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219 Cards in this Set

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What is lateral gene transfer?
It's any transfer, exchange or acquisition of genetic material that differs from the normal mode of transmission from parent of kid (vertical transmission). LGT refers to the transfer/acquisition of genes within a generation and can occur in a genome or between members of different taxa.
How can we tell if a gene is acquired laterally? List 3.
1. Look for the presence of viral or transposable sequences in a genome.
2. Look for sequences unique to a particular genome.
3. Look for phylogenetic incongruence.
Why should you look for viral or transposable sequences for LGT?
Viruses and transposons are agents of gene transfer, so genes near these may have been acquired by LGT.
Why look for sequences unique to a particular genome when looking for LGT?
Genes with sporadic distributions may be newly acquired.
Why look for phylogenetic incongruence when looking for LGT?
It's the most common method and is amenable to all types of genes. It's a disagreement in the phylogenetic tree.
What would phylogenetic incongruence look like from LGT?
Most cases of LGT show up in an anomalous location in a tree. The tree becomes incongruent with phylogenies of the same organisms based on other genes. Looking at one gene, the tree seems to be organized one way, but if you look at the LGT gene, it is organized a different way.
How is LGT different in terms of function from gene duplication?
Genes originating from LGT can provide new functions immediately after being transferred. For example, many strains of bacteria gain virulence genes by LGT which makes them antibiotic resistent.
What are some of the pathogens e. coli can acquire via LGT?
You can still a virulence plasmid into e coli for shigella. E coli can also get dysentery, meningitis, diarrhea, UTI, and HUS genes.
LGT mostly occurs in which organisms?
It usually occurs in single-celled organisms.
What is an example of LGT being crucial for the evolution of multicellular organisms?
Many animals use carotenoids (pigments in plants, bacteria, and fungi that act as antioxidants) to give them distinctive coloration.
What are three examples of carotenoids?
Lycopene in tomatoes
beta-carotene in carrots
alpha-carotene in pumpkins
What kind of animals use carotenoids for coloration?
Flamingos get it from shimp which get it from algae.
Salmon get their coloration from krill.
What is the one example of LGT in eukaryotes?
Aphids have green and pink color polymorphisms. They have genes for carotenoid biosynthesis in their genome. This carotenoid gene is more closely related to the one found in fungi. Aphids are the only animal that produce carotenoids. They probably acquired it from fungi about 100 myr.
What is the typological species concept?
This was the classical idea of speciation. People used to think that members of the same species had similar apearances that are distinct from members of other species. This concept goes back to Plato and Aristotle where there was an ideal form for a species.
What are three ways that the typological species concept can get tripped up?
1. Different species can look alike due to homology.
2. The same species can have polymorphisms, but still be able to interbreed.
3. There can be major sexual dimorphisms.
How did Darwin react to the typological species concept?
Darwin looked at the indistinctness of species' boundaries, particularly the variation in domesticated species, to show that variation exists.
What are the 3 differenct species concepts?
1. Morphospecies (Phenetic) Species concept
2. Biological Species Concept (BSC)
3. Phylogenetic (or Genealogical) Species Concept
What is the Morphospecies concept?
Species are clusters of organisms that are similar based on some characteristics. It takes advantage of the fact that there are often no intermediates between two species. You can classify any group of organisms, but the classification is subjective to the organizer and the specific characteristics she is loooking at.
What is the Biological Species Concept?
Species are groups of actually or potentially interbreeding natural populations, which are reproductively isolated from other such groups. When a group is reproductively isolated, it means that there is no gene flow between the groups. It's the most common definition and is employed by the Endagered Species Act.
What is the only taxonomic category based on the biological process of gene flow?
BSC.
What is the Phylogenetic (Genealogical) Species Concept?
Species are the smallest monophyletic groups (claded) distinguished by a shared derived character. It believes that populations that have been isolated from gene flow will be divergent. It combines features of the phenetic species concept and the biological species concept and can be applied to all types of organisms, living and extinct.
What is essential for the phylogenetic species concept to work?
You have to have a good phylogeny.
What is the downside to using the phylogenetic species concept?
You may end up splitting populations that are the same species based on minor differences or a basepair difference that doesn't really matter.
How do species form?
If species are viewed as genetically separate units, there must be barriers to gene flow, such as isolating mechanisms.
What is the 3 step process to two species being created?
1 species --> divergence --> increase in differences --> 2 genetically isolated species.
What does it mean if two species can't interbreed?
1. no interbreeding
2. no viable hybrids
3. no genetic exchange
What are 4 barriers to gene flow?
1. allopatric speciation (which includes the dumbell model and the peripheral isolate model)
2. Parapatric speciation
3. sympatric speciation
What is allopatric speciation?
It's separated by a physical barrier.
What are the two sub-categories of allopatric speciation?
The dumbbell model and the peripheral isolate model
What is the dumbbell model?
It's a form of allopatric speciation in which a geographical barrier cuts a population in half and then they diverge and become different species.
What is the peripheral isolate model?
It's a form of allopatric species in which a small group leaves the population and is isolated and diverges compared to the former big population.
What is parapatric speciation?
It's where there is a selective gradient and in a population, there is divergent selection across a cline (gradient). You end up forming speciation across a hybrid zone.
What is sympatric speciation?
There is specific speciation of a small group while they are still in the population due to genetic differentiation.
What are the two general kinds of mechanisms keeping species from interbreeding?
1. prezygotic isolating mechanisms - barriers that occur before the zygote is formed.
2. postzygotic isolating mechanisms - barriers that occur after the zygote is formed.
Name 6 kinds of prezygotic isolating mechanisms:
1. They live in the same place, but never encounter one another.
2. Habitat isolation
3. Temporal isolation (by time of day or year)
4. behavioral isolation (they interact, but don't mate)
5. They have sex, but the sperm doesn't transfer.
6. Gametic incompatibility (the sperm transfers, but can't fertilize the egg).
What are 4 kinds of postzygotic isolating mechanisms?
1. Zygotes die early during embryogenesis
2. F1 hybrids are inviable.
3. F1 hybrids survive, but are sterile.
4. Backcross or F2 hybrids are inviable or sterile.
3 main kinds of prezygotic isolating mechanisms:
1. ecological isolation: they live in the same place, but live in different habitats.
2. Temporal isolation: They come in contact, but breed at different times.
3. Behavioral isolation: They come in contact, but don't mate due to courtship differences, different songs, etc.
4. Mechanical isolation: They attempt to mate, but the parts don't work.
5. Gametic isolation: the sperm and egg are incompatible.
What is an example of mechanical isolation?
The escargots whose parts are a different swirl so their junk never meets up. There is also the genital lock-and-key of three different species of fruit flies.
What causes postzygotic isolating mechanisms?
It's because of genetic differences. Two species are incompatible if the alleles fixed at loci in one of the species are incompatible with alleles fixed at other loci in the other species. Hybrids have alleles from both parents at different loci which makes them sterile or inviable.
How does hybrid incompatibility happen?
Dobzhansky and Muller came up with this model independently. It might evolve from epistasis (interaction between loci).
A1B1 --> A2B1 and A1B2 mutations that get fixed on both alleles. If hybrids are majorly selected against, that leads to speciation.
What is epistasis?
The interaction between loci.
What is the hypothetical example for speciation due to enzyme subunits?
You have A1 and B1 subunits that fit together to make a functional enzyme. You get a mutation A2, but it still fits with B1. You get another mutation B2, but it still fits with A1. However, B2 and A2 don't fit together so it can lead to speciation.
What is a real example of the Dobzhansky-Muller speciation hypothesis?
Crosses between Drosophila simulans and Drosophila melanogaster sometimes make hybrids, but the hybrids are sterile. Relative to their common ancestor, mutations have been fixed in each species, the Hmr gene in melanogaster and the Lmr gene in simulans. If you mix these two, the offspring is sterile.
What makes hybrids inviable so often?
It's due to many incompatibilities at locus sites overtime.
What 3 factors did researchers look at when comparing species isolation and genetic distance?
They measured 3 things:
1. Prezygotic isolation when flies from different populations were put together (female preference)
2. Postzygotic isolation when looking at survival/fertility of hybrids
3. Genetic distance in terms of divergence
What did researchers find when comparing species isolation and genetic distance? Name 4 things.
1. Prezygotic and postzygotic reproductive isolation increases with time.
2. The time required for full reproductive isolation is 1-3 million yrs
3. For recently diverged populations, prezygotic mechanisms are a stronger barrier than postzygotic mechanisms.
4. In early stages of speciation, hybrid sterility is almost always seen in males only. Postzygotic isolations evolves more rapidly in males.
How much time is required for full reproductive isolation?
1-3 million yrs
Among recently diverged populations, which isolating mechanisms are strongest?
Prezygotic isolation.
Hybrid sterility is seen almost exclusively in which gender?
The males.
How does prezygotic isolation compare between sympatric and allopatric populations?
Prezygotic isolation is much higher in sympatric populations in which species are overlapping and is lowever in allopatric populations at low genetic distance.
How are natural selection and reproductive isolation related?
Natural selection increases reproductive isolation.
What are the Coyne and Orr results for Drosophila?
Prezygotic isolation is more pronounced in sympatric populations which indicates that female preferences prefers males of the same species. Selection reinforces genetic isolation of populations and favors the establishment of prezygotic isolation mechanisms.
How does female preference react to increased genetic difference?
Females are less likely to mate with males that are more divergent from them genetically.
What is the average exon length?
145 bp
What's the average exon number?
8.8 exons.
What's the average intron length?
3365 bp
What is the size of the human genome?
3.2 Gb (billion bps)
What is the c-value paradox?
There is a discrepancy between genome size and organismal complexity. There are organisms that are less complex than us that have bigger genomes, which is kind of weird.
How did we iron out the c-value paradox?
DNA was purified, cut into small pieces, and melted. The samples were slowly cooled, allowing the DNA to reanneal. You measure the time it takes for everything to reanneal. From shortest to longest time, here are the sequences that reaneal:
foldback DNA < highly repetitive DNA < middle repetitive DNA < single copy DNA
From shortest to longest, what kind of melted DNA reanneals the fastest?
foldback DNA < highly repetitive DNA < middle repetitive DNA < single copy DNA
What is foldback DNA?
DNA that forms hairpins.
What is the makeup of DNA in relation to higher order organisms?
The more complex the organism, the more highly repetitive DNA you tend to have. E coli has almost no repetitive DNA while humans have a lot.
How many genes are in the human genome?
Based on mRNA, we thought that there might be 35K - 140K genes. However, it turns out there are only 20K genes.
Why is there so much repetitive DNA in the human genome?
Transposable elements are viewed as selfish genes that can replicate and transmit themselves at the expense of the host genome.
What are two ways repetitive DNA can expand itself?
1. Transposable elements
2. the passive process of unequal crossing over.
What is unequal crossover? Name the 3 steps.
1. If homologous chromosomes misalign during crossover
2. one crossover product contains an insertion
3. and the other can have a deletion.
Why is there variation in genome size?
It can result from difference among organisms in the rates of deleting DNA. ex. the fugu pufferfish has one of the smallest vertebrate genomes. It's 10% the size of the human genome. It can just get rid of more introns than humans.
How does genome size variation compare to gene number variation among organisms?
Organisms vary 1 million-fold in genome size, but only 200-fold in gene number.
In bacteria, genome size predicts...
gene number. This is not the case in eukaryotes.
Where do new genes come from?
Mainly from gene duplication.
What is gene duplication?
It is the predominant mechanism by which genes with new functions and associated phenotypic novelties arise in eukaryotes.
Duplication:
single ancetral copy gives rise to two copies in a genome.
Tandem duplication:
new copy flanks old copy on the chromosome.
homologs:
two gene copies that diverged from a single ancestor
paralogs:
homologs that initially diverged following a duplication
orthologs:
homologs that initially diverged at a speciation event
gene family:
set of homologous genes diverging due to duplication and speciation.
How often is gene duplication occuring in a genome?
It looks like it is a common and ongoing feature in all genomes. It may be just as important a mechanism of phenotypic evolution as base changes.
2 types of gene duplication:
1. autopolyploidization (whole genome duplication)
2. segmental (gene) duplication
Autopolyploidization:
Nondisjunction of all chromosomes; gametes have twice the ploidy. This is most common in animals and plants that can self-fertilize.
Segmental (gene) duplication:
Gene duplication of a small area, usually involving 1 or a few genes.
What did Susumu Ohno propose?
That gene duplication is the basis for innovation in evolution because it provides new genetic material predisposed toward new functions.
What is the 2R hypothesis?
An hypothesis by Susumu Ohno that there were two rounds of whole genome duplication in the evolution of vertebrates; the first occurring before, and then one after, the divergence of tetrapods and fish, 430 mya.
How can we prove the 2R hypothesis?
By looking at Hox genes. Some large co-linear blocks of genes have 4x copy number in vertebrate lineages. It's unlikely that each gene duplicated independently, although patterns could arise by SD (segment duplication) no WGD (whole genome duplication).
How many young duplications are there compared to old duplications?
There are far more young than old duplications.
On a graph of the number of duplications, what would a whole genome duplication looks like?
It would look like a spike on the graph. We also might expect to see sets of duplicated genes to remain co-linear.
What does the gene duplication graph look like compared to Ohno's hypothesis.
There is a duplication event for the tetrapod split about 450 mya. It's a big band of gene duplication in ancestor of tetrapods (vertebrates with legs). So there is evidence for a whole genome duplication in the vertebrate past.
Why do fish have 4 copies of the Hox gene cluster?
There was a WGD (whole genome duplication) in fish about 300 mya and after that the lineage split from tetrapods.
After gene duplication, name the three ways genes gain new function:
1. Nonfunctionalization
2. Neofunctionalization
3. Subfunctionalization
What is nonfunctionalization?
After duplication, one copy becomes inactivated by mutations because there is no purifying selection to maintain it.
Neofunctionalization:
After duplication, one copy acquired a new function, such as expression in a different tissue or different specificity, and the other maintains its original function. This may result in faster sequence change, especially for amino acid replacement.
Subfunctionalization:
Both copies are partially compromised due to mutations, such that they share same function as a single ancestral copy.
In general, if selection acts on the duplicated locus, what will happen?
It will probably favor a change in function (different pathway or process, or expression in different tissue or stage).
Which kind of change after gene duplication is the most compelling and why?
Neofunctionalization because it is the way that genes with new functions originate.
How is neofunctionalization related to Ka/Ks?
When a gene acquires a new function, we predict that there will be positive selection of the duplicate copy. ie, the Ka/Ks will go up.
How is neofunctionalization evidence for positive selection?
After gene duplication, you can look at the Ka/Ks of the gene. If the Ka/Ks is positive, there has been a point of neofunctionalization and positive selection. Ex: The neofunctionalization of ECP from EDN gene.
What are ECP and EDN?
EDN (neurotoxin): No ribonuclease activity, defense against bacterial pathogen.
ECP (protein): ribonuclease activity, defense against RNA viruses.

ECP came from a gene duplication of EDN. It's an example of neofunctionalization.
What are the 3 mechanisms of gene transfer in bacteria?
1. Transduction
2. Conjugation
3. Transformation
Transduction:
LGT via a bacteriophage.
Conjugation:
Called cell sex, it's the transfer of genetic material from the donor bacteria to the recipient.
Transformation:
Integration of free DNA or plasmids from the environment.
4 ways to tell if a gene is acquired laterally:
1. Look for the presence of viral or transposable sequences in a genome.
2. Look for sequence unique to a particular genome.
3. Look for sequences with atypical base composition (GC content)
4. Look for phylogenetic incongruence.
Name 4 features of prokaryotes:
1. Pro - before, karyon - nucleus
2. usually single cellular
3. small circular chromosome
4. no organelles
Name 4 features of eukaryotes:
1. eu - true, karyon - nucleus
2. often multicellular
3. larger linear chromsomes
4. cell contains organelles
5 members of the 5-kingdom system:
1. animalia
2. fungi
3. plantae
4. protista
5. monera
animalia:
multicellular eukaryotes obtain nutrients by ingestion
fungi:
uni- and multicellular spore-formers obtain nutrients by absorption
plantae:
algae and multicellular plants obtain nutrients by photosynthesis
protista:
unicellular eukaryotes
monera:
all prokaryotes (photosynthesis and absorption)
Why nucleotide sequence did Woese use to create the molecular phylogenetic approach?
16S ribosomal RNA
4 qualities of molecule for molecular phylogenetic approach:
1. heritable: nucleic acid or protein sequence
2. universally conserved: present in all organisms
3. evolve slowly: since organisms are very distantly related
4. easy to isolate large quantities
What paper did Woese write about?
He talked about the three primary kingdoms and wanted archaea to arise first.
How do you figure out which of the 3 taxa evolved first? Name 2 options:
1. Look at which taxon is the most distantly related from the others.
2. Use an outgroup (an organisms on a lineage that indisputably diverged earlier than the taxa in question) too root the tree.
What is the advantage and disadvantage of looking at which taxon is most distantly related from the others to figure out which evolved first?
Advantage: If something is very divergent, it is usually thought to have appeared first.
Problem: What if a particular lineage evolves more quickly? It will be more distantly related, but it may not be ancestral.
What is the advantage and disadvantage to using an outgroup to find the root taxon?
Advantage: The taxon that shares more characters with the outgroup is ancestral.
Problem: Life from another planet? No, but there is a clever way out of this dilemma if you remember that this is a gene phylogeny not an organismal phylogeny.
What particular kind of outgroup should you use when looking for the root taxon of the tree of life?
Look at paralogs that evolved from gene duplication.
What is the parolog used for the root taxon phylogeny?
Hemoglobin
What is the process of gene duplication for hemoglobin? 4 steps.
1. Hemoglobin has 4 subunits, 2 alpha, 2 beta.
2. alpha and beta arose from duplication that occurred in lineage leading to vertebrate.
3. After duplication alpha and beta evolved independently. Your beta globin is more closely related to chimps than alpha globin.
4. the alpha globin is homologous to beta globin and serves as outgroup sequence when examining phylogeny.
To find the root of the tree of life, just find a gene that duplicated...
prior to the diversification of the three domains of life around 2-3 bya.
What is the root of the tree of life?
bacteria.
monophyletic clade:
a clade that contains all the descendents of a common ancestor.
Are prokaryotes a monophyletic clade?
No, because they don't include all descendents of a common ancestor. So it's a paraphyletic clade.
What is 2 problems when making trees?
long branch attraction.
homoplasy
Long branch attraction:
Long branches are fast evolving lineages or deeply diverging lineages that are distant from other species and thus difficult to place on a tree. Long branches tend to clump together on trees even when they are not really related. Worse for some tree methods (parsimony) than others.
2 ways to assess support of a phylogenetic tree:
1. bootstrapping
2. maximum likelihood
Bootstrapping:
randomly subsample the data and determine how often the subsampled datasets support a particular clade in a tree. Bootstrap support for a clade is often written on the basal branch of the clade from 0 (no support) to 100 (strong support).
Maximum likelihood:
ask whether the likelihood of the data is significantly higher for one tree over the other.
Homoplasy:
traits that are similar but are not homologous due to convergence, parallelism, or reversals
example of homoplasy:
octopus and human eyes, bats and birds
Convergence:
going from a different state to the same state of a genetic sequence
parallelism:
same pattern of change in different lineages
reversals:
back mutations in which the nuc sequence goes back to its original state
How can you distinguish between homology and homoplasy?
You can build a tree based on many traits and determine whether a hypothesis of homology or homoplasy is more parsimonious.
What is a gene tree?
A single gene region that has a tree-like genealogy
Incomplete lineage sorting:
a gene tree may differ from species/population tree and from other gene trees sampled from the same individuals.
What is the consequence of incomplete lineage sorting?
It can lead to conflicts among gene trees. Copies of haplotype sampled from different individuals can be traced back to a common ancestor, giving a genealogy for that haplotype.
coalescence time:
time to common ancestor to set of copies.
Phylogenetics:
A tree-like depiction of the evolutionary relationships of species and major groups of organisms. It provides the framework for testing biological hypotheses and tests for the action of natural selection. It can detect the transfer of genes between lineages, or duplication of genes within a genome. It can be used to infer the time scale of evolution and is a fundamental tool in all areas of biology.
Why is it a bad idea to arrange organisms in terms of higher and lower lifeforms?
It can lead to incorrect notions that lifeforms are arranged in a linear hierarchy.
How did Darwin change the idea of higher and lower organisms?
However, Darwin and his contemporaries realized that it should be possible to place organisms
into groups based on (1) their relationships to one another and (2) to their common ancestor,
and to depict them in a manner that resembled a tree
What is the ladder of life?
A tree made by Ernst Haeckel which is a holdover from the great chain of being.
What is phylogeny based on now?
It's based on genome sequences.
What's the timescale for life?
>3 billion years
Microevolutionary processes:
Changes within species or populations: mutation, drift, selection shape evolution within species and populations, leading to population divergence and speciation.
Macroevolutionary processes:
change above the species level: species origination (lineage splitting) and species extinction shape patterns of diversity.
What is wrong with classification schemes?
They are subjective and depend on the particular characters used to differentiate organisms.
How do modern classification systems work?
Moderm classification systems attempt to categorize organisms in a manner that reflects their evolutionary relationships.
What example do most modern taxonomy methods follow?
Linnaeas which made a nested hierarchical scheme.
What are the 7 divisions of a phylogenetic tree?
Kindom
phylum
class
order
family
genus
species
2 ways phylogenetic trees are ordered to determine:
1. their evolutionary relationships (branching order)
2. relative divergence time (most recent common ancestor)
Tree:
phylogeny = cladogram
clade =
monophyletic group = ancestor + all descendents
topology =
branching pattern of the tree
node =
point of speciation
taxon =
sister group = related species from common ancestor
polytomy =
the branching point; many temporal based branches, is a section of a phylogeny in which the evolutionary relationships cannot be fully resolved to dichotomies. In a phylogenetic tree, a polytomy is represented as a node which has more than two immediate descending branches.
paraphyletic groups:
some but not all the descendants of the last common ancestor are included.
All organisms are composites of ________ and _________ characters.
ancestral; derived
apomorphy:
unique, derived trait
sympleisomorphy:
ancestral, primitive trait
synapomorphy:
shared, derived character state. these are the best indicators of evolutionary relationships.
parsimony:
trees with the fewest total character state changes
distance (in relation to phylogeny):
tree that groups taxa according to pairwise distances (proportion of character states shared)
maximum likelihood:
trees that yield the highest likelihood of the observed character state data, given a model of the evolutionary process.
Name 3 phlogenetic approaches:
1. parsimony
2. distance
3. maximum likelihood
What characters are considered in parsimony?
Only shared, derived characters are considered.
4 points of rationale for parsimony:
1. Organisms are related by descent and the closeness of descent means a recent common ancestor
2. Organisms change with time and these changes are passed on to their offspring.
3. Closely related organisms share traits not present in other groups.
4. Considering only these uniquely shared, derived characters provides the best approximation of their evolutionary history
What does parsimony ignore?
All ancestral, as well as all unique characters not present in at least two taxa are ignored.
How do you measure tree length?
Complete branching order determined by a minimum of 5 events.
How could you distinguish the ancestral from the derived state? List 2 ways.
1. Look at the character state in fossils
2. Look at the character state in an outgroup, an organism that is undoubtedly more distantly related that those in question. This will assign directionality to character states.
What is the distance-based approach?
Organisms that more closely resemble one another are more closely related. One simply makes a distance matrix of among all taxa and begin pairing those that are most similar. For example, you could compare the percent pair-wise of a nucleotide sequence.
4 reasons to examine informational macromolecules:
1. the relationship among lifeforms
2. the fate of genes in populations
3. the genetic basis of phenotypic variation
4. how new traits/species originate
Macromolecules:
proteins and DNA/RNA
If two species are more phenotypically similar, they are probably more...
genetically similar. Implied is the logic that organims accumulate genetic differences over time.
What is the source of all genetic variation?
Mutations
Mutation:
Any change in the genetic material.
Point mutation:
Nucleotide base substitutions
small insertions/deletions
Name 7 chromosomal alterations:
1. fusions/fissions
2. inversions
3. duplications of existing DNA
4. translocations
5. deletions
6. polyploidy
7. aneuploidy
How can you acquire new DNA?
Transposable element invasion or the acquisition of foreign sequences through transfer.
Modern definition of mutation:
a change in nucleotide sequence of a genome.
homologs:
genes related by descent from a common ancestral gene sequence
What do mutagens do?
They damage the nucleotide base and result in the mispairing of DNA replication.
transitions:
purine to a purine or a pyrimidine to a pyrimidine
transversions:
pyrimidine to a purine or vise versa
How many possible codon combinations are there?
64
Why is there degeneracy/redundancy in the code?
61 codons code for 20 amino acids.
What is an example of degeneracy in the code?
Most amino acids have multiple (up to 6) codons.
xyU and xyC code...
the same amino acid
xyA and xyG...
almost always code the same amino acid.
AAA --> UAA
nonsense substitution - it makes a stop codon
AAA --> AUA
missense substitution/nonsynonymous substitution
AAA --> AAU
silent substitution
How can you measure the mutation rate?
Look at the number of kids affected by an autosomal dominant mutation. ex: dwarfism
How many cases of dwarfism are due to new mutation?
80%.
How do you measure the mutation rate by equation?
mu = incidence of trait/2
Why would mutations vary over genes? List 4.
1. Target gene size
2. Question of paternity
3. Penetrance
4. Phenocopies
Average mutation rate:
10^-5/gene copy/generation
How many mutations/generation?
32 (haploid)
How many mutations are synonymous?
25%
How many mutations are nonsynonymous?
75%
How many replication/gamete?
200
How many mutations/round of DNA replication?
0.3 mutations
What is the neutralist viewpoint?
Kimura believed that most change at the molecular level is neutral with respect to fitness. Because beneficial mutations are rare and deleterious mutations are purged.
selectionist view:
Most mutations are deleterious.
How often do the 3 mutations occur?
Nonsense mutations: rare
Missense mutation: observed seldomly
silent mutation: most offen
What is the rate of evolution equation?
E = mu x F
What is Ks?
number of synonymous changes
What is Ka?
number of nonsynonymous changes
If Ka/Ks is less than 1...
negative selection is occuring. It's weeding out changes that worsen the protein function.
Ka/Ks = 1...
It's neutral evolution, probably a nonfunctional region.
Ka/Ks>1...
Positive selection - it's promoting changes that are beneficial.
selective sweep:
advantageous mutation arises, fixed by selection along with its linked neutral variants. Also called genetic hitchhiking.
MacDonald-Kreitman Test:
compares the numbers of nonsynonymous and synonymous substitutions in species and the fixed and silent replacement between species. Pn/Ps = Dn/Ds
multiple hits
sites that have mutated more than once.
saturation:
when all the sites, on average have mutated more than once.
4 sites to reach saturation first:
1. noncoding DNA
2. Introns
3. Synonymous
4. transitions
relative rate test:
the rate of molecular evolution is different in different lineages.
How do evolution and population size work?
Evolution of neutral mutations is independent of population size.