Lecture 12a: conservation genetics 1 Flashcards
Lecture outline
- History of genetic diversity study
*Introduction – what is genetic diversity?
*How do evolutionary processes affect it?
*Why is genetic diversity important to the species?
*Impact of population size on genetic diversity.
*Impact of life history of organisms on their genetic diversity.
The beginning of conservation genetics:
1966: New potential: the gel electrophoresis of allozymes
A MOLECULAR APPROACH TO THE STUDY OF GENETIC HETEROZYGOSITY IN NATURAL POPULATIONS.
I. THE NUMBER OF ALLELES AT DIFFERENT
LOCI IN DROSOPHILA PSUEDOOBSCURA
J. L HUBBY AND R. C LEWONTIN
Department Of Zoology, Of Chicago, Chicago, 1966
^ starch gels allowed us to visualise genetic variation in populations that occur at enzyme loci - to identify functional proteins
Early days 1960’s and early 1970’s – learning about variation in populations
crops
Orrewing AL (1969) Development of a program for genetic improvement of douglas-fir in british columbia. Forestry Chronicle 45:395
Konzak CF & Dietz SM (1969) Documentation for conservation, management, and use of plant genetic resources. Economic Botany 23:299
Bennett E (1970) Genetic ecology, genetic resources and plant breeding. Genetica Agraria 24:210-220
Fisheries
Moller D (1969) The relationship between arctic and coastal cod in their immature stages illustrated by frequencies of genetic characters. Fiskeridirektoratets Skrifter Serie Havundersokelser 15:220-233
Fujino K (1971) Genetic markers in skipjack tuna from the pacific and atlantic oceans. Rapports et Proces-Verbaux des Reunions Conseil International pour l’Exploration de la Mer 161:15-18
**Terrestrial animals
(livestock and wild species) **
Rendel J (1970) Conservation of animal genetic resources. Science Journal 6:49
Turner HN (1971) Conservation of genetic resources in domestic animals. Outlook Agriculture 6:254-260.
Grieg JC (1973) The genetic conservation of British deer. Deer 3:10-15
Early example of a study based on wild managed populations
White, CM (1969) Is there a genetic continuity concerned in eyrie maintenance? In Hickey, JJ (Editor) Peregrine Falcon Populations – Their Biology and Decline. University of Wisconsin Press, Madison. pp391-397
The field of study that exists today was led initially by Sir Otto Frankel 1900-1998
key paper: Genetic conservation our evolutionary responsibility Frankel 1974
Frequent contributor to this emerging field in the early period, starting with the resource use theme, but progressively including studies with a broader emphasis. Began with conservation of plant resources and by mid 1970’s became interested in natural variation conservation:
Frankel OH (1970) Genetic resources in plants; their exploration and conservation. Internat. Biol. Prog. Handbook 11. pp469-489.
Frankel OH (1970) Genetic Conservation of plants useful to man. Biol. Cons. 2:162-170.
Frankel OH (1976) Natural variation and its conservation. Basic Life Sci. 8:21-44
What is genetic diversity?
Intraspecific genetic diversity within diploid species can be considered at different levels:
–within an individual (heterozygosity)
–between individuals (within populations)
–between populations
–between species
–between lineages
*Genetic diversity within the individual reflects the proportion of loci that are heterozygous.
*Genetic diversity among individuals in a population is reflected in the diversity of alleles, & the proportion of individuals that are heterozygous at each locus within the population.
*Genetic diversity among populations is often quantified as the genetic distance between them – often measured using Wright’s inbreeding coefficient (next lecture)
*Genetic diversity among species reflects the differentiation that is expected over time by genetic drift or natural selection when populations are reproductively isolated.
*Genetic diversity among lineages within a phylogeny is reflected in the rate and pattern of radiation of that taxonomic group, which will be related to the environment over the relevant time-frame.
Increasing genetic diversity:
Originally acquired slowly over time through mutation:
average neutral rate of point mutations in the nuclear genome is ~8 x 10-9
^ but this varies between taxa, lineages of taxa and across individual genomes
Retention & loss of genetic diversity:
lost or fixed in population through processes of:
genetic drift
natural selection
gained or retained by:
natural selection
migration
Genetic Drift:
random changes in allele frequencies over time in finite populations.
always leads to loss of diversity.
inversely proportional to population size.
dictates survival probabilities of new mutations.
Natural Selection:
The differential survival & reproduction of phenotypes that operates when genotypes (as reflected in phenotype) have different fitness. Individuals with the highest fitness will produce the most offspring, & therefore pass on their traits to a larger proportion of the next generation.
Modes of Selection: ways in which selection can alter traits on an evolutionary timescale:
At least 3 modes:
Balancing (or stabilising) selection
retains heterozygotes or different alleles depending on frequency
Directional selection
leads to the loss of diversity, because one allele is selected and fixed (positive selection) or lost (negative selection)
Disruptive selection
both alleles favoured
Both Balancing and Disruptive selection retain diversity, because both alleles are retained.
Whereas directional selection leads to loss of diversity (selection of one allele at the expense of the other)
Why is genetic diversity important in species?
2 main reasons:
Raw material: rate of evolutionary change in a population is proportional to the amount of genetic diversity available – loss of diversity reduces future evolutionary options
Heterozygosity positively correlated to fitness:
i) positive correlations (Heterosis)
ii) inbreeding depressio
Positive correlation between Heterozygosity and fitness
example 1: Growth rate in coot clam (Mulinia lateralis)
— Larvae collected over 2 week period (Koehn et al. 1988)
^ more heterozygosity = better growth
example 2: 02 consumption in American Oyster (Crassostrea virginica)
(Koehn & Shumway 1982)
^ Less O2 consumption means more efficient – the case in heterozygotes here
example 3: Fluctuating asymmetry in rainbow trout (Oncorhynchus mykiss) (Leary et al. 1983)
^ inbreeding led to assymetry which is usually a sign of inbreeding depression
Example 4: FA among harbour porpoise in the North Sea (de Luna Lopez 2005) —
only traits showing true FA were
compared. 15 microsatellite DNA
markers used to assess diversity.
^ better skull symmetry associated with heterozygosity (as in the trout)
Example 5: Life expectancy
of butterfly Polyommatus coridon (Vandewoestijne et al. (2008)
BMC Biology 6, 46)
^ greater life expectancy in heterozygous
Example 6: Disease resistance
Hoffman et al. (2012, PNAS, Ill , 3775-3780) showed that heterozygosity-fitness
correlations associated With known fitness traits sometimes required very high
resolution analyses to detect,
SNPs in Harbour seal
^microsatelite loci – greater diversity greater resistance to infection and disease
Why should there be a relationship between fitness and molecular markers?
The direct effect hypothesis: fitness correlation as a result of functional overdominance at the scored loci per se. Potentially important in allozyme studies (older studies used this approach).
The local effect hypothesis: fitness correlation as a result of the loci investigated being closely linked to functional loci associated with fitness. Requires a nonrandom associations of alleles at different loci in gametes (linkage disequilibria*) which, for example, are expected in recently bottlenecked-and-expanded populations. *see Frankham et al. pg. 90 for understanding
The general effect hypothesis: fitness correlation reflecting a general genome effect - a result of effects of homozygosity at loci distributed across the genome.
Hansson & Westerberg (2002) Molecular Ecology 11, 2467–2474
Inbreeding depression
Inbreeding increases the frequency of the sexual recombination of alleles that are identical by descent:
deleterious recessive alleles are rare, but more likely to be shared by kin
Increased chance of the combination of deleterious recessive alleles in the homozygous condition.
Effects Of Inbreeding on juvenile mortality in captive populations of mammals (Ralls & Ballou 1983)
^ higher % Juvenile mortality in inbred
^ first demonstration of inbreeding depression – in a study of zoo animals
Genetic drift acts on all populations
Impact is inversely proportional to populations size.
Genetic diversity lost at rate of:
Ht=(1-(1/(2/Ne)))Ht-1
Ne = effective population size
^ size of an idealised population that shows the same rate of decay of Heterozygosity as the observed population.
See in notes graphs from From Evolutionary Biology last year: Illustration of simulated (grey line) and actual (blue line) loss of
diversity over generational time for different population sizes.
^ heterozygosity at generation t is diminished by a factor of 1/2Ne compared to the previous generation (t-1).
4 factors that affect rate of loss of diversity:
(1)Relationship between population size & diversity.
(2)Relationship between census N & Ne.
(3) Population size & extinction rate.
(4)Importance of behaviour & life history
References for factors 1 & 2
(1)Relationship between population size & diversity.
Genetic drift (see Meffe & Carroll): Halocarpus bidwilli Conifer (New Zealand)
& Red cockaded woodpecker (Picojdes borealis)
(2)Relationship between census N & Ne.
Ne smaller than N (after Frankham 1995)
References for factor 3
(3) Population size & extinction rate.
Reed et al. (2003)
experimented with Drosophila
melanogaster and found the more
inbred populations went to extinction
faster.
This simulation analysis. based on 500 replications and the life history Of the elephant seal (Hoelzel Iggg Biol J Linn
Soc 68, 23-39), illustrates the relationship between population size and extinction risk.
Detaills for factor 4
(4)Importance of behaviour & life history
population cycles (e.g. lemmings) approximated by harmonic mean
Migration – arrival of new individuals adds new genes and this reduces loss of heterozygosity
Variance in reproductive success e.g. in polygonous species creates a bottleneck as not all males get to breed
(4)Importance of behaviour & life history:
Demographics: population cycles
Ne influenced most by smallest population sizes in the cycle.
can be approximated by the harmonic mean: 1/Ne= 1/t(1/N1+ 1/N2 +…)
t = number of generations,
N1 = size of population at generation 1,
N2 = size at generation two, etc
(4)Importance of behaviour & life history:
Demographics: migration
Expected rate of loss of H in a population of 100 grizzly bears.
In Isolation
vs
introduce 2 unrelated bears every
(10 years).
see notes for graph - higher level of heterozygosity observed even just with two new individuals every 10 years
(4) importance of behaviour and life history
Variance in reproductive success:
- e,g: polygynous species,
- can consider the effective size of male & female
populations separately to estimate impact on overall
4(NmNf) /(NmNf) - Nm is the effective male population size
- Nf is the effective female populations size.
if all males get to mate then 50/50 but in polygonous species there is bias in mating
see notes for equations
Issues associated with the impact of low genetic diversity on fitness in natural populations led to considerations about how small a population could be and still be ‘OK’
An early consideration was the “50, 500 rule”, first expressed by Franklin in 1980 (in the book by Soule & Wilcox pictured above).
Here’s the idea:
Ne ≈ 50 should be enough to avoid short-term inbreeding depression
Ne ≈ 500 required to avoid long-term erosion of genetic variation in quantitative traits with high heritability (denoted by multiple genes that determine important phenotypes e.g. height or milk production)
In small populations the rate of change in ‘additive’ variance (VA) should be determined by the rate of loss by drift, and the rate of gain by mutation.
deltaVA = V_n— (VA 1 2Ne) (ML = increment in VA per generation due to mutation)
Because at equilibrium AVA = 0, then this reduces to Ne = VA/2Vm
^ Given estimates for these parameters available at the time,
Franklin calculated a minimum Ne of 500
Conservation genetics was going well until Lande suggested there was less need to look at genetics than demographics:
ande (1988) Science 241: 1455-1460 1,710 citations and counting…
Lande’s main points:
1) Echoes the often stated idea that conservation biology is a ‘crisis discipline’ – important decisions often have to be made quickly. At the time genetic work was not a fast process
2) Cites the studies advocating the use of Ne = 500 as the minimum viable population size from a genetics point of view, and suggests that this has led to management plans that ‘neglect other factors that may require larger population sizes for population persistence’ e.g. Allee effect
3) Notes critical demographic factors such as the Allee effect (small populations experiencing low viability and reproduction for ‘non-genetic reasons’), demographic stochasticity, edge effects, and local extinctions.
4) Suggests that gradual inbreeding or reduction in population size may result in relatively little inbreeding depression because selection will purge the population of deleterious recessive alleles when they become homozygous. Studies since suggest mixed effects
5) “demography may usually be of more immediate importance than population genetics in determining the minimum viable sizes of wild populations”
Particular study supporting Lande’s view: Northern Spotted Owl
2500 pairs left at the time (similar now), listed under Endangered Species Act in 1990, requires old growth forest habitat
1984 US Forest Service management plan was based on preserving at least 500 pairs* to maintain genetic diversity
Models based on stochastic demography and habitat occupancy suggested extinction under this plan – habitat too sparse
*note: Nc/Ne considerations not explicit
Genetics and Extinction Frankham
Frankham addresses some of the key issues:
1) Can inbreeding impact the probability that a population will go extinct? YES Cites various experimental studies, and some for natural populations, e.g. Saccheri et al. (1998) on the Glanville fritillary butterfly – 42 populations compared; inbreeding explained 26% of the variation in extinction risk overall.
2) Are species typically driven to extinction before genetic factors can impact (the ‘Lande effect’)? Cites Spielman et al. (2004)
Most species are not driven to extinction before genetic factors impact them. PNAS 101:15261-15264
Do small populations loose evolutionary potential?
Hard to show – should be related to diversity of phenotypes, but Reed and Frankham published a meta-analysis in 2003 and found that the correlation between molecular diversity and life-history traits was low and non-significant. However, Santos et al (2012 J Evol Biol 25, 2607-22) compared experimental founder population size for Drosophila subobscura and found a strong correlation with adaptive potential.
Hoelzel et al. (2019) Conservation of adaptive potential and functional diversity. Cons Gen 20, 1-5
see Seaborn et al. (2021) Global Change Biol. 27, 2656–2668 chart in notes
^ climate change dispersal plastic change allows some adaptation
Mutation meltdown in sexual populations.
i) In large populations, deleterious alleles kept at low frequencies because of selection, but in small populations, drift becomes more important and mildly deleterious alleles become selectively neutral.
ii) Some of these deleterious alleles increase in frequency and reduce fitness – over sufficient time, this could lead to the fixation of deleterious alleles, negative population growth, and a decline to extinction.
iii) Any evidence? Increasing – for example, a study showing fixed deleterious alleles in the ancient genome of the woolly mammoth (Rogers & Slatkin, 2017, PLoS Genetics, 13(3): e1006601)
Northern elephant seal went through a severe population bottleneck. and although now recovered in numbers, retains loss Of function alleles (LOF) that affect female
lifetime reproductive success, and male fertility (Hoelzel et al. (2024) Nat. Ecol. Evol.).
Loss Of Function in genome due to deleterious effect of ‘mutation meltdown’
Summary
1) Loss of genetic diversity reduces future evolutionary options.
2) Positive correlation between variation (within an individual) & fitness - related to both inbreeding depression & the advantage of being heterozygous (heterosis).
3) Intraspecific variation occurs at 3 levels - within the individual, among individuals within a population, & between populations.
4) Heterozygosity is lost as a function of effective population size:
Ht = (1-1/2Ne)Ht-1
5) Effective population size can be much lower than census population size (e.g. often only ~10% in vertebrates).
6) Demographics & behaviour affect effective population size:
1/Ne =1/t(1/N1 + 1/N2 + . . .)
Ne = 4(NmNf)/(Nm + Nf)
