Transcript 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
• Aims of this study
• National approach
• Genetic diversity study
• Selection of populations for conservation
• Relevant points and conclusions
• 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.
Economic
value
Native
status
In situ
conservation
Ex situ
conservation
20 priorities
2262 CWR
Global
distribution
National
distribution
Inventory
Threatened
category
Legislation
Prioritisation at species level
- 8 criteria, 4 methods-
Priority species
Allium victorialis L.
Dianthus laricifolius Boiss. & Reut.
subsp. marizii (Samp.) Franco
20 priorities
Dianthus cintranus Boiss. & Reut.
subsp. barbatus R. Fern. & Franco
Dianthus cintranus Boiss.
& Reut. subsp. cintranus
Priority species
Ecogeographic survey
Field work
Genetic data
Demographic data
Dianthus cintranus Boiss. &
Reut. subsp. barbatus R.
Fern. & Franco
Priority species
Amplified
Fragment Length
Polymorphism
(AFLP)
Priority populations
Threat data
Prioritisation at population level
#
#
# #
#
#
#### #
##
##
##
####
#
•
•
•
•
•
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
• breeding system?
• 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?
• 5 populations, 20 plants/population
• 2 selective MesI and EcoRI primer
pairs
• loci 56-440 bp
Population structure and differentiation:
Descriptive stats:
• Wright’s FST (1951) - Lynch & Milligan
• (1994)
allele frequencies - Bayesian
Isolation by distance:
approach suggested
by Zhivotovsky
• dendrograms
- agglomerative
hierarchical
• Mantel
[pairwise
FST
clustering
UPGMA
(1999) testusing
transformed
to FST/(1‐FST) versus
PCoA
% polymorphic loci/population
AMOVA - based on
Euclidean pairwise
log‐transformed
geographic
genetic diversity - Lynch & Milligan
genetic
distance]distances
(GENALEX v. 6.0)
(1994) forclustering
dominantmethod
markers- for cross• Bayesian
where isolation by distance
• breeders
# private and
alleles
not detected
••
•
•
Natura 2000 sites
Dcb2
Dcb3
Dcb4
Dcb5
Dcb1
Descriptive stats
• total genetic diversity: Ht=0.163
Dcb2
Dcb3
Dcb4
Dcb5
Dcb1
Dcb3
↑Hj=0.170
↑PL=53%
PA=3%
Dcb5
↓ Hj=0.149
↓ PL=46%
↓ PA=2%
(moderate)
• genetic diversity within
populations: Hw=0.152
• inter‐population genetic diversity:
Hb=0.006
OUTBREEDER
Population genetic structure
and differentiation
AMOVA (Analysis of Molecular Variance):
Dcb2
Dcb3
Dcb4
Dcb5
Dcb1
Among populations: 8%
Within populations: 92%
Fst = 0.038 => populations are
little genetically different
OUTBREEDER
Isolation by distance
Dcb3
Dcb3
Dcb1
Dcb1
Dcb2
NO GEOGRAPHIC
PATTERN
671
Dcb3
Dcb4
Dcb5
Dcb1
Dcb2
Dcb2
978
Mantel test => NO
Dcb4
Dcb4
ISOLATION BY DISTANCE
1000
(no restriction to geneflow)
Dcb5
Dcb5
0.001
Dcb2
Dcb3
Dcb4
Dcb5
GENETICALLY VERY HOMOGENOUS!
Dcb1
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)
• 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)
TAXON
POP. POP. SZ. St
THREATS
PRIORITY
Hj St D St # PL St # cl St SUM
St
(%)
Dcb1
0,50
1,00
0,95 0,50 0,99
0,00 3,94
78,80
D. cintranus Dcb2
1,00
0,50
0,91 0,50 0,98
0,08 3,97
79,40
subsp.
Dcb3
1,00
0,00
1,00 1,00 1,00
1,00 5,00
100,00
barbatus
Dcb4
1,00
0,50
0,89 0,10 0,89
0,43 3,81
76,20
Dcb5
1,00
0,75
0,88 0,10 0,87
0,46 4,06
81,20
Ex situ and in situ: Dcb3!
Dcb2
Dcb3 (Condeixa-a-Nova)
↑Hj=0.170
Dcb3
Dcb4
Dcb5
Dcb1
↑D=0.005
↑PL=53%
PA=3%
↑#cl=37
<50 plants
Unknown threats
Outside conservation area
OUTBREEDER
Correlation between neutral and adaptive diversity?
Genetic diversity = evolutionary potential of a species
to evolve and adapt to a changing environment
ADAPTIVE DIVERSITY
NEUTRAL DIVERSITY
• evolution
• migration, mutation, genetic drift…
• reflects the species potential ability • no direct effect on species fitness
to adapt to changing environments
• not affected by natural selection
• 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
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