Evolution & Genetics

Problem of history

different animals have similar parts for different functions - e.g. arms in various animals have very similar structures but they will use them in different ways - why?

Species relationships

Darwin realises that for animals to be related means that they share a common ancestor, and the more closely related they are (e.g. similar biochem.), the more recent that ancestor was.

Descent with modification

Species must not be fixed, but change gradually over time - assures that organisms will be classifiable into hierarchical groups. These groupings represent is the closeness of the common ancestor of all the species involved - (the time since the split).

The problem of design

Organisms everywhere appear well-adapted for their surroundings (or the exact opposite)

Vestigial structures

essentially have no function - e.g. whale’s pelvis

4 components of Darwin’s theory

Variation, heredity, competition, natural selection

Competition

Not all species get to reproduce to the same extent

Homologies

Similarities between organisms due to common ancestry - e.g. pelvis of human = homologous to pelvis of the whale b.c common ancestor

Analogies

Similarities between organisms due to parallel selective pressures (e.g. same environmental pressure/problem)

The modern synthesis

Darwin +Mendel

Phenotype

Some of this is heritable

Genotype

Types of genes you have - variation in this creates variation in the phenotype

Eukaryotes

Cells in animals and plants whose cells contain nuclei and mitochondria

Amino acids

20 different types of them - long chains of them make up proteins

Alleles

Alternate forms of genes

Central dogma

Genes affect the properties of proteins, but proteins do not normally affect the properties of genes. The flow of information is one way.

DNA molecule

Has two strands, each of which mirrors the information in the other through the principle of base pairing

Bonds between base pairings

Hydrogen bonds - b.c. they are weaker and can be broken when needed for transcription

Chromosomes

Long stretch of DNA - DNA is organised into a number of pairs of chromosomes in a diploid organism

Genes

Section of a chromosome coding for a specific protein

Order of bases

= coding for protein - i.e. order of amino acids

Different alleles

Will often lead to the formation of a different sequence of amino acids, therefore a different form of the protein

Sugar-phosphate

Make up backbone of DNA structure

Adenine

Base “A”

Thymine

Base “T”

Cytosine

Base “C”

Guanine

Base “G”

Base pairings

A & T, C & G

Transcription

Hydrogen bonds broken, messenger RNA (mRNA) formed along an open strand and a copy is made of the bases.

Translation

Ribosomes read the code of the RNA and make the proteins like a recipe - 3 bases = 1 amino acid

Codons

Triplets of bases that code for amino acids - T is swapped for U

The genetic code

The mapping from particular codons in the mRNA to particular amino acids in the assembled protein.

The genome

All the genetic material we have

Introns

Contained within genes - non-coding sequences inserted within the code for a particular protein

Exons

The coding sequences within genes

Non-coding DNA

99% of the genome. May be parasitic (i.e. doesn’t do anything).

Transposable elements

Part of non-coding DNA, e.g. “jumping genes” - big lengths of DNA that just get copied

Simple sequence repeats

Another part of non-coding DNA - e.g. ATC ATC ATC - too many reproductions (a mistake) - underpins genetic finger printing

Highly conserved

In relation to some of non-coding DNA - it may have v. important function that we don’t know yet b.c. it’s been preserved in multiple organisms

Diploid

If chromosomes are arranged in pairs (i.e. humans) - two copies of each chromosome - one from each parent

Recombination

During meiosis, the paired chromosomes in the progenitor cell line up next to one another and may exchange DNA, such that a sequence that was originally on chromosome A ends up on chromosome B, and vice versa.

Meiosis

Formation of gametes in the reproductive organs - i.e. progenitor cells from the mother or father with 46 chromosomes split so each gamete has 23 chromosomes.

Linkage disequilibrium

when two genes reside on the same chromosome, there will be some degree of linkage between them. When two genes are linked, the probability of having the grandpaternal copy of gene A is affected by whether you have the grandpaternal copy of gene B.

Haploid cells

gametes

Mitosis

Cells dividing in embryo - replication, chromosomes split and bases are copied

Mutation

Copying error e.g. in mitosis or meiosis. Most “sneak through”

Single-base substitutions

Type of mutation. Transitions - Changes between C and T or between G and A, Transversions - between dissimilar pairs of bases like C and G or C and A

Simple sequence repeat expansions and contractions

Mutation - an extra copy of the repeat motif is added, or one lost

Transposable element insertions

Mutation - the copying of a transposable element such as Alu from one part of the genome to another

Segmental changes

Mutation - big chunks of extra chromosomes - e.g. down syndrome

Deleterious

Harmful

Locus

A particular site in the genome

Linkage study

\
Look at who is affected and who is unaffected \n within a large family, and trace which sections of which chromosomes are shared

Association study

\
Assemble large groups of individuals with and without the trait and compare the frequency of different alleles

Redundant

There are other ways of doing things - e.g. the human genome (coding for amino acids is interchangeable) and biological systems

Mendelian diseases

Mutation caused in genes

Heredity

How far offspring resemble their parents

Mendel

Key scientist - contemporary of Darwin

Pea plant experiments led to discovery of dominant vs. recessive alleles

Homozygous

Having two copies of the same allele - gametes can only be one e.g. eye colour

Heterozygous

Having one of each copy of two different alleles - gametes can be either e.g. eye colour

Independent segregation

This principle means that phenotypic traits controlled by different genes can become separated from each other through the generations i.e. we can observe combinations of genes that we have never seen before in ancestors

Hardy-Weinberg theorem

Theorem that can be used to calculate how common traits should be (i.e. probability). Genotypes always appear in the frequency p^2, 2pq and q^2. (P = freq. of on allele, p = freq. of the other).

Genetic drift

Because populations are finite, allele frequencies do in fact change (a little) by chance from generation to generation \n E.g. if you toss a coin four times, you won’t always get two heads and two tails \n Because of this, neutral alleles change in frequency over time, which means that populations become more dissimilar at the molecular level, even without any natural selection

Called?

Quantitative genetics

Based on phenotypic correlations (genetic component + shared environment component) between relatives. Idea of predicting phenotype from genotype for traits which are not either/or (like being yellow or green), but continuously variable (like height or weight) and where large numbers of genetic loci are involved.

Coefficient of relatedness

i.e. heritability or “h^2” - Works like probability trees e.g. 1/2 x 1/4

Heritability

Number between 0 and 1, reflecting the proportion of variation in that trait in that population which is due to variation in genotype \n Does not say anything about whether something in an individual is ‘due to his genes’

G or A

Letters that represent variation due to genes

C

Letter that represents variation due to shared environment

E

Letter that represents variation due to unique or non-shared environment

Falconer’s estimate of heritability

G = 2 \* (corrMZ – corrDZ)

Malthus

Key thinker: Principle of population

Populations could potentially grow exponentially, but in practice cannot do so, and therefore must be limited by incomplete survival and/or reproduction (e.g. competion)

Reproductive success

the number of descendants an individual leaves

Fitness

Strictly a property of an allele. It is the change in \n frequency of an allele over the generations. It is related to the average reproductive success of all the individuals it appears in

The evolutionarily stable strategy

\
A behaviour that, once common in a population, cannot be out-competed by any alternative behaviour \n Once selection finds an ESS, it keeps the population close to that point

Help collateral kin

Alternative to natural selection to get own alleles into the next generation

c < rb

Hamilton’s rule - (formula)

Calculates cost of kin selection in relation to benefit and relatedness

Inclusive fitness

Your own reproductive success + Help you allow to your kin

Alloparenting

Parenting by a non-biological parent - kin selection allows us to understand why this occurs

Multi-cellularity

Basically the Hamilton rule but in cells. Only gamete cells can reproduce, but normal cells share all their genetic material with the gametes. So if they help the gametes their genetic material is being passed on, which explains why cells put up with their “rubbish life”.

Eusociality

Also helps explain kin selection

Individuals in the population who don’t reproduce, but just contribute to overall function - e.g. ants, bees

Evolutionary transitions

Changes that increase in complexity, but maintain integral components

Intra-genomic conflict

When evolutionary transitions don’t happen as they should

Involves doing stuff that’s good for the gene, but not for the organism as a whole e.g. transposable elements

The mechanisms suppressing competition between genes are not always perfect and genes in the same individual can differ in fitness

Segregation distorters

Another example of intra-genomic conflict

Genetic variants that give themselves an advantage relative to all their competitors

Natural selection

occurs whenever the fitness of one allele at a locus is higher than any of its competitor alleles

Purifying selection

Type of selection - Occurs when an allele that does something useful is fixed at a locus. Whenever mutations arise at that locus, they have lower fitness that the incumbent and thus are weeded out. If they are lethal, they will disappear in one generation. If their negative effect is more moderate, they will persist for some time before disappearing.

Stabilizing selection

Type of selection: people who have mean = have highest reproductive success, e.g. height

Directional selection

Type of selection - leads to change - mean of population does not equal the optimal

Mutation-selection balance

Mutation introduces genetic variation into the population, whilst selection siphons it out. The level in any given population will depend upon the relative strength of the two forces.

Heterozygote advantage

situation where individuals with one copy of a particular allele have higher fitness than individuals with either no copies or two copies.

Negative frequency-dependent selection

Type of selection - This is the situation where a phenotype is associated with relatively high fitness when it is rare, but relatively low fitness when it is common. The result of such a selective regime is that the type stabilizes at an intermediate frequency.

Sexually antagonistic selection

Type of selection - The optimal phenotype may not be the same for males and for females. An allele that increases height may increase fitness when found in a male body, since there seems to be directional selection for height in males, but not when it is found in a female body, since selection on female height is stabilizing.

Adaptationist stance

means reasoning in the following way: if some feature or behaviour is commonly found in a type of organism, then it is probably an efficient design solution to some problem that that organism has faced.

Pleiotropy

When a gene affects multiple traits

Genetic correlations

Evolution does not always produce optimal design - e.g. The Siberian fox farm experiment: when traits hitch hike when one trait is selected

Local maxima

When evolution gets stuck

Reverse engineering

hypotheses derives an expectation of the following form: if the characteristic had been honed by natural selection for the function under test, what design features would we expect it to have? These expectations are often made using mathematical models, but we can use a kind of informal optimality thinking for present purposes. Links to adaptationist stance.

Asexual reproduction

Type of reproduction - w/o another member of their species (on their own)

Clonal reproduction

As a result genome in offspring will be identical to the parents

Isogamous sex

Mating type - more than one sex is needed for reproduction - the gametes don’t differ in size

Anisogamous

e.g. humans - gametes don’t differ in size