Evolution Flashcards
Why should we study evolution?
- Evolution unites sub disciplines of biology via providing common framework
- finding similarities differences and making sense of their functions and origins
What is evolutionary biology? What is the goal?
- the study of evolutionary pathways that led to lifeforms today and how populations continue to change
Goal: to understand origin, maintenance and diversity of life on earth
What does evolutionary biology encompass?
- identification and classification, relationships, adaptations, variation, origins and/or extinction, underlying mechanisms (eg: natural selection)
Why is survival of the fittest not an accurate depiction of evolution?
- generally true, but not exactly accurate because it’s not always the fittest alleles that are chosen.
better : descent with modification
What is descent with modification?
- changes in characteristics over generations
How can we understand how a species has evolved?
- we must know its ancestors and that modifications have occurred
What are the methods of modification for evolutionary processes ?
natural selection, genetic drift, non-random mating, mutation
What is natural selection?
- beneficial alleles increase in frequency due to increased survival and reproductive success of carriers
- Forms become better suited to the environment and increase in frequency in a population over long periods of time
Is natural selection a slow or fast process? Why?
A gradual process! Slight changes occur and over a great period of time will alter the form.
Describe the process of descent with modification via natural selection:
- Individuals possess genetic variations
- genetic mutations change the phenotypes of organisms
- Mutations can increase, decrease, or have no effect on fitness
- mutations can be disadvantageous or neutral, some advantageous which allows for greater survival rates
Result: evolutionary change via naturel selection
How do advantageous mutations result in natural selection?
- allows for that allele carrier to have greater reproductive success and lifespans, that allele will become more common and ‘stronger’
What is the result of an accumulation of advantageous genetic changes within a long period of time?
- produces new species, genera, families, can change taxonomic orders
Describe HIV/AIDs
An intracellular parasite targets helper T cells, hijacks host cells replication machinery, and damages or destroys cells. As more cells are destroyed immune system weakens and cannot fight opportunistic pathogens
What does HIV stand for?
Human Immunodeficiency Virus
What does AIDs stand for?
Acquired Immune Deficiency syndrome
What are some common causes of death for AIDS/HIV patients?
- a weakened immune system becomes susceptible to TB, hepatitis B and C, and cancer (AIDs is not the cause of death but weakens the immune system enough to be taken out easily by another illness)
What is the HIV life cycle?
- Extracellular virus called ‘virion’
- Virion encounters host immune cell: surface protein GP120 binds to CD4 and its coreceptor
- Virion fuses with host cell and RNA and enzymes enter
- HIV’s reverse transcriptase enzyme synthesizes HIV DNA (from the HIV RNA template)
- HIV’s integrase enzyme splices HIV genome into the host cell’s genome
6/7. Host cell transcribes/translates proteins encoded in the virus’ RNA
8/9. Viral proteins and mRNA are packaged into new virions and bud off from host cell membrane before maturing
What are the components of a virion? What does this cause?
- an agent of HIV : consists of very little cell membrane, 2 pieces of RNA, 3 enzymes, surface proteins
What is the minimum concentration of CD4T cells before the immune system begins to collapse?
- 200 cells / mm^2
How can we prevent AIDs/HIV? What are the treatment methods?
- stop them from replicating!
1) AZT azidothymine: prevents HIV DNA from being synthesized
2) HAART: highly active antiretroviral therapy
Describe AZT treatment and its drawbacks
- mimics the nucleotide thymidine and tricks reverse transcriptase, prevents HIV DNA from being synthesized
- issues: when treatment begins patients see a drop in viral load, increases over time until treatment ineffective : treatment less effective over time as virus evolves resistance
–> Greater concentration combated by greater resistance
How does AZT resistance come about?
–> Hypothetically if reverse transcriptase could avoid AZT then the virus would remain unchecked
- mutations that lead to changes in reverse transcriptase amino acid sequence allows enzyme to avoid AZT and change shape of binding site to no longer accept AZT
Describe HAART treatment
- alternative to AZT which develops resistance
- HAART uses multiple drugs at once, requiring an increased number of mutations to achieve resistance (less likely)
- NOT a cure
How did the study of evolution play a role in treating HIV/AIDs?
Understanding evolution and how resistance evolves allowed researchers to devise more effective HIV treatments
–> thanks to evolution studies someone diagnosed at 20 can live to 78
Why does HIV meet the requirements for natural selection?
- variation present: reverse transcriptase is prone to mistakes (half HIV DNA contains more than one error)
- Some of the variation Is heritable (mutation in all daughter visions)
- Not all individuals can survive (AZT blocks)
- Traits which enhance survival more common (resistant mutants become more common)
Evolutionary change via natural selection!
What are the requirements for natural selection?
- Variation present
- variation is heritable
- Not all individuals can survive/reproduce
- Traits which enhance survival/ reproduction become more common
What are the two evolutionary questions throughout the ages?
- how did life begin
- what are organisms so well suited to their environments?
What are the past and present explanations for the evolutionary questions?
Past: supernatural (mythology and divine creation)
Present: natural (process of evolution)
Why do we care about moving to natural explanations from supernatural ones?
all science builds on the work of those that came before, learn from past mistakes, question our own understanding
What is Methodological Naturalism?
- a strategy where one explains the world through laws of nature
- methodological : provides method to explain something and create hypothesis
- naturalism” rather than supernatural
What did methodological naturalism oversee?
Hypothesis testing: must not accept an explanation but test it too.
- helped develop the framework of the scientific method
What is evolution? How was the earth and evolution viewed in the past?
- Evolution : descent with modification over long periods of time
- in the past, earth was though to be young and unchanging (but this does not support the theory of evolution)
Which philosophers acknowledge there may be change?
Empedocles: plants before animals
Xenophanes: Mountains were once underwater
What proved that the earth was older than expected?
- geological evidence (rock strata, erosion, sedimentation rates)
- radiometric dating (4.5 billion years old)
What is our present understanding of the world?
- world is old and ever changing
What is unformitarianism?
- Evidence from geology and Charles Lyell
: Laws of nature are constant in time and space - geological processes have operated over long periods of time in a slow gradual manner
What is catastrophism?
Features arose via sudden cataclysmic events, unlikely to reoccur and impossible to experiment
Who disproved the spontaneous generation theory?
Francesi Redi
What was the former explanation for diversity and well suitedness among living organisms?
- spontaneous generation
- complex life forms arise from non living matter (mudflats –> frogs)
- experiment of flies trapped in jars by Redi disproved this theory
Who was Erasmus Darwin?
Before Darwin, described evolutionary change and the struggle for existence but failed to link the ideas
Who were the pre Darwin people?
- Erasmus Darwin and Robert Chambers
What did Robert Chambers discover? Name the term he coined.
- diversity of species changes gradually over time
- coined the principle of progressive development: new species must arise from old species
- population evolved but not individuals (did not explain why)
What is the Principle of Progressive Development?
- New species must arise from old species
- Organisms have an innate tendency to evolve in a given direction
What did Lamarck propose? What was he known for?
- New more complex species descend gradually from older, less complex species (inheritance of acquired characteristics where individuals evolve)
- famous for being wrong but the first to connect environment to the evolution of adaptations
What mechanism did Lamarck propose for his theory?
- inheritance of acquired characteristics
- habits of an individual bring about changes in its structure which are passed down the generations (incorrect)
What theory came first uniformatarianism or catastrophism?
Catastrophism was first, then uniformatarianism
Describe the pre Darwin theories
Darwin: struggle for existence
Chambers: principle of progressive development, changes occur gradually over time
Lamarck/Baptiste: Acquired characteristics
What were Darwin’s fundamental insights? What do they combine to create?
- the environment selects on variation in traits of individual organisms
- some variants more successful than others
- provides mechanisms (natural selection) that explains trait changes and adaptiveness - All species descended from on (or a few) common ancestor
= theory of evolution by natural selection
What are the 4 lines of evidence for descent with modification (evolution)?
- Species change through time (microevolution)
- Lineages split and diverge (speciation)
- New lifeforms arise from older life forms (macroevolution)
- Common ancestry: all species have arisen from one or a few common ancestors
Describe the first evidence of evolution
Species change through time: microevolution
- microevolution: populations of organisms change across generations
- selective breeding demonstrates such changes
What is microevolution? What proves it?
- populations of organisms change across generations
- selective breeding indicates traits can be selected for
Describe natural vs. artificial selection?
natural selection: evolutionary process where beneficial alleles have a better fitness and increase in frequency (humans may have hand in changing elements of environment)
artificial selection humans select reproducing individuals for desired traits (beneficial alleles play no role)
What is anthropogenic evolution?
- catch all phase for evolutionary changes induce by the actions of humans (climate change, habitat destruction, pollution, overfishing : their impacts on organisms)
what is the 2nd evidence for natural selection (descent with modification)?
lineages split and diverge (speciation)
Describe the fly experiment on different diets to explain speciation
two flies on different diets more prone to mate with those on similar diets : gradual speciation?
What is a species?
- consists of groups of actually or potentially interbreeding population that are reproductively isolated from other groups
(must be able to mate)
Is speciation fast or gradual?
gradual process!
What is the 3rd evidence of evolution?
New life forms arise from older life forms (macroevolution)
What is extinction and succession?
Extinction: all individuals in a species have died out and left no living descendants
The law of succession: animals that inhabit an area will resemble nearby fossils
What are fossils and fossil records?
- fossil records: history of life on earth as recorded by fossil evidence
- Fossils: remains or traces of once-living organisms (~10k or older)
In the use of antibiotics, does the adaptation or resistance in bacteria indicate artificial or natural selective forces?
- natural. not picked by humans or intended, a side effect. Natural resistance to antibiotics.
- natural selection is still considered natural even when organisms are reacting to conditions humans may have altered in the environment.
What is a transitional form?
- if new life forms descended from old ones, fossil records should contain such evidence of a species containing a mix of features between extinct and present day species
Describe the 4th evidence of natural selection
Common ancestry - all species have risen from one or a few common ancestors
What is homology?
- shared characteristics that are a result of common ancestry are greatest evidence for descent with modification
What is true about individuals/groups at the same hierarchal level on a tree of life?
they will resemble each other
- ex: squirrel and deer share more similarities than to frogs
What is a transformational process?
- ensemble changes because each individual member changes
- inheritance of acquired characteristics
ex: smashing course particles into fine dust (all go under change)
What is a variational process?
- ensemble changes because something sorts among the variants in the original ensemble
- natural selection (picks specific and ‘sifts’ them out)
Is evolution variational or transformational?
Variational because through evolution it works on selecting characteristics that increase fitness and increases the frequency of that trait in coming generations
What does artificial selection present?
- selective breedings demonstrates how traits of a population can change over generations
Which gene was involved in the different between wild and domestic tomatoes? How does it work?
- fw2.2 gene: produces a protein that inhibits cell division: more protein = less cellular division = smaller fruit
–> fw2.2 promoter region: on/off switch
How did researchers modify the tomato to identify the variation in the promoter region of the tomatoes?
Modified the domestic tomato by adding the gene to inhibit cell division and create a smaller domestic tomato
- reveals difference in the allele of this gene may be causing size difference
What were the possible routes from small tomatoes to large tomatoes?
- different alleles were present in wild populations
- both large and small fruits were present and we cultivated the large ones - large-fruit alleles arose in already cultivated crops and we encouraged to propagate
Are domestic and wild tomatoes considered the same species? Why or why not?
- they are NOT even though they initially developed from the wild tomatoes
- variation present can lead to modifications in that population over time and even to new species
Was the transition of wild tomatoes to domestic tomatoes because of artificial or natural selection?
- can be both!
- capable of creating entire new species!
What are the steps to the logic of evolution by natural selection?
- individuals within populations differ from one another (variation)
- variations are, at least in part, passed parent to offspring (inheritance)
- some individuals have higher fitness
- The successful individuals succeeded due to variant traits not just luck
What are the 3 components of natural selection?
- variation
- inheritance
- differential reproductive success
Do researchers study traits or the whole organism?
- TRAITS not the organism as a whole
True or false: populations evolve not individuals
true! natural selection works via variation within the populations
What is a major source of variation?
mutations: occur randomly and independently of whether they will be favoured by NS
Do mutations occur for natural selection to select for?
No! They occur independently of whether it will selected for by NS
True or false: Natural selection sorts on phenotype not genotype
- true!
Can phenotype be determine by the environment?
yes! Phenotype can be determined by the environment and by genotype
Explain the purpose of the Oldfield mice experiment as well as their characteristics
- Q: How does natural selection affect coat colour in Oldfield mice ?
and
Does natural selection favour a match between coat and environment colour? - preyed upon by visual hunters, 2 colours
–> darker inland form and lighter beach dwellers - there is variation present within species and within respective populations!
Do the oldfield mice meet the requirements for evolution by natural selection?
- must ask whether it meets requirements
- variation, heritability, fitness (it does, explain why)
Are oldfield mice coat colours inherited?
unsure. we must identify genes involved!
- when the variation is due to genetic variation the trait is heritable
- if the coat colour is light due to environmental factors like sun bleaching it is not heritable
How do we test if variation is heritable or environmental in a species?
- by identifying the genes involved!
What are the genes identified in oldfield mice?
–> Mc1R: controls type of pigment produced and deposited
- two pigments: dark (eumalin) and light (phaeomelanin)
- depends on alpha-MSH which binds to mc1R receptor to produce eumelanin (dark)
- if alphas MSH does not bind to Mc1R produced phaeomelanin (light)
–> also present: agouti
- produces ADP that competes with alpha MSH
- bind to MC1R and blocks production of eumelanin
Describe the role of genes in oldfield mice and how we can determine if variation is genetic or environmental?
- single mutation in Mc1R sequences: reduces ability to bind alpha-MSH
- mutation in regularity region of agouti: higher expression levels of ADP
- it is heritable!
describe how they measured differential reproductive success in old field mice. How did they ensure it was cause and effect rather than correlation?
- 3 different environments: light and dark mice in arena, measured survivors - percent of capture was higher for the mismatched mouse
- removed other factors: silicone mice in natural environments
- same results, match background = higher fitness
How might matching background coats developed in mice? was it quick or slow?
–> say mice with matching produced 1% more offspring than mismatched that gene would double in frequency every 70 gneeraostiond and in a population of 10000 gene frequency could read 100% in a few thousand generations
What are some potentially altering effects that may have altered results of the oldfield mice test?
0- researchers studied traits not entire organisms
- populations evolve not inviduals
- mutations can occur randomly and independalty
- NS sorts on phenotypes not genotype
Describe the case study of beak shape in relation to seed size, and whether natural selection occurred here (did it meet requirements)
Quick Facts
NS acts on individuals, but its consequences occur in populations
Eg; finches with larger beaks survived dorught while others starved, leading to a change in average beak size of the population
NS acts on phenotypes, but evolution consists of changes in allele frequencies
Eg; beak size was the trait being selected but without heritability (a genetic component) evolution could not have occurred
NS acts on existing traits but novel traits can evolve
Eg; new mutations can arise in future generations, and sexual reproduction can lead to new genetic combinations
NS lacks foresight and does not lead to perfection
Is natural selection synonymous with evolution? if no, what is the difference?
NO! NS is a tool used by evolution
- natural selection occurs within a generation, one of several processes of evolution
- evolution: occurs across generations, results from any of the major processes
Is it possible for natural selection to occur without evolution?
yes. for example if big beaked birds survive drought and have children who don’t have big beaks, then it wasn’t heritable and evolution / change will not occur
Why might natural selection not create perfect structures? Provide an example
- NS lacks foresight: does not act in the long run but in the short term, conditions may change later on and a species may be less well suited for the future
ex: blind spot in eye
What is an adaptation?
- an inherited trait that increase and organism’s fitness and is the result of natural selection for its primary function
- increases fitness to both abiotic and biotic environments
- to be considered an adaptation must have been shaped by natural selection
Provide an example of expatation
feathers: today for flight, originally for thermoregulation, sun protection, signalling, and defense
What is an exaptation?
- a trait that currently serves on function today but which evolved from a trait that served a different function in the past
What is a co-opted trait?
- a trait that was formerly for one thing but now serves a new function
- BUT can be multipurpose ie: original function not necessarily lost
Describe exaptions for insects
- treehopper helmets strutter (finish card I’m so tired I need to go to the gym)
What is true about the origins of complex traits?
- will have undergone many changes, have layering of adaptations and exapations
What is gene duplication?
- entire gene or region of genes is duplicated,
- second copy can undergo neofunctionilzation
How does general duplication lay a part in hormone-recport pairs?
- gene duplication could allow second report to mutate and bind new hormones
What is gene sharing:
protein recruited to serve second function elsewhere
What are some arguments against Darwins theory of complex structures?
- critics argued complex traits have no function until fully formed
- what about traits with no known function?
- how and why does variation persist if less fit variants are eliminated
What are the theories for the evolution of complex traits?
- gradual, intermediate steps
- each step itself adaptive, serves same function throughout - Co-opted from another trait
- intermediate steps also functional, complex traits serve new function
What are some constraints on natural selection?
- short term: lack of sufficient variation
- long term: physical constraints, co-evolution, lack of foresight
What are the physical constraints of natural selection?
–> constrained by physical and mechanical laws
eg: can’t have full field of view and stereoscopic vision with only two eyes
What does the ‘evolutionary arms race’ in evolution mean ?
- an organism’s environment is not constant, Natural selection does not have steady target - cannot optimize phenotype
- Ecolutionary arms race: form of coevolution where the species involved each evolve countermeasures to the adaptations of other species
Eg; predator prey interactions
What is co-evolution?
evolutionary change in one species can affect selective conditions for a second species
- as seen in evolutionary arms are
Why might other organisms be important for another organism’s natural selection?
- co-evolution: forms apt of their environment, they evolve countermeasures around each other to adapt to each other
What was carl Linnaeus known for?
- developed classification system still in use today
How did Linnaeus group the animals? What is the order of classification?
- similar species were grouped into hierarchal levels of similarity based on morphology
- domain, kingdom, phylum, class, order, family, genus, species
What is the difference between Linnaeus and Darwin’s theories?
- Linnaeus recognized hierarchal patterns of similarity without reasoning for why
- Darwin provided the why: common ancestry and descent
What are phylogenetics?
- the study of relationships among taxa based on their evolutionary history
What are systematics?
- the study of classifying organisms
What is the goal of phylogenetics?
- to reconstruct evolutionary history of species and understand their pattern of descent
- results typically presented on a phylogeny/phylogenetic tree
What is a taxon?
- group of related organisms placed at branch tip
What are nodes? What are the branch tips?
- nodes: hypothetical common ancestors
- branch tips: descendants
What is true about the phylogenetic orientation and nodes?
- branches can be rotated around any node and still represent the same relationship
What aspect of the phylogenetic tree represents relatedness?
- the distance to the most recent common ancestor represents relatedness
- the more recently 2 groups share a common ancestor the more related they are
What is an ancestral trait?
The character state present in the common ancestor
- trait was present in common ancestor
What is a derived trait?
- any form of that character that arose since divergence from the common ancestor
- a trait that arise from changes to the ancestral state/trait
what are traits in phylogenetics used for? Is the resulting tree accurate?
- for building trees: observe traits of interest to infer patterns
- Infer timing go evolutionary event my mapping traits on a tree
- tree is just a hypothesis, not a given fact .
What are the steps to building a phylogeny?
- select species/taxa of interest
- collect character / trait data
- determine which species have which traits in common
- which traits are ancestral and which are derived
What are the conditions for an ideal case of phylogeny?
- known common ancestor thus we know which traits are ancestral and derived
- each derived trait evolved only once
- once evolved trait was never lost (no reversal!)
What are apomorphies? What is a plesiomorphy?
Apomorphies: (away) unique derived traits
plesiomorphy:(near) shared derived traits
What are synapomorphies? What are symplesiomorphies?
Synapomorphy: shared derived trait
Symplesiomorphy: shared, ancestral traits
What is a clade?
Group of organisms that share a common ancestor and includes all descendants
What are sister taxa?
- taxa derived from same common ancestor
What is polytomy?
unresolved relationship between 3 or more taxa
What are the 3 forms of phylogenetic groups?
- monophyletic, paraphyletic, polyphyletic
Describe the 3 phylogenetic groups
- monophyletic: most recent common ancestor and all descendant of that ancestor = clade
- paraphyletic: includes most recent common ancestor of all members of.a group and some but not all descendant of that ancestor
- polyphyletic: does not include the most recent common ancestor of a group, has at least 2 separate evolutionary origins
Is a clade the same as taxon?
NO!
What is homology?
- shared characteristics that are a result of common ancestry (homologous traits)
What is homoplasy?
- similar character, but not because of inheritance from a common ancestor
- analogy or reversals
What is an analogy?
- character similarity due to convergent evolution (non-homologous or analogous trait)
What are reversals?
- loss of a derived trait with a return to ancestral state
What is divergent evolution?
- closely related organisms diverge from each other due to differing selective pressures
- homologous traits can take on different appearances or functions
What is convergent evolution?
- two or more population/species develop similarities due to similar selective pressures
- develop analogous traits
What are some of the causes of similarity between species?
- homology
- homoplasy
- divergent evolution
- convergent evolution
Why doesn’t Darwins theory explain vestigial traits?
- if NS takes care of things why would they still be there?
What are synapomorphies?
- shared derived traits
What are autopamorphies?
- uniqueW derived traits
What are the ideal conditions for phylogeny?
- known common ancestor (means we know ancestral and derived traits)
- know that derived traits only occur once
- that once evolved, remains (ie: no reversals)
what is the order of linnaen classification?
- domain, kingdom, phylum, class, order, family, genus, species
What are automorphies? What are plesiomorphies?
- derived traits
- ancestral traits
What is the terminology for derived traits?
- apomorphy: derived traits
- autopamorphy: unique derived trait
- synapomorphy: shared derived trait
What is the terminology for ancestral traits?
- plesiomorphy ancestral traits
- symplesiomorphy: shared ancestral traits
What is a clade?
- group of organisms that share a common ancestor and includes all descendants
What is a sister taxa? What is a polymorphy?
sister taxa: taxa derived from same common ancestor
polymorph: unresolved relationship between 3+ taxa
What is another word for clade ?
monophyletic!
what is homology ?
- shared characteristics due to common ancestor (eg; tetrapod limbs)
What is homopolasy?
- shared characteristics but not related to common ancestry (analogy)
What is analogy?
Character similarity due to convergent evolution
What are potential causes of homoplasy?
- common traits with no recent common ancestor
- analogy and reversals
- with reversals a species may have gotten rid of ancestral trait and been reclassified, then originated back to ancestral trait and now looks similar even though they do not have a recent common ancestor
What is divergent evolution?
- closely related organisms diverge form each other due to different selective pressures (eg: tetrapod limbs!)
What is convergent evolution?
- two or more populations/species derive similarities due to similar selective pressers
Why might traits with no known function (vestigial traits) exist?
- on their way out (slowly)
- have unknown function (not actually vestigial)
- not costly to retain
what are the causes of similarity?
homology: similar traits due to common ancestry
homplasy: similar traits but no common ancestroy
- analogy: develops similar traits due to similar selective pressures
- reversals: derived trait evolves back into ancestral trait
What are the two forms of evolution?
Divergent evolution and convergent evolution
What are the requirements for an adaptation?
- inherited trait that increases and organisms fitness: must have been derived form natural selection and serve same primary function as it does today
What is an exaptation?
Trait that serves a different purpose than in the past
eg; feathers: previously for warmth, mating, etc. today for flight!
What were some of Darwin’s fundamental insights?
- individuals have variation - some does better than others, heritable: adaptation, explains why organisms aer well suited to their environments
- all species descended from one (or a few) common ancestors
What are the two fundamental mendelian laws?
- Law of segregation: every individual has two copies of each gene which are separated during gamete formation
2 .Law of independent assortment: which allele is passed on at one locus is independent of which allele is passed at another locus
- exception: linked loci
What is the exception to the 2nd mendelian law? Describe this
- linked loci!
- sometimes traits are linked - alleles located close together on a chromosome: cannot sort independently during meiosis so they only produce 2 types of gametes - only undone through recombination
(typically 4 types of gametes are formed)
What is the process that can unlink loci if they are linked?
- genetic recombination
What are the differences between Mendel and Darwin’s views on heredity?
Mendel: Particulate inheritance: phenotypes may be blended but alleles remain distinct (filters)
Darwin: blended inheritance: once combined cannot be uncombined (blue and red make green forever)
What mechanism describes how variation can remain in a population even once phenotypes have blended?
- Mendel’s particulate inheritance: phenotypes may combine but alleles remain distinct
Does natural selection sort on phenotype or genotype?
- sorts on phenotype: behavioural, physical, and developmental characteristics
How do we get form genotype to phenotype? Describe these processes
Transcription and translation!
Transcription:
- process where complementary antiparallel strand of DNA is synthesized
- RNA polymerase binds to promoter - DNA unwinds - transcription belongs along template strand (in 5’ to 3’ direction)
- products: rRNA, tRNA, microRNA, mRNA
Translation:
- mRNA séquence is translated into amino acid sequence (protein)
- ribosome attaches to mRNA, at start codon (AUG() tRNAs bind and bring amino acids to be linked into chain; stop codon ends translation
- nucleotides grouped into 3 codons; forms 20 amino acids
How many amino acids are there?
20, formed of 3 codons
Why is the genetic code degenerate? Which codon position has the most degeneracy?
The 3rd codon has the most degeneracy because multiple nucleotides code for the same amino acid
What are the functions of proteins? (note; related to gentoypes DNA to phenotypes PROTEIN)
- enzymes; initiate and regulate chemical reactions
- chemical signals between cells -
- regulate DNA expression
- structural functions: form elements of ECM or cytoskeleton
- transportation
What is an exon? What inhibits an exon?
- stretches of DNA that code for protein products
- introns inhabit exons
- introns are non-coding stretches of DNA that interrupt exons and are cut out before translation
What method is used to excise an intron?
-alternative splicing! - cuts out non-coding stretches before translation
- a gene can be cut many different ways and thus encode multiple different proteins
how can multiple proteins be encoded from one stretch of DNA?
- alternative splicing
Which two factors influence gene expression?
- regulatory elements and chromosome structure
what are regulatory elements?
- stretches of DNA that affect rate rot transcription, thereby controlling levels of gene expression
How does chromosome structure regulate gene expression?
- DNA is wrapped around histones to form chromatin
- wrapped tightly, promoter inaccessible so gene is not expressed
What is epigenetic inheritance?
- heritable mechanisms that alter gene expression without changing DNA sequence
- heritable across cell generation; germ lining?
- secondary changes to molecules or histones alter chromatin structure / how tight its packed
- methylation
What is methylation?
- addition of a methyl group to the C-G base pair
- methylated regions interact with proteins that determine chromatin structure
- highly methylated: generally inaccessible to RNA polymerase
What is the main way that epigenetic inheritance occurs?
- methylation: Changes chromatin structure : too tight, inaccessible to RNA polymerase
Describe epigenetic inheritance in the cave fish example
- cave fish do not develop eyes while surface fish do: no mutations in the gene related to eye development
- gene expression differences: decreased expression in promoter regions of >100 eye development related genes; increases DNA methylation at C-G sites
What is cell differentiation?
- methylation and histone modifications alter gene expression in different cell lines
eg; x-chromosome differentiation, developmental plasticity
What is X chromosome differentiation?
- one x inactivated in female mammals by methylation to ensure equal expression of x gene is equal between males and females
- passed onto daughter cells eg; calico cats
What is developmental plasticity?
- adjustment of phenotype to environment (including in utero_)
= eg; pregnant mothers diet impacts Childs risk of metabolic disease later in life
What are the 3 kinds of variation?
- Genetic variation : differences encoded in DNA
- Environmental variation : different environmental conditions alter phenotypes
- Genotype-by-environment variation: different environmental phenotype depending on underlying genotype (some people tan better)
What does phenotype depend on?
- genotype and environment
Does a gene code for a trait alone? What factors impact it?
A gene by itself does not code for a trait but codes for a trait in the context of a particular set of environmental conditions
What is phenotypic plasticity?
- a single genotypes produces different phenotypes in different environments (ecotypes)
What is a reaction norm?
- pattern of phenotypes an individual could develop when exposed to different environments (we see a trend/expected reaction)
What are the 4 methods of new variation originating in a population?
- mutation, recombination (within population)
- immigration and lateral gene transfer ( from outside population)
What are mutations ?
- change to the DNA sequence of an organisms
- the primary source of all genetic variation
How do mutations alter phenotypes?
- mutations can effect phenotypes if they alter expression / function of proteins
What are the types of mutations?
- point mutations, insertions and deletions, gene duplication, chromosomal rearrangement, genome duplication, recombination
what are point mutations?
- transitions (purine with purine, pyrimidine with pyrimidine) and transversions (pyrimidine with purine eg)
- Twice as many ways to change via transversion but transitions are more common
- synonymous (silent), nonsynonymous, nonsense mutation
What are insertions and deletions ?
- addition or removal of one or more nucleotide in a gene
- in frame mutation: adds or removed 3
- frameshift mutations: any insertion or deletion NOT in groups of 3 = affects translations of other codons
what is gene duplication?
Entire gene or region of genes are duplicated
- ie: money with duplicate of enzymes
What is chromosomal rearrangement?
- chromosomal duplication: large portion of chromosome duplicated
- chromosomal deletion: large portion deleted
- chromosomal rearrangement:
inversion: 180 degree rotation in chromosome
translocation: sections of one chromosome moves to another chromosome
What is genome duplication?
- Changes in ploidy: addition or loss of entire set of chromosomes : instant speciation
- usually fatal because animals cannot perform meiosis
- often maintained in plants due to commonality of self fertilization (4n = 2n+2n self fertilizes)
What event leads to instant speciation?
- change in policy: removal or addition of chromsome!
What is recombination?
- available to sexually reproducing organisms (because chromosome come in homologous pairs (not sex))
- crossing over: physical exchange of segments of DNA on homologous chromosomes during meiosis: creates new combines of alleles differing from people
What determines the rate of mutation?
- rates differ by organisms size and genome size
- also among genome regions, sexes, families, tissue type, nuclear and organelle genomes
What are the fitness consequences of mutations?
- mutations can be beneficial, deleterious, or neutral: mutations are random!
- beneficial mutations drive adaptive change but natural and deleterious more common
What are the most common forms of mutations?
- deleterious and natural mutations are more common, but beneficial mutations drive forward adaptations
What is useful about knowing the fitness distribution ?
- means one could predict the likelihood of a beneficial mutation occurring, or how quickly a beneficial allele would spread
If deleterious and natural alleles are more common, how does the genetic quality over time not decrease?
- effects of natural selection favouring the beneficial mutations allows genetic quality to be maintained
How do natural selection and mutation work together?
- Mutations and natural selection work in combination to maintain or even increase a populations mean fitness across generations
What are the 3 consequences of genetic drift?
- in a finite population alleles frequencies fluctuate
- some alleles are fixed, others lost, fraction of heterozygotes in population decreases over time
- separate population diverge in their allele frequencies and in terms of which alleles are present
What are founder effects?
- a subset of population colonizes a new location, genetic diversity depends on which alleles the founding population possessed
- if founders possess rate alleles that allele may become common
what is leading edge expansion?
- colonization of new territory by members of the population near previous range limit
- eg; glaciers retreated, land recolonized by black spruce trees
Is genetic variation reduced in newly colonized regions for the spruce example?
- Nuclear DNA: no reduction in genetic diversity
- mitochondrial DNA: evidence for founder effects
Population bottlenecks can result in rapid fixation or loss of alleles in otherwise large populations because the bottleneck…
- reduces the effective population size
Does drift increase or decrease heterozygosity?
- drift decreases heterozygosity = increase homozygosity
- drift reduces variation, mutation reintroduces it
What is the fixation probability in a small vs large population ?
What are the roles of selection and drift in determining allele frequencies in small and large populations?
Chances of fixation much smaller in larger population
- strong selection+ large population = selection largely determines changes in allele frequencies
- weak selection+ small population: drift largely determine changes in allele frequencies
What are the changes observed in molecular evolution?
- observes how sequences change, not phenotype: may or may not impact phenotype (synonymous, nonsynonymous, nosense)
What was the former belief in molecular evolution? What is the modern understanding?
- initially: if two alleles present, either under balancing selection pr one was one its was out: NS always strong
- 1960s: discovered variation more widespread than NS could be accounted for alone
What is the neutral theory?
- at molecular level:
1. most variation in population is selectively neutral
2. most changes in DNA/amino acid sequences are selective neutral over time
–> most genetic variation in a population is NOT subject to NS (no effect on fitness, no effect on phenotype)
- changes in sequences argued to be a result of drift! (random fluctuation causing differences in sequences - neutral differences)
What does neutral theory say about variation in sequences then?
- occurs through substitution - most are neutral
- most mutations are still deleterious overall, purged form population and don’t contribute to molecular evolution
What does substitution mean in molecular evolution?
- new mutation that reaches fixation
What is the key point of neutral theory?
- suggests alleles can reach fixation by chance (because of drift) rather than selective advantages
What is a pseudogene?
non-functional, typically untranslated DNA segments
- tend to be neutral, mutations within pseudogenes tend to accumulate rapidly
- arise from functional genes and gene deactivation
Why light allelic differences have no fitness consequences?
noncoding regions, synonymous substitutions, nonsynonymous substitutions
What are synonymous substitutions?
- code for same amino acid: silent mutations ; neutral or close to neutral
What are nonsynonymous mutations?
- change protein structure, not neutral BUT some may have minimal fitness effects
What is positive selection?
- selection favours changes at a locus (drives a favoured alleles towards fixation)
- expect more non synonymous mutation -
What is purifying selection?
- selection opposes changes at a locus (ie: removes deleterious mutations)
- expect fewer non synonymous mutations - most removed by selection
Which sites tend to evolve faster?
- sites expected to have minimal effects (neutral: synonymous) tend to evolve at faster rates than non synonymous sites in coding regions
Neutral theory as a null model: does NS still occur?
- natural theory suggest many alleles reach fixation by change rather than selective advantage BUT natural selection still causes change too
- positive selection is still important in driving molecular divergence
Why is neutral theory considered a null model?
- we compare expected values to observed values; infer if NS (or other processes) are occurring of predictions don’t hold
What are the mutation expectations under the neutral model?
- synonymous mutations are expected to evolve by drift, nonsynonymous evolve by drift when neutral
= equal numbers - if selection is occurring, do not expect similar ratios of synonymous to nonsynonymous
What does it mean when there are 6 synonymous to 1 non synonymous substitutions?
- this is purifying selection (NS is occurring) and it is preventing evolving, wants it to stay the same
- selection opposes change at this locus
Does selection need to act consistently across a protein?
- no! is can act differently on different parts of the same protein
How can we determine if selection rather than drift is acting on a locus?
- compare ratio of nonysynonymous to synonymous changes between species
- neutral: all mutations or substances neutral then there Will be equal numbers (drift)
- if selection is occurring do not expect similar ratios (positive or purifying selection may be occurring)
What is the McDonald Kreitman test?
compares pattern of allele substitutions between species populations to pattern of allele polymorphisms within a species population
- under neutral model pN/ps (within pops) = dN/dD (between pops)
-purifying: deterleious mutations create polymorphism within population, unlikely to be fixed - difference within species not populations
positive: beneficial mutations likely to go to fixation: differences between species (ratio larger than within species)
What determines the rate of neutral substitutions?
- rate of neutral substitution = rate at which they arise multiplied by their fixation probability
Is substation rate dependant on population size?
no! substitution rate is independent of population size : neutral subs occur at same rate in population that they do in individuals
What is the probability that a mutation will go to fixation?
- f (a1)
- frequency (1/number of alleles)
ie: population of 200 - f(1/400) = 0.025
What is the difference between substitution at the molecular level and substitution as a function of mutation?
Substitution as a mutation process: a point mutations where one nucleotide replaces another (transition or transversion) to form synonymous,non synonymous, and nonsense
Substitution at the molecular level: in neutral theory
- The process by which a new mutation becomes fixed (most of these mutations are neutral)
Is drift an evolutionary process?
yes it changes allele frequencies
