Transcript Genetic Erosion and Genetic Pollution

Genetic Erosion and Genetic
Pollution : Some thoughts
Nigel Maxted
University of Birmingham
Birmingham, UK
Luigi Guarino
Secretariat of the Pacific
Community (SPC)
Suva, Fiji
Talk Objectives

Review the approaches to the assessment and prediction
of genetic erosion

Distinguish between taxonomic and genetic erosion

Establish tentative indicators of genetic erosion

Some initial thoughts on genetic pollution

Establish tentative indicators of genetic pollution

Prioritising CWR List in Relation to Genetic Erosion and
Pollution
Genetic Erosion

Definition – “Permanent reduction in the number, evenness and distinctness
of alleles, or combinations of alleles, of actual or potential agricultural
importance in a defined geographical area”
(FAO, 1999)

Decrease/loss in (useful?) genetic diversity in a given area over a given time
period
– “X genetic diversity was lost at place Y between time A and time B in the past”
 Need to be able to measure genetic diversity
 Need to define the geographic area
 Need to be able to make comparisons in time
– “X genetic diversity may be lost at place Y between now and a time in the
future”
 Need to extrapolate in time and space
 Need to quantify confidence of prediction

Population change is universal (applies to all biodiversity), can be natural,
there is a need to distinguish between
– Natural changes
– Anthropogenic related population changes
Genetic Erosion
Why genetic diversity is important

–
Maintain viability and evolutionary potential of individuals / populations /
species
–
Direct use by humankind

Genetic erosion associated with ex situ collection or in situ populations

Identification of indicators:
1.
Prophylactic
2.
Assessment
3.
Prediction
Prophylactic Approach


Loss of species (= taxonomic erosion)
Difficult to estimate, but
– IUCN (http://www.iucn.org/) estimate 11,000 species are imminently
threatened with extinction
– Reduction in numbers of crop species (UK Forages; Sackville-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 well
Prophylactic Approach

Loss of genetic diversity (=genetic erosion)
– 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)
Year
Landraces number
1928
200
1938
200
1948
100
1958
≈ 80
1969
35-40
– Quantifying loss examples:
 Akimoto et al. (1999) Oryza rufipogon from Thailand sampling 1985 &
1994 same populations, allozyme analysis = severe decline, rampant
genetic pollution (1996 extinct!)
 De Oliveira & Martins (2002) ipecac from Brazil – indirect and
comparative using Guarino (1995) model
Prophylactic Approach
– Maxted et al. (1997) guesstimate 25-35% of plant
genetic diversity could be lost over the next 12 years
 100% of extinct species
 ?% of remaining extant species
– Largely anecdotal or nomeclaturally based arguments
for genetic erosion: urgent need for rigorous testing
(Brush, 1999)
Prophylactic Approach

Even though imprecise there is a devastating lost of biodiversity at
species and genetic levels, and linked to socio-economic use of diversity,
post Vavilov gave rise to rush to collect in 20th Century

Conservation has a real cost, so must be efficient
– No overall estimate of PGR conservation costs
– Cost of ex situ gene bank conservation alone = US $30.5 million per year
(Hawkes et al., 2001)
– Ex situ gene bank conservation is only 1% of total conservation costs
(Cohen et al., 1991)
– Conservation is expensive!

Use for conservation products
– However, estimate of use of PGR = US $ 500 - 800 billion per year ten Kate
and Laird (1999)
Prophylactic Approach

The need for a prophylactic approach is self evident
– Conserve now to ensure use for tomorrow
 Protection area focus on in situ ‘hotspots’




Ex situ duplication
Increase ‘value’ of landraces (value-added)
Conservation legislation (national, regional, global)
Raise public awareness (professional and general public) in the:
– value of nature
– uses of nature / genetic diversity
– Need for conservation
Erosion Assessment

Direct (measurement of past and current genetic
diversity and relative changes)
– Genetic diversity assessment applying molecular
techniques
 Temporal - compare population’s genetic diversity over a set
time period, re-sampling ex situ conserved populations
 Spatial - compare different population’s genetic diversity at the
same time
– Phenotypic variation
Erosion Assessment

Indirect – any ‘proxy’ factor influencing change in
genetic diversity)
– Population characteristics assessment
 size
 dispersal,
 fecundity, etc.
– Ethnographic assessment
 IK surveys
– Taxon specific assessment
 Taxonomic diversity assessment (vars., races)
 Nomenclatural diversity assessment (landrace names)
 Taxon characteristics (e.g. outbreeders)
Taxon Specific Genetic Erosion

Species with a restricted geographical and ecological range

Species restricted to natural habitats subject to destruction, degradation
and fragmentation

Species poorly adapted to their niche and easily displaced by
competition from more aggressive or alien species

Species found in anthropogenic or disturbed habitats

Species growing in marginal or very localised anthropogenic
environments that are vulnerable to changes in agricultural practices or
land use

Species growing in environments subject to regular natural or humandirected disasters.

Species subject to wild harvesting, over-exploitation and incidental take
Erosion ‘Proxy’ Assessment
– Environment / habitat specific assessment – any factor likely to
result in genetic erosion
 Environmental disturbance or change (local, national, global)
 Natural or artificial habitat loss or modification (local, national, global)
 Over-exploitation (local, national, global)
 Competition from exotic species (local)
 Disturbance (local)
 Disease (local)
 Limited distribution (local)
Prediction of Erosion based on
‘Proxy’ factors
Guarino Model for quantifying the threat of genetic erosion – 24 questions:
1) General
a)
Taxon distribution
Rare
Locally common
Widespread or abundant
b)
c)
Drought
Known to have occurred in two or more
consecutive years
Occurring on average one or more times every
ten years, but not in consecutive years
Occurring less than once every ten years
Flooding
Area known to be very flood prone
Area not known to be flood prone
10
5
0
10
5
0
10
0
Prediction of Erosion

IUCN Red List Categories

Do the categories require adaptation for PGR / CWR use?
Measures to Predict Erosion

Direct
– Molecular analysis of past and current genetic diversity

Indirect
– Ecogeographic / ethnographic projection of genetic erosion
based on past experience
 Use community-based space/time comparisons to identify factors
causative of - or at least correlated with - with erosion
 get taxon or regional based data for these and/or their proxies now
and at time X in the past
 use GIS to map risk of genetic eroson (modeling) for period time X
 now then project from now  time Y
 validate past risk with observed genetic erosion
 refine model for the future
Environment / Habitat Specific
Genetic Erosion

Environment / habitat specific assessment – any
factor likely to result in genetic erosion
– Environmental disturbance / habitat loss /
fragmentation




Drainage work
Dam building
Agricultural development programmes
Road construction, etc.
– Country-wide studies (based on secondary data)
 Ecogeography
 GIS
 Remote sensing
 Aerial 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
• Arachis climates
• Arachis diversity
climates
• Collecting gaps
• Distance from protected
areas
• Risk of genetic erosion
• population density
• soil degradation
• proximity to roads, new
gas pipeline etc.)
The information pyramid
Aggregating information

Detailed local information  national  global level

Affects quantity and quality of information passed along
to decision-makers

Can have a significant effect on the decision-making
outcome

Need to establish a baseline understanding of genetic
diversity for future comparison
12 Genetic Erosion Indicators
1. Relative taxon / variety rarity
2. Relative genetic diversity
3. Extent of occurrence / area of
occupancy
4. Population size (< 5000),
number and isolation
5. Degree and manner of socioeconomic use
6. Geographic location relative
to urban environment

7. Vulnerability to agricultural
changes
8. Vulnerability to natural disaster
9. Presence in protected areas
10. Rare or restricted habitats
11. Threatened habitats
12. Application of complementary
conservation studies (ex situ)
To be applied at national, regional and global levels
IUCN Extent of occurrence / Area of occupancy
Tools to help ID Genetic Erosion

Direct / absolute
– Genetic diversity
studies
– Phenotypic
characterisation
– Regular grid of
permanent sites to
act as a baseline
(Serwinski, 1999)


Indirect / deductive
– Ecogeographic
surveys
– GIS / remote sensing
/ aerial photography
– Ethnographic surveys
–…
Primarily indirect / deductive ?
Genetic Pollution

More than just GMO contaminants!

France wild perennial ryegrass show expected pattern of increasing genetic
distance with increasing geographical distance (Monestiez et al 1994)

UK uncultivated wild grass species Agrostis curtisii shows a similar pattern
but wild perennial ryegrass has lost all trace of a positive relationship
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 Pollution

Introduction of alien genetic diversity into a host genome
– “X genetic diversity from the alien species A was introduced into the
genome of the host species B”
 Deliberate (i.e. Breeding = introgression as a result of conscious human
actions = beneficial)
 Natural (i.e. introgression = beneficial?)
 ‘Accidental’ (i.e. introgression as a result of unconscious human actions =
potentially harmful) = genetic pollution
– “X genetic diversity from the alien species A may be introduced into the
genome of the host species B”
 Need to extrapolate in time and space
 Need to quantify confidence of prediction
‘Accidental’ Genetic Pollution

Need to be able to assess changes in genetic diversity,
identify alien diversity
– Molecular techniques
 Looking for cultivar markers in landrace or wild species e.g. 35% of
maize landraces in Mexico have transgenic DNA
 Numerous studies of gene flow stimulated by GMO debate!

Avoid by geographical isolation, supra-pollination
proximity of alien and host species

Identify species with propensity for genetic pollution
Propensity for Genetic Pollution

Species geographically close to the polluting
species
– Sympatric
– Out-breeders

Closely taxonomically related species to crops!
– Crop are by definition a hotch-potch of alien genetic
diversity
– Crops may have been genetically modified

Gene pool and taxon group
– GP1b, GP2
– TG1b, TG2, TG3, TG4
Conclusion

Prophylactic approach is always preferable as erosion and
pollution cost money!

It is possible to use indicators to assess comparative
probability of genetic erosion / genetic pollution and so
prioritise conservation action

Tools are being developed for predicting genetic erosion, if
not genetic pollution

PGR Forum provides an opportunity to identify indicators
and help meet the CBD COP 2010 targets!
Recommendations for Prioritising CWR List in
Relation to Genetic Erosion and Pollution

–
–
–
–
–

–
–
–
–

?
Highest priority
Taxon related to crops GP1b / GP2 and TG1b, TG2, TG3, TG4
Rare taxa with low population numbers, disparate populations, etc.
Taxa with unique genetic diversity
Taxa restricted to threatened habitats
Taxa vulnerability to agricultural changes
Medium priority
Wild harvested species
Taxa restricted to locations near urban centres
Taxa restricted to rare or restricted habitats
Taxa vulnerability to natural disaster
Lower priority
– Taxa no present in protected areas
– Taxa not duplicated in ex situ facilities
Does rampant genetic erosion / genetic pollution question the validity of in
situ conservation of CWR, if crop CWR introgression is widespread and
genetic diversity is being eroded so quickly?