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Genetic diversity analysis of CWR in Portugal

Genetic diversity analysis of CWR in Portugal. Joana Magos Brehm, Brian V. Ford-Lloyd, Nigel Maxted , Maria Amélia Martins-Loução. Joint PGR Secure/ECPGR workshop: Conservation strategies for European CWR and LR diversity 7–9 September 2011, Palanga, Lithuania. OVERVIEW.

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Genetic diversity analysis of CWR in Portugal

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  1. Genetic diversity analysis of CWR in Portugal Joana Magos Brehm, Brian V. Ford-Lloyd, Nigel Maxted, Maria Amélia Martins-Loução Joint PGR Secure/ECPGR workshop: Conservation strategies for European CWR and LR diversity 7–9 September 2011, Palanga, Lithuania

  2. OVERVIEW • Aims of this study • National approach • Genetic diversity study • Selection of populations for conservation • Relevant points and conclusions

  3. AIMS OF THIS STUDY • To evaluate the genetic diversity and population genetic differentiation of priority species throughout its distribution area in Portugal as a means of obtaining genetic baseline information for future conservation. • To use genetic, demographic and threat data in order to prioritise populations for conservation.

  4. NATIONAL APPROACH: PORTUGAL Economic value Ex situ conservation In situ conservation Global distribution Threatened category National distribution Legislation Native status 20 priorities 2262 CWR Priority species Inventory Prioritisation at species level - 8 criteria, 4 methods-

  5. NATIONAL APPROACH: PORTUGAL Dianthus laricifolius Boiss. & Reut. subsp. marizii (Samp.) Franco Allium victorialis L. Dianthus cintranus Boiss. & Reut. subsp. barbatus R. Fern. & Franco 20 priorities Dianthus cintranus Boiss. & Reut. subsp. cintranus Priority species Ecogeographic survey Field work

  6. NATIONAL APPROACH: PORTUGAL Amplified Fragment Length Polymorphism (AFLP) Genetic data Priority populations Demographic data Threat data Dianthus cintranus Boiss. & Reut. subsp. barbatus R. Fern. & Franco Priority species Prioritisation at population level

  7. Genetic diversity study 1. Dianthus cintranus Boiss. & Reut. subsp. barbatus R. Fern. & Franco

  8. Dianthus cintranus subsp. barbatus • Related crop:carnations (ornamentals) • Habitat:outcrops, mainly limestones • Global distribution:Portugal • National distribution:5 provinces • In situ conservation: not active but part of its distribution occurs within conservation areas • Ex situ conservation:none • Legislation:none • IUCN category (2001): Endangered (EN) • Threats:low precipitation, fires, invasive species, construction, trampling, grazing, trash deposition

  9. Dianthus cintranus subsp. barbatus • breedingsystem? • Dianthus spp. mainly insect‐pollinated (beetles, bees, butterflies, moths…) • some inbreeding in Dianthus spp. • some Dianthus spp. are facultative outbreeders • seed dispersal mechanisms? but seed release by the wind • genetic diversity?

  10. Geneticdiversitystudy 2. Methodology

  11. Amplified Fragment Length Polymorphism (AFLP) • 5 populations, 20 plants/population • 2 selective MesI and EcoRI primer pairs • loci 56-440 bp

  12. Genetic data analysis Population structure and differentiation: • Wright’s FST (1951) - Lynch & Milligan (1994) • dendrograms - agglomerative hierarchical clustering using UPGMA • PCoA • AMOVA - based on Euclidean pairwise genetic distances • Bayesian clustering method - for cross-breeders and where isolation by distance not detected Descriptive stats: • allele frequencies - Bayesian approach suggested by Zhivotovsky (1999) • % polymorphic loci/population • genetic diversity - Lynch & Milligan (1994) for dominant markers • # private alleles Isolation by distance: • Mantel test [pairwise FST transformed to FST/(1‐FST) versus log‐transformed geographic distance] (GENALEX v. 6.0)

  13. Dianthus cintranus subsp. barbatus Natura 2000 sites Dcb2 Dcb3 Dcb4 Dcb5 Dcb1

  14. Dianthus cintranus subsp. barbatus Descriptive stats • total genetic diversity: Ht=0.163 (moderate) • genetic diversity within populations: Hw=0.152 • inter‐population genetic diversity: Hb=0.006 Dcb2 Dcb3 ↑Hj=0.170 ↑PL=53% PA=3% Dcb3 Dcb4 Dcb5 Dcb1 Dcb5 ↓ Hj=0.149 ↓ PL=46% ↓ PA=2% OUTBREEDER

  15. Dianthus cintranus subsp. barbatus Population genetic structure and differentiation AMOVA (Analysis of Molecular Variance): Among populations: 8% Within populations: 92% Dcb2 Dcb3 Dcb4 Dcb5 Fst = 0.038 => populations are little genetically different Dcb1 OUTBREEDER

  16. 671 978 1000 Dianthus cintranus subsp. barbatus Isolation by distance Dcb3 Dcb1 Dcb2 NO GEOGRAPHIC PATTERN Dcb3 Dcb2 Dcb4 Dcb5 Dcb1 Mantel test => NO ISOLATION BY DISTANCE (no restriction to geneflow) Dcb4 Dcb5

  17. Dianthus cintranus subsp. barbatus Dcb2 Dcb3 Dcb4 Dcb5 Dcb1 GENETICALLY VERY HOMOGENOUS!

  18. Selection ofpopulationsfor conservation 1. Criteria used

  19. Criteria DEMOGRAPHIC DATA: population size THREAT DATA : number of threats GENETIC DATA: • genetic diversity (measure of molecular diversity) • # polymorphic alleles (measure of genepool richness) • # common (population frequency >0.05) and localised alleles (in <50% of populations) (modified from Marshall & Brown 1975) • inter‐population genetic distance (measure of how similar populations are)

  20. Integration of all data • Standardisation to 1, integrated in a sum per population and transformed into % using the highest score as the reference value of 100% • Priorities: populations with higher % (Delgado et al. 2008)

  21. Selectionof populationsfor conservation 2. Results

  22. Integration of all data

  23. Dianthus cintranus subsp. barbatus Ex situ and in situ: Dcb3! Dcb3 (Condeixa-a-Nova) ↑Hj=0.170 ↑D=0.005 ↑PL=53% PA=3% ↑#cl=37 <50 plants Unknown threats Outside conservation area Dcb2 OUTBREEDER Dcb3 Dcb4 Dcb5 Dcb1

  24. Relevant points and conclusions

  25. Neutral versus adaptive diversity • Correlation between neutral and adaptive diversity? Genetic diversity = evolutionary potential of a species to evolve and adapt to a changing environment • ADAPTIVE DIVERSITY • evolution • reflects the species potential ability to adapt to changing environments • NEUTRAL DIVERSITY • migration, mutation, genetic drift… • no direct effect on species fitness • not affected by natural selection

  26. Conclusions • AFLP successfully used to obtain genetic baseline information on priority CWR: D. cintranus subsp. barbatus is an outbreeder, with genetically homogenous populations and moderate values of genetic diversity, low but significant levels of genetic differentiation, most genetic variation within populations • Genetic + demographic + threat basic data => suggest target populations for in situ and ex situ conservation of Portuguese priority CWR: D. cintranus subsp. barbatus: Dcb3

  27. Genetic diversity analysis of CWR in Portugal Joana Magos Brehm, Brian V. Ford-Lloyd, Nigel Maxted, Maria Amélia Martins-Loução Joint PGR Secure/ECPGR workshop: Conservation strategies for European CWR and LR diversity 7–9 September 2011, Palanga, Lithuania

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