic change remains to be investigated in detail, but these processes are critical to predicting how species will adapt to changing environments.
De Woody A., Bickham J.W., Michler C.H., Nichols K.M., Rhodes O.E, Woeste K.E. (eds) 2010. Molecular approaches in natural resource conservation and management. Cambridge University Press. 374 pages. ISBN 978-0-521-51564-1
Kremer A., Le Corre V., Petit R.J., Ducousso A. 2010. Historical and contemporary dynamics of adaptive differentiation in European oaks. pp 101-116
Genetic linkage studies in forest trees started within the application of allozymes in the late 1980s, and were refined as DNa marker technology improved. This book edited by Chittaranjan Kole makes a review in 2006 about the existing genetic maps and their application in genetics breeding in forest trees. The eight chapters include Populus trees, pines, spruce, eucalypts, Fagaceaea trees, black walnut , Douglas fir, and Cryptomeria japonica.
I coordinated and coauthored the review on Fagacea trees, updating the state of knowledge in Castanea, Quercus, and Fagus, and on comparative mapping between Querus and Castanea as well.
The chapter on Fagaceae comprises 4 sections
Construction of genetic linkage maps
Comparative mapping between Quercus, Castanea and Fagus
Genes mapped in oaks and chestnuts
Kole Ch. (ed) 2007. Genome mapping and molecular breeding in plants. Volume 7. Springer Verlag. 232 Pages. ISBN 978-3-540-34540-4
Kremer A., Casasoli M., Barreneche T., Bodénès C., Sisco P., Kubisiak T., Scalfi M., Leonardi S., Bakker E.G., Buiteveld J., Romero-Severson J., Arumuganathan K., Derory J., Scotti-Saintagne C., Roussel G., Bertocchi M.E, Lexer C., Porth I., Hebard F., Clark C., Carlson J., Plomion P., H. Koelewijn, and Villani F. 2007. Fagaceae: comparative Genetic Mapping in Fagaceae. pp 161-187
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In the early 1990s INRA initiated a research project to investigate the level, distribution and dynamics of genetic diversity of tropical trees in French Guiana. Starting from scratch, the project aimed at identifying likely ecological and biological determinants of genetic diversity. The project selected a set of 15 species exhibiting contrasting life history traits (pollen and seed dispersion, flowering phenology, succession, spatial distribution etc..). The research was conducted within the Paracou well known large scale and long term experimental plot. For each species, the level and the spatial distribution of diversity was described within the Paracou stand. Furthermore genetic processes as mating system, phenology of flowering, and gene flow were also monitored. In 2004 when this book was published, we reviewed the results obtained after 10 years of investigation.
I contributed to the setting in up of the genetic lab in Kourou and the research project on genetic diversity of forest trees in French Guyana, together with Henri Caron and Eric Bandou. CIRAD also joined the project shortly after the start. In this book I provided an outline of the project and coauthored the review on the distribution of genetic diversity in 10 species.
Gourlet-Fleury S., Guehl J.M, Laroussinie O. (eds) 2004. Ecology and Management of a Neotropical Rainforest. Elsevier. 308 pages. ISBN 2-84299-455-8
Kremer A., 2004. The genetic diversity of forest tree species in French Guiana. p147-148
Caron H., Bandou E., Kremer A. 2004 Multilocus assessment of genetic diversity in tropical trees in Paracou stands. p160-171
This special issue of Forest Ecology and Management gathers the manuscripts 16 invited speakers that came to the DYGEN conference organized within the European parliament in Strasbourg in 2002. The conference was organized while the results on the distribution of genetic diversity have accumulated on a European scale thanks to the financial support of the EU within the first framework programmes. The conference was intended to fill the gap between basic resarch conducted in the area of population , evolutionary and ecological genetics, and the implementation of their results in conservation genetics.
Kremer A., Reviron M.P. 2004. Dynamics and conservation of genetic diversity in Forest Ecosystems. Forest Ecology and management, Volume 197, issue 1-3, 338 pages
What are the relative contributions of evolutionary history, genetic processes, and demographic dynamics to the extant distribution of genetic diversity in trees? These are central questions in population genetics, and concerns for the management and conservation of tree populations. In traditional population genetics, these issues have been investigated through theoretical approaches using simplified evolutionary scenarios. Computer simulations allow to extend these predictions to more realistic situations. Finally predictions from theoretical work and simulations can be confronted to genetic surveys conducted with nuclear and organelle markers in natural populations.
A conference organized in Kourou (French guiana) in 2000 gathered investigators using these different approaches to provoke thoughtful discussions between practicioners and theoreticians on these issues. Comparisons were made between theoretical expectations, computer simulations and experimental results.
Degen B., Loveless M.D., Kremer A. (eds) 2002. Modelling and experimental research on genetic processes in tropical and temperate forests. Empraba Amazonia Oriental. 198 p. ISBN 85-87690-14-0.
Gerber S., Mariette S., Streiff R., Bodénès C. Kremer A. Using oaks to compare microsatellites and AFLP markers for parentage analysis. p 69-77
Le Corre V., Kremer A. The response of forest tree populations to natural selection: variability and differentiation of adaptive traits and their underlying loci. p 102-108
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This is the special Issue of "Forest Ecology and Management" entirely dedicated to the paneuropean distribution of chloroplast diversity in European white oaks. This continental wide survey was conducted within the FAIROAK project supported by the European Commission, and is a collective achievement of 13 labs. In addition to the genetic survey, microfossils data were extracted from the European pollen data base, and jointly anlyzed with the genetic data, thus allowing to reconstruct post glacial colonisation pathways. The special issue comprises 4 synthetic papers and 9 regional papers addressing local and regional distribution of chloroplast haplotypes.
Kremer A. (ed.) 2002. Range wide distribution of chloroplast DNA diversity and pollen deposits in European white oaks: inferences about colonisation routes and management of oak genetic resources. Forest Ecology and Management, 156, Vol 1-3, 224 pages.
The 1990 decade was a period of intense research to develop useful genetic markers that could be applicable at a large scale for monitoring the distribution of genetic diversity in natural and domesticated plant and animal populations. The DG XII Biotechnological Unit of the European Commission supported collaborative research projects called "Molecular Genetic Screening tools". This book is a deliverable of the consortium of labs of these projects and was aimed at investigators of all disciplines, with interests in the conservation, population biology, taxonomy, evolution,management, breeding and industrial applications of plant and animal diversity. The book is divided in five parts: DNA extraction, Basic screening methods, Sources of probes and primers, Data analysis, and case studies. My contribution is in the section on data analysis, where we we describe methods for estimating diversity and differentiation, and the allelic and nucleotidic level and for nuclear and organelle DNA.
Karp A., Isaac P.G., Ingram D.S. 1998. Molecular tools for screening biodiversity. Plants and animals. Chapman & Hall. 498 pages
ISBN 0 412 63830 4
Kremer A., Petit R.J., Pons O. Measures of polymorphism within and among populations. p 299-311
The availability of large numbers of molecular markers in the 1990s has overturned scopes and perspectives in many fields of genetic research. This book tackled the new questions that markers allowed to address at that time in the areas of quantitative, evolutionary, population genetics and breeding applications. The original french version of the book was published in 1998, and it was updated in an english version in 2003. I emphasized the application of molecular markers in population genetics, by addressing diversity and gene flow. In the updated version, a comparative analysis was made across different types of markers that were available in those days.
De Vienne D. (ed) 2003. Molecular markers in plant genetics and biotechnology. Science Publishers 236 pages.ISBN 1 57808 239 0
Kremer A., Mariette S. 2003. Molecular markers in population genetics. p 125-149
Most of the chapters of this volume are based on invited lectures presented during th 4th International Consultation on Forest Genetics and Tree Breeding in Beijing, China, August 22-28, organized by IUFRO (International Union of Forest Research Organisations). What were the motivations of this conference ? As stated by Csaba Matyas, editor of the book, it was timely to review achievements and suggest future contributions of new approaches in forest genetics on issues that have global significance. There are at least four very serious challenges to mankind, which are related to forestry and to forest genetics which demand active involvement:
catastrophic depletion of forest resources
acute shortage of firewood
environmental threats to forests in industrialized regions
impending effects of predicted climate changes.
We took this opportunity to present our first results regarding the prediction of differentiation of adaptive traits, in comparison to their underlying genes, using a simulation approach. These predictions were further compared observed values compiled in provenance tests.
Matyas, C. (ed.) 1999. Forest genetics and sustainability. Kluwer Academic Publisher. 288 pages. ISBN 0-7923-6011-7
Kremer A.,Le Corre V., Mariette S. Population differentiation for adaptive traits and their underlying loci in fores trees: theoretical predictions and experimental results. p 59-75
This special issue of Annales des Sciences Forestières comprises presentations made at the first conference of the IUFRO working party "Genetics of oaks". Despite their economic and social importance and world-wide distribution, oaks had received at that time very scanty attention regarding genetics. The objectives of the conference were to review the pioneering research results, to present current research projects in oak genetics in different countries, and to discuss opinions on controversial issues. The conference and proceedings were divided in 5 sections: Taxonomy and interspecific variation, Hybridization and sexual reproduction, Intraspecific variation, Vegetative propagation, Tree improvement.
I chaired the working party, and organized the meeting. This was also the opportunity to make a review of our first results regarding the distribution of genetic diversity in European oaks on the basis of isozymes, and the very first results with DNA markers.
Kremer A., Savill PS, Steiner KC 1993. Genetics of oaks. Annales des Sciences Forestières 50, Suppl 1, 1-472
Kremer A., Petit R.J. 1993 Gene diversity in natural populations of oak species, Annales des Sciences Forestières, 50, Suppl 1, 186s-202s
Daubree J.B., Kremer A. 1993. Genetic and phenological differentiation between introduced and natural populations of Quercus rubra L. Annales des Sciences Forestières, 50, Suppl 1, 271s-281s
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This book is one of the very first review on genetic diversity of European trees at a continental scale using genetic and molecular markers available by the late 1980s (terpenes, isozymes, RFLPs). The review builds on the invited presentations to a workshop that was organized in 1990 at the University of Gottingen. After a series of technical introductions regarding the different maker technologies available at that time, results of genetic surveys are shown for major European broadleaves (beech, oaks, chestnut) and conifers (Norway spruce, Silver fir, Scots pine and Maritime pine). The books closes with two applications of markers techniques in breeding operations.
We made a comparative analysis of the distribution of genetic diversity at tne nuclear and organelle, and showed for the first time the contrasting outcome of population differentiation at these two levels.
Müller-Starck G., Ziehe M. 1991. Genetic variation in european populations of forest trees. Sauerländer's Verlag. 271 p. ISBN 3-7939-0790-2
Kremer A., Petit R.J., Zanetto A., Fougère V, Ducousso A, Wagner D, Chauvin C Nuclear and organelle gene diversity in Quercus robur and Q. petraea. p 141-167
Northern red oak (Quercus rubra L.) is an exotic species in Europe, which has been widely planted across the continent since its first introduction at the end of the 17 th century. Before it became considered as an invasive species. During the late decades of the last century, it was the first broadleaved planted species in France. Its widely use stimulated research about the seed sources to be used and the silviculture to be applied for the species. The monography published by INRA was collective effort of tree secientists to assembel the existing knowledge on the issues, and the research going on in silviculture, ecology, physiology, pathology and genetics. I contributed to the editing, translated chapters of american colleagues, and authored research articles that I conducted on Quercus rubra.
Timbal J., Kremer A., Le Goff N., Nepveu G. 1994. Northern red oak (in french). INRA editions. 564 p. ISBN : 2-7380-0479-2
Kremer A., Daubree J.B., Jung Müller B. Genetic diversity of introduced populations in France (in french) p 25-45
Timbal J., Kremer A. Botanical, morphological and biological characters of Northern Red oak (in french). p 45-53
Kremer A., Daubree J.B. Mating system and gene flow (in french). p 417-425
Kremer A. Genetic improvement of Northern red oak in France (in french). p 424-443
This Special Issue of "Revue Forestière Française" is entirely dedicated to forest tree improvement encompassing topics ranging from theory of selection to practical application as production of reproductive material in seed orchards or by vegetative reproduction. On the theoretical level, it goes from basic concepts in artificial selection, to breeding strategies, and to improvement goals. At the applied level, it covers examples of tree improvement programmes in temperate and tropical species, deployment methods and consequences in silviculture and management. The issue adopts purposely a popular science approach making concepts and methodological issues accessible to a large public.
Kremer A. 1986 Variation of the genotypic expression (juvenile-mature correlation, and genotype-environment interaction). A quantitative and mechanistic approach (in french). Revue Forestière Française, 38, Special Issue, 40-48
Kremer A. 1986 Selection methods and strategies (in french). Revue Forestière Française, 38, Special Issue, 89-100
Kremer A. 1986 Chêne rouge d'Amérique (in french). Revue Forestière Française, 38, Special Issue, 165-167
This is how the editors introduced the book. in 1985. "In many parts of the world we are witnessing the change of the forest tree to a cultivated plant, probably the most recent domestication process of the plant world. In this process risks are taken and mistakes are made, but as can be expected when we start from fundamentally wild forest tree populations yield increases per unit area have often been very large. In domesticating trees we must be aware of the considerable risks taken in order to increase yields. To some extent yield increases are inevitably gained at the expense of ecological stability".
I contributed to this debate by using a component approach, by subdividing a complex trait as growth into numerous additive and multiplicative components, taking as an example pine growth. The results show that components do not contribute independently to the integrative traits, but trade offs and compensation occur along the path. Methods are proposed to measure the degree of compensation.
Tigerstedt P.M.A., Puttonen P., Koski V. (eds) 1985. Crop physiology of forest trees. Helsinki University Press. 336 pages. ISBN 951-45-3705-X
Kremer A. Componenet analysis of height growth, compensation between componenets, and seasonal stability of shoot elongation in maritime pine (Pinus pinaster Ait.) p203-218