Genetic Erosion and Genetic Genetic Erosion and Genetic Pollution : Some thoughtsPollution : Some thoughts

Luigi GuarinoLuigi GuarinoSecretariat of the Pacific Secretariat of the Pacific

Community (SPC)Community (SPC)Suva, FijiSuva, Fiji

Nigel MaxtedNigel MaxtedUniversity of BirminghamUniversity of Birmingham

Birmingham, UKBirmingham, UK

Talk ObjectivesTalk Objectives Review the approaches to the assessment and Review the approaches to the assessment and

prediction of genetic erosionprediction of genetic erosion

Distinguish between taxonomic and genetic erosionDistinguish between taxonomic and genetic erosion

Establish tentative indicators of genetic erosionEstablish tentative indicators of genetic erosion

Some initial thoughts on genetic pollutionSome initial thoughts on genetic pollution

Establish tentative indicators of genetic pollutionEstablish tentative indicators of genetic pollution

Prioritising CWR List in Relation to Genetic Erosion Prioritising CWR List in Relation to Genetic Erosion and Pollutionand Pollution

Genetic ErosionGenetic Erosion Definition – Definition – “Permanent reduction in the number, evenness and “Permanent reduction in the number, evenness and

distinctness of alleles, or combinations of alleles, distinctness of alleles, or combinations of alleles, of actual or of actual or potential agricultural importancepotential agricultural importance in a defined geographical area” in a defined geographical area”

(FAO, 1999)(FAO, 1999)

Decrease/lossDecrease/loss in (useful?) in (useful?) genetic diversitygenetic diversity in a given in a given areaarea over a over a given given time periodtime period

– ““X genetic diversity X genetic diversity was lostwas lost at place Y between time A and time B in the at place Y between time A and time B in the past”past”

Need to be able to measure Need to be able to measure genetic diversitygenetic diversity Need to define the geographic Need to define the geographic areaarea Need to be able to make comparisons inNeed to be able to make comparisons in time time

– ““X genetic diversity X genetic diversity may be lostmay be lost at place Y between now and a time in the at place Y between now and a time in the future”future”

Need to Need to extrapolateextrapolate in time and space in time and space Need to quantify Need to quantify confidenceconfidence of prediction of prediction

Population change is Population change is universal universal (applies to all biodiversity), can be (applies to all biodiversity), can be natural, there is a need to distinguishnatural, there is a need to distinguish between between– Natural changesNatural changes– Anthropogenic related population changesAnthropogenic related population changes

Genetic ErosionGenetic Erosion Why genetic diversity is importantWhy genetic diversity is important

– Maintain viability and evolutionary potential of individuals / Maintain viability and evolutionary potential of individuals / populations / speciespopulations / species

– Direct use by humankindDirect use by humankind

Genetic erosion associated with Genetic erosion associated with ex situex situ collection or collection or in situin situ populationspopulations

Identification of indicators:Identification of indicators:

1.1. ProphylacticProphylactic

2.2. AssessmentAssessment

3.3. PredictionPrediction

Prophylactic ApproachProphylactic Approach Loss of species (= taxonomic erosion)Loss of species (= taxonomic erosion) Difficult to estimate, butDifficult to estimate, but

– IUCN (http://www.iucn.org/) estimate 11,000 species are IUCN (http://www.iucn.org/) estimate 11,000 species are imminently threatened with extinctionimminently threatened with extinction

– Reduction in numbers of crop species (UK Forages; Sackville-Reduction in numbers of crop species (UK Forages; Sackville-Hamilton, 1999)Hamilton, 1999)

Year 1924 1973 1998

Number of grass species 13 6 2

Number of legume species 7 4 1

Number of other dicot species 4 5 0

Total 24 15 3

Taxonomic erosion must involve loss of genetic diversity as wellTaxonomic erosion must involve loss of genetic diversity as well

Prophylactic ApproachProphylactic Approach Loss of genetic diversity (=genetic erosion)Loss of genetic diversity (=genetic erosion)

– Extremely difficult to quantify, evidence is often anecdotal (FAO Prague Meeting, 1999) or Extremely difficult to quantify, evidence is often anecdotal (FAO Prague Meeting, 1999) or nomeclaturally based as for potato landraces on Chilean island of Chiloe (Ochoa, 1975)nomeclaturally based as for potato landraces on Chilean island of Chiloe (Ochoa, 1975)

– Quantifying loss examples:Quantifying loss examples: Akimoto Akimoto et al.et al. (1999) (1999) Oryza rufipogonOryza rufipogon from Thailand sampling 1985 & 1994 from Thailand sampling 1985 & 1994

same populations, allozyme analysis = severe decline, rampant genetic same populations, allozyme analysis = severe decline, rampant genetic pollution (1996 extinct!)pollution (1996 extinct!)

De Oliveira & Martins (2002) ipecac from Brazil – indirect and comparative De Oliveira & Martins (2002) ipecac from Brazil – indirect and comparative using Guarino (1995) modelusing Guarino (1995) model

Year Landraces number

1928 200

1938 200

1948 100

1958 ≈ 80

1969 35-40

Prophylactic ApproachProphylactic Approach

– Maxted Maxted et al.et al. (1997) guesstimate (1997) guesstimate 25-35% of 25-35% of plant genetic diversity could be lost over the plant genetic diversity could be lost over the next 12 yearsnext 12 years 100% of extinct species100% of extinct species ?% of remaining extant species?% of remaining extant species

– Largely anecdotal or nomeclaturally based Largely anecdotal or nomeclaturally based arguments for genetic erosion: urgent need for arguments for genetic erosion: urgent need for rigorous testing (Brush, 1999)rigorous testing (Brush, 1999)

Prophylactic ApproachProphylactic Approach Even though imprecise there is a devastating lost of Even though imprecise there is a devastating lost of

biodiversity at species and genetic levels, and linked to socio-biodiversity at species and genetic levels, and linked to socio-economic use of diversity, economic use of diversity, post Vavilov gave rise to rush to post Vavilov gave rise to rush to collect in 20collect in 20thth Century Century

Conservation has a real cost, so must be efficientConservation has a real cost, so must be efficient– No overall estimate of PGR conservation costsNo overall estimate of PGR conservation costs– Cost of Cost of ex situex situ gene bank conservation alone = US $30.5 million gene bank conservation alone = US $30.5 million

per year (Hawkes per year (Hawkes et al.,et al., 2001) 2001)– Ex situEx situ gene bank conservation is only 1% of total conservation gene bank conservation is only 1% of total conservation

costs (Cohen costs (Cohen et al.,et al., 1991) 1991)– Conservation is expensive!Conservation is expensive!

Use for conservation productsUse for conservation products– However, estimate of use of PGR = However, estimate of use of PGR = US $ 500 - 800 billion US $ 500 - 800 billion per year per year

ten Kate and Laird (1999)ten Kate and Laird (1999)

Prophylactic ApproachProphylactic Approach The need for a prophylactic approach is self The need for a prophylactic approach is self

evidentevident

– Conserve now to ensure use for tomorrowConserve now to ensure use for tomorrow Protection area focus on Protection area focus on in situin situ ‘hotspots’ ‘hotspots’ Ex situEx situ duplication duplication Increase ‘value’ of landraces (value-added)Increase ‘value’ of landraces (value-added) Conservation legislation (national, regional, global)Conservation legislation (national, regional, global) Raise public awareness (professional and general Raise public awareness (professional and general

public) in the:public) in the:– value of naturevalue of nature– uses of nature / genetic diversityuses of nature / genetic diversity– Need for conservationNeed for conservation

Erosion AssessmentErosion Assessment Direct (Direct (measurement of past and current measurement of past and current

genetic diversity and relative changes)genetic diversity and relative changes)

– Genetic diversity assessment applying molecular Genetic diversity assessment applying molecular techniquestechniques

TemporalTemporal - compare population’s genetic diversity over - compare population’s genetic diversity over a set time period, re-sampling a set time period, re-sampling ex situex situ conserved conserved populationspopulations

SpatialSpatial - compare different population’s genetic - compare different population’s genetic diversity at the same time diversity at the same time

– Phenotypic variationPhenotypic variation

Erosion AssessmentErosion Assessment Indirect – any ‘proxy’ factor influencing Indirect – any ‘proxy’ factor influencing

change in genetic diversity)change in genetic diversity)

– Population characteristics assessmentPopulation characteristics assessment size size dispersal, dispersal, fecundity, etc.fecundity, etc.

– Ethnographic assessmentEthnographic assessment IK surveysIK surveys

– Taxon specific assessmentTaxon specific assessment TaxonomicTaxonomic diversity assessment (vars., races) diversity assessment (vars., races) NomenclaturalNomenclatural diversity assessment (landrace names) diversity assessment (landrace names) Taxon characteristicsTaxon characteristics (e.g. outbreeders) (e.g. outbreeders)

Taxon Specific Genetic Taxon Specific Genetic ErosionErosion

Species with a Species with a restricted geographical and ecological rangerestricted geographical and ecological range

Species restricted to natural habitats subject to destruction, Species restricted to natural habitats subject to destruction, degradation and fragmentation degradation and fragmentation

Species poorly adapted to their niche and easily displaced by Species poorly adapted to their niche and easily displaced by competition from more aggressive or alien speciescompetition from more aggressive or alien species

Species found in anthropogenic or disturbed habitatsSpecies found in anthropogenic or disturbed habitats

Species Species growing in marginal or very localised anthropogenic growing in marginal or very localised anthropogenic environments that are vulnerable to changes in agricultural environments that are vulnerable to changes in agricultural practices or land usepractices or land use

Species growing in environments subject to regular natural or Species growing in environments subject to regular natural or human-directed disasters.human-directed disasters.

Species subject to wild harvesting, over-exploitation and incidental Species subject to wild harvesting, over-exploitation and incidental taketake

Erosion ‘Proxy’ AssessmentErosion ‘Proxy’ Assessment

– Environment / habitat specific assessment – any factor Environment / habitat specific assessment – any factor likely to result in genetic erosionlikely to result in genetic erosion

Environmental disturbance or change Environmental disturbance or change (local, national, global)(local, national, global)

Natural or artificial habitat loss or modification (local, national, Natural or artificial habitat loss or modification (local, national, global)global)

Over-exploitation (local, national, global)Over-exploitation (local, national, global)

Competition from exotic species (local)Competition from exotic species (local)

Disturbance (local)Disturbance (local)

Disease (local)Disease (local)

Limited distribution (local)Limited distribution (local)

PredictionPrediction of Erosion based of Erosion based on ‘Proxy’ factorson ‘Proxy’ factors

Guarino Model for quantifying the threat of genetic erosion – 24 questions:Guarino Model for quantifying the threat of genetic erosion – 24 questions:

1)1) GeneralGenerala)a) Taxon distributionTaxon distribution

-- RareRare 1010-- Locally commonLocally common 5 5-- Widespread or abundantWidespread or abundant 0 0

b)b) DroughtDrought-- Known to have occurred in two or more Known to have occurred in two or more

consecutive yearsconsecutive years1010

-- Occurring on average one or more times every Occurring on average one or more times every ten years, but not in consecutive yearsten years, but not in consecutive years

55-- Occurring less than once every ten years Occurring less than once every ten years 0 0

c)c) FloodingFlooding-- Area known to be very flood proneArea known to be very flood prone 1010-- Area not known to be flood proneArea not known to be flood prone 0 0

Prediction of ErosionPrediction of Erosion IUCN Red List CategoriesIUCN Red List Categories

Do the categories require adaptation for PGR / CWR use?Do the categories require adaptation for PGR / CWR use?

Measures to Predict ErosionMeasures to Predict Erosion DirectDirect

– Molecular analysis of past and current genetic diversityMolecular analysis of past and current genetic diversity

IndirectIndirect– Ecogeographic / ethnographic projection of genetic Ecogeographic / ethnographic projection of genetic

erosion based on past experienceerosion based on past experience

Use community-based space/time comparisons to identify Use community-based space/time comparisons to identify factors causative of - or at least correlated with - with erosionfactors causative of - or at least correlated with - with erosion

get taxon or regional based data for these and/or their get taxon or regional based data for these and/or their proxies now and at time X in the pastproxies now and at time X in the past

use GIS to map risk of genetic eroson (modeling) for period use GIS to map risk of genetic eroson (modeling) for period time X time X now then project from now now then project from now time Y time Y

validate past risk with observed genetic erosionvalidate past risk with observed genetic erosion

refine model for the futurerefine model for the future

Environment / Habitat Specific Environment / Habitat Specific Genetic ErosionGenetic Erosion

Environment / habitat specific assessment – Environment / habitat specific assessment – any factor likely to result in genetic erosionany factor likely to result in genetic erosion

– Environmental disturbance / habitat loss / Environmental disturbance / habitat loss / fragmentationfragmentation Drainage workDrainage work Dam buildingDam building Agricultural development programmesAgricultural development programmes Road construction, etc.Road construction, etc.

– Country-wide studies (based on secondary data)Country-wide studies (based on secondary data) EcogeographyEcogeography GISGIS Remote sensingRemote sensing Aerial photographyAerial photography

Priority areas for collecting wild Gossypium in Africa

• Climates associated with high diversity

• High risk of genetic erosion– soil degradation– cattle density– human population growth

• Collecting gaps• High accessibility

Priority areas for collecting wild Arachis germplasm in

Bolivia

Data sources USDA, CIAT, FAN, WCMC

• ArachisArachis climates climates• ArachisArachis diversity diversity

climatesclimates• Collecting gapsCollecting gaps• Distance from Distance from

protected areasprotected areas• Risk of genetic Risk of genetic

erosionerosion• population densitypopulation density• soil degradationsoil degradation• proximity to roads, proximity to roads,

new gas pipeline new gas pipeline etc.)etc.)

The information pyramidThe information pyramidAggregating informationAggregating information

Detailed local information Detailed local information national national global global levellevel

Affects quantity and quality of information passed Affects quantity and quality of information passed along to decision-makersalong to decision-makers

Can have a significant effect on the decision-Can have a significant effect on the decision-making outcome making outcome

Need to establish a baseline understanding of Need to establish a baseline understanding of genetic diversity for future comparisongenetic diversity for future comparison

12 Genetic Erosion 12 Genetic Erosion IndicatorsIndicators

1.1. Relative taxon / variety Relative taxon / variety rarityrarity

2.2. Relative genetic diversityRelative genetic diversity

3.3. Extent of occurrence / area Extent of occurrence / area of occupancyof occupancy

4.4. Population size (< 5000), Population size (< 5000), number and isolationnumber and isolation

5.5. Degree and manner of Degree and manner of socio-economic usesocio-economic use

6.6. Geographic location relative Geographic location relative to urban environmentto urban environment

7.7. Vulnerability to agricultural Vulnerability to agricultural changeschanges

8.8. Vulnerability to natural disaster Vulnerability to natural disaster

9.9. Presence in protected areasPresence in protected areas

10.10.Rare or restricted habitatsRare or restricted habitats

11.11.Threatened habitatsThreatened habitats

12.12. Application of complementary Application of complementary conservation studies (conservation studies (ex situex situ))

To be applied at national, regional and global levelsTo be applied at national, regional and global levels

IUCN Extent of occurrence / Area of IUCN Extent of occurrence / Area of occupancyoccupancy

Tools to help ID Genetic Tools to help ID Genetic ErosionErosion

Direct / absoluteDirect / absolute– Genetic diversity Genetic diversity

studiesstudies– Phenotypic Phenotypic

characterisationcharacterisation– Regular grid of Regular grid of

permanent sites permanent sites to act as a to act as a baseline baseline (Serwinski, 1999)(Serwinski, 1999)

Indirect / deductiveIndirect / deductive– Ecogeographic surveysEcogeographic surveys– GIS / remote sensing / GIS / remote sensing /

aerial photography aerial photography – Ethnographic surveysEthnographic surveys– ……

Primarily indirect / deductive ?Primarily indirect / deductive ?

Genetic PollutionGenetic Pollution More than just GMO contaminants!More than just GMO contaminants!

France wild perennial ryegrass show expected pattern of increasing France wild perennial ryegrass show expected pattern of increasing genetic distance with increasing geographical distance (Monestiez genetic distance with increasing geographical distance (Monestiez et alet al 1994)1994)

UK uncultivated wild grass species UK uncultivated wild grass species Agrostis curtisiiAgrostis curtisii shows a similar pattern shows a similar pattern but wild perennial ryegrass has lost all trace of a positive relationship but wild perennial ryegrass has lost all trace of a positive relationship between genetic distance and geographical distance (Warren et al., 1998)between genetic distance and geographical distance (Warren et al., 1998)

Species Lolium perenne Agrostis curtisii

Regression coefficient for FST on distance -1.05 x 10-4 7.77 x 10-5

Significance * ***

r2 1.9% 7.0%

Genetic PollutionGenetic Pollution IntroductionIntroduction of of alienalien genetic diversitygenetic diversity into a host genome into a host genome

– ““X genetic diversity from the alien species A X genetic diversity from the alien species A was introducedwas introduced into the genome of the host species B”into the genome of the host species B”

Deliberate (i.e. Breeding = introgression as a result of conscious Deliberate (i.e. Breeding = introgression as a result of conscious human actions = beneficial)human actions = beneficial)

Natural (i.e. introgression = beneficial?)Natural (i.e. introgression = beneficial?) ‘‘Accidental’ (i.e. introgression as a result of unconscious human Accidental’ (i.e. introgression as a result of unconscious human

actions = potentially harmful) = genetic pollutionactions = potentially harmful) = genetic pollution

– ““X genetic diversity from the alien species A X genetic diversity from the alien species A may be may be introducedintroduced into the genome of the host species B” into the genome of the host species B”

Need to Need to extrapolateextrapolate in time and space in time and space

Need to quantify Need to quantify confidenceconfidence of prediction of prediction

‘‘Accidental’ Accidental’ Genetic Genetic PollutionPollution

Need to be able to assess changes in genetic Need to be able to assess changes in genetic diversity, identify alien diversitydiversity, identify alien diversity– Molecular techniquesMolecular techniques

Looking for cultivar markers in landrace or wild species e.g. Looking for cultivar markers in landrace or wild species e.g. 35% of maize landraces in Mexico have transgenic DNA35% of maize landraces in Mexico have transgenic DNA

Numerous studies of gene flow stimulated by GMO debate!Numerous studies of gene flow stimulated by GMO debate!

Avoid by geographical isolation, supra-pollination Avoid by geographical isolation, supra-pollination proximity of alien and host speciesproximity of alien and host species

Identify species with propensity for genetic Identify species with propensity for genetic pollutionpollution

Propensity for Genetic Propensity for Genetic PollutionPollution

Species geographically close to the Species geographically close to the polluting speciespolluting species– Sympatric Sympatric – Out-breedersOut-breeders

Closely taxonomically related species to Closely taxonomically related species to crops!crops!– Crop are by definition a hotch-potch of alien Crop are by definition a hotch-potch of alien

genetic diversitygenetic diversity– Crops may have been genetically modifiedCrops may have been genetically modified

Gene pool and taxon groupGene pool and taxon group– GP1b, GP2GP1b, GP2– TG1b, TG2, TG3, TG4TG1b, TG2, TG3, TG4

ConclusionConclusion

Prophylactic approach is always preferable as Prophylactic approach is always preferable as erosion and pollution cost money!erosion and pollution cost money!

It is possible to use indicators to assess comparative It is possible to use indicators to assess comparative probability of genetic erosion / genetic pollution and probability of genetic erosion / genetic pollution and so prioritise conservation actionso prioritise conservation action

Tools are being developed for predicting genetic Tools are being developed for predicting genetic erosion, if not genetic pollutionerosion, if not genetic pollution

PGR Forum provides an opportunity to identify PGR Forum provides an opportunity to identify indicators and help meet the CBD COP 2010 targets!indicators and help meet the CBD COP 2010 targets!

Recommendations for Prioritising CWR Recommendations for Prioritising CWR List in Relation to Genetic Erosion and List in Relation to Genetic Erosion and

PollutionPollution Highest priorityHighest priority

– Taxon related to crops GP1b / GP2 and TG1b, TG2, TG3, TG4Taxon related to crops GP1b / GP2 and TG1b, TG2, TG3, TG4– Rare taxa with low population numbers, disparate populations, etc.Rare taxa with low population numbers, disparate populations, etc.– Taxa with unique genetic diversityTaxa with unique genetic diversity– Taxa restricted to Taxa restricted to threatened habitatsthreatened habitats– Taxa Taxa vulnerability to agricultural changesvulnerability to agricultural changes

Medium priorityMedium priority– Wild harvested speciesWild harvested species– Taxa restricted to locations near urban centresTaxa restricted to locations near urban centres– Taxa restricted to Taxa restricted to rare or restricted habitatsrare or restricted habitats– Taxa Taxa vulnerability to natural disastervulnerability to natural disaster

Lower priorityLower priority– Taxa no present in protected areasTaxa no present in protected areas– Taxa not duplicated in Taxa not duplicated in ex situex situ facilities facilities

?? Does rampant genetic erosion / genetic pollution question the Does rampant genetic erosion / genetic pollution question the validity of validity of in situin situ conservation of CWR, if crop CWR introgression conservation of CWR, if crop CWR introgression is widespread and genetic diversity is being eroded so quickly?is widespread and genetic diversity is being eroded so quickly?