Transcript The early history of population genetics

Genes, genetics and natural selection
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Darwin’s theory of natural selection explained macroevolutionary patterns in terms of
population-level processes
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The birth of modern genetics led initially to a battle between the Mendelians and the
Darwinians
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The neo-synthesis saw the coming together of genetics and evolutionary thought. The
selfish gene is just a (very elegant) restatement of this fact.
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Patterns of molecular evolution have generated many more controversies, notably over
the neutral theory.
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The processes of speciation and extinction are still very little understood, however
important progress has been made in understanding what types of genetic differences
can lead to reproductive isolation
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What Darwin said
Organisms produce too many offspring
Heritable differences exist in traits influencing the
adaptation of an organism to its environment
Organisms that are better adapted have a higher chance of
survival
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Galton’s law of regression to the mean
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Characters are correlated between relatives
– height, hereditary genius
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But over time, deviations from the mean tend to be diluted
– Great men have less great sons!
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Natural selection cannot produce persistent change
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Mendel’s peas
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x
AA
x
aa
Aa
x
Aa
AA/Aa &
3
aa
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Rediscovered c. 1901 by de Vries, Correns and Tschermak von Seysenegg
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Mendelians versus biometricians
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Mendelians
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Adherents of Galton’s conclusion that natural selection is ineffective
Evolution proceeds in large steps (saltational)
Mutations of discrete nature
Natural selection cannot work because of regression towards mean
Bateson, de Vries
Biometricians
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Adherents of gradualist, Darwinian view
Variation is truly continuous
Large mutations happen, but are not very important
Pearson, Weldon
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Nilsson Ehle’s wheat (1909)
Genotype
AA
Aa
aa
BB
Bb
bb
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Morgan and the fly-room
(Sturtevant, Muller and Bridges)
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Discovered crossing-over (cM)
Proved chromosomes carried
hereditary factors
Showed heritability of bristle
number in Drosophila
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Fisher’s results on genetic variation
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First widely read mathematical treatment of selection
Three types of quantitative trait
– Continuous (weight, height, milk yield)
– Meristic (bristle number in Drosophila)
– Discrete with continuous liability (disease susceptibility)
Frequency
Phenotypic variance = s2P
Trait value
σ P2  σ A2  σ D2  σ I2  σ E2
Phenotypic
Additive
genetic
Dominance
Epistatic
Environmental
Genetic
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Estimating the genetic component of quantitative traits
Offspring
value (y)
y=a+bx
XX
X
X
X
σA
Cov(x, y)
2
b=
= h = 2
Var(x)
σ
2
X
X
X
X
X
X
P
X
Mid-parent value (x)
m
mS
Dm  h2 (mS - m)
Selection
response
Trait value
Trait value
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The neo-synthesis (1920s-1930s)
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Contributions to a coherent Darwinian view of evolution by natural selection
from geology, palaentology, natural history, cytology, genetics, and
populations genetics
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Variation in natural populations
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Mimicry in butterflies
Industrial melanism in moths
Pin and thrum flower forms in Primula
Darwin’s finches
Sickle-cell anaemia
Birth weight
Disease
All maintained
by natural
selection +/recurrent
mutation
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The selfish gene
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The evolutionary theory of Haldane, Fisher and Wright is a gene-centred view
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considers whether a new mutation will spread through a population
NOT what is best for the population
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However, natural selection acts on the set of genes it finds in an individual
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The correlation of relatedness over evolutionary time will determine whether of nor the
fitness interactions between genes are important in shaping evolution
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Y chromosome genes
Green-beard genes and kin recognition
Selfish genetic elements (segregation distorters, cytoplasmic male sterility, sex-ratio
distorters)
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Can natural selection explain
• Mimicry?
The photo shows unpalatable swallowtail
model species (left) and palatable
mimetic forms of female Papilio memnon
(right). At bottom is the Papilio memnon
male. This polymorphic, female-limited
Batesian mimicry was first described by
Alfred Russel Wallace (1865).
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• Social insects?
A Camponotus
japonicus ant sharing
honey with another ant
Mother
Sister
Daughter
Father
brother
son
Niece or
Nephew
female
0.5
0.75
0.5
0.5
0.25
0.5
0.375
male
1
0.5
1
0
0.5
0
0.25
Haplodiploid
Relatedness in haplodiploid insects
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Kin selection
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Work by Hamilton, Price and others showed the importance of interactions between
relatives in explaining biological patterns
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JBS Haldane
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“I would be willing to lay down my life for 2 brothers or 8 cousins.”
rb  c  0
Relatedness
Cost to actor
Benefit to receiver of action
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• Sex-related characteristics?
Stalk-eyed fly
Irish elk
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Two or three theories of sexual selection
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Fisherian runaway process
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Good-genes
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Females have an asymmetric preference for a male trait which varies in the population
Males with the favoured trait are more successful in mating irrespective of whether they
are better adapted to their environment
The population will shift towards the new trait
Requires covariance between trait and female preference
Sexually selected traits are indicators of good genes (Hamilton and Zuk)
E.g. the wattle on a rooster indicates parasite load
Costly traits and the handicap principle
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Costly traits can evolve as honest signals of quality as females will always benefit from
being choosy
(Doesn’t have to be a good genes argument)
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Species-level selection? (Stanley 1975)
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Higher-level selection leading to long-term changes in clade morphology can occur if…
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Speciation rates are correlated with parameters of life-history/ecology
OR extinction is selective
AND rates of speciation and extinction are uncoupled from what natural selection
favours within populations
Evidence?
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Major extinctions were highly selective
Planktotrophic gastropod molluscs have lower extinction rates than those with direct
development BUT the fossil record shows a relative increase in the number with direct
development (higher speciation rates?)
Completely asexual lineages (e.g. some rotifers, fish, lizards) usually at tips of trees,
suggesting they are short-lived
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Evolution at the molecular level: The molecular clock
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The number of differences between genes at the molecular level correlates with the time
separating the species (Zuckerkandl and Pauling 1962)
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The rate of substitution is constant over time
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Sarich and Wilson (1967) used the molecular clock to estimate the human-chimp split as
5MY – previously thought to be 14MY
Doolittle et al. (1996)
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Does natural selection explain molecular evolution?
Kimura (1968); King and Jukes (1969)
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Constancy of rate of molecular evolution (the molecular clock)
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More important regions of proteins evolve at a slower rate than less important
domains
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High levels of protein polymorphism
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High rates of molecular evolution (about 1.5x10-9 changes per amino acid per
year – even in living fossils!)
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Kimura’s neutral theory
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The majority of changes in proteins and at the level DNA which are fixed between
species, or segregate within species, are of no selective importance
The rate of substitution is equal to the rate of neutral mutation
k  f neutral μ
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The level of polymorphism in a population is a function of the effective population size
and the neutral mutation rate
π  4 Ne μ
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Polymorphisms are transient rather than balanced
Frequency
NOW
Balanced
NOW
Transient
Time
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Detecting natural selection at the gene level
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Bursts of amino acid substitution in lineages
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Amino acid changes concentrated at sites within proteins
– HLA
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Specific footprints in patterns of genetic variation
– Genetic hitchhiking
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Speciation and extinction
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How do new species arise?
– Gradual accumulation of differences between geographically separated
populations exposed to different selective pressures - allopatric
– Rapid event associated with change in lifestyle (e.g. host-plant preference,
mating song, chromosome number, hybridisation) – sympatric
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How can we study the process of speciation?
– Hybrid zones
– Genetic footprints
– Analysis of reproductive isolation
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Why do species go extinct?
– Major extinctions in evolutionary history
– Anthropogenic extinction
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The biological species concept
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A species is a population whose members are able to interbreed freely under
natural conditions
– Many species can hybridise when brought together (e.g. ligers & tions)
– Where do primarily asexual species fit in? (e.g. bacteria)
– Many species complexes (particularly plants, e.g. elms)
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Phylogenetic - Individuals within a species are more closely related to each
other than to any other organisms
– Gene trees versus species trees
Congruent
Incongruent
E.g. Only 52% human
genes closest to chimps.
Rest are (H,(C,G)) or
((H,G),C) Satta et al.
(2000)
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Allopatric speciation
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Vicariance events
– Mountain, river, marsh, forest arises and separates populations
– E.g. numerous species boundaries at Pyrenees
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Peripatric
– Populations at periphery of species range get separated and diverge
– May be associated with ‘founder’ events
– E.g. island species
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Centrifugal
– Contraction of species range leads to differentiation among refugial
populations, which overwhelm peripheral populations (like Wright’s shifting
balance)
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Islands – extreme allopatry
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New and unusual species often form on islands associated with reduced
competition and broadening of potential ecological niches
Gigantism
Flightlessness
Occupation of
Unusual niches
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Vertebrate species richness
Geographical patterns in species richness
Energy (evapotranspiration)
Species richness in the US
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Sympatric speciation
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Speciation over over-lapping populations due to change in
– Host-plant preference (Rhagoletis)
– Local adaptation in association with the evolution of pre-mating isolation
(Chiclid fishes in lake Victoria)
– Changes in courtship song (crickets)
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Maybe driven by sexual selection?
– Birds of paradise
– Leipdoptera
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Studying speciation – ring species
Greenish warblers
in Asia
The two overlapping Siberian
forms have different song
patterns
Elsewhere, the pattern varies
more or less continuously
with an EW axis of increasing
complexity
Irwin (2000)
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Studying speciation - hybrid zones
Pyrenean hybrid zone in Corthippus parallelus
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The genetics of speciation
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Gradients in allele frequency across hybrid zones indicate that some genes can
cross the genetic barrier
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Variation in gradient indicates some genes are linked to factors generating
hybrid incompatibility
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Studies on Drosophila show some variation is shared between species while
others are only in one
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Haldane’s rule
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In crosses between two species, if one sex is missing or sterile it is the
heterogametic (XY) sex
X Y
Mammals
Bird
Butterflies
Male
Female
Female
X X
Female
Male
Male
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Interactions between genes on the X and autosomes are ‘imbalanced in the
heterogametic hybrid
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‘Speciation genes’ can be mapped in Drosophila between related species
– Only one putative speciation gene has been found (but it is very interesting)
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Chromosomal speciation
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New plant species can form when species hybridise
– E.g. Wheat, Helianthus petiolaris and H. annuus
x
Years of
natural selection
Natural experiment
Similar set of
chromosomal
segments retained
Artifical selection
x
For viability
Lab experiment
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Taxonomic survivorship curves
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Van Valen’s Red Queen hypothesis
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Deterioration in the environment of a species caused by continual adaptation
of competitors leads to a constant per unit time risk of extinction, so a
geometric distribution of species survivorship times
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Based around idea that ecology is a zero-sum game
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The Permian extinction
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Largest extinction in the history of life – 251 MY ago
80% marine species went extinct in 1MY
9 orders of insect and therapsid reptiles lost
Associated with massive volcanic activity, large increase in CO2 and global
warming
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The K/T mass extinction
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65 MY ago
15% marine invertebrate families and 45% genera lost
Extinction of the dinosaurs
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Evidence for the asteroid theory (Alvarez et al. 1980)
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Iridium spike at K/T boundary
– High concentrations in extraterrestrial objects
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Soot in same layer
Shocked quartz crystals
Putative crater off Yucatan peninsula
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BUT all can also be produced by
volcanoes?
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Historical anthropogenic extinctions
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Wave of extinction of large animals in Australia around time of appearance of
first humans (c. 50,000 YA)
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Worldwide, there is no evidence of Indigenous hunter-gatherers hunting
nor over-killing megafauna. The largest regularly hunted animal was
bison in North America and Eurasia, yet it survived for about 10,000
years until the early 20th century. For social, religious and economic
reasons, Indigenous hunters harvested game in a sustainable manner.
http://www.amonline.net.au/factsheets/megafauna.htm
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However, in the last 300 years there have been 27 extinctions of large
mammals on continents and 55 on islands (including Australia)
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Factors endangering species
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Habitat loss
Exotics
Pollution
Over-harvesting14%
Disease
88%
46%
20%
2%
(43 % UK plant species exotics)
(Wilcove et al 1998)
Number
of
species in
group
Vertebrates
Mammals
Birds
Reptiles
Amphibians
Fishes
Subtotal
Number of
Number of
Number of
% of total in
% of total
threatened
threatened
threatened
group
assessed
species in
species in
species in
threatened in
threatened in
2002
2002*
4,763
9,946
7,970
4,950
1996
1,096
1,107
253
124
2000
1,130
1,183
296
146
2002
1,137
1,192
293
157
25,000
52,629
734
3,314
752
3,507
742
3,521
24%
12%
4%
3%
24%
12%
25%
21%
3%
7%
30%
18%
IUCN Red list 2002
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