Evolution

Lecture 1
- The platonic - Aristotelian- Judaeo-Christian world view of Essentialism and Teleology
-Darwin's theory of biological evolution is a synthesis of these two streams of thought
- Plato initially placed in essentialism
- Foremost in the philosophy of Plato was the concept of two co-existing worlds, a perfect world that
we conceive with our intellect and an illusionary world that we perceive with our senses
- Plato, variation in plants and animals were merely imperfect representations of their essential or
ideal form

- Teleology - Belief in a divine order or purpose to life
- Aristotle ordered species according to Great Chain of Being or Scala Naturae
- Species were fixed forms, simple to complex and Church adopted this, with addition of angels and
God above Man
- All species characteristics are purposeful
Natural Theology and Taxonomy
- Carlus Linnaeus sought to bring order to diversity of life in his text Systema Naturae, dedicated to
the greater glory of God and who was the one who founded modern taxonomy by developing the
system of Latin binomial nomenclature
- Linnean classification - hierachial, but not evolutionary, Genus species
- Based on morphological similarities and assumption of fixity of species and not evolutionary
descent
-K, P, C, O, F, G, S
- Initially 600 animals classified by Aristotle, then in 1600AD, 1000, and in 1758AD, 4400 animals
numerous plants
- 3 million today, believed to be 30-50 million
PHYSICAL SCIENCES
- replaced will of God or Aristotelian teleology with a concept of efficient cause
- meaning what once was seen as the purpose for which events occur was changed to a mechanism
that cause events to occur
- Gravity replaces faith and sun replaces earth as the centre of the solar system

- Cuvier - founder of modern vertebrate palaeontology
- life's history recorded in fossil containing strata
- Each stratum characterised by unique fossils
-the older the strata, the more differing was present from modern organisms to the one found in the
fossil
- Extinction common to earth's history
- He believed in Doctrine of Special Creation and fixity of species, even though with evidence of
evolution found by him
- CATASTROPHISM - theory that major changes in the Earth's crust are a result of catastrophic events
rather than from gradual processes of change
Hutton

- GRADUALISM - theory that profound change is the cumulative result of slow continuous process eg
great canyons formed by slow erosion
Time between Adam and Even to birth of Jesus, biblical age of the Earth, 6000 years
- Lyell added to Hutton, influencing Darwin
- Earth must be ancient, more than 6000
- Very slow and subtle processes over time provided dramatic changes

Sociology and Economics
- Malthus - intrinsic rate of increase in human pop will lead to imminent food shortage and mass
starvation, industrial revolution
- Darwin came to realise that many more are born than can possibly survive
Lamark - Transformism
- organisms arise from inanimate matter by spontaneous generation and progress towards greater
complexity
- particular path of an organism's evolution is guided by a changing environment, first basis of idea
of adaptation
- Differential use of disuse of organs during an individual's life is transmitted to subsequent
generations resulting in inheritance of acquired characteristics
- Transformism conflicted with Catastrophism
Darwin's finches.
Observation #1 - Members of a population often vary in their inherited traits
2- All species can produce more offspring than their environment can support and many of these
offspring will fail to survive and reproduce
Inference #1 - Individuals whose inherited traits give them a higher probability of surviving and
reproducing in a given environment tend to leave more offspring than other individuals
2 - Unequal ability of individuals to survive and reproduce will lead to the accumulation of
favourable traits in the population over generations
Concepts
1. Organisms beget like organisms - stability in process of evolution
2. In most species, number of individuals in each generation that survive and reproduce is small
compared to the number initially produced
3. In any given population there are chance variations among individual organisms and some of the
variation is inheritable
4. Some variations enable individuals to produce more offspring than others, inherited favourable
variations tends to become more common from one gen to the next, process known as natural
selection
5. Given sufficient time, natural selection leads to accumulation of changes that differentiate groups
of organisms from one another, ie different species from an original one.
Darwin - change not stasis, is the natural order
Lecture 2
- Darwin considered actions of natural selection to be so slow that they were not observable directly
- Artificial selection
- Visible results of AS confirmed heritability of characters and the extent of variation hidden in the
gene pool of most species
- Darwin used examples from breeding experiments as evidence for his theory on the importance of
natural variation and the role of selection in evolution below level of species, ie forces of change in
gene pool
- Process known as microevolution
- Natural selection at the level of gene frequencies and even morphological characters can be rapid
and easily measured
- Macroevolution
- origin of species and the historical patterns of species origins and extinctions
- 5 principle categories of evidence for macroevolution
- large number of diversity and number of species
- particular kinds of organisms were found in particular geographic areas
- fossil record which showed organisms had a long history, had changed through time and had also
become extinct
- homologous structure of diverse organisms, implying a historical relationship or common ancestry
- adaptation which provided evidence of selective forces in environment and the imperfection of
adaptations which suggested historical constraints on evolutionary change
- Microevolution, the rapid evolution of viruses such as HIV
- Various substances used to affect the reproductive cycle of HIV, however when this occurs and
agent is applied, majority of HIV cells will be killed/removed however there will be a very small
population of cells that contains resistance to such an agent. These cells will still be able to continue
in the replication cycle, and produce offspring that also have this resistance, eventually producing a
100% population that is a resistant to the specific agent that was initially present to aid and prevent
infection/disease
Macroevolution
- Fossil Record - evidence of continuity and descent with modification, not due to catastrophic
events and catastrophism
- Absence of transitional fossils, missing links
- shows evolutionary changes in various groups of organisms
- Homology
- Similarity among different organisms
- Homologous structures - structures that are the result of common ancestry
-structures can be used for different functions and so might or might not appear similar
- Homologous structures that are left over, structures that are of marginal importance, known as
vestigial structures, remnant features that served the ancestor
- Skeleton of snakes contain vestigial pelvis and leg bones, illustrating ancestors could have walked
- Homology also in terms of genes
- Convergent Evolution
- Distantly related organisms resembling one another, independent evolution of similar features in
different lineages
- Evolving independently however adapted to similar environments in similar ways, resemblance is
said to analogous due to convergent evolution, share function but not ancestry
- Homologous - share ancestry but not necessarily similar function
- Biogeography
- the geographic distribution of species
- Continental drift
-Endemic species of plants and animals
- Ancestry from mainland organisms, then new species arise when in new land and environment

Lecture 3
- Darwin was unable to provide a valid mechanism for how to explain hereditary
- How inherited characteristics are transmitted from generation to the next
- why inherited characteristics are not blended out but instead disappear and reappear in later
generations
- how variations arise on which natural selection acts
Mendelian genetics and Darwinian evolution reconciled, forming basis of synthetic theory of
evolution
Modern Synthesis summarised
- Ample genetic variation arises and is contained in populations by random process of mutation,
recombination and chromosomal changes and not directed by responses according to organisms
needs, ie adaptions
- Evolution in pop influenced by natural selection in particular, as well as by gene flow and random
genetic drift, and characterised by changes in gene frequency
-Adaptive genetic variation produces small stepwise changes in phenotypes, accumulating gradually
in evolutionary lineages over long periods of time
- Divergence of geographical isolated pop is unimpeded and gradually leads to speciation and
reproductively isolated groups
- Continued gradual accumulation of genetic differences, under principal guiding force of natural
selection, results in new taxa above species level, by same processes that produce new species
- Population genetics - process of change in allele frequencies of a population or gene pool
- population - interbreeding group of organisms, defined and united by gene pool
- gene pool - sum of all alleles of the genes in individuals in a population
- Species - group of populations that potentially/actually interbreed in nature and are reproductively
isolated from other populations/species
- Evolution - result of accumulated changes in composition of gene pool
- Individual organism is said to be a temporary vessel holding a small sample of the gene pool for a
brief moment in time

- Maintenance of variability in populations
- Hardy and Weinberg used a mathematical formula displaying how both dominant and recessive
alleles survive in a pop and how dominant alleles do not simply drive out the recessive ones
- Formula shows genetic recombination, that occurs in each generation of diploid organisms, does
not by itself change gene pool
- They considered behaviour of alleles in an idealised population in which specific characteristics
were present
- no mutations occurring
- no migration or gene flow, no net movement of organisms into or out of pop
- No drift, population is large enough that chance alone will not alter allele frequencies
- Panmictic, or random mating
- No natural selection occurring, offspring of all possible matings are equally likely to survive to
reproduce in next generation
-State that the frequencies of alleles and genotypes in a pop will remain constant from gen to gen,
provided Mendelian laws are present, not linked genes
- Describes hypothetical population that is not evolving


- Mutation regarded as only significant factor capable of bringing about evolutionary changes,
including origin of new species and forms of new complexes of organisms

- Focussing on evolutionary changes in populations, we define evolution on smallest scale, known as
microevolution, change in allele frequencies in a population over generations
- Allele frequency affected by natural selection, genetic drift and gene flow

Lecture 4
- Extent of genetic variation in a pop, major determinant of capacity for evolutionary change
- Natural populations hold wide range of genetic variation
- Synthetic theory accordance - principle agent of changes in composition of the gene pool is thought
to be natural selectio
- Other agents of change in a natural population is
- Mutation - source of true genetic novelty, change in sequence of bases in DNA of organism,
producing new alleles, immediately changing gene pool of population
- Random event
- Rare, due to high fidelity of DNA replication but contribution of mutation is substantial on a
population wide basis
- Mutation rates are usually low that it does not determine direction of evolutionary change
Maintaining variation
- Sexual reproduction
- Diploidy
- Outbreeding
-Heterozygote advantage
Losing Variation
-Inbreeding
- Genetic drift
Restoring Variation
-Gene flow
Gene flow
- movement of alleles into and out of populations or sub populations, potentially introducing new
alleles or altering proportion of alleles already present
-Can counteract effect of natural selection and tends to maintain homogeneity in population
Genetic Drift - phenomenon in which certain alleles increase or decrease in frequency, potentially
even disappearing as a result of CHANCE events
- More evident in small populations than larger ones
- Founder effect - when a few individuals of a population are separated from the rest of the
population, establishing a new population with a different gene pool to that of the original.
- Wind blowing away birds from population, indiscriminately blowing away some individuals but no
others
- Population bottleneck - sudden change in environment, that drastically reduces the size of the
population and only a few remain
- As if the population has gone through the bottleneck, reducing its size, bottleneck effect
- By chance, certain alleles may be over or under represented in this new small population and some
alleles may even be absent.
1. Genetic drift is significant in small populations
2. Genetic drift can cause allele frequencies to change at random
3. Genetic drift can lead to loss of genetic variation in a population - loss in alleles over time,
evolution depends on genetic variation, can influence how effectively a population can adapt to a
change in the environment
4. Genetic drift can cause harmful alleles to become fixed - population survival can be threatened.

- Non random mating causes change in proportion of genotypes but may or may not affect allele
frequencies in population

Sexual Reproduction
- most important factor in promoting genetic variability in populations of diploid organisms

Outbreeding and Inbreeding
- Mechanisms that promote outbreeding, promote variability, while inbreeding (mating between
close relatives) results in loss of variation and increased homozygosity, increased susceptibility to
diseases, inbreeding depression
-Common in small captive populations, and populations that have experienced bottleneck genetic
drift.
- Consanguineous matings more likely to produce homozygous for otherwise rare autosomal
recessive genes

Diploidy
- Variability is preserved by this, and it shelters rare recessive alleles from selection
- Creates a recessive refuge for deletrious alleles, some of which causes serious disease in humans
- In terms of heterozygote superiority, natural selection promotes to preserve variability, in some
cases, such as sickle cell anaemia in areas where malaria incidence is high
- The heterozygote is more advantageous than either homozygous genotype, increasing chances of
survival and reproduction of that individual. Thus heterozygote is selected either homozygote
- Heterosis, hybrid vigour, is a result of either heterozygote superiority or masking of effects of
recessive alleles

Lecture 5
Natural selection - differential reproduction of genotypes resulting from interactions between
individual organisms and their environment
- Synthetic Theory - natural selection is the major force in evolution
- Natural selection operates wherever genotypes differ in fitness, where fitness is measured by
genotype's rate of increase relative to other genotypes
- Natural selection categories are stabilising selection , directional selection and disruptive selection
- Stabilising - favours intermediate phenotypes over extreme phenotypes and narrows variation in
population
- Directional - favours one extreme phenotype over another, and moves whole mean of population
towards one end. Variation remains the same
- Disruptive - Favours extreme phenotypes over intermediate, change in distribution of population
phenotypes, with decreasing amount of intermediate and increase in extreme phenotypes
- Fourth is said to be frequency dependent selection - fitness of phenotype decreases as it becomes
more common in population, and increases as it becomes less common

- Sexual Selection - Darwin - results from competition for mates, thought to be responsible for
elaborate mating displays and secondary sexual characteristics in some species

- Result of natural selection is adaptation
- Microevolutionary scale - gradual variation that follows geographic distribution, cline, and distinct
phenotypes of same species occupying different habitats are said to be evidence of adaptation
- Macroevolution - coevolution, convergent evolution and divergent evolution, evidence of
adaptation
Coevolution - result of selective forces exerted by interaction between species
Convergent Evolution - different ancestors, unrelated species come to resemble each other in some
attribute as a result of adaptation to similar selection pressures
- Divergent evolution - related species, related population becoming dissimilar, sometimes leading to
new formation of species
- Influences of genetic drift and gene flow may counter balance forces of selection
COEVOLUTION - Mimicry, Mullerian Mimicry, Batesian mimicry, the selective forces that are applied
due to interaction between organisms.
Lecture 6
- Phylogeny
Evolutionary development and history of a species. Common ancestry. Phylogenetic
classification takes into account the similarities that are homologous.
- Species defined as group of natural populations who can interbreed with each other successively
and are reproductively isolated from members of other populations
- Allopatric Speciation and Sympatric Speciation, Allopatric with geographically isolated populations
and sympatric without. Sympatric thought to occur mainly in plants through polyploidy (increase in
genome number), resulting in hybridisation, can occur in disruptive selection also
- BSC - Ernest Mayr

-Allopatric- considered to be the most the most common mode of speciation
-Dispersive - chance movements to new habitats
- Vicariance - geographic disruption of distribution
-Sympatric - can also be assortative mating creating genetic discontinuities
-Autopolyploidy and Allopolyploidy - auto -derived from same species, - allo - from different species
-auto has a meiotic error, whereas allo has mitotic and meiotic error
- Microniche adaptation producing new species

- Through genetic isolation, key event of speciation occurs
- Reproductive isolation mechanisms
- Prezygotic and postzygotic
- Pre zygotic mechanisms include spatial, temporal, behavioural, ecological and morphological
differences between populations
- Post zygotic mechanisms, after fertilisation, inlcude zygotic mortality, reduced reproductive success
and reduced viability and fertility of hybrid, or hybrid breakdown
-Habitat - populations live in different habitats and do not meet
-Temporal - mating or flowering occurs at different seasons or times of day
-Behavioural - little or no sexual attraction between males and females
MATING
-Mechanical (morphological) - structural differences in genitalia or flowers prevent copulation or
pollen transfer
-Gametic - male and female gametes fail to attract each other or are inviable
FERTILISATION
-Reduced hybrid viability - hybrid zygotes fail to develop or reach sexual maturity
-Reduced hybrid fertility - fail to produce functional gametes
- Hybrid breakdown - offsprings of hybrids have reduced viability or fertility
-Cetaseans have few post zygotic isolation mechanism, thus majority is pre zygotic
- Macroevolution, considered product of 4 patterns of evolutionary change, phyletic change,
cladogenesis, adaptive radiation and extinction
- Phyletic change or anagenesis is a gradual change within a single lineage over time
- Cladogenesis, evolutionary change produced by branching off of populations from each other to
form new species
-Cladogenesis said to be what produces diversity of species over time
-Adaptive Radiation - rapid formation of new species from a single ancestral group, characteristically
to fill in a new ecological zone - also convergence, example of marsupials and mammals, yet similar
characteristics between them, analogous
- Extinction - disappearance of a new species from the earth
- Punctuated Equilibrium can be said to be a fifth pattern of macroevolution - where new species
appear in bursts of rapid speciation among small peripheral populations, they displace the existing
species, which become extinct, persist for long periods of time with little change and then abruptly
become extinct.
- 5 mass extinction events, with recent one ending the dinosaurs and potentially allowing adaptive
radiation to occur for mammals
-Gradual or punctuated
-Punctuated displays speciation occurred relatively rapidly















Lecture 7
- Phylogeny -evolutionary history
- Every taxon should be monophyletic in a phylogenetic system, every taxon consisting of organisms
descended from one common ancestor
- Similarities should be homologous over analogous, result of common ancestry rather than the
adaptation to similar environments
- Morphological, molecular characteristics, fossil evidence and patterns of embryonic development
are used for evolutionary systematics

- Two new methodologies proposed for classification, numerical phenetics and cladistics
- Numerical phenetics - relies solely on scoring of equally weighted similarties and differences among
groups, without regard to homology or analogy - grades of change
-Cladistics - based on entirely branching relationships, determined by shared evolutionary derived
characteristics, and ignores overall similarties - clades
-Taxon - group of species of higher order taxonomic groups
- Traditional view, based on fossil evidence, closest relatives to whales were thought to be
carnivorous hoofed animals, mesonychians
- Recent analyses of DNA sequences, hippos are closer relatives to whales
-Fossil records of walking whales, with distinct ankle bone, similar to artiodactyls, was due to
convergence rather than homology
-Ancestral characteristics - characteristics inherited with little or no change from remote ancestors
- Derived - characteristics which have undergone recent change and may be shared only by closely
related species or taxa

- Cladistics emphasise monophyletic classification
-Grades - groups which have evolved new adaptive features
-Clades - which are groups including only monophyletic branching events









Lecture 8
-Homo sapiens, our own species
- Two living groups of primates are prosimians and anthropoids
- Modern prosimians, lemurs, bush babies
-Anthropoids include New World and Old World Monkeys and hominoids - apes and humans
- 3.6 to 1.4 million years ago, groups of hominins lived that walked erect, small, ape like skull
- Closest living relative to homonins, including present day humans are the chimpanzee
-Homo erectus - 1.6 million to 300,000 years ago
-Tall, body structure skeletal wise, similar to modern humans, skulls much heavier
-H. erectus, stone tools, fire

- Archaic H. sapeins - larger brains and smaller teeth than H. erectus
- Neanderthal fossils, date about 300,000 to 35,000 years ago, period of last glacial advance
-Neanderthal had fire, inhabited caves, hunted large animals, probably wore clothing. Use of stone
tools and burial of dead, sometimes with food and weapons
- Cro Magnons, modern humans, replaced Neanderthal,
- Two models for transition from archaic to modern
- Multiregional model - geographically distant populations of archaic humans linked by gene flow
slowly evolved into modern humans over last 700,000 years, phyletic change or anagenesis, gradual
transition from one form into another
-Eve Hypothesis - modern humans originated in Africa less than 200,000 years ago and spread rapidy
throughout Europe and Asia, replacing Neanderthals. Example of cladogenesis, branching of lineages
into separate species and extinction of one species
-Fossil evidence of co existence between Cro Magnons and Neanderthals present

-Analysis of mtDNA, all humans are descendants of common maternal ancestor, living 200,000 years
ago
-Homo erectus, leaving Africa, 200,000 years ago
- Between C and D, use of tools, early
- Hominins and apes - bipedal locomotion and larger relative brain volume
- Neanderthal - symbolic representation, complex arose with Cro Magnons





Lecture 9

On a macroevolutionary scalre
-Mass extinction, impact between earth and asteroid or comet travelling at a speed of more than
10km/sec
- Energy liberated causing environmental disasters, such as storms, tsunamis, cold and darkness,
greenhouse warming and acid rain and global fire
- Mammals were able to fill in ecological zones with the removal of dinosaurs
-Punctuated equilibrium presented, opposing gradual equilibrium
-Bursts of rapid speciation among small peripheral populations
-New species replace many of the previously existing species
- Species persist for long periods of time, with little change, the abruptly become extinct
-Paleozoic, Mesozoic and Cenozoic
- Permian extinction, then Triassic, then extinction, then jurassic, and cretaceous, and then
cretaceous extinction
1. iridium anomaly layer
2. laminar deformation of quartz grains
3. basaltic spherules
- boundaries between Cretaceous and Tertiary Period
-all evidence for extra terrestrial impact for extinction of dinosaurs

Microevolution - Population bottlenecks increased risk of disease in African Cheetahs
- fewer than 20,000 in sub Saharan Africa
- During Pleistocene and Pliocene, at least four species and four subspecies of cheetahs present
- Towards Pleistocene, monophyletic cheetah species survived, while all others abruptly became
extinct in North America, Europe and Australia
-Extinction reasons may have included
- environmental cataclysm of human hunting pressure
- rapid environmental change
-epizootics (diseases) related to domestication
-Inbreeding depression present in Cheetah, aberrant sperm
- Reduced levels of genetic variation relative to other species
- Hypothesis that cheetahs species survived an intensive inbreeding period, due to population
bottleneck
- Increased spermatozoa abnormalities
- decreased fecundity
-high infant mortality
-increased sensitivity to diseases