natural selection 2

Question 1

Estimating generational change in allele freq for A1 due to selection based on relative fitness under HWE

Answer 1

The formulation given below allows us to estimate the generational change in allele frequency for A1 due to selection based on relative fitness under HWE (HWE = Hardy Weinburg Equilibrium)

deltasP = pqs(ph+q(1-h)/1-2pqhs-q^2s

Question 2

Example of directional selection: Scarlet Tiger Moth

Answer 2

The medionigra (dark wing) allele in the Scarlet Tiger Moth (Panmaxia dominula)

– decline of the ‘medionigra’ (M) allele.

Work done over the years by RA Fisher, EB Ford, PM Sheppard and others:
- Calculated expected loss rate compared to actual record (see graph in notes)
- So since it matches observation is it due to natural selection?
- Not necessarily – it could it just be about temperature and not selection for allele frequency at all.
- This was proposed based on wild-caught larvae held in the lab at constant temperatures

(Owen & Goulson 1994) see charts in notes:
Infact it was found that variation may be due to where moths were raised rather than temp.

Jones (2000) challenged this idea
“The maximum and minimum daily temperatures and the monthly average temperatures have been measured at the time and site of pupation and metamorphosis of P. dominula. These field observations show that the frequency of medionigra and the temperatures measured both at the sites of pupation and in air near the ground in Cothill Fenare unrelated. Thus the laboratory experiments have been misleading and do not help to explain the decline and annual fluctuations in the frequency of medionigra in the Cothill population of P. dominula”

Later, O’Hara (2005, Proc. R. Soc. B 272, 211-217)
modelled the pattern of variation over time and suggested that both fluctuating levels of selection and genetic drift may be important

Conclusion:
- Although a model based on section against the M allele with s=0.1 and h=0.5 fit the observed trend, we couldn’t confirm selection as the driver
- Suggestions that it was instead environmental temperature were suggestive, weren’t fully supported
- Later models incorporating both selection and drift were consistent with the trend, but still not causative proof

Question 3

Example of directional selection: Peppered moth study

Answer 3

Peppered moth (Biston betularia) and industrial
melanism. (Based on various papers by H.B.D. Kettlewell and colleagues)

Mutation for peppered moth melanism is due to a transposable in intron I of the Cortex gene. In (a) the candidate region element is shown, refined in (b) and the indel shown in orange. (Van’t Hofet al. (2016) Nature 534)

Question 4

Example of directional selection: Finch beak variation

Answer 4

Rosemary and Peter Grant spent decades on the Galapagos island, Daphne Major observing finches — major drought in 1976-77 affected beak depth in the medium ground finch (see Boag and P. R. Grant 1981 Science 214:82)

Abzhanov et al (Science 2004 305: 1462 1465)
suggested that the change in beak thickness could be due
to changes in the expression of just one ‘growth factor’
gene: Bmp4

Genome scans revealed more loci likely associated with bill size and foraging strategy among Geospiza sp.
“HMGA2 has been associated with variation in height, craniofacial distances, and primary tooth emption
in humans”. WIFI inhibits the developmental control gene ‘WNT’.

Further evidence for natural selection among the Galapagos finches comes from the observation that extensive morphological variation, evidently adapted to local habitat, has evolved in spite of relatively little differentiation at neutral genetic markers. The finch phylogeny (left) is based on non-coding DNA sequence data: Sato et al. 2001 Mol. Biol. .Evol. 18:299-311

Question 5

Another way to look for evidence of selection at the level of individual genes is to consider the rate of non-synonymous vs synonymous change

Answer 5

Another way to look for evidence of selection at the level of individual genes is to consider the rate of non-synonymous vs synonymous change

dn/ds < 1
This suggests that deleterious non-synonymous changes are being removed by selection. We call this ‘purifying selection’

dn/ds > 1
This indicates that positive selection has caused some amino-acid substitutions

dn/ds = 1
This suggests that amino-acid substitutions have been neutral (or it could be a balance between positive and purifying selection)

See Parmley & Hurst (2007) Bio Essays 29, 515-519

One caveat to be aware of: Sometimes synonymous changes can have functional relevance, e.g if they affect splicing or the rate of protein production

Question 6

Population level comparisons

Answer 6

Looking for deviations from expectations (in this case a measure of population differentiation that assumes neutrality)to find evidence for positive(directional) selection

Question 7

FST

Answer 7

— ranges from 0 to 1
— e.g: if F ST = 0.15, this suggests 15% of genetic variance can be explained by differences among populations.

• if 0 = panmixis (no subdivision, random mating occurring, no genetic divergence among populations)
• values up to 0.05 = low genetic differentiation
• > 0.25 = very great genetic differentiation
• 1 = complete isolation (extreme subdivision).
  — F ST typically calculated based on data from multiple genes.

Question 8

Evidence of local adaptation in the copper rockfish?
Buonaccorsi et al. (2002) Can. J.

Answer 8

In the end the authors thought isolation and genetic drift was the most likely explanation

Question 9

Population Genomics of Parallel Adaptation in
Three spine Stickleback using Sequenced RAD Tags
Hohenlohe et al 2010

Answer 9

Freshwater vs saltwater: Screening across genomes
found peaks of differentiation (FST), some too high to be
explained by neutral differentiation alone.

stickleback genome estimates:
41% regulatory
17% coding
42% probably regulating

Question 10

Focal genes and more genome scans

Answer 10

Build on what you know about a particular gene as a candidate gene to see if it relates to the environment e.g as HSP70 gene was studied in evolution canyon (Israel):
Differential expression of HSP70 gene in two habitats
that differ in microclimate for Drosophila melanogaster
“Evolution Canyon”
(Michalak al. 2001 PNÅS 98: 13195-13200)

Question 11

Another genome scan example:
Change of conditions from surface to deep-sea

Answer 11

changes occurring:
- hydrostatic pressure (main change)
- thermal gradient
- salinity gradient
- oxygen minimum layer

see: https://doi.org/10.1038/s41559-018-0482-x
Genomics of habitat choice and adaptive evolution
in a deep-sea fish (Michelle R. Gaither et al)

1000-1500m is an important habitat boundary various aspects of physical oceanic properties show a transition at this depth

60 genomes sequenced.
Most comparisons showed correlated genotype frequencies, but all comparisons with 1800m showed strong evidence for selection associated with habitat depth (violated the assumption of correlated genotype frequencies).

For 9 outlier SNPs (single nucleotide polymorphisms), the comparison by genotype shows fixed genotypes at
1800m and segregating at lower depths 6 loci showed fixed non- synonymous changes in coding genes.

Neutral loci (-50K) no difference by depth
OBSLI : one of loci with non-synonymous changes
that suggest functional differences (Obscurin aka OBSLI)

Question 12

Balancing selection

Answer 12

Two main types:

Overdominance: this occurs when h < 0 – also known as ‘heterozygote advantage’.

Frequency dependent: in this case the allele will be, e.g. favoured when rare, but disfavoured when common (or visa-versa) - tends towards an equilibrium value. A similar effect can come about when the environment changes over time.

Question 13

Overdominance examples:

Answer 13

Sickle cell anaemia

Homozygote suffers disease (crystal aggregations in blood that can block capillaries),but heterozygote has only mild form, and is at the same time resistant to malaria

It is an autosomal recessive disease caused by mutation in the β-globin gene – a Glutamic acid to Valine substitution in one of the Hg chains that together bind O2

MHC Class II gene polymorphism

selection for heterozygotes in immune system genes preserves essential variability

Question 14

Frequency Dependent Selection:

Answer 14

Positive:
Fitness increases as an allele becomes common, &
decreases as allele becomes rare.

Negative:
Fitness increases as an allele becomes rare, &
decreases as allele becomes common.

Question 15

Example of positive frequency dependence:
Müllerian Mimicry

Answer 15

First described by the German zoologist Fritz Müllerin 1878

Unpalatable species mimic each other when they overlap in geographic range to reinforce signal to predators

Their bright coloration is an ‘aposematic’ signal to the potential predator

Question 16

Example of negative frequency dependence:
Batesian mimicry

Answer 16

The mimic species is itself palatable, but resembles a distasteful model species.

This is only effective if the mimic species is rare compared to the model species.

Genetic polymorphism can be promoted when the palatable species adopts several different model species to mimic -expected since the mimic needs to remain relatively rare

Question 17

Other types of frequency dependence

Answer 17

Temporal patterns – in this case a characteristic maybe an advantage part of the time (for example during certain seasons), while another characteristic may be an advantage at other times. If the net benefit balances, the two characteristics may be preserved.

Spatial patterns – microhabitat variation can define separate niche space within the same environment/geographic area. In this case, individuals may adapt to different microhabitats – a potential path to speciation.

Question 18

Lab experiment of disruptive selection

Answer 18

Isolation by disruptive selection (Thoday & Gibson,1962)

This experimental study showed that disruptive selection could work in principle. Two populations of drosophila were subjected to differential selection for 12 generations.

Question 19

Natural example of disruptive selection

Answer 19

The Lazuli bunting provides a natural example of disruptive
selection
(see Greene et al. 2000 Nature 407: 1000-1003).

Both dull and bright yearling males attracted mates, and had more successful broods - causing selection for both extremes.

Question 20

Wright’s Shifting Balance Theory of evolution.

Answer 20

A novel idea that integrates directional selection and random genetic drift:

Wright felt that the interaction between genes (epistasis) is likely very important, and that gene combinations would define a fitness landscape. Directional selection would move a population towards an adaptive peak, but in finite populations genetic drift could move a population off a peak, through a trough and onto another(potentially higher) peak.

Wright envisioned three phases:

l)An exploratory phase where a population may be on a peak (better than ‘nearby’ options, but not the best)
- The action of small groups explores new combinations. Most stay on the suboptimal fitness peak (reasonably successful). but some get caught in adaptive valleys (unsuccessful).

2)Drift and selection promote movement to a higher peak
- selection causes the groups that are in the adaptive valleys
to move towards new higher fitness peaks

3)Eventually the success and dispersal of individuals on the highest peak promotes success overall.
- groups at higher fitness peaks off migrants helping other groups move to higher fitness peaks.

So does it happen?

-It’s phases 1 and 3 that are controversial
- phase 2 is just directional selection and no longer controversial.
- There have been proposed examples, e.g. Mallet (2010) Shift happens! Shifting balance and the evolution of diversity in warning colour and mimicry. Ecol. Entomol. 35, 90-104

Question 21

Phenotypic plasticity : why wait for evolution if you can do it yourself?

Answer 21

Phenotypic developmental plasticity is the potential for a given genotype to develop different phenotypes in different environments. A striking example in the world of trees is the Jeffrey pine (Pinus jeffrey) which adapts its shape to the weather.

common garden experiments using Arctic Char also illustrate phenotypic plasticity
(Parsons et al. (2011) 9101.2011.02301.x )

see in notes schematic graphs showing reaction norms according to plasticity

Question 22

Population density and palatability in crickets - linking phenotypic plasticity and evolution of aposematism

Answer 22

In this study by Sword (2002, Proc. Royal Soc. B 269, 1639-1644) there is a relationship between population density and palatability that suggests a role for phenotypic plasticity in the evolution of aposematism (being unappetising)

Question 23

genetic assimilation

Answer 23

The process by which plasticity may facilitate evolution by natural selection is called ‘genetic assimilation’.
A ‘sigmoidal’ reaction norm may be affected by selection or drift. (see notes for cricket example)

Question 24

Summary

Answer 24

1) There are now many examples of directional selection, both for phenotype and at the molecular level, though determining that positive selection is the motive force can be difficult

2) Evolution by balancing selection can be due to either selection for heterozygotes(such as in sickle cell anaemia), or frequency dependent selection (which can be positive, negative or related to temporal/ spatial variation in the habitat)

3) Evolution by disruptive selection can be due to the positive selection of different forms, or to selection against the heterozygote.

4) A theory that incorporates both natural selection and genetic drift is Sewell Wright’s shifting balance theory, whereby a fitness ‘landscape’ can be explored by drift, and peaks climbed by natural selection.

5) Phenotypic plasticity allows for some phenotypic variation for a given genotype, and may facilitate the evolution of traits by natural selection. The ability to be ‘plastic’ is also something that can evolve