Transcript Realistic population and molecular genetic tools for genetic

Realistic population and
molecular genetic tools for
genetic assessment
(a simple minded, but pragmatic
view!)
Brian Ford-Lloyd
What will I talk about?
1. Definitions
2. Molecular and Popgen Background
3. The CWR list
4. Easy guides to erosion
5. Genetic pollution
6. Application of methodologies
7. CBD targets
8. When to do Molpopgen?
1. Definitions
• Genetic erosion
– a permanent reduction
in richness or evenness
of common localized
alleles
– or the loss of
combinations of alleles
over time in a defined
area ( after Guarino)
• Genetic pollution
– gene flow from
transgenic (or nontransgenic ?) crops to
natural populations
2. Some background
• sampling variation or drift causes loss of
genetic variation in small populations
• effective size, Ne, not actual size N,
determines the rate of this loss
• in natural populations Ne is less than N
• difficult to obtain an estimate of the ratio
Ne/N
An example of Ne /N
• Papaver dubium:
– 50% of all seed set from 2% of plants
– This gives a ratio of Ne /N of 0.07
– Papaver plants set 75% of seed by selfpollination
– Ratio reduced to 0.024
Minimum viable population (MVP)
• ‘The minimum size of a population which
will allow us to reduce the loss of genetical
variation and heterozygosity by the
inbreeding caused by drift to an acceptable
level’
• (there are several other definitions)
wild
Beta Ne?
In situ conservation
• for species like P. dubium a population size of N = 5000 is
reasonably safe
• populations of herbaceous CWR such as wild wheat, in which
the density of plants is often around 10 per m2, occupy only
about 500 m2 of ground
• for a tropical forest dipterocarp (density can be as low as only 2
per km2), a population of this size would require a reserve of
2500 km2!!!
Important information at the gene level
• Effective population
size
– Level of heterozygosity
– Inbreeding
• Change in allele
frequency
• Genetic diversity
• Allele richness
• Gene flow
• Genetic drift
– genetic erosion
• Natural selection
– erosion and pollution
• Migration
– pollution (erosion) or
replenishment
Molecular markers/DNA profiling
•
•
•
•
•
•
Arbitrarily primed markers (RAPD/ISSR) -?
AFLPs -?
SNPs/DNA sequence -?
EST based markers -?
isozymes/allozymes
SSRs (microsatellites)
– Yes because they are co-dominant, but.....
Are there primers available for species
on the CWR list?
• Out of 160 random
CWR taxa (genera)
surveyed:
• 29% had SSR primers
available in the
published literature
CWR genera with SSR primers:
Acer
Aegilops
Albizia
Allium
Arachis
Armeniaca
Asparagus
Avena
Begonia
Cannabis
Castanea
Citrullus
Corylus
Cynodon
Dianthus
Diplotaxis
Elymus
Eruca
Eryngium
Festuca
Ficus
Fragaria
Geum
Gossypium
Iris
Lactuca
Lolium
Lupinus
Malus
Nigritella
Olea
Pelargonium
Pinus
Plantago
Prangos
Prunus
Pterocarya
Ribes
Rosa
Salix
Sinapis
Sophora
Sorbus
Taraxacum
Tripolium
Vicia
Vitis
Zostera
CWR genera without primers:
Abutilon
Achillea
Aconitum
Agave
Agrostis
Alternanthera
Amygdalus
Anthericum
Apium
Aquilegia
Artemisia
Atriplex
Atropa
Axonopus
Berberis
Bituminaria
Broussonetia
Calliandra
Capparis
Carum
Ceratonia
Chamaecytisus
Chamaemelum
Chrysanthemoides
Cichorium
Cleome
Colocasia
Consolida
Convallaria
Cordia
Corynephorus
Crocus
Cryptotaenia
Cynara
Cyperus
Dalbergia
Daucus
Digitalis
Drosophyllum
Elaeagnus
Epimedium
Fagopyrum
Flaveria
Furcraea
Galega
Halimodendron
Hedera
Helleborus
Hippocrepis
Hydrocotyle
Iberis
Imperata
Isatis
Juglans
Juncus
Laurus
Lavandula
Lens
Leucaena
Limodorum
Linum
Lotus
Ludwigia
Maclura
Matteuccia
Melissa
Mentha
Mercurialis
Monochoria
Myrrhis
Narcissus
Nasturtium
Nigella
Onobrychis
Ornithopus
Osmunda
Papaver
Parietaria
Phacelia
Phalaris
Phleum
Phoenix
Phyla
Poa
Polemonium
Portulaca
Ranunculus
Rhododendron
Rubus
Rumex
Sagittaria
Salvia
Sambucus
Santolina
Scilla
Securigera
Sesleria
Silphium
Stachys
Syringa
Tetragonia
Thymus
Trapa
Trigonella
Tulipa
Vaccinium
Valerianella
Vallisneria
Verbena
Vincetoxicum
Viola
Vulpia
Xanthium
3. The CWR list
• The CWR list has around 20,000 species
• In theory we could undertake detailed
genetic assessment of genetic
erosion/pollution on over 6000 taxa using
SSRs
• If we wanted to, and had the resources
• and.......
A huge task!
The key issues might be:
• How can we assess the majority of our
CWR species simply and easily?
– and minimise genetic erosion/pollution
– and maximise genetic diversity in in situ
conservation
• How do we prioritise the taxa for molecular
population genetic intensive study?
– (workshop 2?)
4. Simple and easy guides?
• Information on breeding system
– around 80% of diversity is within populations
of outbreeders
– most diversity is among populations of
inbreeders
Further simple guides:
• Effective and actual population sizes are not
the same
• But, actual population size can be a rough
guide
• Will give us an idea about erosion if actual
population is getting smaller
Resampling?
• If populations are staying the same size,
then molecular population genetic analysis
may be needed only once
• If population size is decreasing, then may
need resampling - when? how often?
Other simple guides:
• Taxonomic diversity
– assuming diversity is spread across taxa,
ensuring that subspecific taxa are conserved
should ensure that diversity is conserved
• Ecogeographic diversity
– populations that have different adaptive norms
will be genetically diverse
• Red data listing
– what genetic information is revealed?
5. Genetic pollution
• “It is clear that spontaneous hybridisation
and introgression of genes from
domesticated plants into wild relatives is a
common characteristic of domesticated
plants”
– Ellstrand, 1999
conventional
or transgenic
Genetic pollution:
• The Gene Pool Concept will
provide an indicator of the CWR
species that are vulnerable, but
• 22 out of 25 of the World’s most
important crops have evidence of
natural hybridisation with one or
more wild relative
• This could extrapolate to over
18,000 (90%) of our CWR species
wheat
rice
maize
soybean
barley
sorghum
millet
cotton
rape
beans
sunflower
potato
sugarcane
cassava
oats
coconut
coffee
cowpea
rye
oil palm
sweet potato
olive
grape
Can genetic pollution affect genetic
diversity?
Data not
involving
transgenes
• gene flow can cause change in genetic
diversity
– in 12 different studies, diversity in introgressed
populations was greater
• can gene flow cause extinction?
– more data are needed
– it is ‘speculated’ that hybridisation may have
caused extinction of CWR of Capsicum, date
palm, hemp, maize, sweet pea
6. How to apply assessment
methodologies?
• Other prioritisations first, then • are any subspecific taxa seriously threatened?
• are any major habitats/regions threatened?
• are most populations’ sizes declining (outbreeding
species) ?
• are some populations’ sizes declining (inbreeding
species) ?
• do sampled populations contain significant genetic
diversity?
– if yes, then only re-sample if change in population size
Monitoring genetic pollution?
• Bottom line - measure gene flow
– need FST and molecular markers
• Could assess:
– occurrence of hybrids and hybrid derivatives
(morphological)
– fitness of hybrids/hybrid derivatives
– spread of hybrids/hybrid derivatives
• Must be over large timescale, large
geographical area, large sample size
7. CBD 2010 targets and WS5
CWR list &
Euro+Med
A: Focal area
B: Indicator for
immediate testing
C: Possible
indicators (require
further development)
Status and trends
of the components
of biological
diversity
Threats to
biodiversity
Trends in
abundance
and distribution of
selected species
Trends in genetic
diversity of ....
cultivated plants...
Number and cost
of alien invasions
8. When to do molecular population
genetics?
Red
Data
Listing?
• if most populations’ sizes are declining (outbreeding
species) ?
• if some populations’ sizes are declining (inbreeding
species) ?
– and/or because any one major habitat/region is
threatened
– and/or because any subspecific taxon is
seriously threatened
• then sample and do molpopgen to establish whether
populations in protected areas are adequate, or which
populations to protect
A realistic message?
• Don’t - plan to do molpopgen first
• Do - molpopgen last or even not at all
– when other guides have been examined
– when other assessments have been done
• Do - use molpopgen as last resort to:
– select best populations for in situ conservation
– monitor populations or critical situations
• Don’t - use molpopgen to prioritise CWR
list!