Realistic population and molecular genetic tools for genetic assessment (a simple minded, but pragmatic view!) Brian Ford-Lloyd.

Realistic population and molecular genetic tools for

genetic assessment

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 non-transgenic ?) 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 self-

pollination

– 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)

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!!!

wildBeta Ne?wildBeta Ne?

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

AcerAegilopsAlbiziaAlliumArachisArmeniacaAsparagusAvenaBegoniaCannabisCastaneaCitrullusCorylusCynodonDianthusDiplotaxis

ElymusErucaEryngiumFestucaFicusFragariaGeumGossypiumIrisLactucaLoliumLupinusMalusNigritellaOleaPelargonium

PinusPlantagoPrangosPrunusPterocaryaRibesRosaSalixSinapisSophoraSorbusTaraxacumTripoliumViciaVitisZostera

CWR genera with SSR primers:

AbutilonAchilleaAconitumAgaveAgrostisAlternantheraAmygdalusAnthericumApiumAquilegiaArtemisiaAtriplexAtropaAxonopusBerberisBituminariaBroussonetiaCalliandraCapparisCarumCeratoniaChamaecytisus

ChamaemelumChrysanthemoidesCichoriumCleomeColocasiaConsolidaConvallariaCordiaCorynephorusCrocusCryptotaeniaCynaraCyperusDalbergiaDaucusDigitalisDrosophyllumElaeagnusEpimediumFagopyrumFlaveriaFurcraea

GalegaHalimodendronHederaHelleborusHippocrepisHydrocotyleIberisImperataIsatisJuglansJuncusLaurusLavandulaLensLeucaenaLimodorumLinumLotusLudwigiaMacluraMatteucciaMelissa

MenthaMercurialisMonochoriaMyrrhisNarcissusNasturtiumNigellaOnobrychisOrnithopusOsmundaPapaverParietariaPhaceliaPhalarisPhleumPhoenixPhylaPoaPolemoniumPortulacaRanunculusRhododendronRubus

RumexSagittariaSalviaSambucusSantolinaScillaSecurigeraSesleriaSilphiumStachysSyringaTetragoniaThymusTrapaTrigonellaTulipaVacciniumValerianellaVallisneriaVerbenaVincetoxicumViolaVulpiaXanthium

CWR genera without primers:

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.......

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?)

A huge task!

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, 1999conventionalor 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

wheatricemaizesoybeanbarleysorghummilletcottonrapebeanssunflowerpotatosugarcanecassavaoatscoconutcoffeecowpearyeoil palmsweet potatoolivegrape

wheatricemaizesoybeanbarleysorghummilletcottonrapebeanssunflowerpotatosugarcanecassavaoatscoconutcoffeecowpearyeoil palmsweet potatoolivegrape

Can genetic pollution affect genetic diversity?

• 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

Data notinvolvingtransgenes

Data notinvolvingtransgenes

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

A: Focal area

Status and trendsof the componentsof biological diversity

Threats to biodiversity

A: Focal area

Status and trendsof the componentsof biological diversity

Threats to biodiversity

B: Indicator forimmediate testing

Trends in abundanceand distribution ofselected species

B: Indicator forimmediate testing

Trends in abundanceand distribution ofselected species

C: Possibleindicators (require further development)

Trends in genetic diversity of ....cultivated plants...

Number and costof alien invasions

C: Possibleindicators (require further development)

Trends in genetic diversity of ....cultivated plants...

Number and costof alien invasions

CWR list &Euro+Med

CWR list &Euro+Med

8. When to do molecular population genetics?

• 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

RedDataListing?

RedDataListing?

• 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!

A realistic message?