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EVOLUTIONARY BIOLOGY OF ANIMALS
History of Evolutionary Thinking
•

Evolution is a fact (with lots of evidence to back it up) and a theory (repeatably tested by
hypotheses)
...


•

The evidence for evolution is universally shared features (homology), hierarchical
classifications in phylogeny, biological relationships, geological history and geographical
distributions

•

Darwin’s evolution – population change over generations, with gradual change and
speciation driven by natural selection
...
Beak size in Darwin’s finches is very heritable
...
It then reduced in
subsequent generations

•

Hybrid speciation – two species blend to form a unique non-interbreeding species

•

Evolution – change in the DNA sequence over many generations, whether by natural
selection or genetic drift

•

Humans, whether consciously or unconsciously, impact of everything we interact with

•

Early hunter gatherers avoided hunting large and dangerous prey – exerting an unconscious
selection for large dangerous prey

•

Neolithic revolution – the start of agriculture
...

Began taxonomic classification based upon observation, and used comparative anatomy
...
Didn’t believe in evolution, and
attributed the gradation in nature to the great chain of being

•

Great chain of being - hierarchical structure of all matter and lifestarting with God and
through to angels, demons, stars, moon, kings, princes, nobles, commoners, wild animals,
domesticated animals, trees, other plants, precious stones, precious metals and other
minerals

•

Al-Jahiz 781-869AD – muslim scholar from Baghdad
...


•

Linnaeus 1707-1778 – created the binomial nomenclature, and order, kingdoms and classes
...
Believed in the
essentialist species concept
...
This paved the way for later evolutionists
...
Within species
variation is attributed to varying amounts of the essence
...

Understood the species concept, and described a new timeline of the earth, with 7 epochs
...


•

Lamarck 1744-1829 – proposed idea of species change based upon increasing complexity
and change through the same genetic line, and it being a very slow environment driven
process
...


•

Lamarckism – the whole giraffe thing (hypothesised adaptation over time via the inheritance
of acquired characteristics) but after many, many generations, making the speciation
imperceptibly slow – shows understanding that something is changing over generations

•

Darwin and Lamarck both recognised evolution, just had different mechanisms
...
Darwin thought
Lamarck’s book was rubbish but agreed that they had similar conclusions even if the method
of change was different
...


•

Saint-Hilaire 1772-1844 – Comparative anatomist, looked at homologies (which formed the
basis of evidence for evolution)
...
Studied the
internal anatomy of vertebrates and invertebrates
...
Destroyed the natural order as grouped animals into phyla howing no
evidence of increasing complexity, but believed man was different
...


•

Catastrophism – the idea that the earth has been shaped by rapid dramatic events at the
end of epochs, as opposed to gradual changes like erosion – not testable

•

Uniformitarianism – the idea that things have changed gradually and that all processed
which created this landscape can still be found in operation today - testable

•

Principles of the correlation of parts – Cuvier’s idea that all organs in an animal's body are
deeply interdependent
...

Eg
...
Therefore, all features must be in line for a function
...
Already was used by botanists

•

Erasmus Darwin 1731-1802 – Doctor and poet, believed that all species (including humans)
were descended from a prehistoric marine microorganism
...
Pre-Darwin evolutionist
...


•

In science the credit goes to the person who convinces the world – not to whom the idea
first occured

•

Malthus 1766-1834 – Said that not everyone can survive - if population growth outstrips
food supply there will be famine – restoring the population to a maintainable level

•

Alfred Russell Wallace and Charles Darwin presented the idea of natural selection in a joint
paper to a Linnean society meeting

Summary: Many people contributed to the theory of evolution in a gradual process
...
Al-Jahiz understood survival of the fittest
...
Buffon understood the species concept and that species were adapted to their
environments, and that the earth is ancient
...
Lamarck believed in evolution driven by the environment but
that acquired characteristics were inherited
...
Three separate
people arrived at natural selection as a mechanism for evolution
...


•

Nuclear chromosomes are linear, with psuedoautosomal regions at ends for recombination
(genes in the middle don’t move)

•

Cytoplasmic DNA like in mitochondria and chloroplasts is circular

•

Possible changes include: substitutions, indels, chromosome breakages and fusions,
duplication of genes and genomes (increasing the copy number), inversions,
pseudogene formation (eg if moved and no longer worked), and acquisition
of horizontally transferred DNA from plasmids or transposons

•

SNPs – Single nucleotide polymorphisms, or single base substitutions
...
Rare codons are heavily selected against in highly
expressed genes but can not be an issue in rarely expressed genes
...
This
increases diversity, but may plateau as there is a limit the maximum changes as site
saturation occurs, and proteins still must be able to work

•

Mutations are not necessarily independent as one mutation can increase the chance of
another

•

Chromosome fusions and rearrangements – very common in families like shrews
...


•

Gene duplication can be useful – the duplication and subsequent diversification of spider silk
genes has lead to the ability to occupy many niches – different AA sequences which
determine properties like stretch leads to different fibres, leading to different spinning
manners, and different morphologies
...
It
is much bigger than its ancestor, and most of the duplicated genes stay functional
...
This is why genetic fingerprinting works, as the error rate in the regions is
so high and therefore individual

•

Recombination – an important part of meiosis, mixing up allele combinations (doesn’t occur
in mitochondria – there is complete linkage between genes)
...
This results
in very different genomic content in gametes
...


•

Asexual organisms can’t recombine so cannot rid themselves of bad mutations

•

Changes can occur as a result of a repair – eg in gene conversion where one allele is repaired
by copying a homologous allele
...
Can be caused by misaligned DNA sequences in nonhomologous recombination

•

Transposable elements – genetic elements capable of moving from one location to another,
often leaving a copy behind, thereby increasing their number
...
There are different classes of transposable elements:

Class I – retrotransposons - leave a copy of themselves
behind
...
Are the most common
type in bacteria, eg IS elements in E
...


•

Recombination among transposons on different chromosomes or at different sites on the
same chromosome can cause inversions, translocations and deletions as recombination
relies on pairing of matching gene bits and transposable elements all match – fucks shit up

•

Virogene – strain found in baboons and cats – who are not closely related
...
Those that aren’t are generally removed by
natural selection

•

In the short term, changes to genomes are normally changes in allele frequency, not
generation of new alleles
...
Heterogeneity in the environment may lead to this change or to
alleles being lost forever

•

In long time frames mutation is the more important driving force in genome evolution,
changing genome size and content

•

Mutation determines the rate of adaptation
...
It has evolved
multiple times in 3 different ways, but all to the same gene

•

Evolution is dynamic – it can go back and forwards
...
Eg the melanocortin system (set of genes) determines colour patterns as
well as other traits like immunity – darker wild vertebrates are more aggressive,
sexually active and resistant to stress than lighter individuals (although may just
invest in different life stages)
•
Species with a large genome (aka high C-value, the total amount of DNA per
cell) develop more slowly than small genome species

•

Comparative genomics – when looking at evolutionary changes often have to compare
genomes to see changes (eg dolphins have similar changes in brain structure as primates), or
to show which genes may be responsible

Summary: Changes in DNA can be small or large
...
Understanding what changes persist is useful as it tells us what we
might expect to evolve in a particular time frame, and it helps us understand how the evolutionary
patterns we see today have come about
...
It is
also important to remember that
natural selection has no
foresight/purpose – it cannot try
to make things, and only favours
changes that are useful in the

present, not which will become useful
•

Dali’s elephants couldn’t exist because as body mass must be proportional to femur
diameter
...
Eg, when domesticating
silver foxes in Russia, they selected only
for tameness
...

These changes included the fox becoming
spotted, coming into heat every 6 months
and becoming more 'dog-like
...
It occurs at random, and
whilst most mutations are (mostly) harmless and
few are deleterious, even fewer are immediately
beneficial
...

This mutation has evolved multiple times (convergent)

•

Coat colour does have an impact on fitness: darker mice are predated upon more in light
habitats and vice versa

•

Even small differences in fitness can lead to big change: 1% more offspring in light habitats
for light mice would lead to a 100% increase in allele frequency in a population of 10,000
within a few thousand generations – short in an evolutionary timescale sense

•

Anything over 5% difference is strong natural selection

•

Fitness = 1 – s (selection coefficient) – s=0 is no selection, s=0
...
When in the gutter only a new
mutation will allow the drunk to leave it

•

With this analogy, the starting point is also
important – if you start on the left you may
be more likely to go left

•

Frequency-independent selection – the
fitness of the phenotype is not directly
dependant on the frequency of the trait in
the population

•

Directional selection – or positive/negative selection – leads to fixation or elimination of an
allele
...
Eg, sickle cell
anaemia, where the homozygous recessive is lethal,
but the heterozygote is anaemic but reduces the
growth of
the malaria
parasite
(but only
advantageous if in a malaria risk area)

•

Underdominance – or heterozygote disadvantage –
where the heterozygote has a lower fitness than

homozygotes - very rare in the real world, but lab tests have made mouse models of Lupus,
where the heterozygotes develop the auto-immune disease
•

Frequency dependent selection – where the cost and benefits of a trait depend upon its
frequency in the population
Positive – the fitness of the phenotype increases as the frequency of the trait
increases – eg Jeremy the snail, anatomy flipped so couldn’t mate as his sex organ
was on the wrong side
...
Works on polymorphic species with different
morphs (eg colour), where the common ones are predated on more than the rare
(search image)
...
Eg, when lots of left handed scale eating cichlids are around, prey learn to
protect their right side – increasing the gains and therefore fitness of right mouthed
fish who bite on the left

•

Fishers sex ratio model – a form of negative selection
...
If female births are rare, then parents predisposed to bearing
females will have more grandchildren – spreading the female-bearing allele
...
Does not result in adaptation
(like natural selection)
...
Occurs in
all populations as no population is infinite

•

Alleles at all loci are subject to random genetic drift, but not all alleles are not necessarily
subject to natural selection

•

Neutralist-selectionist debate – whether random genetic drift or natural selection is the
primary driver of evolution

•

Assume all change to be neutral (random) unless proved to be selection – can be the null
hypothesis for evolution

•

Wright-fisher model - describes the sampling of alleles in a population with no selection, no
mutation, no migration, non-overlapping generation times and random mating
...

Advantageous alleles may not become fixed, especially if
the population is small or selection is weak
...
It also causes
heterozygosity to increase over time

•

The smaller the allele frequency the higher chance of
losing it

•

Bottlenecks cause drastic changes in allele frequencies –
founder effects accelerate genetic drift via random
bottleneck effect

•

Eg, in a large number of islands each with 10 inhabitants, and all islands were founded by Aa
heterozygotes
...


•

Although Darwin viewed inheritance as a blending process, Mendel’s peas demonstrated
the law of inheritance of discrete elements
...
Natural selection
works on standing genetic variation within populations, but there are physical constraints to
what is possible
...
Evolution has no foresight, and
natural selection can only act on presently beneficial variation, not what will be useful in the
future
...
Predators are known to favour common morphs, leading to rare morphs having
an advantage

•

If there was positive frequency dependent selection instead then the rare morph would be
eliminated – the negative maintains the diversity

•

As opposed to frequency, there may be a minimum number of a morph required
...
Tri are better at identifying the quality of fruit
whilst di are better at detecting camouflaged predators
...
If individuals are closely related, then unequal ratios can persist as individuals
do not gain the same relative advantage to being the one to produce more of the rare sex
...
Eg low reproductive-effort female bank voles are favoured at low
densities, but at high densities females who produce many young have a higher survival and
fitness (rare phenotype)

•

Mimicry is a good example of adaptation to a biotic factor – they adapt in response to the
other species around them

•

There are three types of mimicry:
Batesian – harmless organisms mimicking harmful species – eg hoverflies
and wasps
Mullerian – harmful mimicking harmful – eg noxious butterfly species
mimicking other noxious species (reinforces predator aversion)
Cryptic mimicry – (harmless) species mimicking something in the
environment – eg stick insects, crab spiders on flowers etc

•

Mimics are influenced by both density and frequency dependence depending on
type: more Mullerian mimics is good for a mimic, whereas more mimics is bad for
a Batesian or cryptic mimic

•

Not all variation is adaptive
...
But the areas with more
morphs than expected were not due to more adaptations: hybridisation of previously
isolated populations caused new shell colours

•

Pleiotropy limits adaptation as it can create a tug of war situation
...
Eg mimicry is controlled by a supergene collection of
genes (which are unlikely to be separated by recombination)
...
Can be
due to:
Prezygotic barriers – pre-mating, eg mating calls aren’t compatible
Postzygotic barriers – post-mating, eg embryo can’t develop
Or a combination thereof

•

Allopatric speciation – a physical barrier splits a population into two (can be altitude, river
etc – what is a barrier to one species is not necessarily to another), causing reproductive
isolation, each new range has its own equilibrium
...
Eg Anoles lizards
currently have parapatric distributions, but allopatric speciation followed by expansion into
newly suitable ranges is the most likely explanation

•

In R
...
America) – pending sympatric speciation?

•

Adaptive radiation – rapid diversification and speciation to fill various available niches
...
There’s a random element to what gets to the island first, but there is always
adaptive radiation to the same functional groups

•

Adaptation can be driven by changes in resource availability
...
Size was suggested to be due to increased competition
on the island (r/K)
...


•

Phylogenies can allow us to infer the evolutionary
history
...
strigata and S
...
Partula also have thick shells and nonpigmented mantles
...


•

Speciation can be determined by only a single gene: chirality (direction of the coil) is
determined by a single gene, which leads to reproductive isolation between lefties and
righties – however they will not eventually become new species as snails show the
phenotype of their mothers – it isn’t related to their own genome, so they cannot pass it on
(a sinistrally coiled snail may have the genetics to coil dextrally but his mother was sinistral)

•

Sexual reproduction allows the removal of deleterious homozygous recessive mutations

•

Asexual reproduction allows an exponential increase in population size (2n)

•

Some species have populations of both, eg flat worms which can cycle between states

Summary: Pleiotropy can limit rates of diversification and adaptation, as can high levels of gene linkage
...


Population differentiation and phylogeography
•

Mating is assumed to occur randomly in a population

•

If there are no barriers to dispersal, and mating can occur at random between subpopulations then the population is panmictic

•

Genetic exchange is mediated by the movement of individuals
...
Normally only report if significantly above zero (not the actual value)
...
Have to use genetic
markers to find the subdivision, then use the markers to find if there is inbreeding

•

The amount of genetic exchange between populations (in a meta-population) depends on
the strength of selection: if there is no selection then migration tends to homogenise gene

frequencies between populations
...
Eg only resistant insects can survive on pesticide sprayed
fields – regardless of the incoming novel genes
•

Effective population size (Ne) – the number of individuals contributing to the next
generation (more important than the absolute population size)
...
It may not be obvious who is
contributing, eg in bees Ne = 1
...
Eg Soay sheep have drastic population crashes in
harsh winters, losing genetic variation
...
Size can recover from crashes, but diversity can’t
...
Unequal sex

ratios lowers Ne, as if only one male contributes to the next generation, relatedness in the
next generation is much higher
...
Variance in reproductive success between individuals
also lowers Ne – if some are more successful then their genes are overrepresented in the
next generation and the diversity is lower
...
The is a separate Ne for each population in a
metapopulation
...


•

Linyphiid spiders live in disturbed agricultural habitats can disperse long distances by
ballooning but only 40-60% do
...
There is a small number of long distance migrants (most don’t go too far)
...
Like genetic hitchhiking
...
This sweeps the
infected females alleles to a higher frequency, reducing diversity
...
Usually found on large-scale geographical ranges, but
sometimes can be local
...
Eg the three most likely migration routes through Europe after the last ice age:

Grasshopper – One genetic type spread across the whole of Europe and
colonised it before the other two species could get out (from behind
mountains – still very cold at the top), leaving them little space
Hedgehog – All three species get out at the same time and colonise their
own little bit of Europe
Bear – Iberian and Eastern species get out and colonise, but the Italian
species remained stuck behind the alps
...
This is
done genetically (often with
mitochondrial DNA)
...


•

Each dot is a mutation, whilst each
circle’s size is the number of
individuals with that genotype,
and the colour is the geographical
location of these variants
...
We cannot know which the right way is,
so leave all options in
...


•

These historical explanations for current distributions
are vital to understanding current patterns of genetic
variation
...
It
can form what appears to be patterns but are in fact
due to chance

Summary: Genetic variation in populations is sensitive to population size (and Ne), dispersal, migration,
variance in reproductive success, unequal sex ratios, and past colonisation events

Human evolution
•

All studies use one, or a combination, of four approaches:
Archaeology – analysis of ancient samples
Anthropology – studies change in human culture, society and morphology
Linguistics – study of language and structure
Molecular Genetics – to assess evolutionary change and relationships

Arc
ha
eol
og
y

An
thr
op

•

Some studies use comparative approaches, eg comparing humans to apes

•

Some studies use contemporary (modern) populations

•

Some use ancient samples (or preserved material)

•

Archaeological samples which can be dated are good for studying human migrations
...
Conclusions
drawn from artefacts often are based on multiple types of samples

•

Can get quite a lot of detail
...
Analysis of the isotopes in his enamel and
bones show where he grew up (isotopes are absorbed with food and are stored in the body
and are variable with location)
...


•

Social brain hypothesis - suggests that primates evolved large brains to manage their
unusually complex social systems

An
thr
op
olo
gy

Lin
gui
stic
s

Mo
lec
ula
r
Ge
net
ics

•

Machiavellian Intelligence hypothesis – suggests that large brains evolved in response to
intense social competition, with a better survival if you can use and exploit others in the
social group, without causing disruption or aggression

•

These hypotheses were formed from comparative analysis
of primates
...


•

Can also compare genes between humans and chimps,
with fewer active genes for olfactory receptors and no
bitter taste receptors in humans
...
The study was based upon
the loss and gain of homologous words
...


•

Can use phylogenies to show the diversification of language
clades
...
This can then be
interpreted in terms of likely historical processes (eg migration or population expansion)
which arrived at the current distribution

•

Analysis of 120 different proteins across Europe, mished into a PCA, show a series of clines
across Europe, with a division (or hybrid zone) in scandinavia like the phylogeographic
studies of animals
...
Eg, in the below maps, colour
indicates the proportion of each ancestral strain now found in bacteria at each location
...
Maternal mitochondrial genomes support the place of origin being sub-Saharan Africa
roughly 100,000 years ago

•

A consequence of this is that African populations have much higher diversity and are the
oldest lineage

•

The most recent common ancestor of all humans lived 100-200 thousand years ago – which
fits with the out of Africa hypothesis

•

The type of genetic marker can determine the strength of the study:
Mitochondrial DNA - maternally inherited, with no recombination, so
provides an unbroken link to ancestral grandmothers
Y chromosome – paternally inherited, with an unbroken link to ancestral
grandfathers
Autosomal DNA – inherited equally from both parents, but is hard to
sequence as there is too much noise from heterozygotes (the two sequences
are on top of each other)
...
Only europeans and asians share
DNA with neandertals – not africans
...
These changes may have affected
appearance, energy, and metabolism
...
The genome of the Denisovan girl was used to
calculate the % similarity to modern day humans
...
As
there was a high level of homozygosity, it was shown that the population size of the
Denisovans had remained small

•

Y chromosomes are linked to geographic
locations, at global and local scales (left)

•

Just because you have DNA from
somewhere, eg Africa, does not make you
African or show your true origin

•

There are higher percentages of male genes
further from Norway, as women did not
generally go on crusades
...


•

Models assume no mutation, no random
genetic drift and no selection
...
Distributions are not random
...


Summary: It can be hard to tell whether variation is a result of natural selection or
if it is neutral
...
Huge recent advances have been
made into ancient human DNA that is thousands of years old
...
Advances have also been made in the ability to obtain and interpret
variation in modern DNA from entire genomes
...
Looks at new lineages arising and existing
lineages becoming extinct
...


•

Eg, in social spiders either sociality breaks down as the population is
not related enough, or it gets so inbred that the fitness decreases –
then new lineages arise

•

Lineages can seem to persist (eg the same morphology is found even after a species is
extinct), but the trait has just re-evolved

•

Microevolution – smaller scale changes like alterations of gene frequencies in populations
(which can in turn lead to bigger changes)

•

There is a grey area between micro and macroevolution

•

Fossil – any trace of past life
...
This becomes less precise as the sample gets older due to error
...
They can be used as a marker
to date rocks by – eg if species X are here it must have formed when that species was
prevalent
...
Multiple tracks were visible, and other marks like ripples showed that it was
terrestrial (as the sand was windblown – this had to be demonstrated)
...


•

The bones were previously thought to be a different species, but when reexamined they were found to belong to an unknown species of plesiosaur (showing the
difficulties in identification)
...
Eg a CT scan of the
inner ear of pterosaurs showed that the balance organ and relevant brain portion were very
large, indicating that they were very agile when flying, and capable of catching prey midflight
...
This can be interpreted
as evolutionary change
...
Eg, mammal-like reptiles with mammal-like jaw
muscles are shown, and other fossils show mammalian type traits slowly appearing in
reptiles in stages

•

Some fossils have characteristic that are intermediates, eg Archaeopteryx is a feathered bird
like organism which still has dinosaur features
...
Eg, horseshoe crabs are morphologically similar to forms from 200mya
...
Eg, body colour, snail shell banding patterns

•

These terms can also be used for genes or even SNPs, although if sequences have many
changes it can make non-related sequences appear similar
...
To look at
this, the phylogeny must be reliable

•

In the Cambrian explosion we suddenly see many new animal types, fully formed and with
no intermediates
...
The fossil record is incomplete and doesn’t show the earlier evolution
2
...
There was a predictable exponential increase in the number of organisms at
this time due to an ecological vacuum – a load of new niches opened up,
and organisms diversified to fill them

•

Many species are not represented in the fossil record, either
because they were not suitable fossil material, they didn’t live
in the right place, or were very rare

•

Therefore, the causes of diversification during the Cambrian
explosion are still uncertain
...
High levels of iridium and extraterrestrial amino acids
found in strata from that time period support the suggestion
that it was caused by an asteroid hitting earth (but extinction
and iridium levels don’t match exactly which could be due to
fossils moving strata – another issue with dating)

•

Fossils can also tell us about loss of organisms
...
This could be because they had a broader geographic range (like
metapopulaions), but being more widespread may mean more probability of being fossilised
– the record could be biased towards certain species

•

You can estimate diversification and extinction rates from fossil records and molecular
phylogenies of current species
...
DNA has been attained from samples
which are thousands of years old, but normally DNA hits for them are modern contaminants
...
DNA just doesn’t
actually last that long

•

mtDNA is a lot easier to attain, as there are many more sequences per cell

Summary: Fossils are either of ancestors of modern species, or organisms for which there are no
descendants
...
The record is incomplete as only some
parts of some organisms can be fossilised, and only under ideal conditions
...
The fossil record can
give us an idea of what has existed, and morphology and genetics can show the relationship to modern
animals, but there are still many questions

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