Eve Final Flashcards
Codon bias influenced by
-mutational bias and genetic drift
Natural selection
Gene expression
Translational efficiency
Codon bias
No random usage of synonymous codons to encode a given amino acid
(Different codons that correspond to the same amino acid appear at different frequencies in the genome)
Codon bias example
Mutations from G to A and from C to T are TWICE AS COMMON
(Tends to favor accumulation of codons with A and T bases)
Natural selection as a cause of mutation bias
translation of highly expressed genes is most efficient when their codons correspond to transfer RNA that are common; so selection favors these codons
Can also favor codons that produce messages that are less prone to translation errors
Codon bias driven by selection
tends to be stronger in genes that are highly expressed and in species with very large population sizes such as free living microbes
Codon bias and population size
Species with smaller population sizes drift, overwhelms, whatever selection actions anonymous mutations, and codon bias is very weak or absent
STRONGER IN LARGE POP
Synonymous mutations weakly selected, in LARGER POP…
Selection MORE IMPORTANT; Ns»>1
SMALLER POP MORE INFLUENCED BY DRIFT
Male driven evolution
male germ line mutation rate is higher than the female germ line mutation rate, the Y chromosome is exposed to a more hostile mutation environment so its going to incur more mutations per generation
Y chromosome evolves very very fast
mutation rate. Is 3 x greater
Nonsynonymous sites are more
Clock-like than synonymous sites
dN
Non synonymous site
Expected dN/dS for a “typical” gene
<1
Expected dN/dS for a gene coding for an unconstrained protein
=1
Recurrent directional selection
dN/dS >1
What requires dN/dS»1
Very conservative test for adaptive evolution, as large numbers of selective fixations
Directional selection and evolution rate
Very rapid evolution
What does a smaller dN/dS ratio suggest
rates of protein evolution are slowed down by functional constraint
Recurrent directional selection ratio; dN/dS»_space;1
Very RARE
have to have a lot of amino acid changes going through under selection
Very frequent adaptive evolution has been acting on it
BIG dN/dS tells…
evolving adaptively - potentially its biology is changing
Examples of genes dN/dS >1
- Vertebrate immune system
- Viral coat proteins, other pathogens
- Reproduction related genes
More powerful way of detecting adaptive protein divergence (compared to dN/dS) ?
McDonald-Kreitman (MK) test
McDonald Kreitman test
Under the null hypothesis (neutral evolution), polymorphism and divergence result from genetic drift
Rapidly evolving proteins should also show high levels of protein polymorphism within species
Polymorphic and fixed a.a variants are compared to polymorphic and fixed synonymous variants
Can only detect recurrent adaptive fixations and can only reject if there are sufficient numbers of variants in a gene
A protein under very LOW FUNCTIONAL CONSTRAINT should show a lot of
Protein polymorphism
diverging very quickly between species
Gene under STRONG CONSTRAINT
should show very little polymorphism at amino acid level and show be evolving very slowly at the protein level between species
polymorphism is
positively correlated with recombination
stronger selection/lower recombination
larger hitchhiking effects
hitchhiking effect
as the copies of the beneficial mutation spreads to higher frequency, the neutral variance linked to them hitchhike to higher frequency
mutation becomes fixed, genetic variation is eliminated in the region nearby
Hitchhiking: Regions further from beneficial mutation
Regions of the chromosome further from the beneficial mutation retain variation because recombination joints together chromosomes that carry the beneficial mutation with chromosomes that carry neutral variants
polymorphism remains at regions farther away on the chromosome
this is a telltale sign used by geneticist to find evidence of recent adaptation
background selection
rather than the spread of beneficial mutants having this effect on the genome, its the removal of deleterious mutations that have this effect on the genome
Introduce mutation but selection removes that chromosomal region out
(basically reducing effective population size of chromosomes)
rapid spread of beneficial allele to intermediate frequency
generates long regions of linkage disequilibrium
evolution of human skin pigmentation
indirect result of selection on thermoregulation
- selection for hair loss
- COMPENSATORY selection for skin pigmentation
theory for evolution of lighter skin
selection for vitamin D related traits at high latitudes
more pigment protecting against folate depletion at low latitudes carries a cost and is unnecessary at higher latitudes
light skin alleles evolution
significant amount of lighter pigmentation seems to have evolved independently in groups of European and Asians
eye color: before or after
eye color might have evolved before pigmentation
Species: BSC
groups of actually or potentially interbreeding populations, which are reproductively isolated from other such groups
GENE FLOW (reproductive isolation) is focus
cryptic species
isolated but with little phenotypic differentiation
problems with BSC
asexuals
extinct groups
gene flow between “good” species
breeding experiments impractical
phylogenetic species concept
two populations are species if they are different in MORPHOLOGY, DNA
species are often
reproductively isolated AND phenotypically diverged
speciation is the
evolution of reproductive isolation or the absence of gene flow between two populations is required for them to no longer exchange genes with each other
mechanisms of reproductive isolation
pre zygotic
post zygotic
premating barriers
features that impede transfer of gametes to members of other species
potential mates do not meet
potential mates meet but do not mate
postmating
mating occurs, but zygotes are not formed
postzygotic barriers
hybrids are formed but have reduced fitness
extrinsic
hybrids have low fitness for ENVIRONMENTAL reasons
not well adapted
cant obtain mates
intrinsic
low hybrid fitness is independent of environmental incompatibility
Haldane’s Rule
when hybrid breakdown is differentially expressed in the two sexes, the HETEROgametic sex is usually affected more severely
which appears first; sterility or inviability
hybrid sterility often appears before hybrid inviability
Most common mode of speciation
Allopathic speciation
Allopatric speciation
Two populations have to become geographically separated to eventually evolve these reproductive isolating mechanisms
Might be able to reproduce if they come back together; depends how diverged they are
Allopatric divergence
populations that are more geographically distant from one another have accumulated more genetic differences from each other
More reproductively isolated they are
The more geographically different the population are the less likely they are to meet
Strength of sexual isolation is correlated with
Geographic distance
Are sister species sympatric
Rarely sympatric
Is speciation likely to occur on small islands
Less likely to occur on small islands
Taxa in which gene flow is high, such as bats have speciated only on very large islands while taxa in which gene flow is very limited such a snails have speciated on small islands’
speciation is more likely to occur on larger islands, and in species with restricted gene flow
How is gene flow influenced by isolating mechanisms
Play a role in RESTRICTING GENE FLOW
Come back together= Secondary contact
Interaction after secondary contact
newly formed species can then coexist as distinct populations if they are selfish sufficiently reproductively isolated
Dobzhansky Muller Model
model posits that genetic incompatibilities between diverging populations, arising from mutations at different loci, can lead to reduced fitness or reproductive isolation in hybrids upon secondary contact. These incompatibilities contribute to the process of speciation by creating barriers to gene flow between populations
Dobzhansky-Muller incompatibilities
refer to the negative genetic interactions that occur between genes from different populations that have diverged from a common ancestor, leading to reduced fitness or reproductive isolation in hybrids.
arise due to the accumulation of mutations in isolated populations and can contribute to the process of speciation by creating barriers to gene flow.
Incompatibilities are effect of what
Incidental effect of DIRECTIONAL SELECTION
Isolation evolution rate
Rate is greater than rate of genetic drift
Males are completely sterile- suggests that isolating mechanisms evolve very, very fast
there hasn’t been enough time for genetic drift to lead to any significant genetic differences between the three species yet they are strongly isolated from each other
What do clades that have strong sexual selection show
Tend to be more species rich
Why might speciation rates be higher in some groups than in others
Dispersal and opportunities for allopatry
Variation in mating systems or the intensity of selection
Assortative mating
Pattern of mating where individuals with similar phenotypic or genotypic traits preferentially mate with each other
Reinforcement
Isolation is DIRECT result of SELECTION ON TRAITS PROMOTING ASSORTATIVE MATING (non-heterozygote)
Factors working against reinforcement
Gene flow into hybrid zone
Alleles increasing Assortative mating may have deleterious pleiotropic effects outside hybrid zone
Alleles favoring Assortative mating may not be strongly genetically associated with alleles reducing hybrid fitness
Reinforcement applies where
There’s at least some gene flow occurring
Opposing forces in contact zone
Selection and gene flow
Gene flow tends to
Homogenize the population (reducing genetic differentiation and increasing genetic similarity)
What happens if selection wins
Reinforcement occurring; lead to completion of speciation event
Data required to support reinforcement
Hybridization occurs in nature
Hybrids have reduced (but non-zero) fitness
Assortative mating is stronger in contact zone
Character displacement
A pattern; occur in species pairs that are completely isolated ( not experiencing reinforcement)
Sympatric drosophila species pairs tendency to show isolation
Strong tendency to show greater isolation at lower genetic distances compared to allopatric species pairs
Evolved much stronger pre mating/pre zygotic isolation
Sympatric speciation
Prob rare
Unlikely due to no impediment to gene flow
“Magic traits” that influence ecological and reproductive isolation make speciation more likely
Many supposed examples might just be rapid evolution in allopatry with range expansion leading to current sympatric speciation
Allopatric speciation is STRONG NULL hypothesis
Sympatric speciation
two populations can become different species without ever experiencing allopatry
so their ranges remain overlapping the entire time and somehow they still evolve reproductive isolation from eachother
POSSIBLE example of sympatric speciation
African cichlid radiatons in lakes Malawi, tanganyika and Victoria
Best examples of sympatric speciation
Due to culturally driven reproductive isolation
Strong sexual selection very likely to
Lead to higher rates of speciation than those with NO SEXUAL SELECTION
How do changes of ploidy affect speciation
changes of ploidy often lead to instantaneous isolation or speciation
for example, if you cross two diploids and you get a tetraploid, then this offspring is now isolated from each of the different diploid species completely
Haldane’s Rule explanations
- Faster X evolution
- X-A incompatibilities that are recessive are EXPOSED in the heterogametic sex
Why do phylogenetics
Basic description of nature
Often interesting from an organismal perspective
Detecting evolutionary patterns
Taxa
Anything from individuals to “higher” levels such as genera, phyla, etc
Characters
Anything measured from DNA sequences to highly complex traits
Sequence alignment between two or more species
A hypothesis about nucleotide homology
Phenetics
Organisms that are more similar share a more recent common ancestor compared to organisms that are LESS SIMILAR
Cladistics
Branching patterns can be reconstructed based on shared derived character states, known as synapomorphies
Premise
Only one true tree of life; shared derived character state can only be explained by virtue of inheritance through a common ancestor
“Ancestral” character state can ALSO result from
Reversal to the ancestral state in a lineage
Outgroup method
Assumes state in the outgroup represents ancestral state, which may not be true if there has been considerable evolution in an outgroup
Fossil record usage
Poor fossil record may cause incorrect inferences
Not applicable on all taxa or characters
Developmental biology may be used to
Infer ancestral/derived states
Derived states may appear LATER in development than ancestral states
Homoplasious characters
Can lead to conflicting patterns (due to parallel and convergent evolution)
Rapid radiations
Rapid speciation events
Internal branches very short
Shared derived character states are just not there to provide the info you need to have confidence about which species are more closely related to which other species
What are slow evolving molecules used for
Used to resolve deep evolutionary history
Want to have as FEW parallel convergent changes as possible
What are rapidly evolving molecules used for
Used to resolve recent history
Reconstruct very short time scale evolution
Incomplete lineage sorting (ILS) in recently separated populations may result in
DISAGREEMENT between gene trees and species trees
Influenced by amount of ancestral variation and the timescale of separation
Incomplete lineage sorting
occurs when ancestral genetic variation is not sorted into distinct lineages within a population before speciation events
Comparative method
Search for general patterns of evolution
Correlated evolution of particular traits
Temporal patterns of trait evolution
Independent contrasts
if we have two traits that we measure in species A and B and they DIFFER in these two traits
those differences must have evolved since that ancestor
the evolution between A and B differ from evolution in C and D
a tree and two different traits that are evolving
how strong is case that this trait is correlated with evolution of this other trait
LOOK FOR: how many independent times did this trait evolve on the tree
When that trait evolved, did the other one evolve at the same time ??
Bipedalism is a
Key event in hominid history
- reduced galloping speed and tree-climbing ability
- greatly increased efficiency of walking
- humans unusual in ability to run for long periods of time
- climate cooling and drying in Africa, leading to pressure to forage more widely might have been the agent of selection
Bipedal how long ago
7 mya
Deviation from the expected relationship of brain versus body size
Massively deviated
Common ancestor with H. Sapiens
800,000 years ago
Protein overlap and chimps, Neanderthals, and humans
Several proteins at which chimp and Neanderthal are identical, and human is DIFFERENT
Non-African chromosomes have more…
Neanderthal ancestry than African chromosomes
Who were the Denisovans
Archaic hominin group from Denisova Cave in Siberia
Sister to Neanderthal
Diseases and Humans
Múltiple diseases have jumped to human in RECENT past (malaria, tuberculosis)
Agriculture led to HIGH POPULATION DENSITIES and close interaction with domestic animals
Origin of alleles contributing to RECENT HUMAN ADAPTATION
Some alleles have their origin in introversion event from ANCIENT hominins (ESPA1 and high altitude adaptation)
Pigmentation alleles and alleles associated with w diet (Inuits)
Human health effects due to mismatch between our ancestral biology and our recent environment?
Like w wisdom teeth
- skulls of pre-industrial farmers exhibit lots of dental problems
- skulls of ANCIENT HUNTER GATHERERS have FEW dental problems
SO COMMON?
- were chewing a lot more
-jaw bones aren’t as big now
Possible effects of agriculture and the rise of cities
HIGH POPULATION DENSITIES led to infectious disease such as measles, mumps, influenza, smallpox
Some infectious diseases jumped from domesticated animals to humans
Do modern lifestyles increase BREAST CANCER risk?
Women are not always pregnant or lactating now so we have MORE menstrual cycles which means more cell division
Hygiene hypothesis
Cleaner environment leads to lower rates of childhood infection
Sometimes hace adult immune systems that OVERREACT
Old friends hypothesis
In the absence of ancestral pathogens, our immune systems don’t even develop properly
Also lead to OVERREACTION
Genes involved in oncogenisis
About 1% of genes in the genome
Which cells produce cancer
Mutations in stem cells
Cancer is produced by competition among
Clonal lineages generated by somatic mutations
Renal cell carcinoma; evolutionary divergence poses PROBLEMS for THERAPY
Primary tumor on kidney sent metastases into the lung and chest wall
Therapies sent to treat primary would miss variation in the mestastes
Gene duplications often result in
Unequal crossing over
Human phenotypes associated with copy number variants
Parkinson’s, autism, color blindness
Orthologous
Genes that diverged from common ancestral gene by phylogenetic splitting
Paralogous
Loci in the same species or different species that descended from different duplicate genes in ancestral species
A1 and b2
Potential case of adaptive variation related to gene dosage in humans
Amylase
Subfunctionalization
A gene performs two functions at once, duplication and divergence occurs, and now on copy performs one function and one performs the other function
Neofunctionalization
One gene performs one function, duplication and divergence occurs, one gene KEEPS performing ancestral function, and other gene is free to get NEW FUNCTION
Gene duplications can give us…
Can lead to novel traits!
Approach for detecting HGT
Phylogenetic discordance
Amount of genes in unicellular organisms
Seem to have the least amount of
New genes
One could arise in non genic DNA and it becomes transcribed and favored somehow
Maybe spread under directional selection
