Lectures 4-6 Flashcards
Who came up with the theory of particulate inheritance
Gregor Mendel
Who believed in the theory of blending inheritance
Darwin
What was the theory of blending inheritance
heritable factors blend to produce an intermediate phenotype
Why does the theory of blending inheritance not work
because if offspring phenotypes must always be intermediates of parents, all individuals would look the same after just a few generations
What are the 3 laws of the particulate theory
Law of segregation
Law of independent assortment
Law dominance
What is law segregation
individuals possess two alleles at each gene – one from each parent
What is law of independent assortment:
genes for separate traits are passed on independently from parents to offspring (NB this is not always true - remember linkage disequilibrium?)
What is law of dominance
recessive alleles will always be masked by dominance alleles
What are Darwins four postulates after the modern synthesis
- As a result of mutation, gene flow and recombination, individuals within populations are variable for nearly all traits.
- Individuals pass their alleles on to their offspring intact.
- More offspring are produced than can survive.
- The individuals that survive and reproduce are those with the alleles that best adapt them to their environment.
What were the two schools of thought on genetic variation within populations until 1960
Classical and Balanced
What did the classical school think
Genetic polymorphisms are rare and mainly deleterious. At each locus, the best allele should be fixed by natural selection
What did the balanced school think
Large amounts of genetic variation are maintained in populations. At each locus, polymorphisms are maintained by “balancing” natural selection
Was the classical or balanced school right in there thinking
Turned out to be both wrong… but to be fair, they didn’t have any data!)
When is it reasonable to use phenotype as a proxy for genotype
for discrete variation, where a trait follows a simple Mendelian inheritance pattern e.g
When is it not reasonable to use phenotype as a proxy for genotype
When you have continuous traits such as height as continous traits are mostly polygenic (controlled by many genes)
Ways you can visualise genetic (protein) variation
gel electrophoresis
microsatellite genotyping
Why was the classical school wrong
polymorphisms are not rare
Why was the balanced school wrong
no evidence that selection maintains all the variation
Who argued for neutralism in the selection-neutralism debate
Motoo Kimura
Who argued for selection in the selection-neutralism debate
John Maynard-Smith
What is the neutralism stance on the evolution at the molecular level (DNA sequence)`
Most variation at molecular level is selectively neutral, fixed by genetic drift
Most non-neutral mutations eliminated by selection
(does not suggest that morphological, physiological and behavioural features evolve by random genetic drift – such features evolve by NS, its just that this make up only a small part of overall molecular variation
What is the selectionism stance on the evolution at the molecular level (DNA sequence)`
Substantial portion of the genome affected by selection
Selection acts on many genes, and also affects linked sites
Reasons why variation is maintained (briefly)
various mutational mechanisms/
recombination, natural selection, gene flow recombination
What is the observed genotype frequency
the proportion of a population that has a certain genotype
What is allele frequency
proportion of a given allele in the population
How to work out the total amount of alleles in sample
number in a sample x2
What are the assumptions of hardy weinburg equilibrium
a. infinitely large population size
b. no mutation
c. no selection
d. no gene flow
e. random mating
What can we test with Hardy weinburg equilibrium
test whether evolution is occurring and see if one or more assumptions are being violated
What is genetic drfit
– random fluctuations in allele frequencies occur as a result of ‘sampling error’ between generations in finite populations
What can genetic drift lead too
Can lead to the replacement of old alleles by new alleles (and the trait they confer) – non-adaptive evolution
What are some differences between natural selection and genetic drift
GT is non adaptive and can affect all loci/alleles
NS is adaptive evolution and favours mutations that give an adaptive advantage. Does not necessarily affect all alleles
What is a similarity between genetic drift and natural selection
Both cause allele substitutions – evolutionary change – in populations
What happens when alleles drift towards fixation
the freq of heterozygotes decreases.
What is the bottleneck effect
Specific case of genetic drift
occurs when some event causes a drastic reduction in the size of a population. Usually results in loss of genetic variation
What is the founder effect
A colony formed by a small number of founders will suffer loss of genetic variation – rare alleles are likely to be lost
What is census size
Number of individuals in a population
What is Ne
effective population size ie
The size of an ideal theoretical population that would lose heterozygosity at the same rate as the actual population’.
What 3 factors influence effective population size
1) Variation in the number of progeny. If some individuals have more offspring than others, Ne will be reduced
2) Overlapping generations
Individuals mate over multiple generation.
Offspring may mate with parents. They carry identical copies of the same genes, so the effective number of genes in the population is reduced.
3) Unequal numbers of males and females
How do fluctuations in population size influence Ne
All populations fluctuate in size – the rate of genetic drift is higher in small populations, so Ne is more strongly affected when population is small
What is F
coefficient of inbreeding
What is inbreeding
Mating between related individuals
When does the inbreeding coefficient increase more rapidly
increases more rapidly in small populations than in large populations.
Evidence for inbreeding depression on Florida panther
Tail kink
Cryptorchidism (>80% males) & deformed sperm
Poor fecundity
High parasite load and disease susceptibility
Atrial septal defects
What is inbreeding depression
When inbreeding reduces reproduction and survival
Consequences of inbreeding
Reduces heterozygosity
Exposes rare deleterious recessive alleles (as homozgotes)
Loss of genetic diversity
Similarities between inbreeding and genetic drift and what are the consequences
Both related to population size
Both have similar effects in terms of reducing genetic diversity
Both increase risk of extinction in small populations
This is why genetic diversity is one of the three global conservation priorities of the IUCN
Both key forces in evolution, especially in small populations
Genetic drift influences genetic variability predictably , how is that beneficial
if we can measure genetic variation at genes not under natural selection, we can compare patterns of DNA variation from real populations to reconstruct population history
Why is is important to know effective poulation size, not just
Not all individuals in a census will contribute to the next generation. Thus, genetic drift and loss of heterozygosity will be greater than expected as the population is effectively smaller than it really is.
What is genetic rescue due to
Gene flow
Example of genetic rescue
1995 Florida Panther N ≈ 25 with inbreeding depression (last lecture!) … 95% likelihood of extinction in 20 years…
1995 – Eight pumas introduced from Texas (historically linked)
1995-2007 Population size stabilises! Hz increases! - Survivorship increases! - Inbreeding traits decrease!
What can cause population structuring
Natural aggregations
Fragmented habitats
What can population structure lead to
It can cause population subdivision and lead to genetic differentiation among subpopulations
What can cause genetic differences between populations , and in turn, structural differences
Random processes such as genetic drift and mutations
Deterministic processes such as gene flow and selection
What is the Wahlund effect
Reduction in Hz caused by structure (shown by pooling two populations together)
What does a large F mean
A larger F means there is greater population subdivision (or inbreeding)
How can population structure be quantified
quantified using Wrights F (fixation) statistics
What is Wrights F (fixation) statistic equation
F = (H,exp – H,obs)/H,exp
where Hexp is heterozygosity expected under HWE = (2pq) and Hobs is the heterozygosity observed
What will cause a low H,obs
Lower Hobs is produced by subdivision into smaller populations -diverging through genetic drift or selection (and/or non-random mating in populations).
What are the 3 hierarchical levels of total F (inbreeding coefficient)
Individual
Subpopulation
Total population
How to calculate Fis
Fis = (Hs - Hi)/Hs
What is Fis
Fis measures - population structure (inbreeding) in individuals relative to subpopulations,
What is Fit
measures - population structure (or inbreeding) in individuals relative to the total population
How to calculate Fit
, FIT = (HT - HI)/HT
What is Fst
measures - population structure (or inbreeding) in subpopulations relative to the total population
How to calculate Fst
FST = (HT - HS)/HT
In terms of F (inbreeding coefficient) , what is Hi
Hi this is the OBSERVED heterozygosity of individuals
In terms of F (inbreeding coefficient) what is Hs
expected Hz in subpopulations – according to HWE
In terms of F (inbreeding coefficient) what is ht
expected Hz in total population – according to H
What happens to genetic structure is there is no migration
With no migration, genetic structure will increase over time due to genetic drift
What equation shows that genetic structure (Fst) accumulates fastest in small populations
FST = 1 – (1 – 1/2N)^t
What is gene flow
movement of gametes or individuals among populations
What are the models of gene flow
Isolated population distribution – Island Models
Patchy population distribution – Stepping Stone Models
Continuous population distribution – Isolation-by-distance Model
What is the island model of gene flow
Discrete populations with individuals migrating from one population to another with equal probability (p)
Model is not realistic in natural populations
What is the stepping stone model of gene flow
Individuals migrate to neighbouring populations with a defined probability (p) that differs according to factors (e.g. distance)
More realistic
Model is computationally difficult beyond 2 dimensions and most organisms inhabit multidimensional space
What is the distance by isolation model
Even distribution of continous overlapping populations
Individuals less likely to migrate to more distant sites
Neighbouring populations are genetically similar
Realistic - used in computer simulations
How to work out expected change in allele frequency per generation due to gene flow
∆p = m(p2 - p1) p1 = allele frequency in recipient population
p2 = allele frequency in donor population
m = proportion of alleles entering a
population through immigration
what is migration-drift equilibrium
When the level of gene flow matches the level of genetic drift
How are gene flow and genetic drift opposing
genetic drift leading to the divergence of populations and gene flow homogenising them.
What is the isolation by distance model
Based on the theory that migration between continuous populations decreases with increasing distance
Direction of migration is random
It terms of isolation by distance model, what is a neighbourhood
= group of individuals from area 2σ wide
Migration distance is measured as the standard deviation σ (sigma) of the migration distribution
What is the relationship between Nb and Nm
Nb is analogous to Nm in the island model: an indicator of gene flow
What are direct methods of estimating gene flow
Mark-and recapture studies
Can be accurate, but don’t take into account what proportion of migrants contribute to gene flow + short term
Tracking marker alleles over a short number of generations
Directly reflects gene flow, but unrealistic in natural populations + short term
What are indirect methods of estimating gene flow
Statistics derived from allele frequencies
Directly affected by gene flow and long-term, but can be difficult to interpret
If you have a high Fst value, what does it mean
Highly significant population subdivision
What does it mean to have a low Fst value
Very little population subdivision
How is genetic drift usually measured
using F statistics
What mechanisms can counter homogenisation by gene flow
Selection (& sexual selection) can act to counter the effects of gene flow at the whole genome-level, or at specific genes
