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Hardy-Weinberg equilibrium (HWE)
One locus with 2 alleles at HWE: p2 + 2pq + q2 = 1
HWE illustrates an important principle: random mating of individuals
is usually equivalent to random union of gametes (alleles)
Assumptions of HWE
•Random Mating
•large population size (no drifting)
•no selection
•no migration
•no mutation
Implicit assumptions:
•sexual reproduction
• nonoverlapping generations
•normal mendelian segregation of alleles
• equal fertility of parent genotypes
• equal fertilizing capacity of gametes
• equal survival of all genotypes
Is this realistic? Probably not.
Linkage equilibrium
•Alleles at separate loci are expected to segregate independently
during meiosis. They show linkage equilibrium.
Example:
• 2 loci with alleles A1 and A2; B1 and B2 their frequencies will be p1 and p2 and q1
and q2.
•Possible gametes A1B1; A1B2; A2B1; A2B2
• Genotype frequencies will be the product of constituent allele frequencies
Linkage disequilibrium
Linkage disequilibrium = a deviation from random associations of
alleles at different loci
• Linkage disequilibrium can be caused by :
- chance events
- population bottlenecks
- recent mixing of different populations
- selection
• Linkage disequilibrium is important because:
- It is common in threatened species with small populations
- evolutionary processes are altered
- functionally important genes may exhibit linkage disequilibrium
- can be a signal of recent admixture of populations
LECTURE THREE:
EVOLUTION IN LARGE
POPULATIONS: SELECTION
Influences upon genetic diversity and the evolution of
populations
Genetic Drift
Mutation
Natural Selection
Migration
The need to evolve
• environmental change is ubiquitous
– Pests, parasites, novel competitors, anthropogenic change,
global warming, new diseases
• Species must adapt and evolve to avoid extinction
Ecological responses to recent climate
change
(Walther et al. (2002) Nature 416: 389-395)
Ecological responses to recent climate
change
(Walther et al. (2002) Nature 416: 389-395)
Ecological responses to recent climate
change
(Walther et al. (2002) Nature 416: 389-395)
The need to evolve
• environmental change is ubiquitous
– Pests, parasites, novel competitors, anthropogenic change,
global warming, new diseases
• Species must adapt and evolve to avoid extinction
The “Red Queen Hypothesis”
(Van Valen, 1973)
• species must continually evolve in order to avoid falling behind
competitors
Adaptation
• 3 forms of adaptation: Physiological, behavioural and genetic
Physiological adaptation: change in metabolism or biochemistry to
deal with an environmental problem
Example: High-altitude adaptations in vertebrate haemoglobins
• Increased blood O2 affinities at
altitude
• Linked to structural changes in
haemoglobin molecules
Weber (2007) Respiratory Physiology
& Neurobiology vol 158 132–142
Adaptation
Behavioural adaptation: the things organisms do to survive
Example: feeding specialisations in bottlenose dolphins in Shark
Bay, WA
• Subset of population uses
sponges to probe substrate
for fish
• Recent co-ancestry
• Vertical social transmission
among females
• Cultural transmission of tool
use?
Krützen et al. (2005) PNAS vol 102 8939-8943
Adaptive evolution
Adaptive evolution: long term evolutionary changes in response to
natural selection upon superior genetic variants
• Adaptive evolutionary changes in animals have been
documented in:
- morphology, behaviour, colour, prey size, body size, life history,
disease tolerance and resistance, biocide resistance, tolerance
to pollutants.
• Plants evolve in response to:
- soil conditions, light regimes, water stress, flooding, air
pollution and herbicides. Plant populations adapted to diverse
ecological conditions are so common that they have their own
term, called ecotypes.
Rapid adaptive evolution in Darwin’s finches
Case study: evolution of Darwin’s finches caused
by a rare climatic event (Grant and Grant, 1993
Proc. R. Soc. Lond. B 251 111-117)
• Darwin’s finches studied continuously on Galapagos Is. Daphne
Major since 1973
• Major El Nino 1982-83 causing 8 months rain
• Plant and seed communities changing introducing new selection
pressures
• Directional selection for longer, slender beaks better adapted for
eating smaller seeds
Unpredictable Evolution in a 30-Year Study of Darwin’s
Finches
(Grant and Grant, 1993 Science 296: 707)
Adaptive evolution and explosive
speciation in cichlid fish
Kocher, T (2004) Nature Reviews Genetics 5: 288-29
• Genetic adaptation and adaptive evolution is ubiquitous in species
that have genetic diversity
Adaptive evolution
• Take home message: Adaptive evolution is ubiquitous in plants
and animals that have genetic variation
• Adaptive evolution is important in the following conservation
contexts:
- Preserving evolutionary potential
- Adaptation to marginal environments
- Genetic adaptation to captivity
- Adaptation of invasive species
- Outbreeding depression
Natural Selection
Natural Selection
• Differential survival and reproduction in nature that favors
individuals that are better adapted to their environment
• eliminates of less fit organisms and genetic variants
• Moulds the variation made available by mutation, drift and
migration
• Adaptive changes occur only by natural selection. During the process
of adaptation, natural selection can enhance, retain or eliminate
variants
Evolving populations are complex
systems
• Evolving populations are complex systems influenced by mutation,
migration, selection and chance operating within the context of the
breeding system
Competition
Climate
Disease
Loss of
genetic
diversity
Zygotes
SELECTION
CHANCE
SAMPLING
deaths
Adults
Mating
MIGRATION
Gametes
Selection of mates
MUTATION
Introduction to Conservation Genetics 2
Fig 6.1 Evolving pop as complex systems.ppt
Selection
• Alleles whose carriers produce fertile offspring that survive to
reproductive age increase in frequency
• Alleles whose carriers produce fewer offspring decrease in frequency
• Selection operates at all stages of the life cycle:
- Acquisition of mates
- Mating success
- Fertlization success
- Number and survival of offspring
- Longevity
- Pollen production
- Pollination success
- Zygote viability
- Dispersal ability
Selection decreases the frequency of
deleterious alleles
• Consider selection against a recessive lethal, Chondrodystrophic
dwarfism in California condors
• Recessive homozygotes die but heterozygotes have normal survival
Modelling the impact of selection against chondrodystrophy: refer to table 6.1 and Example 6.1
Selection increases the frequency of
advantageous alleles
• Consider adaptive evolutionary change, industrial melanism in the
peppered moth
• Melanic moths first recorded in 1848
• By 1900 99% of population melanic
• Frequency of M (melanic) allele increases
until eventually fixed
• Rate of change depends on the strength of
Selection against the non melanic form or the
selection coefficient, s.
Modelling adaptive evolutionary change, refer to Figure
6.4, Box 6.2
Selection models
• The impact of selection depends
on:
- Strength of selection (selection
coefficient, s)
- Mode of inheritance
- Allele frequencies
Selection is stronger on some loci and
characters than others…
Selection is stronger on some loci than others…
For equivalent circumstances, selection has a greater impact on
haploid loci than on autosomal diploid loci. Sex-linked loci are
intermediate (refer to table 6.2)
Selection is stronger on some characters than others…
– introns / microsatellites
– proteins
~ weak
~ moderate
– MHC
~ stronger
• All still relatively weak compared to selection on morphological
or quantitative characters
• Eg. selection coefficient at MHC typically ≤ 1%
Selection on quantitative characters
• Variation is determined by several loci and environmental effects
• Selection affects phenotypic means and variances
3 forms of selection on quantitative characters:
Directional selection: favours
phenotypes toward one end of
the distribution and shifts
mean towards that extreme
Stabilizing selection: favours
phenotypic intermediates and
reduces variation about the
mean
Disruptive Selection: favours
both phenotypic extremes and
increases variation about the
mean
Case study: directional selection
Undesirable evolutionary consequences of trophy hunting in
Bighorn sheep Coltman et al. (2003) Nature 426, 655-658
Directional selection: favours phenotypes toward one end of the
distribution and shifts mean towards that extreme
Case study: stabilizing selection
Stabilizing selection for birth weight in humans after Mather, 1973
Stabilizing selection: favours phenotypic intermediates and reduces
variation about the mean
Case study: disruptive selection
Disruptive Selection: favours both phenotypic extremes and
increases variation about the mean
Disruptive selection and then what? Rueffler et al. (2006) TREE 21,
238-245; Schulter and McPhail (1992) The American Naturalist 140:
85-108
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EVOLUTION IN LARGE
POPULATIONS: INTERACTIONS
OF MUTATION, MIGRATION
AND SELECTION
Mutation
• Sudden genetic change in an allele or chromosome
• ALL GENETIC DIVERSITY ORIGINATES FROM MUTATION
• Single locus mutations are generated by base substitutions,
additions and deletions, gene duplication events and by insertion
and excision of mobile elements
• Mutations that affect fitness traits are most important to
conservation biology
• Silent or neutral mutations are still important as molecular
markers
Mutation rates vary across loci and
characters
• Generally speaking, mutation rates are low and can often be ignored as
an evolutionary force
Mutation is a recurrent process
• Mutations continue to arise over time.
• Modelling the impact of mutation on a population:
A1
p0
u
Frequency of A1 in the next generation:
A2
q0
p1 = p0 (1-u)
Change in frequency of the A1 allele:
∆p = p1 – p0
Substitute for p1:
∆p = p0 (1-u) – p0
∆p = -up0
• Genetic diversity takes hundreds to millions of generations to be
regenerated by mutation (refer to box 7.1)
Mutation occurs in both directions
• The balance between forward and reverse mutations (up = vq)
results in an equilibrium
A1
p
u
v
A2
q
u
q̂ =
u+ v
Example: What is the equilibrium frequency of the A2 allele in a case
where the forward mutation rate (u) is 10-5 and the reverse mutation
rate (v) is 3x10-6
u
q̂ =
u+ v
-5
10
q̂ =
= 10/13 = 0.77
-5
-6
10 + 3x10
Equilibrium frequency of A2 (q) = 77% . Equilibrium A1(p) = 1 - 0.77 =
0.23
Mutation-Selection balance
• Most mutations are deleterious and their removal by selection is slow, thus
they accumulate within the genome. This is referred to as the ‘mutation load’
•High cumulative rate of deleterious mutations is kept in check by selection mutation-selection balance
Autosomal recessive
u
q̂ = √
s
Refer to Pg 149 of text derivation and table 7.4 for expressions for other modes
of inheritance.
Migration
• Population differentiation through selection and genetic drift is
slowed by migration (gene flow)
∆q = q1 - q0 = q0 + m (qm – q0) – q0
= m (qm – q0)
Importance of mutation, migration
and their interactions with selection
to conservation
• genetic diversity lost by chance and selection is regenerated by
mutation
• forced migration through translocation can be used as a
management tool to recover lost genetic diversity in small
threatened populations
• migration can reverse inbreeding depression
• inbreeding results in exposure of rare deleterious alleles in the
mutation load leading to reduced reproduction and survival
• understanding these interactions allow us to tease apart the
effects of the various forces upon natural populations, leading to
improved understanding of the study system
3 Founders
NEXT LECTURE:
GENETIC
CONSQUENCES OF
SMALL
POPULATION SIZE,
MAINTAINING
GENETIC DIVERSITY
G1
G2
G3
Genetic Drift /chance events
Mutation
Relevance of Mutations in Populations
• Mutations are the source of variation, but the process of mutation
does not itself drive genetic change in populations
• Mutation rates (probability that one allele changes to another
allelic form in one generation) are too slow
Relevance of Mutations in Populations
•Mutation works best in larger populations
•In large populations, nearly every conceivable mutation will occur,
which gives natural selection the chance to “try them out” and retain
the few beneficial ones
• For species that have lost substantial proportions of their genetic
variation, regeneration by mutation may take a million or more
generations (unlikely to occur during the lifespan of the species)
• Mutation is almost entirely ineffective in generating useful variation
in small populations and probably too slow to help species of
conservation concern
Migration
Migration
• Genetically effective migration from another population will replace
lost, or introduce new, variation to a population
• Migration reduces differences among populations generated by
mutation, selection or chance
• reduced migration limiting geneflow leads to random differentiation
among sub-populations
With gene flow –
panmixia, or one
population
Without gene flow –
population
fragmentation and
subdivision
Migration
• Migration increases genetic diversity within a population according
to:
- the proportion of migrants in the “new” population (i.e. the postmigration population)
- the difference of allele frequencies in the migrants compared to
those of the “old” pop.
Old popn
Migrant popn
New popn
Original population plus
migrants and their new
alleles or different
frequencies. Therefore,
Diversity increases.
Migration
• Increased loss of alleles by drift in small populations is
counterbalanced by the greater impact of an individual migrant
• Very few migrants are needed to prevent differentiation of
subpopulations by drift at neutral loci
Fst = measure of
population differentiation
Nm = no. of individuals in
the pop X no. of migrants
per generation