Molecular tools to assess genetic diversity: Examples. from temperate and tropical forests. Reiner Finkeldey. Freiburg, Workshop Oct 2009

Transcription

1 Freiburg, Workshop Oct 2009 Molecular tools to assess genetic diversity: Examples from temperate and tropical forests Reiner Finkeldey 1

2 Outline/objectives 2 Presentation for workshop Objectives (here: conservation) and methods Role of molecular methods in conservation and biodiversity research Neutral markers; case studies and examples Quercus in Romania Hagenia in Ethiopia Blighia in Benin Final considerations and conclusions Muammar Gaddafi speaking more than 90 minutes to the United Nations General Assembly, Sept magnifier_pos-2.html

3 Conservation and molecular markers Conservation of genetic diversity will remain empty talk until we begin to understand how the diversity we wish to conserve is distributed in space (BAWA and KRUGMAN, 1990). Limitations of marker-based studies Neutral markers Relation to important (adaptive) traits? No knowledge for most endangered taxa! 3 Map of CpDNA haplotypes of Hagenia abyssinica in Ethiopia

4 Population genomics in conservation genetics Search for functionally important diversity Relation to adaptive traits E.g. climate change (Relation to traits of economic importance) Links between tree improvement and conservation Genomic resources needed Focus on model taxa Populus, Pinus, Eucalyptus, (Quercus),??? 4 (Tuskan et al., 2006)

5 Some limitations of population genomic approaches in conservation genetics of forest trees Complete amino acid sequence of Dhn3 in oaks and 3D structure of the enzyme (Vornam et al., in prep.) Phenotyping of long-living trees can be challenging Selection of important traits depends on environment Preliminary results Small effects of single genes Candidate gene approach risky Focus on model taxa limits development of genomic resources for endangered non-model species With insertion EMBL Acess No: AM Without insertion EMBL Acess No: AM

6 Genetic inventories with neutral and adaptive genetic traits Evolutionary factors past Mutation Migration/ Gene flow Mating system Drift Selection Neutral markers Genetic inventories Genetic variation within populations among populations present 6 Adaptive genetic diversity Evolutionary adaptive potential future

7 Genetic inventories at neutral markers Are results relevant for conservation genetics? Hybridizing oaks (Quercus spp.) in Romania Hagenia abyssinica in Ethiopia Blighia sapida in Benin 7 Quercus robur; Thomé (1885)

8 Curtu, A.-L., Finkeldey R. and Gailing O. (2004). Comparative sequencing of a microsatellite locus reveals size homoplasy within and between European oak species (Quercus spp.). Plant Molecular Biology Reporter 22: Example I: Hybridization among oaks Section Quercus Q. robur Nutrient-rich, wet soils Q. petraea Well-drained, more acid soils Q. pubescens Xerophile Q. frainetto Xerophile-mesophile Section Cerris Q. cerris Xerophile Bejan Forest (45 51 N, E), Carpathian mountains in westcentral Romania (Curtu, 2006) 8

9 Case study 1: Evolutionary biology of oaks Curtu, A.L., Gailing, O., Finkeldey, R. (2007). Evidence for hybridization and introgression within a species-rich oak (Quercus spp.) community. BMC Evolutionary Biology 7: 218 Example I: Hybridization among oaks 9 Morphologically intermediate trees are indicated with numbers and arrows

10 Case study 1: Evolutionary biology of oaks Curtu, A., Gailing, O., Leinemann, L., Finkeldey, R. (2007). Genetic variation and differentiation within a natural community of five oak species (Quercus spp.). Plant Biology 9: Example I: Hybridization among oaks Six nuclear microsatellites, seven isozymes Low to moderate differentiation at most loci Strong allele frequency differences at some loci 10

11 Case study 1: Evolutionary biology of oaks Curtu, A.L., Gailing, O., Finkeldey, R. (2007). Evidence for hybridization and introgression within a species-rich oak (Quercus spp.) community. BMC Evolutionary Biology 7: 218 Example I: Hybridization among oaks robur pubescens petraea frainetto 11 Software STRUCTURE; Pritchard et al. (2000)

12 Case study 1: Evolutionary biology of oaks Curtu, A. L., Gailing, O., Finkeldey, R. Pollen-mediated gene flow and hybridization in a mixed forest of oak species (Quercus spp.). In prep. Example I: Hybridization among oaks Investigation of progenies from 8 seed parents Example: seed parent no. 251: Q. pubescens 31% external pollen 10 successful parents within stand No. 5: putative F1 hybrid pubescens x robur No. 111: putative F1 hybrid pubescens x petraea Evidence for Introgression 12

13 Curtu, A. L., Gailing, O., Finkeldey, R. Pollen-mediated gene flow and hybridization in a mixed forest of oak species (Quercus spp.). In prep. Example I: Hybridization among oaks Introgressive Generation F 1 forms Total 1 Sample size Percentage (%) Adult trees Offspring

14 Curtu, A. L., Gailing, O., Finkeldey, R. Pollen-mediated gene flow and hybridization in a mixed forest of oak species (Quercus spp.). In prep. Example I: Hybridization among oaks Q. petraea Q. pubescens Q. robur Q. frainetto 14

15 Example I: Hybridization among oaks Asymmetrical gene flow Hybridization and introgression confirmed Species identity maintained by Asymmetrical gene flow Selection against (most) hybrids and intermediates; outbreeding depression Maintenance of different adaptive properties of species Enhancement of adaptive potential by (rare) hybridization Q. petraea Q. pubescens Q. robur Q. frainetto Introgressive Generation F 1 forms Total Selection against hybrids Sample size Percentage (%) Adult trees Offspring

16 Example II: Genetic variation of Hagenia in Ethiopia Material 25 populations (all known in Ethiopia) Investigation of Phenotypic diversity Leave traits Dendrometric traits cpdna haplotypes AFLPs 16

17 Example II: Genetic variation of Hagenia in Ethiopia 17

18 Example II: Genetic variation of Hagenia in Ethiopia spatial distribution of cpdna haplotypes and variation at AFLPs AFLPs H T : F ST : H j : PPL:29.9% 90.7% SM 18 Taye et al. Plant Syst Evol (2009)

19 Example II: Genetic variation of Hagenia in Ethiopia In situ conservation priority areas Ex situ conservation priority areas Priority populations for domestication 19

20 Example III: Blighia sapida (Sapinadaceae) in Benin 20

21 Example III: Blighia sapida in Benin Agroforestry systems Evergreen and late successional Homegarden...

22 Example III: Blighia sapida in Benin Type Stand Sample size Field/ Fallow AFLPs/nSSR s cpssrs N Dali Segb Kandi Bouk Touk Para Glaz Sava Total Forest Pene Bass Adja Zogb Pobe Methods Phenotypic traits dendrometric traits fruit traits AFLPs 375 fragments nssrs 4 polymorphic cpdna haplotypes 1 polymorphic cpssr locus 22 Agon Total Ekue et al. (2009a, 2009b, in prep.)

23 Example III: Blighia sapida in Benin Touk Segb Bouk NDali Pene Bass Sava Adja Zogb Pobe Agon Kand Para Glaz Nei s div: AFLPs H E : nssrs bp 40.8 % 135 bp 44.1 % 145 bp 15.1% ccmp7 haplotypes Field/Fallow stand Forest stand Frequency

24 Example III: Blighia sapida in Benin AFLPs Forest stands Field/Fallow stands P Value % Forest Br ns PPL ns H J ns nssrs A R ns H E ns 24 Br : Band richness; PPL : Percentage of polymorphic loci; H J : Nei s gene diversity; A R : Allelic richness; H E : Expected heterozygosity

25 Example III: Blighia sapida in Benin Stand F ST values nssrs AFLPs 6 forest field/fallow All

26 Example III: Blighia sapida in Benin Main results Significant correlation spatial/genetic distance different origin of field/fallow stands in NE AFLP: R = 0383, P < nssr: R = 0.199, P < 0.05 AFLP nssr - Fst) no indication of losses of diversity in field/fallow stands Fst / ( Implications for participatory approaches in conservation; farmer-led domestication Ln (Geographic distance)(km) 26

27 Final remarks, conclusions Methods Out-dated or state of the art? Appropriate for particular question/hypothesis drift, reproduction system (incl. hybridization) Selection, (local) adaptation Mix of methods! Most economical solution 27 SNPs (Gibson and Muse 2004)

28 Final remarks and conclusions Automation potential of new marker types (e.g. SNPs) must not be overlooked Detailed information on population structures irrespective of function of observed variation Potential use of SNPs also as informative neutral markers Potential of new technologies for non-model species e.g. 2nd generation sequencing technologies recognized, but must be exploited Genes mirror geography in European humans: Investigation of > SNPs in more than Europeans (Novembre 2008) 28 (Novembre 2008)

29 Final remarks, conclusions Approx flowering plants Threats to global biodiversity (including forest genetic resources) Land use change Ecosystem (forest) degradation Mainly in the tropics Climate change 29

30 Thanks to Lucian Curtu (Quercus spp.) 30 Taye Bekele (Hagenia abyssinica) Marius Ekué (Blighia sapida)

31 Thank You for Your attention! 31 Fidel Castro, record holder: 4 hour 29 minutes at UN general assembly