Genes, genetics and natural selection

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Genes, genetics and natural selection

• Darwins theory of natural selection explained
  macroevolutionary patterns in terms of
  population-level processes
• The birth of modern genetics led initially to a
  battle between the Mendelians and the Darwinians
• The neo-synthesis saw the coming together of
  genetics and evolutionary thought. The selfish
  gene is just a (very elegant) restatement of this
  fact.
• Patterns of molecular evolution have generated
  many more controversies, notably over the neutral
  theory.
• 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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Galtons law of regression to the mean

• Characters are correlated between relatives
• height, hereditary genius
• But over time, deviations from the mean tend to
  be diluted
• Great men have less great sons!
• Natural selection cannot produce persistent change

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Mendels peas
AA x aa
x
Aa x Aa
x
AA/Aa aa
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1
Rediscovered c. 1901 by de Vries, Correns and
Tschermak von Seysenegg
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Mendelians versus biometricians

• Mendelians
• Adherents of Galtons 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
• Adherents of gradualist, Darwinian view
• Variation is truly continuous
• Large mutations happen, but are not very
  important
• Pearson, Weldon

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Nilsson Ehles wheat (1909)
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Morgan and the fly-room (Sturtevant, Muller and
Bridges)

• Discovered crossing-over (cM)
• Proved chromosomes carried hereditary factors
• Showed heritability of bristle number in
  Drosophila

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Fishers results on genetic variation

• 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
Phenotypic
Additive genetic
Dominance
Epistatic
Environmental
Genetic
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Estimating the genetic component of quantitative
traits
Offspring value (y)
y a b x
X
X
X
X
X
X
X
X
X
X
X
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)

• Contributions to a coherent Darwinian view of
  evolution by natural selection from geology,
  palaentology, natural history, cytology,
  genetics, and populations genetics
• Variation in natural populations
• Mimicry in butterflies
• Industrial melanism in moths
• Pin and thrum flower forms in Primula
• Darwins finches
• Sickle-cell anaemia
• Birth weight
• Disease

All maintained by natural selection /- recurrent
mutation
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The selfish gene

• The evolutionary theory of Haldane, Fisher and
  Wright is a gene-centred view
• considers whether a new mutation will spread
  through a population
• NOT what is best for the population
• However, natural selection acts on the set of
  genes it finds in an individual
• The correlation of relatedness over evolutionary
  time will determine whether of nor the fitness
  interactions between genes are important in
  shaping evolution
• 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
Relatedness in haplodiploid insects
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Kin selection

• Work by Hamilton, Price and others showed the
  importance of interactions between relatives in
  explaining biological patterns
• JBS Haldane
• I would be willing to lay down my life for 2
  brothers or 8 cousins.

Cost to actor
Relatedness
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

• Fisherian runaway process
• 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
• Good-genes
• 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
• Costly traits can evolve as honest signals of
  quality as females will always benefit from being
  choosy
• (Doesnt have to be a good genes argument)

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Species-level selection? (Stanley 1975)

• Higher-level selection leading to long-term
  changes in clade morphology can occur if
• 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?
• 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

• The number of differences between genes at the
  molecular level correlates with the time
  separating the species (Zuckerkandl and Pauling
  1962)
• The rate of substitution is constant over time
• 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)

• Constancy of rate of molecular evolution (the
  molecular clock)
• More important regions of proteins evolve at a
  slower rate than less important domains
• High levels of protein polymorphism
• High rates of molecular evolution (about 1.5x10-9
  changes per amino acid per year even in living
  fossils!)

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Kimuras neutral theory

• 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
• The level of polymorphism in a population is a
  function of the effective population size and the
  neutral mutation rate
• Polymorphisms are transient rather than balanced

NOW
NOW
Balanced
Transient
Frequency
Time
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Detecting natural selection at the gene level

• Bursts of amino acid substitution in lineages
• Amino acid changes concentrated at sites within
  proteins
• HLA
• Specific footprints in patterns of genetic
  variation
• Genetic hitchhiking

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Speciation and extinction

• 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
• How can we study the process of speciation?
• Hybrid zones
• Genetic footprints
• Analysis of reproductive isolation
• Why do species go extinct?
• Major extinctions in evolutionary history
• Anthropogenic extinction

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The biological species concept

• 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)
• 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

• Vicariance events
• Mountain, river, marsh, forest arises and
  separates populations
• E.g. numerous species boundaries at Pyrenees
• Peripatric
• Populations at periphery of species range get
  separated and diverge
• May be associated with founder events
• E.g. island species
• Centrifugal
• Contraction of species range leads to
  differentiation among refugial populations, which
  overwhelm peripheral populations (like Wrights
  shifting balance)

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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
Flightlessness
Occupation of Unusual niches
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Geographical patterns in species richness
Vertebrate species richness
Energy (evapotranspiration)
Species richness in the US
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Sympatric speciation

• 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)
• 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

• Gradients in allele frequency across hybrid zones
  indicate that some genes can cross the genetic
  barrier
• Variation in gradient indicates some genes are
  linked to factors generating hybrid
  incompatibility
• Studies on Drosophila show some variation is
  shared between species while others are only in
  one

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Haldanes rule

• In crosses between two species, if one sex is
  missing or sterile it is the heterogametic (XY)
  sex
• Interactions between genes on the X and autosomes
  are imbalanced in the heterogametic hybrid
• Speciation genes can be mapped in Drosophila
  between related species
• Only one putative speciation gene has been found
  (but it is very interesting)

X
Y
X
X
Mammals Male Female Bird Female Male Butterfli
es Female Male
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Chromosomal speciation

• New plant species can form when species hybridise
• E.g. Wheat, Helianthus petiolaris and H. annuus

Years of natural selection
x
Natural experiment
Similar set of chromosomal segments retained
Artifical selection For viability
x
Lab experiment
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Taxonomic survivorship curves
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Van Valens Red Queen hypothesis

• 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
• Based around idea that ecology is a zero-sum game

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The Permian 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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The K/T mass extinction

• 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)

• Iridium spike at K/T boundary
• High concentrations in extra-terrestrial objects
• Soot in same layer
• Shocked quartz crystals
• Putative crater off Yucatan peninsula
• BUT all can also be produced by volcanoes?

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Historical anthropogenic extinctions

• Wave of extinction of large animals in Australia
  around time of appearance of first humans (c.
  50,000 YA)
• BUT
• However, in the last 300 years there have been 27
  extinctions of large mammals on continents and 55
  on islands (including Australia)

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.ht
m
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Factors endangering species

• Habitat loss 88
• Exotics 46
• Pollution 20
• Over-harvesting 14
• Disease 2

(43 UK plant species exotics)
(Wilcove et al 1998)
IUCN Red list 2002