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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
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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Mendel’s peas
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x
AA
x
aa
Aa
x
Aa
AA/Aa &
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Characters are correlated between relatives
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– height, hereditary genius
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But over time, deviations from the mean tend to be diluted
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Natural selection cannot produce persistent change
aa
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– Great men have less great sons!
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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Nilsson Ehle’s wheat (1909)
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
Genotype
AA
Aa
aa
BB
Biometricians
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Bb
Adherents of gradualist, Darwinian view
Variation is truly continuous
Large mutations happen, but are not very important
Pearson, Weldon
bb
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Fisher’s results on genetic variation
Morgan and the fly-room
(Sturtevant, Muller and Bridges)
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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)
Discovered crossing-over (cM)
Proved chromosomes carried
hereditary factors
Showed heritability of bristle
number in Drosophila
Frequency
Phenotypic variance = σ2P
Trait value
2
P
Phenotypic
Additive
genetic
=
2
A
+
2
D
+
Dominance
2
I
+
2
E
Epistatic
Environmental
Genetic
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The neo-synthesis (1920s-1930s)
Estimating the genetic component of quantitative traits
Offspring
value (y)
y=a+bx
X
X
X
X
X
X
X
X
X
b=
X
X
Cov(x, y)
= h2 =
Var(x)
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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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A
2
P
X
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Mid-parent value (x)
µ
µS
∆µ = h2 (µS - µ)
Selection
response
Trait value
Mimicry in butterflies
Industrial melanism in moths
Pin and thrum flower forms in Primula
Darwin’s finches
Sickle-cell anaemia
Birth weight
Disease
Trait value
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The selfish gene
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Mimicry?
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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Can natural selection explain
The evolutionary theory of Haldane, Fisher and Wright is a gene-centred view
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All maintained
by natural
selection
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).
Y chromosome genes
Green-beard genes and kin recognition
Selfish genetic elements (segregation distorters, cytoplasmic male sterility, sex-ratio
distorters)
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Kin selection
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Social insects?
A Camponotus
japonicus ant sharing
honey with another ant
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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
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
Cost to actor
Relatedness
Benefit to receiver of action
Haplodiploid
Relatedness in haplodiploid insects
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Two or three theories of sexual selection
Sex-related characteristics?
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Fisherian runaway process
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Good-genes
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Stalk-eyed fly
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)
Irish elk
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Species-level selection? (Stanley 1975)
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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
Higher-level selection leading to long-term changes in clade morphology can occur if…
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The molecular clock
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
Doolittle et al. (1996)
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Kimura’s neutral theory
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!)
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
The level of polymorphism in a population is a function of the effective population size
and the neutral mutation rate
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= 4Ne
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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Speciation and extinction
Bursts of amino acid substitution in lineages
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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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Amino acid changes concentrated at sites within proteins
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Specific footprints in patterns of genetic variation
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
– Genetic hitchhiking
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The biological species concept
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Allopatric speciation
A species is a population whose members are able to interbreed freely under
natural conditions
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– Gene trees versus species trees
Incongruent
Peripatric
– Populations at periphery of species range get separated and diverge
– May be associated with ‘founder’ events
– E.g. island species
Phylogenetic - Individuals within a species are more closely related to each
other than to any other organisms
Congruent
Vicariance events
– Mountain, river, marsh, forest arises and separates populations
– E.g. numerous species boundaries at Pyrenees
– 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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Centrifugal
– Contraction of species range leads to differentiation among refugial
populations, which overwhelm peripheral populations (like Wright’s shifting
balance)
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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Islands – extreme allopatry
New and unusual species often form on islands associated with reduced
competition and broadening of potential ecological niches
Gigantism
Vertebrate species richness
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Geographical patterns in species richness
Flightlessness
Energy (evapotranspiration)
Occupation of
Unusal niches
Species richness in the US
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Sympatric speciation
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Studying speciation – ring species
Speciation over over-lapping populations due to change in
Greenish warblers
in Asia
– 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
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
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
Pyrenean hybrid zone in Corthippus parallelus
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Haldane’s rule
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Chromosomal speciation
In crosses between two species, if one sex is missing or sterile it is the
heterogametic (XY) sex
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New plant species can form when species hybridise
– E.g. Wheat, Helianthus petiolaris and H. annuus
x
X Y
Mammals
Bird
Butterflies
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Male
Female
Female
X X
natural selection
Female
Male
Male
Natural experiment
Similar set of
chromosomal
segments retained
Interactions between genes on the X and autosomes are ‘imbalanced in the
heterogametic hybrid
Artifical selection
x
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Years of
‘Speciation genes’ can be mapped in Drosophila between related species
For viability
– Only one putative speciation gene has been found (but it is very interesting)
Lab experiment
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Taxonomic survivorship curves
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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The K/T mass extinction
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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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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Historical anthropogenic extinctions
Iridium spike at K/T boundary
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– High concentrations in extraterrestrial objects
– BUT
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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?
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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Factors endangering species
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Habitat loss
Exotics
Pollution
Over-harvesting
Disease
88%
46%
20%
14%
2%
(43 % UK plant species exotics)
(Wilcove et al 1998)
Number of
species
in
group
Vertebrates
Mammals
Birds
Reptiles
Amphibians
Fishes
Subtotal
Wave of extinction of large animals in Australia around time of appearance of
first humans (c. 50,000 YA)
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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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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