Excerpts of the Minutes of the ANR-BIOADAPT FLAG Kickoff meeting

Transcription

1 Excerpts of the Minutes of the ANR-BIOADAPT FLAG Kickoff meeting Avignon, France, January 2013

2 Table of contents Excerpts of the... 1 Minutes of the ANR-BIOADAPT FLAG Kickoff meeting... 1 Schedule for joint FLAG/TipTree meeting in Avignon... 3 Project and partner presentations... 5 Technical workshops... 5 Genotyping workshop... 6 Phenotyping workshop... 7 Modelling workshop... 8 Executive meeting Sampling strategy Measurements of environmental variables RTEs Paper writing workshop Paper Paper Paper

3 Schedule for joint FLAG/TipTree meeting in Avignon The FLAG Kick-off meeting has been held jointly with the TIPTREE Kick-off meeting. Tuesday 15/01 (Plenary, URFM room Belvedère) 9h30 Ivan Scotti : Presentation of FLAG project (INRA-KOUROU) 10h00 Sylvie Oddou-Muratorio : Presentation of TipTree project (INRA- AVIGNON) 10h30 Ophélie Ronce: EVORANGE project : aims and main results (ISEM) 11h15: break 11h45 Santiago González-Martínez: Results of the LINKTREE project- Ecology meets genetics (INIA-CIFOR) 12h30 Bart Muys: Presentation of EFIMED and experience with forest management scenarios and stakeholder involvement (EFIMED) 13h00: lunch 14h00 Jean-François Dhôte : Climate change and research needs for public forest management (ONF) 14h30 Frank Schurr: Data-driven models of eco-evolutionary dynamics in forest trees (ISEM) 15h00 Hendrik Davi : Local adaptation to climatic gradients: application of a Physio-Demo-Genetics simulation model to European Beech populations (INRA- AVIGNON) 15h30 Myriam Heuertz : The scale of genetic structure and adaptation in a widespread tropical tree, Symphonia globulifera (INIA-CIFOR) 16h00 Rosane Collevatti: Geographical Patterns in Neutral, Quantitative and Adaptative Genetic Variation in Cerrado Tree Species (Universidade de Goiás) 16h30: break+ photo 17h00 Ivan Scotti : Molecular and quantitative genetics of local adaptation in tropical trees 17h30 Delphine Grivet, Giovanni Vendramin: Adaptive variation, environmental gradients and demography in Pinus pinaster and Pinus halepensis (INIA-CIFOR & CNR-FIRENZE) 18h00 Arndt Hampe: PERSisting at the LIMit: Genetic structure, hybridization and performance of Quercus robur at the species southwestern range margin Wednesday 16/01 Morning - plenary, URFM room Belvédère 9h00 Sascha Liepelt, Bruno Fady, Giovanni Vendramin: Genetic variation in candidate genes of Abies alba along ecological gradients (UNI-MAR, CNR- FIRENZE, INRA-AVIGNON) 9h30 Thomas Källman: Genetic and phenotypic diversity in experimental populations of Picea abies from Sweden (UNI-UPSALLA)

4 10h00 Lars Opgenoorth, Giovanni Vendramin : Description of experimental plots, sampling design and selection of candidate genes in Picea abies in Germany and Italy (UNI-MAR, CNR-FIRENZE) 10h15 François Lefèvre: Considering evolutionary processes in adaptive forestry (INRA-AVIGNON) 10h45: break 11h15 Hadrien Lalagüe : Looking for signature of adaptation over short-scale spatial climatic gradient: an experimental genomic and simulation approach in Fagus sylvatica (INRA-AVIGNON) 11h40 Sylvie Oddou-Muratorio: Adaptive potential of a drought-prone Fagus sylvatica population 12h00: Introduction of the technical workshop 13h00: lunch Wednesday 16/01 14h00-16H00: Technical workshops (Small groups) 1) Genotyping and sequencing activities (Room Belvédère)- Moderators: Ivan Scotti, Bruno Fady 2) Functional traits (Room Ventoux)- Moderator: Hendrik Davi 3) Modeling activities (Room PSH)- Moderators: Frank Schurr, Sylvie Oddou- Muratorio 16h00: break 16h30-18h00 Side meetings Harmonization of experimental activities within species Abies alba: UNI-MAR, CNR-FIRENZE, INRA-AVIGNON Picea abies: UNI-UPSALLA, UNI-MAR, CNR-FIRENZE Pinus sp: INIA-MADRID, CNR-FIRENZE, INRA-AVIGNON Tropical species: INRA-KOUROU, Universidade de Goiás, INIA-MADRID Other topics (ongoing ANR projects..) 20h00: dinner at Le Petit Louvre Thursday 17/01 -Plenary, room Belvédère 9h00 Synthesis of the technical workshops (one representative of each workshop) 10h00: Integrative workshops to connect the different experimental, modeling and stakeholder activities (1) Harmonization of experimental activities AMONG species (Moderators :Beppe Vendramin, François Lefèvre) 11h00: break

5 (2) Connections between experimental results/issues and modeling approaches (Moderators: Santiago González-Martínez, Ophélie Ronce) (3) Stakeholder engagement and connection between biological models and scenarios of adaptive sylviculture (Moderators : Bart Muys, Bruno Fady). 13h00: lunch 14h00 FLAG: executive meeting (1) decisions to be taken (2) timing of the task 15h00 Tiptree: executive meeting (1) decisions to be taken (2) timing of the task 16h00: break 16h30-18h00 Side meetings Friday 17/01 9h00 - plenary, room Belvédère Writing workshops * List of possible topics for common papers to be produced during FLAG/tipTree projects 1- Synthesis papers Concept paper on local adaptation Variation of selection gradient on functional traits from juvenile to adult stage Synthesis on heritability, genetic and environmental correlations for functional traits 2- Research papers Efficiency of genotyping/sequencing approaches (RADseq?) Respective importance of directional vs stabilising selection in tree populations 13h00: lunch, and of the meeting Project and partner presentations Nineteen talks have been given, with the aim of showing the aspects of each partner s research that converge upon FLAG objectives. Project and partner presentations have been merged into a zip file (Presentations_KOM-Avignon-2013.zip) and distributed by Bruno Fady (see his message of January 21). The file is however no longer on the website but is available from Ivan Scotti upon request. Technical workshops Three technical workshops have been held to discuss methodological choices to be made in the project ( beyond the general project plan, which is not modified):

6 genotyping, phenotyping and modelling. The participants to each workshop have focussed on the need to establish common methods for genotyping and modelling and a set of common phenotypic traits to apply to all species. Genotyping workshop Three main topics are addressed: (a) best strategy to apply next-generation genotyping; (b) how to make use of available genomic resources (c) how to efficiently make the link between tasks 2,4 (detection of selection) and task 5 (association mapping). (a) The strategy chosen for Task 1 (genotyping in natural populations for the detection of loci under disruptive selection) is to genotype in pools. The alternative option use of individual samples is discussed, because of potential problems with unequal representation of individuals within pools (unequal representation of pools in a run is less of a problem here because we do not crosscompare pools). Allelic frequency differences among populations (rangewide, landscape-scale gradients and cohorts). Thus we need allelic data from individual genotypes (but info on frequency needed at population level). Thus we could generate data with pooled individuals (but problem with statistical power? Problem with accessing reliable frequency data, yes, but good data has been provided in the literature from pools of 10 individuals with AFLP). Anonymous strategy is fine, but we could also go candidate gene approach. In case no signature of disruptive selection is detected locally (i.e. in samepopulation subdivision tests), a fall back proposal is made: to sample ecotypically different, geographically distant populations (this will require independent analyses to take into account demographic history of populations). Moreover, it is recalled that adaptive traits are mostly multilocus, so use of available methods that test differentiation at several loci together is recommended. It is equally important not to drop good candidate genes (known to have a function in the response to the targeted ecological gradients) that may show weak signatures of selection. (b) For several species, it is possible to rely on existing resources (from LinkTree etc.) and develop more markers in addition to what will be generated from the FLAG Rad-seq. The partners are welcome to make use of available genomic resources for all Tasks whenever they feel it useful for answering the Project s questions, and they can use their own budget for this action, provided that this does not prevent them from realising the project globally. It is however stressed that the added value of multiple species is generalization of conclusions on adaptation (nb and proportion of loci under selection, type of genes under selection, type of optimum phenotypes under varying environmental constraints, etc). Such cross-species and cross-environment comparisons are only feasible if all species are treated equally.

7 (c) The project s original rationale is to first identify loci under divergent selection (task 3) and then test whether these loci are associated to functional traits (Task 5). However, given that for some species genomic resources are available (see (b)), there might be no need to temporally and conceptually strictly link tasks 3 and 5. Tasks 2-3 should be carried out for all species (see (b)), but task 5 can be carried out independently. [...] Phenotyping workshop [ ] Main conclusions of the workshop [C1] We have to distinguish traits that are expected to be directly related to fitness (e.g. radial growth, survival, seed production; the so-called performance traits ) from traits under selection in a given environment (e.g. resistance to drought, cavitation, phenology of budburst, etc; functional traits ). Performance traits have to be measured over all sites and all species if possible, whereas the functional traits to measure may be specific of the environmental gradient and of the species. [C2] Making a lot of measurements can be time consuming. Consequently, perhaps relative values of traits, not absolute quantitative value (for instance not an exact account of cones number) can be sufficient. [C3] Some traits are easier to measure that others: The performance traits for seedlings are easy to measure: survival and height growth. Performance traits for adults are more complicate to measure, as mortality rate and tree fertility are often related to diameter and past growth, a measure of age, past tree ring increment and diameter is the minimum. The estimation of fertility is obviously also useful but due to masting behavior, we need several years of measurements or use a proxy of average fertility (scares of cones on branches for instance). Two performance traits currently lack in our measurements: the seed mass and seed quality that clearly control the rate of germination. It is easy to measure and we have to add it. An important functional trait is phenology, which can be measured on adults and on seedlings. When drought drives the environmental gradient, leaf traits have to be measured on adults, but on seedlings we have to add roots investment estimation that requires destructive measurements. We can also collect branches on adults and send them to wood platform in Biogeco to assess cavitation vulnerability using CAVITRON (see with Biogeco). Finally, the impact of climate variations on trees can be assessed through tree ring increment and measurement on mean sensitivity to climate.

8 Some guidelines for measurement in the field: Collect as much environmental data as possible, at plot and individual level, those data that make sense for the traits that are under consideration. Include measures of the environment: climate, but also competition (i.e. density). Identify environmental gradients that actually have an effect on the selection gradient. Keep in mind that added value of multiple species is generalization of conclusions on adaptation (nb and proportion of loci under selection, type of genes under selection, type of optimum phenotypes under varying environmental constraints, etc). In the wet tropics, there might be difficulty in finding adaptation to drought. Perhaps it is adaptation to water-logging that should be targeted. Keep in mind that measured traits may be under selection in a different way depending on age. There may be different genetic correlations between traits depending on age. Trees at different ages may not be in the same environment (/ not have the same niche) although they are in the same place. Three proposals: The first one is to collect phenotypic data already available in worldwide TRY database to assess the variations of these traits between populations and across environmental gradient. The second proposal is quite challenging. It consists in creating a common seed bank of TipTree and FLAG projects. The seeds can be collected this summer, common measurements of seed mass and seeds quality can be achieved and then a common garden can be planted. One ancillary possibility is to take a sample of this material to assess impact of stresses. Some facilities can be provided from ANAES services French projects. [ ] We envisaged three altitudes, 10 mothers per altitude 30 seedlings per seed tree. For fitness proxy, it is not the solution. Association in situ or cross transplantation will be more useful. The third proposal can be a common collect of cores for tree ring increment and branches for cavitation on adults of several sites. Two things, we have no discussed about, what about the saplings and what about the link that can be made between adults and seedlings. Common garden under greenhouse is maybe the only way to avoid the impact of the change of light environment between seedlings and adults and between seedlings in different situations. What about herbivory? Modelling workshop [C1] A rapid overview of the state of the art regarding the species included in TipTree project (Table 1). Those six species correspond to large number of different study cases from a modeling perspective, even if the targeted

9 scenario (the most interesting to investigate) is common for most of them and relate to persistence under CC (ie demographic collapse) [C2] [ ] [C3] Moreover, an important issue is to what extend the models developed should be species-specific (aiming at providing realistic scenario for the evolutionary dynamics under CC). Alternatively, general model could be developed (two last lines in Table1), with the objective of providing a better understanding of adaptation in age-structure populations. [C4] The way experimental data (in particular genomic data) can be incorporated into models need to be refined (see discussion below on genetic architecture). [C5] Note that a major outcome of the modeling activities is to assist the choice of the functional traits critical for the targeted scenario. However, it poses organizational challenges (timing of the WP)

10 Table 1 : For each species included in TipTree project, modeling tools available of under developments, targeted scenario to be studied Species Model available * Scenario Region/Scale Data within TipTree Fagus sylvatica CASTANEA, PDG, PHENOFIT Persistence under increasing temperature Mont Ventoux demography and drought Abies alba CASTANEA, (PDG) Persistence under increasing temperature and drought Pinus halepensis Quercus robur Picea abies Eperua falcata General strategic model General strategic model CASTANEA, PHENOFIT (will be done by Isabelle Chuine) General model for evolution of serotiny (Tonnabel et al J.Ecol) NOTG (for carbon stocks) CASTANEA, PHENOFIT CASTANEA will be parameterized by Hendrik Persistence under increasing fire frequency Persistence under increasing drought Phenological responses to climate change, Demographic Persistence under increased drought and increased flooding Persistence and expansion under climate change Phenological responses to climate change Mont Ventoux & 2 other gradients W part of range (Italy, France, Spain) Extremadura Entire European range Guyana demography, seed dispersal, lots of quantitative genetics General discussion Genetic architecture of the traits is expected to make big differences in evolutionary dynamics under CC (in particular for the evolution of genetic variances) ; see Gomulkiewicz, R., Holt, R.D., Barfield, M., & Nuismer, S.L. (2009) Genetics, adaptation, and invasion in harsh environments. Evolutionary Applications, 3,

11 Include environmental models where variation is not clinal, but patchy (e.g. in Medit. species) and population models with low effective population size (e.g. above (= low drift effect) and below 100). Silvicultural scenarios need to account f or landscape changes, including land use changes (importance in Tropics). Link with other projects which deal with forest management. Project MOTIVE includes a database of climate scenarios. Couple models from Linktree with those in MOTIVE that output ecosystem services (and decision support). Include uncertainty in scenarios and communication of decision support (not really the case in MOTIVE) How can the no regret options be defined? No regret options might mean scenarios where outcomes are acceptable for society (including forest managers). Use scenarios that can be used for education of forest managers and policy makers. Include social considerations in scenarios (as social representations of forests are usually the first impediment to change). Natural regeneration is the cheapest and easily done option for forest management (in France). Include specific ecosystem services (that may differ regionally) in the scenarios. Climate change is often not believed to be happening by numerous foresters. Executive meeting Sampling strategy. For Tasks 2-3, sampling strategy will consist of two gradients wherever possible, with two extreme sub-populations sampled in each. Twentyfive individuals, as unrelated as possible, should be collected. A spatially structured sampling scheme, with a Vitruvian man shape, is suggested by Myriam Heuertz. This sampling scheme allows both efficiently sampling population diversity and efficiently studying Spatial Genetic Structure (see figure 1). To grant that all distance classes are covered, while under the constraint of a sample size of 25 trees, it is suggested that trees are mostly sampled in the body, arms and legs of the plot, plus few scattered trees on the outer circle.

12 Figure 1. Leonardo da Vinci s Vitruvian man and Myriam s sampling scheme [...] It is suggested to make more at least two libraries with different enzymes for increasing alignment potentials (this needs to be checked). It is also stressed that, since loci under selection identified by RAD are to be used to design SNP genotyping experiments in task 5, there must be sufficient sequence length on both sides of each SNP to accommodate primer design; therefore, attention will have be paid to the average length of sequenced RAD tags. Measurements of environmental variables: at least crude characterisation of soil texture and depth as well as topography (see this with the experts); Measurements at the individual level: competition index, wood cores, soil samples, vegetation cover in 1 sq m plots, slope, orientation of slope, diameter and height, health and ontogeny index (adventitious roots and pneumatophores for Symphonia). [...] RTEs: Should we use half-sib families or unrelated seedlings? Unrelated seedlings are comparatively superior for association mapping; however, in many cases RTEs have already been established and will be used as-is. [...]

13 Paper writing workshop Three papers are considered as useful/central for the project, and will be planned for writing in year Paper 1 Micro-environmental adaptation: there is room for a paper on this, different from the classical local adaptation papers. Also look at the temporal aspect (seedling banks, seed banks) as a way to escape bad conditions. Overlapping generations: little work on it, except in CAPSIS. Overlapping generations slow down drift (simulations made by Myriam with Olivier Hardy). Nevertheless, overlapping generations seem to have little effect on Ne. Make the scope very clear. Associate this to a review on within-population and between-populations distribution of diversity for both markers and traits, as a function of life-history traits or other traits. The question would be why there is so much variation if it is maintained by selection, this is a thing to look at. Correlation between the diversity of environment a population lives on and the genetic diversity of traits. Description of plots with environmental and phenotypic variation. Santi, Myriam, Ivan and Sylvie set the general topics. Postdoc 1 (see Executive meeting) will take this in charge. Then there will be a writing workshop to wrap it up. A collection of relevant literature will be gathered and distributed among partners. The reference list will be posted on the project s website ( Paper 2 Meta-analysis of local adaptation: there is room for a meta-analysis paper on patterns of altitudinal variation and genetic diversity in plants. Rosane, Bruno and Katy take care of this. Paper 3 Variation of selection gradients and response to selection across ontogenetic stages: General topic : There is a room for a synthesis paper dealing with the variation in selection patterns acting at different life-stage of long-life species. It is important to consider both the variation of selection gradient together with the variation of quantitative genetic parameters shaping response to selection. It is also important to consider that both environment and ontogenic stages vary between adult and seedlings stage. So the broad topic of this synthesis paper could be Synthesis on heritability, genetic and environmental correlations for functional traits across life-stage

14 Remark: how far this issue may be connected to the niche theory: is there different niche between niche at adult stage and juvenile stage Contents : The synthesis should include results of breeding program and what they can learn: how a trait at early stage relates to trait at adult stage responsiveness to selection; evolvability. Note that literature biased in favor of species with little age difference at juvenile and adult stage (fast-growing tree). There is a magic figure in the literature: correlation >0.8 for trees after 12 years old. Consider the problem of maternal effects. Inbreeding issue: Francois, Sylvie, Hendrik, set the general topics. Katy Csillery (TipTree Post-doc a URFM) will take this in charge. Need/opportunity to associate colleagues working with fishes.