Evolution

Evolution: Change in (biological) entities over time

Origin of Species: written by Charles Darwin in 1859
Scala Naturae: chain of being, a ladder of increasing complexity
Carrolus Linneaus: Father of taxonomy (hierarchy of nested sets groups within groups)
Paleontology: The study of fossils/rocks
Catastophism: Cuvier, what we have today is a leftover of species that survived catastrophes
Lamarck: suggested that forms come into being as modifications of previous forms
Mutation: changes in the original genome
Homology: similarity resulting from common ancestry
Analogy: Converse of homology
Convergent evolution: feature evolved in two different times and places on the tree of life
Transitional form: an organism that is intermediate between an ancestor and a descendant in a evolutionary
sequence.
Polygenic inheritance: phenotype influenced by several genes
Directional Selection: one end of distribution selected against
Disruptive Selection: Intermediate phenotypes selected against
Stabilizing Selection: extreme phenotypes selected against
Allele: an individual gene variant at a locus
Genotype: the combination of 2 alleles in an individual
Neutral alleles: mutations that dont affect fitness
Harmful alleles: reduce fitness
Beneficial alleles: increase fitness
Gene-flow: alleles introduced to a population from other populations
Gene pool: sum of all alleles at all gene loci in all individuals
Allopatric speciation: geographic barrier blocks gene flow between populations
Sympatric speciation: new species arise within range of parent population
Fusion: Dont undergo sympatric speciation even though they have separated, failure to speciation
Reinforcement: Have a reproductive barrier less likely to make the disasterous choice, number of hybrids being
produced declines - Speciation can be favoured further
Exaptation: Structures adapted for one function are coincidently used for another function
Homeotic genes genes that are involved in embryologic development which specifiy which segments of the
ebryo develop into
Taxonomy: naming and identification of taxa species and groups of species
Phylogenetics: of evolutionary trees (phylogenetic trees/phylogenies)
Monophyletic group (Clade): An ancestor and all of its descendants
Paraphyletic group: An ancestor and some, but not all, of its descendants
Polyphyletic group: A group that does not include its own most recent common ancestor (= 2+ branches
artificially grouped together)
Relative Dating:
Absolute Dating:
Indirect Dating:
Adaptive Radiations: is the evolution of ecological and phenotypic diversity within a rapidly multiplying lineage.
Peptidoglycan layer between (complex polymer of sugars and amino acids




Lamarcks Ideas:
1) Pattern
a. Living world made up of many separate lineages with independent origins
- simpler organisms havent had much time to evolve as those that are more complex
b. Each lineage progresses (strives) towards greater complexity/perfection
2) Process/Mechanism
a. Use-and-disuse, and Inheritance of acquired characters (Lamarckism)
- If you use a body part more than other parts, this part will become more developed than other
part
- Features that you acquire during your lifestyle will be passed onto your offspring
- Note that the INDIVIDUALS EVOLVE
Darwins Ideas:
1) Pattern
- Living things united in a single branching tree of relationships
- The history of life on earth is a branching tree, species changing into species over time
- A point where one lineage divides into two divisions happen more than once in a tree
- Look at the fork closest to the end Most recent Common Ancestor of the two divisions (A + B)
- Descent with modification Species A and B are similar because of their shared history prior to
their last common ancestor
- But species A and B also differ because of independent changes in their lineages after divergence
from their last common ancestor
- This fits with Linnaean classification Tree of Life fits well to hierarchical classification

2) Process
- Evolution occurs primarily because of the action of Natural Selection
- Key point: individuals of a species belong to populations
- Note that populations evolve, not individuals
Natural Selection Ingredients:
1) Heritable Variation
- Individuals in a population are born differing in many traits (many features)
- Many traits can be passed on from parents to offspring (i.e. are heritable)
- Ex: shells that are all belonging to snails, shell patterns are heritable

2) Excess Production
- In any population, more offspring are produced than needed to maintain it (usually many more)
- When resources are limited, many of the offspring do not survive (or at least, dont reproduce
successfully)
- Excess production leads to competition: the struggle for existence some will succeed, some
will not
- But because of their differing traits, some individuals have an advantage i.e. will produce more
viable offspring on average
- This is the concept of fitness

Then advantageous traits increase in frequency
- Heritable traits that helped individuals to have more viable offspring on average will tend to be
passed on to those more numerous offspring
- With time, these traits will tend to become more frequent in the population (& disadvantageous
traits will become less frequent)
- This is evolution (the population has evolved)
- Prevalence of a trail increases, the physical traits represent this in a population

Natural selection over time results in adaptive evolution (adaptation) - organisms well suited to their
environment

Evidence of Natural Selection
Warfarin Resistance in Rats
- Only a few rats that had mutations with warfarin resistance
- Once warfarin was introduced, the rats with resistance were more successful and this mutation
was passed on
- Over the next couple of years, they stopped poisoning with warfarin, the frequency of warfarin
resistance declined
- Shows: Editing rather than creative mechanism needs variation to act on
- Shows: Contingent on time and place - happen to be disadvantageous when poison not used
Evidence for Tree-of-life and descent with modifications
Homology
Similarity resulting from common ancestry
a) Standard anatomical structures structures with different functions but the same form

b) Vestigial Structures structures with little or no function derived from more complex structures
ex: human appendix, remnant hind-limb bones in whales (later)
c) Embryological Homologies Organs that share a common function during development, but
have a very different form/function once developed
E.g. pharyngeal pouches in vertebrate embryos
Comes gills in fishes Become Eustachian tubes in mammals
d) Molecular Homologies Homologies at the biological level
- e.g. The universal genetic cods

- reflects evolutionary events that take place over time

Analogous Structures (converse of homology) similar functions but very different structures (similarity
not from common ancestry)
convergent evolution: feature evolved in two different times and places on the tree of life


Biogeography
- The geographic distribution of organisms
- Some taxa (groups of similar species) are restricted to certain locations (endemic, not
ubiquitous)
- Explanation: descent from a common ancestor that lived in that location

Fossil Record
- Descent with modification predicts transitional forms
- Order of appearance in fossil record
- Examples: whales (fully aquatic mammals)
o Dorsal fin, blowhole, tale adaptation to a fully aquatic lifestyle
o Lack hind-limbs
o Forelimbs lack distinct fingers
o Dorsal fin, caudal flukes
o Nostrils on top of head etc.
- and birds (powered flight)
- A series of many transitional forms link modern whales to land-dwelling mammals

Modes of Selection





Oscillating directional selection in fluctuating environments
- does not need to go in one direction
- ex: rainfall in Galapagos Islands, seed size, and finches
- Seeds that are big and hard, you need a large beak to get food
- Seeds that are small, you need a smaller beak to get food
- In rainy years, increase in small beaks
- In dry years, need a more robust beaks
- Because the environment is changing, the distribution of a phenotype is constantly changing
directions
- Fitness is more than survival
- Can have a longer life time, but less offspring if behaviour doesnt allow it to mate

Sexual Selection
- Effectively a special case of natural selection
- Competition for mating opportunities
- Results in adaptations that increase mating success
o But can actually reduce change of survival

Intrasexual selection
- Competition within one sex (usually males) for mating opportunities
- Adaptations: Armaments physically competing

Intersexual selection
- One sex (usually females) chooses mate from (competing members of) other sex
- Ornaments visually competing
Evolution of populations
Fixed alleles: Whole population is homozygous at locus
Polymorphic loci: two or more alleles in population, each present at some frequency

Microevolution: Change in the frequencies of different alleles in the gene pool over generations
At the extreme, change can mean fixation of an allele, or loss (extinction) of an allele.

Hardy-Weinberg Principle: describes expected relationships between allele and genotype frequencies
when there is no evolution

p + q = 1
p
2
+ 2pq + q
2
= 1
p
2
,q
2
= Expected frequencies of the two homozygote genotypes
2pq = Expected frequency of heterozygotes

Assumptions of Hardy-Weinberg
1) No net mutations
2) Random mating
3) No natural selection
4) Large (infinite) population size
5) No migration (no gene flow)
Violation of these assumptions usually signals evolutionary change

Causes of microevolution
Mutation (trivially)
Non-random mating
Natural selection
Genetic drift
Gene flow
Of these, only natural selection results in adaptive evolution

Gene Flow
Dispersal of gametes (e.g. pollen) or migration
Gene flow from population with different allele frequencies change in allele frequencies
Gene flow can introduce new alleles to a population

Random Genetic Drift
Sampling error
Can lead to fixation (or extinction) of alleles in the absence of natural selection. if no new
alleles are being introduced

Drift, population size and frequencies
Rate of drift related to population size
Faster in small populations than large
Random: Neutral allele at frequency 0.5 is equally likely to eventually be fixed or to go extinct
[In theory, chance of eventual fixation of a neutral allele is the same as its frequency]

Genetic bottlenecks
Breeding population is very small for a time
Genetic drift powerful: allele frequencies change, many alleles fixed or go extinct.
= Lower genetic diversity overall, even if population later expands in numbers
Some rare alleles can increase in frequency
= Possibility of high frequencies of harmful alleles (even fixation of slightly harmful alleles)

e.g. High prevalence of particular normally rare genetic diseases in isolated human populations
- Ellis-van Creveld Syndrom
- ~1000x more common in a particular Amish group than in general population

Endangered populations/species
- Genetic diversity (gene pool) can be increased by adding individuals from other populations
(enforced gene flow)
- Captive breeding programs manage matings to preserve remaining genetic diversity
Preserving Allelic Variation
Diploidy hides recessive alleles from selection when they are rare.
- e.g. earlier cystic fibrosis example: q =~0.02; ~1 in 25 Europeans are carriers; Only 1 in 2500 are
homozygous.
Natural Selection can sometimes favour allelic variation: Balanced Polymorphisms, e.g.:
Frequency-dependent selection
Heterozygote advantage (= overdominance)
Inverse Frequency-Dependent Selection: Rarity increases relative fitness of a variant
e.g. the scale-eating fish
left and right mouthed scale eating fish tend to eat scales off the plank of a fish
Sickle-cell anemia (a case of Heterozygote advantage)
Single locus recessive genetic disease
ss homozygotes - severe illness, high mortality while young: Fitness of ss much lower
than SS or Ss
But, Ss confers resistance to malaria (deadly)
Malaria absent: SS, Ss similar fitness
Malaria prevalent: Ss confers higher fitness than SS
** learn this as an example
What is a species?
Morphological Species Concept: based on morphological similarity. (Molecular sequencing is now also
used)
Biological Species Concept:
Inter-fertility: populations that interbreed to produce fertile offspring
Reproductive Isolation: Do not normally successfully interbreed in nature with other species

Speciation
- Reproductive barriers inhibit gene flow between populations, allowing evolutionary divergence
- Prezygotic barriers: act before fertilization
- Postzygotic barriers: act after fertilization


Prezygotic Barriers Postzygotic Barriers
1. Habitat isolation
2. Temporal isolation
3. Behavioural isolation
4. Mechanical isolation
5. Gametic isolation (gamete
incompatibility)
1. Hybrid Inviability
2. Hybrid Infertility
3. Hybrid Breakdown
(pages 490-491)

Geographic Barriers:
(Mountain ranges, rivers, open water, lake
formation, land bridges)
- Either barrier forms during history of
species or rare migrants cross existing
barrier.
- Ex: Isthmus of Panama: formed 10-3
million years ago, isolating population
of many species

Evolution after separation:
- Natural selection to different
environments (adaptive evolution)
- Genetic drift (especially in small isolated
populations)
- Migrants found new small population in
peripheral habitat
Speciation
Allopatric speciation: geographic barrier blocks gene
flow between populations
Sympatric speciation: new species arise within range
of parent population
Requires a barrier to gene flow within a geographic
region
Host switching by specialist herbivores or
parasites (habitat/behavioural isolation)
Disruptive selection, favouring evolution of
reproductive barriers between individuals
with different phenotypes?
Polyploid speciation in plants



- mutation
- Having more than two sets of
chromosomes
- Can cause speciation in sympatric plant
populations, gene flow is reduced
between polypoloid and normal
individuals
- Reproductive isolation, genetic isolation
occurs


If contact re-establishd between evolved allopatric populations:
1) Complete reproductive barriers evolved:
populations now classic biological species OR












Fusion: Dont undergo sympatric speciation even
though they have separated, failure to speciation
Reinforcement: Have a reproductive barrier less likely to make the disasterous choice, number of
hybrids being produced declines - Speciation can be favoured further
Evolution of complex features
(Darwin proposed evolution through many small steps, every step should improve fitness)

1) Functioning Intermediates
- In many cases, simpler forms of complex structures are potentially functional
o Evidence: Organs of different complexity in related species
o Tep-wise evolution plausible
o Ex: Functional eyes of different complexity in different living molluscs
2) Modification of existing structurs
- Exaptation: Structures adapted for one function are coincidently used for another function
o Ex: Birds are related to dinosaurs. The original function of the feather was not for flight.
Feathers in non-flying dinosaurs were used foro thermoregulation or display
3) Larger steps than imagined by Darwin
- Changes in developmental regualtion
- Origin of novel genes (gene duplication)
o Evolution of developmental regulation: mutations affecting genes that control
development small genetic change can result in lage coordinated changes in
phenotype
o Homeotic genes genes that are involved in embryologic development which specifiy
which segments of the ebryo develop into
Hox genes: control indentity of segments along developing animal body
o Evolutionary modification of rates of growth during development


Phylogenies and Systematics
Systematics: study the diversity of life
two components
Taxonomy: naming and
identification of taxa
species and groups of species
Phylogenetics: of
evolutionary trees
(phylogenetic
trees/phylogenies)

Binomial Names Genus species

Different groups on trees
Monophyletic group (Clade):
An ancestor and all of its
descendants
Paraphyletic group: An ancestor and some, but not all, of its descendants
Polyphyletic group: A group that does not include its own most recent common ancestor (= 2+
branches artificially grouped together)


How do we infer phylogenies?
Character states (possible homologies)
Morphological features, etc.
Identities in DNA / protein sequences
Distribution of character states among
organisms reflect evolutionary relationships (see next
slides)


What if there is a conflict?
i.e. character state distributions are not all consistent with the same tree
Convergent evolution (analogy not homology - see lecture 2)
Reversals (e.g. loss)
Compare many (all) possible trees
Parsimony criterion: best tree is the one that implies fewest evolutionary changes.

Molecular Sequence Data
Phylogenies usually constructed by comparing molecular sequences (e.g. DNA, proteins).
A site in a set of aligned DNA sequences is a character: Different bases at site are the states



Phylogenies of genes
Evolution of genes themselves is often of interest
e.g. tracing history of gene duplication, or of
gene transfer between genomes
One of many aspects of the disciplines of
molecular evolution and genome evolution
Aligned molecular sequences (DNA, proteins) can
be used to infer relationships among organisms,
Genes themselves have evolutionary trees, which
can be studied to understand their history, (e.g. gene
transfer)


Macroevolution
Sedimentary rock is where most fossils are
found.

Relative dating
Order of appearance in strata
Index fossils to compare locations

Absolute dating
Radiometric (Isotopic decay)
Ancient sedimentary rock and
organic material hard to date directly
Radiometric dating used to directly
date volcanic (igneous) rock.
e.g. Potassium-40 Argon-40
dating

Indirect dating of sedimentary rock and fossils associated with datable volcanic layers






End-Permian Mass Extinction
~250 million years ago
Most devastating mass extinction.
Extinction of ~90% of species on earth
Many large taxa went totally extinct
(e.g. ~50% of Families)
Ultimate Cause:
Volcanic activity??
End-Cretaceous mass extinction
~65 million years ago
Most recent big mass-extinction
Extinction of ~50% of species on earth
e.g. dinosaurs (other than
birds)
Several marine invertebrate
groups
Cause
Asteroid impact (probably)
Adaptive Radiations: is the evolution of ecological and phenotypic diversity within a rapidly multiplying
lineage.
Rapid speciation and evolutionary change in underexploited habitats
Regional:
e.g. colonisation of new island chains
World-wide:
Following mass extinction events.
Replacement in fossil record.


The major lineages of life
(page 515)
- Since ancient times: 2 kingdoms:
animals and plants
- In 1970: five-kingdom scheme:
o Animalia
o Plantae
o Fungi
o Protista
o Monera (prokaryotes)

Some problems with the five-kingdom scheme
- Imperfect fit to phylogeny
o Protista and Monera are paraphyletic groups, not monophyletic (lecture 5)
- No formal taxon for Eukaryotes
Importance of Prokaryotic Life
On Earth for >3 billion years
Most of biological activity in many ecosystems
Ocean
Soil
More prokaryotes than human cells in body
Cause many major diseases & infections
Biotechnology

Typical prokaryotes
Small, simple in structure
Single cells, sometimes simple colonies
Little compartmentalisation of cell
Compact genome
Usually one chromosome (plus plasmids)
Most of DNA is coding: usually 1-6000 genes
Efficient
Growth when resources are scarce, and/or
..very rapid growth and reproduction when resources plentiful
Some species can reproduce every 20 mins under ideal conditions (by binary fission)

Metabolic diversity (examples)
Photoautotrophy (photosynthesis) in some groups:
Harvest light energy; Convert CO
2
into new organic carbon - as in plants
But also
Chemoautotrophy: Obtain energy from oxidising inorganic chemicals; Convert CO
2
into new
organic carbon
e.g. Sulfide (H
2
S) oxidisers

Evolution by acquisition gene transfer:
Some Plasmids
Lateral (Horizontal) gene transfer between genomes
Now recognised as extremely important evolutionary process in prokaryotes

Bacteria
Most diverse Domain
Most of the well-known prokaryotes
Includes all known disease-causing prokaryotes
- Cell Surface
- Usually two bounding membranes: Plasma membrane and outer membrane
- Peptidoglycan layer between (complex polymer of sugars and amino acids)
- Some instead have plasma membrane only
- Usually with thick peptidoglycan wall













A few important types of bacteria
- Spirochetes
- Gram-positive bacteria
- Cyanobacteria (photoautotrophs)
- Proteobacteria

Archaea
Some (many) are extremophiles
Some are extreme thermophiles (some grow at 110C; usually also chemautotrophs)
Some are extreme halophiles (salt-loving)
Many are methanogens - produce methane as a waste product of (anaerobic) energy
metabolism.
Dominant biological source of methane.

Archaea Cell surface
No outer membrane; no peptidoglycan
Membrane lipids chemically different from those of both Bacteria and eukaryotes



Archaeal membrane lipids
(Branched chains, Ether-linked)

Bacterial or Eukaryotic membrane lipids
Some prokaryote-cell-like features of mitochondria and plastids
Similar size
Divide by binary fission
Have ribosomes (Prokaryotic-like)
Have their own genomes!
Encode some RNAs, and proteins that are translated on the organelle ribosomes















Protists:
The first eukaryotes were single cells
Most of the major lineages of eukaryotes alive today are still single-celled protists
Very abundant in most ecosystems
Important photosynthesisers (algae)
The major predators of prokaryotes
Parasitic protists cause some major diseases