Test #1 Flashcards
Misconception about Darwin
The importance of Darwin himself – people think that only he came up with theory or that all scientists were against him and he revolutionized the idea –> NOT TRUE
- Misconception = that he came up with his ideas suddenly all on hos own –> In reality – his grand idea didn’t come about in a vaccum
***Darwin was just in the right place at the right time to get the credit BUT he was not the only person
What led Darwin to his ideas (overall)
He was alive at the point of intersection of intellectual processes that led people towards this direction
***NOTE: He was NOT the only person to connect the dots at the time of connection
Darwins concluions were…
An inevitable outcome of broader perspectives at the time – the reason that he gets too much credit (it wasn’t as revolutionary as people make it seem)
Persectives in the past (limitations on people)
At Darwins time – it was hard to have sufficient perspectives for one person –> Took time to draw out that perscteive to think about areas that you weren’t around
Understanding Earth’s age
Took time to know that earth is older than what we know –> hard to get that persective
Importance of Empirical Thought
Once scientific empirical thought took hold = increased understanding of earth iteself –> THEN applies this to biological systems
Who set the stage for Darwin’s profound realization
- Nicholas Steno
- William Smith
- James Hutton + Charles Lyell
Darwin (Overall)
Great Naturalist
***He travelled = gave him first hand persective on the variety of the world + how wide the world was
***His ideas did NOT come about in a vacuum
How did Darwin draw his conlusions
Drew conclusions from years of observations of species in their natural envirnments + Fossils + patterns of traits in domesticated animals
- He had first hand expriences of variety of world + how wide the world was from travelling
Key Developments before Darwin
- Antiquity of the world
- The relationships among organisms
Nicholas Steno
Overall: Established the underlying Premise of geology
- Dutch Bishop
- First real academic realization of what FOSSILS are
Example – Shark Teeth – before they didn’t connect that they came from living things
- Notes distirbution of fossil marine animals in terrestial rocks
- Developed idea of straigraohy
- Was only looking at local rocks
- had understanding of geology –> understood that we can study earth via studying rocks
***made a system to study rocks within his region
Stratigraphy
Study of the layers of rocks in terms of chronology
***Idea was developed by Nicholas Steno
Steno + Stratigraphy
He developed idea of straigraohy – he found that the laters reprented chronology – that diffrent layers are diffrent events in geologic history
William Smith
English Surveyer
Overall: Was able to see the big picture of stratigraphy – connected rock formation in diffreent parts of Britain –> Aligned rocks in one area to rock layer in a different areas based on fossils (found the same types of fossils in layers but in diffreent places = knew they had to be from the same time)
- Notes that the strata from across england showed remarlable consistencey in the fossils that they hold
- Found strata can be identofied across wide geographic span by “index fossils”
- Broadened Stratography – NOW not just in one place
- Understood earth on larger scale
***Did his work because looking for mines
Index fossils
Fossils that serve as diagnostics for a particular geologic period
***Index fossils = indicate layer
What did Smith see?
He connected rock formation in diffrent parts of Britain –> Aligned rocks in one area to rocks in layer in different area – saw the same change over time
- Saw that particular layers of rock in different parts of the world can be aligned by fossils in the layers
James Hutton + charles Lyell
Overall: Found that processes that have built and shaped geologic strata are essentially the same as the processes we see at work today
- Understanding geologic processes NOT just patterns anymore
Suggested: that the grdaual nature of these porcesses indicates that earth MUST be expreml;ey old
- Thought about porcesses happening today and how they scale over time to create what we see
- Understood what happened in Past + When we scale up rate of ongoing processes wbnough to see large scale processes we see – wouold mean that earth need to be much older than people thought before
What came from Hutton + Lyell
Created Uniformitarism
Uniformitarism
Natural Laws observable around us now are also responsible for events of the past
- Means that the properties of the universe have not foundationally changed over time –> Same processes for history of earth.
- Means that the same laws of nature are not changing from expeirmnet to expeimnet
**Idea that the present is the key to the past
**Really important in science
***Came out of geology
Why is Uniformitarism important in scinece?
Because it means that the same laws of nature are NOT changing from experiment to experiment – very important in science
Things in geology that affected biology perspective
- Found that the earth is old
- Makes sense of broadening persiectives
- Explains things by sclaing up ongoing processes – don’t need supernatural explinations for things
Relationships among organisms (overall)
Broader view of the living worls arts to take shape around that time – it took leaving small town to broaden persepctive
Linneus
Overall: father of taxonomy + binomial nomenclature – made hiearch –> Tied together all we know about life forms
- Gave comprehensive volume for how living world is connected
- Classified and named over 12,000 species of plants and animals
- Searched for divine plan in relationship among taxa
- Though species are immutable (Do not change) – BUT he still found connction between them
- Found connections between living things
- Set ground of perscetive for people to make DWM
Buffon
Naturalist – started grappeling with ohysical mechanistic explinations of the earth and living world long before Darwin
OVERALL: recoignized the improtnace of patterns in biogeography
- Observing regional differnces among species led some to start thinkning that species might not be immutable
- one of the first naturalists to begin expressing teh ideas that species may change over time
- Paying attentoon to differnece between organisms of the same species
- Thought about the idea that species change through time
Question: How did differences come about – does it show that organisms change across space
Biogeography
The study of distribution of species across space – observing regional diffreences among species led some to start thinkning that species might not be immutable
Example:
1. Wolves – North America/Siber = Large Vs. tropical = Small
- Moose – Alaska Vs. Scandanavia
Buffon realization
Thought about the idea that species change through time – did it by how species are distributed across the world –> Disrubution might tell us about how organisms might change
Question: How did differences come about – does it show that organisms change across space
***Shows that the idea of species changing over time did not start with Darwin
Buffon Ideas
Thiought all soecies were made in Europe and then they dispersed and degraded
Lamarck
Overall: Described how traits of organisms are matched to their envirnments and habitats
- Said traits of organisms match their envirnments well –> came up with how organisms change over time + how change is tramitted thorugh time
- Thought species change over time
- First to develope a cohesive thory in how organisms evolove
***Came up with 1st theory of how heredity works BUT he was wrong
Lamark’s heredity
Said that traits of organisms match the envirnment well –> came up with how organisms chnage over time + how chnage is transmitted through time
HAD IDEA OF AQUIRED INHERTIANCE
Who was the ifrst to develope a cohesive thoery in how irganisms evolove?
Lamark
Lamarkism
Change in organisms brought by natural physical processes
Contains:
1. Force of coplefications (Spontenous generation) – increase in complexity through time
1. Force of adaptations (Aquired inheritance) – match body to envirnment – idea of how organisms chang over time
Example – Giraffes necks get longer
***Had idea of aquired inheritance
Cuvier
Father of paleontology from a biological persective – put fossils in biological context
Geeatest contirbution – realuzation of excitcion – credited with deomnstrating that extiction is real
- realized that geologic history was charachterized by waves of diffrent fauna
- Still thought species were immutable
- Thought ecosystems are created and destroyed over again
Cuvier ideas
Idea of catastophism – thought that ecosystems are created and destroyed over and over again
How did Dawrin make observations
Restless young man – joined the company of naval vessel at 22 00> circumnavigated the globe – giving breadth of perscetive on nagural world that few with his interstes and training experinced
***Because of this = he made observations of living and geologic world
Darwin’s observation in context
He was making these observations about the worlkd in the intelecual context
Inevitability of Darwin’s conclusions
His ocnclusions were inevitable – this view of life was coming into focus anyway
- He was NOT the only person with ideas at the time
Dawrin was thw the first person to put all of the peices together BUT he sat on his ideas for a decade
***We give darwin too much credit – it was inevitable conversion of intersection
How do we know that Darwin’s conclusion were inevtiable
Becayse Wallace had independelet arrived at the same conlsuions – shows that the conclsuions were inevitable because it actuallt did happen somegere else
Wallace
He came up with the same conclsuoons as Dawrin independeley – he was more eager to announce his finidngs= spurred Darwin to publish his work
Dawrin + Wallace
came up with same conclsuions – wallace was more eager to announce his findings = spurred Darwin to publish his work –> Darwin gets credut becayse he was rocher
***Shows influence of class politics
Componenets of Darwinian Evolution
- Pattern
- process
Pattern of Darwinian Evolution
Common decent – Descent with modification
Process of Darwinian Evolution
Mechanisms for how changes arrive – process = natrual selection
Which is more acceoted pattern or processes
People NOW accept natural selection (process) more than the pattern
- The common decent thing is the thing that people don’t like
AT Darwins time it was the opposite – people didn’t accept the mechanism
Why didn’t people accept mechanism at Darwin’s time?
- They didn’t have the math to show the mechanism at the time
- They didn’t have the genetic idea at the time – didn’t know about heredity
Two models for explaining patterns of biodiversity
- Special Creation
- Descent with Modification
Modern science
Essnetially we are confronting models with data to disprove models
Example – comparing models of special creation with DWM
Special Creation
- Species are immutable (unchnaging)
- Lneages fo NOt diverge
- Species are created seperatley
- Species are geniologically independet – not fundementally realted to each other
How did they combine special creation + fossils
There was an idea that all things were created at one point and existed over time
***They didn’t really think that this was true because they knew extictions happen because of fossils = they thought that species are made at once and then die and a new species is made
Overall: idea that species pop in and out of existence
Descent with Modification (overall)
- Species change thorugh time
- Single lineases give rise to many – diverge
- Old forms beget new forms – connects round history of life –> genologically realted
- Species are geniologically related
- Requries the earth to be vastly older than recorded human history – requires a huge amount of time for this to occur
Lines of evidence for Descent with Modification
- Do species change over time
- Does special occur?
- Do new forms arise from old?
- Are different Groups of organisms related
Do species change over time OR are they fixed in traits?
We know that species change over time because we can make them change – we domestricate things = we chaneg theor traits over time = we know that their can change
How do we make species change
We domesticate things = we know that species change over time
Evidence of species changing over time
- Artifcial Selection
- Applied Breeding (domestication)
Evidence for populations changing undeer human control
Artifical selection – seen in scientific experiments –> shows species change over time
- Can see change in behavioer
- String interfences
- Often modest expected change
- experiments can also involove exposing popularions to experimental conditions and measuring for heretible change
Example – do experimnet with mice runing on treadmill – only take the fastest mice and breed them
Agents of selection in selection experiment
Humans – if doing selection experiment = people impose selection –> humans are the agents of selection
Second type of experiment that shows species change over time
Experimental evolution –> expose populations to experimental conditions and measure for heretible chnages
Experimental evolution
Take population and expose to new conditions – see change
***SHows that species change over time
Example – Threespine sickle back
Threespine sickle back experimnet
Overall: Taking population and exposing to new conditions to see change
Threespine sickback = occurs in marine and freshwater popultions
- The freshwater popultions = have better cold tolerance
- When take diffreent popultions from nature and carfully test the thermo tolerance in lab reared genertaion THEN tranfer them to expeirmntal ponds with cold conditions
- DOES NOT have acrtive control breeding – not purposfully putting the cold tolerant fish with cold tolerant fish
Result: When bring them back into the lab and have offspring under contrlled conditions –> the offsrping cold tiolerance imporved by 2.5 degrees in just 3 generattions – minimum temperature of gish improves –> now they can maintain homeostatsis in coldeer envirnment
- exposure to colder –> have phenotypic shift
- NOT picking only the cold tolerant – all of them can made
Applied Breeding
Domestication – shows that species change over time
Morphological change in applied breeding
Applied breeding = shwos there can be morphological chnage (physical chnage – change to body structure)
History of Applied breeding
We have a long history of selevctive breeding fo domestic plants + Animals giving rise to unambiguous answer that species DO change over time
Example #1 – Dogs – share common ancestory
- Wolf = common ancestory –> have morphological shift becased on humans applying selective pressure (getting different breed of dogs)
- Morphologic change can be seen in cranium
- Would say that they are different species beased on morphology if you didn;t know that they were all one
Example #2 – Can be seen in plants (we domesticate plants too = we know species change over time) –> Wild mustard
- The common wild mustard plant was domestricated to make many plants –> all domestirca forms of same common ancestral plant
Does speciation occur?
ANSWER: YES – many expamples of recent on-going speciation in nature
Speciation
One lineage splits into two seperate lineages
Do new forms arise from old?
YES
Evidence:
1. Biogeographhical + paleotological evidence –> Seen in law of sucession
2. Transitional Fossils
What connects organisms across history of life?
Old forms giving rise to new forms
Law of Succession
Correspondance among fossils and existing faina dn flora in spaces
***Evidence that do forms arise from old
- Correspondance across modern organisms and possible origins in the same space –> Modern organisms in a space corresponds to the fossils in that space
Example #1 – Australian fossils that are mammals are marsupials BUT asiam mammals are placentals
Example #2 – Apes – see modern and fossils in the same place
Example #3 – Sloths –> they are ONLY found in the new world – connects modern fossils in the same regions
Wallace Line
Differentates faina of asian origin with fiana of australian origin
- Seperates placentals Vs. Marsupials
***Seen in fossils + existing organisms
What do we expect to see in the fossil record IF new forms arise from old?
Exoect to see fossils with mixes of Ancestral and Novel traits
Transitional Fossils
Fossils with mix of ancestral and novel traits – ties groups of organisms over time
Example – Dinasours with feathers
Misconception about Transitional Fossils
That they are link between two things
Transitional Fossils are NOT link between two things – they are a branching point with a mix of traits
- they are NOT direct loinks rather they are reprenstative of organisms that shared a common ancestor with a group near a branching point
Predictions about transitional fossils
Based on gaps between existing organisms and ones in the fossil record = we can make predictions about what transitional form to expect
- In some cases paleotologists have been very sucessful with this
Example – evolution of whales
Evolution of Whales
Whales = hoof mammals
- Evolution of whales from terrestrial ungulates in the Eocene to Ocean going + Krill feeding giants of today
- once found where to look = found the set of transition fossils to connect the dots
Connectivity in the living world
IS NOT along a single tradectory – NOT a straight line
- People think that evolution is a single tradjectory – that it is a direct progression within a single lineage over time –> NOT TRUE
EVOLUTION – is NOT a singloe lineage – have branching diversification over time = need to contextulaize thorugh fossils
Example of Transitional Fossils
Whales – conects 2 kinds of hippos and 2 kinds of whales
Start = mammal – know many steps occur in trantion
- Can see fossils with hind limbs –> orginals that ahve all BUT one feature
- Orginal mammal = not direct ancsetor BUT is part of the processes
- Can see existing organisms with lens
- Example transitional form = filter feeder + some no teeth
- Still living organisms can be transitional forms
***Transitional forms shows mix of trauts that allows us to understand developement
Homology
Charachteristics shared among orgnaisms because they were inherited from a common ancestory
***homolgous traits
- Similarities = biologically meaningful NOT just coincidence – they are because of a common ancestor
Example of homology
- Mammal Limb Bones
Evidence that different groups of organisms are related
- Homology
Mammal Limb bones
Limbs = highly conserved –> ecen if they are in diffrent shapes and sizes and have different purposes
Better Forms of homolgous traits
There are better forms for homolgous traits for their function BUT they are confined by shape in ancestory
Places homology is seen
- Vestigal traits
- Atavism
Vestigal Structure
A useless rudimentary version of a trait that is a function in related taxa
- Reminent of traits in ancestors
Example
1. Psudgogenes
2. Moden Whales
3. Appendix
Psudogenes
Non-functional copies of coding genes
Example – Vitamen C synthesis in Primates
- Humans need to ingest vitaman C BUT other animals don’t –> this is because hour ancestors were furgavors = they were not limited in vitamn C –> there was a mutation that stopped vitamen C. production BUT there was no bad effect because we got enough Vitamen C in diet = kept mutation
Whales + Vestigal traits
Modern whales = have no hind limbs BUT they have a pelvis bone that is not attatched to anything because ancestors had hind limbs
Appendix + Vestigal trait
Appendix = was thought to have NO use BUT now we think it may play some role in gut microbiome
Atavistic Traits
Reappearnce of ancestral traits in individuals
- Provised evidence of homology in developmental pathways
Example – more than 2 nipples
Use of Atavistic traits
Provide evidence of homology in developmental oathways – mutation in development occurs that re-turns on a gene
***We can manipulate atavistic traits ourselves
Manupulating Atavistic traits
We can manipulate appearnace of atavistic traits – can exeperimentally trun on latent homolgous developmental pathways
- Evo-Devo + evidence for homlogy in developmental pathways -- look at how ancestral pathways work
Example – make chicken that can grow teeth
Patterns of homology
Describe relationships among taxa –> Because homology is based on common ancestry it leads to specific nested patterns of traits among relation organisms
***Makes nested patterns of traits among organsims
- Nested rather than Vendiagram
- nested with each other
- Nested in the same sense as the standrad taxonomic hiearchy – refected in classifciation system
Where else can homology be seen
Have homology in DNA and protein sequences
***have the same nesting sturcture in genetics as we do in traits –> Genologic nesting
Have:
1. Orthologs
2. paralogs
Orthologs
Homolgous genes between species – across species
Paralogs
Homlogous genes that diverged within a lineage
***genologics relate to each other within sme species
- Genes related within ONE genome
What makes paralogs
Paralogs = result of gene duplication events – genologics related
- Gene + chromosome + Whole genome duplication event
What forms the basis for modern phylogentics
Orthologs + Paralogs – genologics related to eachother
Example recent gene duplication
A recent duplication of DNA sequences around nueron gene PMP22
***makes PMP-22 flanked on both sides by CMT1A repeat
- RT repeats that flanks = can be bad --> can end up losing a copy or end up with two during recombination - Nearby repeates make the region prone to mitotic probelms - Erroes in duplciation can lead to disease
Charcot-Marie tooth diease
Errors in duplication in PMP22 because of RT repeats that flank both sides
***loss of genes = get disease
When did duplication event in PMP-22 occur?
Occured sometimes bteween most recent common ancestor of homo + pan + gorllia and most recent common ancestor of homo and pan
***Repeat is found in homo + pan
- Pan = chimps + babones
- Humans + Chimps + Baboes = have copies
Why are PMP-22 repeate NOT convergent evolution
NOT convergent evolution because the traits are NOT adaptive
Why are PMP-22 repeate NOT convergent evolution
NOT convergent evolution because the traits are NOT adaptive
Two broad compoenents of Darwin’s ideas
- pattern – common Descent
- Process – mechanisms for how change arises over time –> process that generates diversity + process that connects diversity
Two overall changes that led to Darwin’s ideas
- Change in geologic thought
- Change in biologic thought
BOTH led to Darwin’s ideas on pattern
Intelecual setting for Darwin’s breakthroughts
- Break through on pattern in Geology (led to pattern)
- Breakthrough on pattern in biology (led to pattern)
- Breakthrough on Process – Malthus (led to process)
Malthus affect
Affected both Darwin + Wallace (Darwin + Wallace both read his work)
- Gave breakthrough to figure out process – mechanism for how change arises over time
Malthus (overall)
Was one of the first people to really think about teh mathamatic reality of human demography
- We would now call what he did “demography”
- he put numbers to issues of human populations – made many models
- He realized the remarkable power of unchecked population growth
***At the time people were thinking about mathamatic models for population growth
Demography
The study of population structure
Importance of Malthus
His line of thought was critical fro Darwin + Wallace idea of natural selection as the mechanism of change
- critical for coming up with MECHANISM
What did Malthus find?
He realized the remarkable numerical power of unchecked population growth
- Realized math potential in how reproduction oppertates that makes population growth unstable process
Showed that the way popultions grow through time = leads to massive growth UNLESS it is in check
Malthus opinion on population growth
He viewed this intrinsic property of populations (that unkecked growth) as a source of great human sufferering
What did Malthus finding show?
Means that something needs to hold population growth back – without check the population is unstable and unsustainable
Geometric/Exponential growth
Population is increasing by constant rate per individual over time
Geometric Vs. Exponetial growth
Geometric = discrete units of time
Exponential = continous time
***Difference between the two = how you keep track of time (discrete vs. continous time)
Arithmetic growth
Population increase by a constant amount over time
- Increase by a constant amount of individuals
***Different than versions where you add individuals based on the density of the popultion – this does not take into account the density of the population
Two types of growth
- Arithmetic
- Geometric/exponential
Arithmetic growth equation
Yt = Yo + XT –> JUST a linear equation
T = time
Overall – Number of individuals X Time (because adding the same number of individuals each time no matter how big or small popultion is)
- Each generation as set number (X) individuals added to the populton
Example – start with 1 person and add 2 people each generation
1 –> 3 –> 5 –> 7 –> 9
- Adding a fixed number each time
***Creates linear popultion growth (Always adding 2 individuals each time)
Exponentailo growth equation
Yt = Yo X X^t – for each generation t -> X offspring PER individual are added
- Adding X offspring per individual (Y)
Example – start with 1 individual and the popultion grows at a rate of 2 individuals per generation
1 –> 2 –> 4 –> 8 –> 16
***Much more rapid growth than arithmetic model
What type of growth is seen in popultions
Most is exponental growth –> seen in almost all real popultions in nature
- Seen by looking at reproduction
What type of growth did Malthus notice
Exponential growth – he notives this because we are NOT actually in an exponental model = means that there is some outside force that needs to be occuring
Who is included in growth models
We only look at growth from the persective of females –> THEN once do equations add back in males
- only look at females + female offspring
- Then you can apply the sex ratio for a given popultion (often assume 50:50) –> THEN can add males back in
Example – if in the end you calculate 32 indivudals THAT means 32 females –> Assuming 50:50 ratio - means your total popultion is 64 (32 + 32)
***Works IF we know things about the sex ratio
Malthus equations (image)
Fibonachi
Came up with sequnce to try and come up with a model for popultion growth – it was an attempt to put numbers to popultion before malthus
What did Malthus realize
He considered exponential growth from the perspective of human popultions and agrucultural surplus – he realized that growth was a BIG problem for humans
Malthus + agriculture
He realized that exponential growth was a BIG probelm for humans – what would it do to agruculture?
Asked if we could save up resources to suppert humans
Answer: NO – human technology can’t keep pace if going unchecked = he thought that we were always on the edge of catastrophe
- Mortality would be higher if growth rates go unchecked
- Even with increases in production – agriculturakl surpluses would still inevitably lead to famine
What stops us from being in a state of catastrophe
Mortaloty rates stop us from being in a state of catastrophe
- High mortality rates stops catastrophe – most individuals due before reproduction in order for popultions to stay stable
- What prevents us = high level of background morlatlities to counterect popultions from rapid exponetial growth
***If most don’t survive = more stable popultion
Does growth models hodl true for most animal popultions
YES – numbers held true for most animal popultions – also found that mortaloity is a fundemental property of most popultions
What explains constant growth (what explains ability to mainatin expo growth model and not be unstable)
Variation in survival + reprduction
Mathlthuianism + Darwin
In natural popultions and humans (at the time) most individuals born into the popultion don’t actually contribute to the next generation
***This view of a struggle for existance as intrinsic to all popultions = critical to the formation of Darwin;s ideas for a mechanism
***Because most of popultion isn’t surviving –> means there is a variation in success = got Darwin + Wallace thinking
Uniquness of Darwin’s mechanism
The idea of the mechansim was not completley unique –> the importance of Darwin’s work was in coupling the process with the pattern
- Widening the scope of selection to encompess all of the loiving world
STILL – he wasn’t the only one to come up with his conlcuoon –> wallace came up with the same idea – spurred Darwin to finally publish
Importance of Darwin
Coupling the process + Pattern
Orginal Word Model of NS
Based on 4 tesable posutalates
- Built on a set of 4 postulates that are testable to epxlain data
***All postulates are testable
Why did natural selection remain controversial
Because Biology and Math had to catch up
- We didn’t have a mechanism for inheritance –> hard to prove
- Mendle have us some idea –> use it for small traits BUT coupling mechansism of inheritance for complex variation too time to build understanding
- Anylzying variation in popultions – ststistics
- Answer to many probelms
What was more accpeted for darwin + wallace
The pattern was accepted by scientofic community + public within 10 years BUT the mechansim of natural selection was controversial for longer
- Mechanism of natural selection was not accepted for another 50 years
- Mechansim remained controversial because testing is hard to do
NS postulates
NS is simple due to 4 key postulates
***Each postulate is testable BUT tesing is not always easy
- Populations are variable – variation within populations
- Traits are heretible
- Variation in survivorship + reproductive sucess
- Surivivorship + reproductive success vary as a function of traits
Postulate #1 – Populations are varaible
Populations differ in:
1. Morphology – body shape + Size + Structure
2. Color (ex. Sgells of snails)
3. Physiology (Ex. Cold tolerance + metabolic variation)
4. behavior
5. Life history traits (Ex. Growth + development + number of offspring/gametes)
6. Immunity (Ex. being resistant to disease + pathogens)
***This is fairly intuative – easy to see
- Certainly seen in human populations (Ex. Distrubution of height – math shows amount of variation)
***Can see how selection drives varaition
Where can variation be seen?
- Seen in human popultions – Example is disribution of height (math shows the amount of variation)
- See genetic variation within popultion – can see varaition in genome
Example – HMHC antiogen protein in immune system- Gene in MHC = has over 1,000-2,000 allleles in human popultion
***Have varaition in physical (in phenotype) + vaiation in allele in genome
What is the hardest postulate to test
Postutlae #2 – traits are heretible
What do we mean in posulate #2 – traits are heretible
NOW we know about genetics BUT here we mean about heritablity = LOOKS across generation
Heretibility
Means that there is some connection between the phenotypes of one generation and the next
***Means that the offspring will look like the parents
- Means that there a function in offspring that is in the parents - makes many connections between phenotypes in offspring and parents
***Very hard to demonstrate/show
What do we mean by “traits are heretible”
If we think in discrete generations – what we mean is simply that the phenotypic distribuition of generation 2 is at least partially a function of the phenotypoic distribution of their parents
Complexity of heretiability
Heretabiloity = rather complex in practice
***A trait can have a clear genetic basis BUT not be heretible in a straight foward way at the popultion level
Example – Genetic dominence –> NOT negating heritability BUT comlicats it
***Means that the second generation looking like their parents is more complicated than “just looking the same” – because of complex heritability patterns
***Traits can be heretible BUT not in a straight foward mechanism
Example – dominence –> complicates the 1:1 parent phenotype:offspring phenotype
- complicates the fact that the next generation will look exactley like the parents
Why is postulate #2 hard to measure?
Because heretibility is complicated
Example of heretibility
- Look at heights – looks at the children/sibling heights vs. the average height of both parents
- Can see the mathamatic connection
- Explains genes
- Fits statistically significant line in parents vs. offspring
- Hard to do things to contril for envirnment variation
- Mesuring beak size in parents vs. offspring
- The relationship between the two could be because of genetics OR could be because of shared envirnmental factors
- En
Second reason why is it hard to test heretibility
Because envirnmental factors affect traits – the correltion between parents and offspring could be because of shared envirnment
Second reason why is it hard to test heretibility
Because envirnmental factors affect traits – the correltion between parents and offspring could be because of shared envirnment
Postulate #3 – variation in survivorship + reproductive sucess
***Very easy to see + testable
***This postulate is almost universally true in natural popultions
Exceptions to Posutlate #3
Cases where a popultion is in the midst of exponetal growth
***When it isn’t true it is transient – only occurs for a few generations
Example of times when not true:
1. Invasive species – if colonizing a new habitat = grow rapidly until it hits its limits
2. If bounding back from an epidemic
***The rapid growth does not last for long –> if it did it would become overrun with organisms – means that almost ALL of the time you can check off postualte #3
Example of popultion in exponetial growth
Hex crane – we started conserving them to ensure their survival –> they are in exponential growth pahse while they are getting higher BUT they are only able to do this because people are ensuring their survival
- Won’t last forever
Example where postualte #3 is not true
What types of popultions does Postulate #3 work for?
Works for R and K stradegy populations
R stadegy
Investment optimized to the number of offspring – faster replication = put more babies hoping to survive
Example – octopus
Example R stradegy
Octupus –> makes 0.25 million ocotopi each generation
- replication rate = 125,000 (for females only – 250,000/2)
- Each octopuc gets pretty large
***If they were in exposnetial growth and all octopus survive to reproduce (meaning there is no variation in surivival + reproductive sucess) THEN by generation 4-5 the octopu would exceed the mass of the earth
- This is the reason why differential survival + reproduction needs to be true
K investment stradegy
Investment optimized for care and or development of offspring
- Produce fewer offspring BUT hope all surive –> add more resources to make sure they do
Example – elephants
Example K stradegy
Elephants – If they all survived to reproduction – in 44 generations they whole earth would be elephants
- Means that even for the slowest growing organisms postulate #3 needs to be true (still need to have variation in survival + reproduction)
Most important postulate
postulate #4 – survivorship + reproductive vary as a function of traits
What do we mean in Postulate #4 – surovorship + reproduction vary as a function of traits
Means that variation in survival is mathamatically connected to varaition in traits
- Survive and reproduce as a function of varying traits
- means that rates of mortality and reproductive sucess are NOT uniformly distributed across the population in regard to certain phenotypes
- Means that individuals with a certain phenotyoe value are more likley to survive + reproduce
Example of uniformlity distributed
In the image – the trait is not affecting survival –> there is no diffrence in suvivorship between individuals with trait or without the trait
- In this case natural selection is not active
- Have uniform distribution
Uniform Distrubution = no correlation = failes the 4th postulate
Uniform distribution
probability of y does not vary as a function of x - everyone in the population has the same chance of surviving and reproducing, regardless of phenotype
***Means that natural selection is NOT active – fails 4th postulate
Not uniform Distribution
Image = not uniform distirbution – one trait value (individuals with certain traits is NOT surviving) BUT trait values in the center (individuals with different traits) are surviving
***have a difference between survivorship –> means that what trait you have matters for survival
- there is a relationship between trait and survival
- Trait = affects probability of survival
- here posulate #4 is true
Example where postulate #4 is true
Coat color in mice –> whether mice survive is based on coat color
In dark soil = dark coast allows you to camaflouge better = survive better
In light soil = want light coat
***There is a connection between coat color and liklihood of surviving
Example of Natural Selection
Gulls – In a field of Golden Rods
NOTE: many insects = specialists for golden rods –> Many inescts make a Gull on the Golden Rods
***Goldren Riods = well studied in evolutionary studies
Insects Making Gull
Gull = purely plant tissue
Insects induce it in the plant –> then insects lay egg in the plant and the plant secretes hormones to trick the plant to make a structure that benefits the insects
- The Vascular tissue = adds defensive compunds around the Gull - Making the Gull is ONLY costly to the plant --> the plant is really making a house for parasite - Affects plant replication - Gull = puts fitness cost on plant - Gull = hujacks the plants genome
Example – What shapes the evolution of Gall size
Look at 4 postulates:
1 – Is the Gall size variable –> YES
2 – Is the Gall size heritable –> YES
- Hard to test
3 – Do all flies continue to the next generation – is there variability in survivorship – YES
4 – Is fly survival and reproduction uniformly distributed – YES
- Look at natural history
***All 4 postulates are true = makes a relationship between probability of survival and size of gall = selection is occuring
Testing if gall size is hertibles
Grow clones (meaning that they have the same genotype) in greenhouse and look at parent vs. offspring
How do you know that all flies continue to the next generation
In 3 generations = it would be over 15 million flies if there was no diffreence in survivorship AND we know that most flies don’t move more than 25 meteres – since we do not have 15 million flies in 25 meters = know there there is differntial survival + reprduction
Seeing fly survival and reproduction is uniformly distributed
Look at Natural history + look at Gall size
***record gall size and open them up to record the fate of the fly larvea (look at gall size vs. survival)
Need to look at the parasotic insects that attck Gall flies
1. Beetle – most get attacked by beetle –> WITH beetles there is some varaition in survival BUT mostly the same atttacj rate no matter the Gall size –> Means that the attack rate IS uniformly distributed = there is no difference in survival because of Gall size = means natural sleection is NOT occur
- here survival rate is the same for all gall sizes
- Wasp species –> The probability of getting attacked by a wasp increase as gall size decreases
- at 25 nm you are almost immune to wasp –> Here there is a relationship between the trait and suvivorship = means that natural selection is occuring
- Not uniformly distrubuted = having the trait affects your survivorship = NS is occruing
Why doesn’t Gall size just continue to increase – why are they not all Huge Galles
Why is there NOT runaway selection
- Wasps are NOT the only source of mortality
Example – birds also each the galls (birds eat the insects in them)
- Birds go after the bigger galls (bigger galls have lower survival)
MEANS that there is selection in both directions –> the intermediate size is the best
Result: Get stabilization state – NOT getting runaway selection because NS is not just optimizing one thing at a time
- There is a difference acorss popultions + difference across years – NS process = go back and forth all of the time
- Looking at different locations and within the same feild in different years the gall sizes change and they change in different conditions –> NS regimes are NOT fixed through time – forces imposing NS change so have long term dynmanic shift
Runaway selection
When the traits just most so far from to be the most fit (Ex. Gall size just ciontniuing to increase to be HUGE galls)
Stabilizing Selection
Individuals with the intermediate trait values have the highest fitness –> When teh intermediate trait is favored
- Sleection won’t go in one direction forver because the end point is not the best – the best is something in the middle
Ex. Gall size – because bigger is good for bird protection but small is good for wasp protection = the intermediate size is the best
Physical Fitness + Darwinian Fitness
They can be related BUT they might not be
Fitness in Vernacular
Conjured a lot of meanings – Strength + Stamina + Speed
Darwinian Fitness
The extent to which an individual contributes to future generations
- Not neccesarily what we think of as “fitness”
***amount of individual you contribute to the subsequent generation
***Need to think of it in terms of LIFETIME reproductive output
Survival + Fitness
We often think of “survival of the fitest” BUT survival is not enough
***Survival is a neccessary compoennet of fitness BUT it is not enough for fitness
Survival = only ONE part of it –> Need to survive to the point of reproduction – survival is needed for fitness BUT also need reprouctive component (need repriductive sucess)
What is needed for fitness
- Survival
- Reproduction
NEED – survival + reproductive success
Firness = Survival –> Reproduction
Post reproduction survival in Fitness
AFTER reproduction – can still survive after reprpduction –> That survival might not have to do with fitness because you already reproduced the amount you will in your lifetime
***Shows that survival is NOT the only part of fitness – some types of survival might not even be part of fitness such as survival after reproduction
Components of Fitness
We can define many compennets of fitness (BUT they are organism soecific)
Example for sexual organism:
Surival –> Mating success –> Fecundity
- Need to survive to the point of reproduction
Fecundity
Number of offspring you produce + can include parenting sucess
- Includes parenting sucess IF offspring learn traits because then you arte keeping them alive
- This is NOT inclduing genes of offspring traits
***Part of mom’s fitness = how well she can protect her kids BUT her genes are not part of the kids fitness
Mating Sucess
Looking at traits that might contribute to mating sucess
Example – competition with males + locating a mate + co-population + fertlization
- You might have a moose that is good at getting a mate but his sperm doesnt work making his fitness zero
Is offspring survival part if fitness of parents
Depends of the traits in question – need to think about whose fitness it is
- Part of mom’s fitness = how well she can portect her kids (that is mom fitness) BUT part of kids fitness is based on the genes from mom
Fitness in life histories with multiple mating events
Need to think of it in terms of LIFETIME reproductive output
Have survival –> Mating success –> Fecundity –> GOES BACK to survival
KEY for seeing if trait affects fitness = does it affect lifetime reproductive sucess
***Fitness = might not only have a single round of reproduction – if life historiues with multiple mating events
Key for seeing if trait affects fitness
Does it affect lifetime reproductive success
Example Orthology
Duplication evnet in PMP22 gene – makes sense as homologs that arose in common ancvetro of human + chimp + baboes after split wioth gprilla
- Shared because of homlogy –> tells us about biological reality of relationships of organisms
Molecular homology
- Junk DNA
- Look at functional things that are homologous –> look at biochemical pathways
- Often have homologous biochemical pathways –> same genes for enzymatic function because of homologty
-Same mechanisms + pathways because inherited from a common ancestor
Example – Aquition of mitocondria - Many biochemical underpinning s of life were laid down a very very lomg time ago
- Often have homologous biochemical pathways –> same genes for enzymatic function because of homologty
Molecular homology = extent way beyond closley relate mamales
Why is Junk DNA good evidence for homology?
Good evicence because can’t be convergent evolution
Aquisistion of mitocondria
Example of molecular homology – occured because MRCA of all extant Eukaryotic organisms
- Homologous across ALL Eukaryotic
- Critical in history of life
- Impirtant molecular homology
Time in evolution – need to contemplate the time involoved
To know time = look at time scale for porcess in the world and then scale up
Example – whales (Time from evolutuon)
Mammal –> Whales = took 55 MY
- Huge chnage in physiology + Morphology
- 55 MY = brief in the hirtosy of the earth
- 55 million years vs. history of animal life → small – 10% of animal life as we know it
- Histiory if all animal life vs,. History of the earth → animals = very small part in history of the earth
History if form = very small – took all of the time befire to build all biochemical processes
ALL took tremednous amount of time – change from 1 generation to the next = can be scaled up to the history of life
- Diversity seen in animal life today = looking at huge time scale
Transional fossils misconception
People think that transtional fossiles = direct missing link
***They are not missing link they are just a branch between two points – represents a brant that has some chnages but not all
- Branching point shows things that are no longer alive BUT show us the order and where these things occured
Point of TF = that they tell us the order of events –> tell us the order of evolution – show us the order and where these things occured
When can population evolove
If the 4 postulates are trie
Exponetial growth Example – Aligator snapping turtle
Example of a popultion that people think might be slow growing – shows that they would still become unstable very fast
- Have potential for out of control growth (Expo growth) in population that we think would be slow
Prompt: Each female lays 15 eggs at a time (15 eggs per clutch)
- In the current popultion the ratio of males to females in the offspring is 2:1
Question – if we introduce a male and female turtle into the lake –> how many total (male + female) grandchilren will they have if all of the females survive to reproduce
Reminder = ONLY include females in the equations
We know:
- Yo (starting popultions) = 1 –> because only females are included in teh equation – start with one male and one female BUT only include the ONE female in equation
- T = 2 geneterations – because asking for grandchildren = Parents –> Children –> grandchildren = 2 generations
- X = 5 eggs –> Because we know that its is 15 TOTAl egges per clutch (which includes male and female eggs –> Apply the 2:1 ration = 10:5 males:females = 5 female eggs per clucth (ONLY inlude females in equation)
- yT= ?
Yt = 1 X 5^2 = 25 Females –> X:25 (2:1) –> 50:25 –> 50 + 25 = 75 – Answer: 75 total in 2 generations
- 75 grandturtles come from just one clutch of eggs in each generation
IN REALITY – a female thyat survives to adulthood has an everge lifespan of 70 years
- If a turtle as her first clutch at 12 = she has 58 clutches in her lifetime
MEANS her reprodctive rate = NOW 290 (Because 5 X 58 clutches) –> 290 female eggs in lifetime
THEN Yt = 1 X 290^2 = 84,100 female granturtles
apply 2:1 –> 252,300 total grandturtles
- If they all survived – in just 2 generations = 252,300 – know that this won’t actually happen because everyone surviving almost never happens
How should we think about fitness
Need to think about fitness as a whole
To think about fitness (consequnce of individual adding to gene pool) = need to think about survival and reproduction – need to think of BOTH survival AND reproduction
When we’re thinkning about traits and variation we need to ask “what are the conseqeunces of contributing to the gene pool in the next generation”
***Fitness is sometimes counter intuative
Fitness logic
Fitness is sometimes counterintuative – the biggest + stringest + fastest + feircest isn’t neccesarily the fittest
Example – Fitness of Gulls
- Can look at it in two ways they can get kills
1. humans shooting the seagulls –> here there are no traits that would protect them
- Whether they get hit = by chance –> there is no heritable traits that are under selections in this context
2. Using Trained raptors – they chase the individual –> maybe there is a trait tat plays a role in whether they get eaten by a falcon
- Can catagorize the dead bird based on muscle density (Have normal + More + less) – most of the indiviudals were normal but had some that were higher and some that were lower
RESULTS:
1. For the shooters – the probability of survival is the same –> therte is a unifrom distrubtion across trait values – survival is not impacted by muscle condition
2. For the falcones – still have the same muscle distribution across popultion BUT now the probability of survival is NOT the same
- poor muscle = less likley to survive (might be less agile + Slower)
- normal msucle = higher survival than the other two
- More musle = likley to get killed –> SHOWS that higher musclar physical fitness here DOES NOT EQUAL biologic fitness (Example of counterintuative to how we think of physical fitness)
Here – intermediate os the best = example of stable selection
Example #2 of counterintuative fitness – Dogs
Question – Which of these dogs has the highest fitness
Fitness = depends on the conetxt – can only define fitness in the answerment the organisms is currnetley in
Answer: We can’t know which will repdouce more just by looking at them – the actual condition of the organisms + their ability to interact in the envirnment doesn’t mean anything about reproductive sucess
- Fitness of the Left = zero – bevcause he has no testicles BUT we would not know that inofmration without bieng given it
- Fitness of the right is greater than 1 assuming it can breed
NOTE – need to keep in mind lietime repdouctive sicess
Example #3 of fitness – Dung beetle
Dung bettle fitnes can be counter intuative for reprductive sucess among fertile individuals
- The Dung beetle males = build tunnels for females and girad them – while the big heavily armored males are fighting the smaller hornless ones sneak into the tunnel and mate with the females = results in 2 stradegies for reproductive fitness
OVERALL – shows that fitness is NOT straight foward – shows that fitness is complicated and we need to keep that in mind
Here = have 2 forms of fitness:
1. Smaller (no horns) –> bypass the fighting males and sneak in
2. The bigger ones guard and then mate with females
***This helps explain why we still have smaller males – shows slection for one direction and the other
Key points regarding humans
- Wehn we talk about Darwinian fitness we are NOT making value judgements – we still have to think about lifetime reproductive sucess (and this is not always easy to preduct)
- If we make analogies to humans – to get fitness in humans = we just think about reproductive sucess
- We cannot make value judgements on phenotype –> way we use fitness = hard to seperate from the biologic definition
Misconceptions about evolution
- individuals evolve – REALITY = selection acts on individuals BUT individuals don’t evolove
- Natural sleection can see into the future – it cannot
- Selection adds more varaition – REALITY is that selection acts on existing varaition in popultions
- Selection results in perfection – NOT TRUE
- Selection favors complexity – NOT TRUE
- Being evolutionarily advancd – subjective
Level of evolution vs. Level of selection
Evolution = population level
- Evolution = allele change from one generation to teh next –> change in allele frequencey in a popultion over time = populatoions evolve
Selection = acts on individual – fitness is based on individual
Selection = acts on individual BUT indoividuals don’t evelopve populations eveleve
Change in individual
Change in individual IS NOT evolution – change in an individual is JUST development
Darwin vs. Lamark’s views
The crux of the difference between darwin vs. lamarsck was veiws on the mechnaism behind decent with modification
- Lamarck = change in indivual that is passed down
Natural selection looking into the future
Natural selection = CAN’T look into the future
- NS = purley mathamatic process within parental generation
Result = evolution lags a generation behind the selective pressures
- NS is bloind to the future – it can only repsind to the conditions in the cirrent generation at the time –> NOT prepparing for the next generation
- NS = only responds to the crrent envibrment – not looking to the future
- ONLY the current conditions affects differnce in repdouction and survival
Lag in NS
Because NS can’t look in the future = have a lag a generation behind the selective pressure
- The popultion adapts to parents conditions – the offspring might be in different conditions that they might not be well adpated for
- Offspring are adapted for their parents enovrment = have lag
- Evolution is a step behind if the conditions are changing rapidly
Example – Avgerage Gall size changes from year to year – the Gall size is optimal from the past year = have lag
- Size of galls in one generation = based on parent conditions
Variation + Selection
Selection acts on the existing varaition in a given popultion – IT DOES NOT add new genetic varaition
***Nothing about Natural selection makes varaition – NS is not adding variation BUT that doesn’t mean that novel traits are not evolving
How do novel phenotype evolove
- reshuffling of genetic varaition
- NS is in concert with two evolutionary forces (Mutation + Migration) – Get novel varaition through mutation + Migration
Example of selection acting on existing varaition –Avergae oil in kernel
Start = have 4-6% – Avg = 5%
THEN selected for increased oil content –> Pushed popultion outside of the bounds from the start BUT it moves outside of the bounds ONLY based on exiting variation (pushes outside ONLY because natural selection is reshuffling)
Have 3 genes that influence kernel Oil – all three have allele for 5% phenotype BUT some individuals might have an allele than increase the oil
- The +2% alleles = at low frequencey in the orginal popultion
- Each +2% allele contributes to varaition – likley to have 1 +2 alelle per indivual in the popultion BUT then as NS acts on the popultion you can have more indivudals with the +2% allele – the +2 alleles are bieng elected for – NOW you are increasing the amount of +2 alleles in the popultion – with the increase frequnecey there is a higher change than an indivual gets 2 +2 alells – now you have multiple + 2 alleles = now have increase in oil content
- As NS acts on the popultions –> the indivuals with +2 alelles are selection = increase frequnecey of +2 allele = increase chances of getting + 2 allele
HERE = you are reshuffling the varaition that is already there – you change the allele freqeunecey –> Leads to you pushing outside the bound of the parent population
NS + phenotypic bounds
NS takes varaition and psuhes the distrubution outside of bouns of parents varaition – outside of phenotypic bounds of distrubution because of reshuffling
***Mutation and migration explains novel phenotypes even more so
Selection + Perfection
Selection does NOT result in perfection
***Evolution is constrained – evolution can’t optimize all traits simultanously
Example – Galls – Can’t optimize protection from wasps and protection from birds at ones – because they are conflicting traits (one is bigger and one is smaller) = can’t optimize both at once = constrained
Selection + Complexity
Selection DOES NOT favor coplexity – life has increased in complexity iver time BUT NOT because selection is favoring complexity
- It is intuative that complex orgainsms exist now that didn’t in the past –> potential complexity of animal life – might see this history and assum ethat there is a reason that NS favors complexity
Fitness + complexity
Fitness can just as easily incluse loss of complexity as it gain include gain in complexity
***People think that becoming less complex = de-evolution –> It is not de-evolution – just regular evolution (fitness in these cases is just getting rid of complexity)
Lamarck + Complexity
Part of Malarcks ideas was thinking that a driving force was to increase complexity over time
Exmples of Loss of complexity
- Flightless birds – came from flighted bird (flight = more complicated = means that things decrease in complexity)
- Organosms living in caves = lose eyesight
- Many insects = live sessile life
- Parasitc organisms = lose complexity (some thing that ere are more parasitic organsims than any other = means that this loss in complexity happens a lot)
If Natural Selection doesn’y favor complexity –> How did we increase in complexity
Example – Drunkard’s walk – if a drunk person stumbles out of a bar and he doesn’t know where he is going
- he is walking from the wall –> Gutter
HERE – it is inevutable that he will end up at the wall
- Since he can’t go back past the wall = he will eventually end up in the street – because there is a limit in one directed imposed by the wall = he needs to end up on the street
SAME THING = happens with complexity over time
- In evolution we have a limit “Gould’s left wall of biocompleicty” – we have evoloved in a compltley random way (we go back and forth in both directions) BUT we can’t go past the wall
- IF the wall wasn’t there = then the space of complexity would spread to both sides (because less and more complex would happen) – since it is going in both directions in this case the average complexity would stay the same BUt the variability will change
- BUT with the wall = can’t go past a certain point in one direction = vraiabluty can increase (can go in one direction) BUT can’t go in the other = the average complexity CAN ONLY increase because there is a limit on one side that we can’t go past
***In this way a directionless process leads to big increase in complextity iver time – inevitable paty of process
Increase in complexity process
Increasing complexity arises from a passive undirected process
- NS process is NOT in the direction of complexity (it is a directionless process) YET we have an increase in complexity
- We evoloved in a completley random way – go back and forth in both directions BUT we can’t gp past the “wall”
***In this way a directionless process leads to big increase in complextity iver time – inevitable part of process
**Get overall increase in complexity BUT without Natural selection actually favoring complexity because natural selection does not favor complexity
**Still get pattern of increase in complexity in directionless process
Drunkards wall in evolution
In evolution = have a limit (similar to wall in drunkard’s example) – the wall = Gould’s “left wall of biocomplexity”
- This wall = limit to lack of complexity that we can have – it is the least complex thing that can still be alive –> we can’t go past it
Being Evolutionaryly advanced
VERY subjective – humans think that they are the most advanced BUT that is completley subjective
- Humans have not evoloved more than any other organisms –> all orgainsm today have been evoliving for the same amount of time
Example – Humans vs. Platapus
- Humans = evloved live birth + mamamary glands after they split from platapus – since this evolution is more recent = seems more adavanced BUT that is just our perspective
- Platapus – evoloved their own traits ince the split (venom + electroreception – they can feel the nerves of other fish) –> from the perspective of the platapus they are more advanced
What prevenyed Universal accpetance of NS for decade?
Some gaps in knowldge
1. The nature of novel varaition (people didn’t know where novel varaition comes from)
2. The natire of inheritance
- Many of the critisms were reasonable given the level of understanidng – critisms makes sense based on what people knew
***Issue = was acceptance of the mechanism of change – NS wasn’t beleived
Understanding the nature of varaition
Peolpe did not know this = didn’t beleive NS
- Commanality of mutation was not appreacted until genetic work with Drosphilla in 1900s STILL the natire of mutations importance for evolution was questioned for decades
Question about mutation in evolution
Is it one rare mutation or is it a build up of many small minor ones (Gradual vs.. Saltation
NOW = we know that saltation is not how it works most of the time – we know it is usally small changes over time
Saltation
Jumping – Idea that there is a mutation that just reframes whole organism and then acts quickly on it
- People thought IF this is the way it works then mutations would cerate monsters
- Question = was evolution dirven by catastrophic mutations that lead to “hopeful monsters”
Nature of inheritance understanding during darwin
Mendle was active around the time The origin of species was published BUT his work remained obscure for decades – Mendles work wasn’t published at the time and was not rediscvievred until the end of the 19th century –> people didn’t now how inhertanve worked + the ideas at the time didn’t work well with how natural selection works
IN the meantime popular ideas about inheritance didn’t work well with Darwinian selection
Idea of Inheritance during darwins time
Blending inheritance –> people thought that some asoect gets passed on and there is some blending that mix to make offspring
- People know that offspring look like parents BUT thought it was a blend of traits
***Blending = doesn’t work well for evolution by NS
- Blending = not a mode of inheritance that allows evolution to persist
Example – Start with an all blue population → THEN have a spontaneous mutation that makes a red color → Say the red is favored → if blending of traits is true the offspring would have a mix of red and blue = would get purple offspring – some might say purple and some might mix more with blue = goes back towards blue
- In this case the intial red gets dilluted over time (NOW you have a dilluted version of the mutations and never get the red again)
***In blending you never get the instial red again – the effect of the mutation doesn’t matter because it is always diluted through time
- If this was true NS wouldn’t work
What was the mechansim of evolution missing
The mechanism of evolution was missing a mode of inheritance
Issue with blending inheritance
It does not work well with evolution by natural selection – because over time you only get a dilluted version of the mutation (never get the original mutation again)
- Keep losing the phenotype – new variation goes away
- Varaition goes away
Debate about traits after mendle’s work
Discrete vs. Continous traits – if we have discrete genes how can we see continous traits (Such as height + cold tolerance)
Question: How do we reconcile the discrete in Mednle’s work with continous traits
Debate of Discrete vs. continous triats
Had two camps:
1. The Mendials
2. The Biomatricians – measured things and found that very few things lined up with mednles work (they found that there were very few discerete traits + couldn’t see significant Mednelian genetcics)
Question: How do we reconcile the discrete in Mednle’s work with continous traits
Continous trait
Can be any value – not discrete trait
Ex. Cold tolerance + height
Issue in Mednle’s experiments
HE got lucky – the traits that he happened to work with just happened to be discrete traits (they were all or none traits)
- He only looked at discrete traits
- Part of the reason it took people a while to know how heretibility worked is that continous traits often include many genes –> when people found Mendel’s work and looked at some organisms there were some traits that worked BUT there were some that were more complex in nature such as continous traits – so they did not know how heretibility if its not as simple as Mendle’s
***It took deciades of people arguing to understand to connect complex phenotypic varaition and heredity
OVERALL – people had issues with Mendle’s work because his work failed to epxlain the heredity in continous traits
Quanatative genetic
The study of Heretability of complex traits
Modern Synthesis
The reconcilliation between the Mendelian and Biometric ways of thinking with Darwinian Evolution
IF people know Natural selection based on phenotypes VS. people know how heretibility works – THEY needed a way to bridge the two
Modern Synthesis = shifted towards genetic understanding of evolution and biologic varaition
***led to paradigm shift
Point of Modern Synthesis
Shift towards a genetic understandng of evolution and biologic variation
- Modern Synthesis = need to think of evolution as genetics and allele frequency
***reframed evolution explictiley around popultion
***The new persective allowed us to refarme the postulates of Natural selection
Importance of recolciloing mendelains and biometricians
There was this impediment to understanding eveolution because of the debate – reconciling the camps allwoed us to have an undertsanding that modern biology uses today
***Reconciliation = occured because of modern synthesis
What did modern synthesis look at
studies natural selection as mechanism and other mechanisms of evolution – understanding change over time
Understanding of genetics during modern synthesis
During the time there was a framework of understanding basic genetics – now scaling up the basic genetics of the family level – allowed us to understand the mechansim of change
MS in my own works
Basically there was this debate where they had continous traits and Mendle’s finsings couldn’t epxlain the heretibability behind them – this was an impediment in understanding natural selection as the mechansim for evolution
***This debate was reconciled by the modern synthesis
AFTER the reconcilation they wwere able to turn the phenotypic undertsanding of evolutrion and synthesisze that with waht we know about how heretibility works
The synthesis then reframed evolution to be on popultoon level + scaled up our undertanding of geentics to popultoion lavele –> ON the popultion level we can now understyand mechnaism of change and using that new understanding we reframed the postulates of natural seleection.
- NOW have genetiocs worked into Evolution by NS
***Modern synthesis = explains evolution as a fundementally genetic process
Outcome of Modern Synthesis
Restated the four postulatesin explicitly gebetic terms
MODERN synthesis = explains evoluton as a fundementally genetic process
***The postulates are the same conceptutally but are tweaked to be about genetic varaitions
Postulate #1 After Modern Synthesis
Varaition among individuals results from mutations creating new alleles arsing and segregating in populations
- Varaition had to do with varaition in alleles
BEFORE – was about phenotyouc variation – now making it about genetic varaition
Postulate #2 After Modern Synthesis
The inheritance is the result of allelic variation passing from parents to offspring
- Traits are heretible
BEFORE – phenotypic varaition – NOW allele varaition – connects parents phenotypc to offspring phenotypes
***Connects offspring phenotypes to parents phenotypes
Postulate #3 After Modern Synthesis
Through differential survival or reproductive sucess not all individuals contibute the same amount to the following generation
- Really just the same thing (nothing is different)
Postulate #4 After Modern Synthesis
The probability of contributing to the next generation varies as a function of an individuals genotypes
- Alleles at a locus affect if you survive and reproduce
- Shows genetic version of Natural selection
BEFORE – stating the relationship between phenotype and S/R BUT now S/R are difefrent based on genotype
Charts before and after Modern synthesis
Before = looking at charts that compared phenotype to the probability of survival AFTER looknig at charges that look at genotype and probability of survival
BECAUSE phenotype is based on genotype = can compare the proabbility of suvival between genotypes (because the diffreent genotypes is what leads to the phenotypes that allow some to survive more)
Quanative genetics
Understanding the connection between selection and variarion on alleles to phenotypic distribution
- Looking at how envirnment affects variation + how Heredity occurs + How the genotypic distrubution responds to Natural selection
***Understanding the connection between discrete inheritance and continous traits
Why is it important to talk about genetics in evolution
Because evolution is the change in allele frequncies in popultion through time = need to establish the rules by which alleles are passed between generations
We are building a null model –> rule of inheritance between phenotype are used to make null models in popultion genetics
Making null models in popultion genetics
Make null models using the rules of inheritance between phenotypes
Gene
The discrete functinonal unit of heredity – refers to any variable geentic locus
- Parent –> Offspirng – is NOT diluted
***What sticks around in generation of offspring
Gene in other context vs. gene in this class
In other contexts – gene often refers to a segment of DNA that contains a transcribed region andnits regulatry regions
This class – think of gene as more than just protein coding region
- We think of it more broadly because there are parts of the genome that affects phenotypes = affects heredity + we are still intersted in variation that doesn’t lead to phenotypes
- In evolutioon – we are intersted in heretible varaition more broadly that jist protein regions
Locus
Specific location in the genome
Genome
Total herediatry information in an organism
Genotype
The specific allelic composition of an individual at one or more loci
Variant at a locus – doesn’t need to be a protein coding gene
Gene duplication evens
Have one locus that duplicates and inserts somewhere else in the genome
Example – Say we have a gene duplication event mutation where a locus sequnce gets copied to another location (identical sequnces) – Is this two genes or 1 gene?
ANSWER: 2 genes – because it is 2 loci (gene = any variable genetic locus)
- It can be the exact same protein but since it is two loci = it is two genes
***Because they are two loci = they are inherited seperatley (can be passed down irrespective of each other) = 2 genes
Alleles
Variant forms of a genetic locus
Example – can have. aC instead of a T OR can have an Indel OR can be varaint bases near each other than are inherited together
***Different alles could affect phenotype BUT can have two alles that still make teh same phenotype (diffreent sequnce but still leads to same phenotype)
IMAGE – thigs on the side = shows the phenotype for each locus
Polymorphism
When there are multiple variants
Gamete
Specialized haploid cells resulting from meiosis (in sexually reproducing taxa)
Meiosis (overall)
Diploid –> Haploid (makes sperm/egg)
Calculating how many possible gametes can be produced
2^n – n = number of pairs of heterozygous chromosomes OR number of heteozygous loci
***Based on the genotypes across homologous chromsomes = can look at all of the possible gametes produces
Example – 2 alleles at 2 loci = 2^2 = 4 gametes
Why are Mednle’es “Laws” and not Laws
Because his “laws” are NOT absolutley strict – they are good most of the time but they are not asbolute
Mendle’s “Laws”
- Law of Segregation
- Law of independent assortment
Law of segregation
Homologous chromsomes seperate during meiorsis so that ONLY one copy of each gene (one allele per locus) occurs in each gamete
- If the parents are diploid )have 2 copies of each locus) –> only one copy ends up in gametes
- Each gamete carries one copy into the gamete pool to form zygotes
***This is the closest one to a law – because it works most of the time
When does Law of Segregation Breakdown
- Non-disjuction events + Mitotic errors
- Can get 2 copies OR no copies
Example – trisomy 21
- Chromosomal fissions –> large scale chromosomal events
Law of independent assortment
Allelic varaition at different loci are passed to offspring independently
- The probability of getting one allele at one loci is independent from the probability of getting a different allele at a another loci (alleles at different loci are inherited independently of each other)
- Alleles of difefrent genes are inherited independently of each other
***ALL multi loci gametes possibilities are equally likley
- The probabilities of alleles at different loci being inherited are indepent of each other
***leads to a mix of mom and dad alleles in gametes (because might get mom at one loci but dad at a different loci)
When is the law of independent assortment true?
True when the loci are on different chromosomes + If the loci are far apart on the same chromosome
Recombination
Swapping of alleles between homologous chromosomes – Likley to happen a few times on each chromosome during meiosis
END – a new version (with a mix of maternal and paternal alleles) ends in gamete
How to know if two loci are indepent
They are independent if the likleyhood of a gamete with both loci is 25%
BECAUSE if they are indepent then can multiply probability
P(one allle at loci 1) = 0.5 (If have 1 M and 1 P = Probability of Either M or P is 1/2)
P(one allle at loci 2) = 0.5 (If have 1 M and 1 P = Probability of Either M or P is 1/2)
P(one allle at loci 1) X P(one allle at loci 2) = 0.25
***If they are independent then the chance of getting both is 0.25
IF the frequency is NOT 0.25 then ther are NOT indepent (iof the freqincey is 1 or 0 then they are completley dependent)
Linkage
Deviation from expectation that two alleles are indepent of each other
***If the chance of getting 2 alleles is not 0.25 then they are NOT indepent = they are linked in some way
When does Independent assortment occur
- During metaphase
- During recombination
Recombination + Indepentdent assortment
IF you have recombination then you are equally likley to get ALL combinations of alleles (MEANS that alleles at different loci are indepent of each other) BUT if recomnbination is not equally likley then you change the probability of getting combinations of alleles = Lose independent assortmement
Deviations from Independent Assortment
- Linkage
Deviations from Independent Assortment
- Linkage
Linkage
Unlikley for cross over to happen when close together = NOW has some alleles occuring together more than others
- Have a non-random distribution of multi-loci genomes (Not 0.25 for all)
Example More AB than ab or Ab = Means that A and B are no longer inherited indepentley of each other
***Often due to a physical linkage – close proximity of the same chromsomes BUT not always
Recombination
Event in meiosis that generations haploid multi-locus genotypes that differ from the parents
- get genotype that neither oarent has
What is included in Independent Assortmant
- Recombination (within chromsomes)
- Lining up of chromsomes on metaphase plate (Assortment of chromosomes)
- Always have this
Importance of recombination
Important part of independent assortment – anything that limits recombinations = causes devaitions from mendle’s laws
Do you always have Independent assortment between different chrosmomes
YES
Do you always have independent assortment within chromosmes
NO – might have linakge = no recombination = no IA (THIS IS A TIME WHERE MEDNLES LAW BRAKS DOWN)
Linkage
Any breakdown of independent assortment
MEANS that allels at different loci are inherted together more than exopected by chance – alleles at different loci are not being inherited independently of each other
EXAMPLE – if AB is more likley than ab (means that A and B are no longer inherited independently of each other)
Modifier models
We can change models to account for linkage
Modifier models
We can change models to account for linkage
Probability and Law if independent assortment
Because the probability of inheriting alleles at different loci are indepent = can multiply the probability of getting the allels
Ex. P(red allele at locus 2 on chromosome 1) = 0.5
P(organe allele on chrosmome 2) = 0.5
Probability of getting Red AND organe = 0.25
***Because they are inherited independently of each other = can multiply them together
What will proabbility be is IA is true?
The proabbility of all possible gametes will be in equal propertions
Punnent Squares (Overall)
Visual representations of the probabilityes of getting a specific gamete – visual representation of probability of genetic varaition from 2 individuals
- Shows Mendle’s Laws
***Stems from mendles first two laws
What do punnet squares show
- Show Mendle’s Laws
- Show varaition in gametes – shows the types of offspring and the frequencey at which they occur
Punnet Square for single locus
***Can look at the frequency at which genotypes occur
Punnet Square for Two loci
Can see that there are 4 haploid gametes per individuals THEN look at how each indiviudlas gametes combine to pass to zygotes
***Can see genotype and phenotype frequncey
TWO LOCI genotype ration – 9:3:3:1
Genotype Frequcney in Dihybrid cross
We are able to determine the frequncey of genotypes in the next generation from the gamete pool of the mating pair
- Can see the probability of producing 2 phenotypes
What is the result of Punnet square
You can see the frequencey of genotypes in the next generation form the gamete pool of the mating pair
- Can se the gamete pool in the cross (result of the cross is the gamete pool)
- can see the probability of producing certain phenotypes
Gamete pool
The set of all copies of all gamete genotypes in a populations that could potentially contribute to subsequent generations
***Is the inside of the punnet square
What is the punnet square
A representation of the probabilities of zygote formation across gamete pool
Calculating probability of zygote with particular genotypes – what is the probability of forming a zygote with aabb
Option 1 – Look at square –> Can see 1/16
Option 2 – There is only ONE way that aabb forms (if sperm has ab and egg has ab)
P(ab sperm) = 0.25
- becasue have 4 possible sperm and all of them are equally likley
P(ab egg) = 0.25
- because have 4 possible egg and all of them are equally likley
P(aabb) + 0.25 X 0.25 = 0.0625 = 1/16
***Since P(ab sperm) is independent from P(ab egg) = the probability of both of them happening is the product of their independent probabilities
Example – what is the probability of Aabb Zygote
Since producing Aabb with ab Sperm and Ab egg is Mutauklay exlusive from produving Aabb with Ab sperm and ab egg = can add their probabilities together (CAN ADD for ME)
- We wait the probaility that either one OR the other will happen → MEANS that teh combinaed exclusive events are additive
AND vs. OR in probabilities
AND = X
OR = +
Independent statement (AND statement) = multiply
Exclusive statement (OR statements) = add
Expanding mindset of mednialn genetics
We can take the mindet of probabilitu events in gamete pool and use it to build a model of mendelian genetics at the population level
Complication to mendelian genetics
- Dominance
- Epistasis
Dominance
The phenotypic affects of one allele masks the phenotyopic affect of another allele at the same locus
- Interferance between 2 alleles at the same locus
- Effect from interaction of many alleles at once locus
- One allele interacts with the other allele that affects phenotype
***It is a type of interaction between allelic varaition at a locus (one allele is masking another) BUT really are habing an interaction between two alleles
Issue with dominance (why it is a complication)
Is a complication – because it blocks the contribution of one of the parents = interferes with heritability across generation (complicatioes the observation of the correlation between parent phenotyope and offspring phenotype)
***Breaks down the straightfoward relationship between the phenotype of the p[arent and the phenotye of the offspring
Misconception with inheritance
We need to stop thinkning that inheritance is compltley dominent or completely recessive – there can be different degrees of dominence and recessive
- Not everything is just domient and one is recessive
- Many alleles have intermeduate levels of affects
- Dominence itsself can take different forms
Example of dominance – eye color
1 Copy of A = stops all phenotypic affects of a
***We know A is dominent to a because the heterozygous Aa look like the homozygous AA
How does dominence happen?
Depends on the molecular affects of the alleles
Tow ways that dominance is generated:
1. Haploinsuffciencey – dosage affect
- 1 copy of something is not enough to do snoething – need expression of both copies to gave a phenotype
- If only have one copy of allele expressed then not passing the threshold to see the phenotype
Example – might need enough of an enzyme to get over the activation energy
- Dominance negitive affect – protein interactions (based on what proteins can interact to form dimers or multimers)
How should we thoink about traits
Traits should be thought about as being determined by the whole genotype rather than just the presence of one allele
Looking at genotypes + fitness
You can think of the affects of genotypes with fitness as the phenotype
- can see the relationship of fitness and alleles (can think of fitness as just another phenotype)
Example – is the fitness of the heterozygote like the fitness of the AA or aa
- Can also be incompltelet dominent where Aa is in the middle of aa and AA (this is what is happening most of the time
Can teh recessive allee increase fitness
YES – fitness affects of a mutation can be purley recesisve
(fitness of aa can be higher than Aa and AA)
In the chart – AA is still dominant because Aa is like AA and not aa
Aa as incompletley dominant
Here have incomplete dominenace – likely in between
***Assume that this is happening most of the time
Fuel for evolutionary forces
Variation
How do we get information about dominance vs. recessive
Natural History
Dominanece vs. Epistasis
Dominance = interaction within one locus
Epistasis = interaction between different loci
Epistasis
An effect of the interaction among multiple loci on a phenotype (or fitness) such that the joint affects differ from the sum of the loci completley
- Means that you can't just add up all of the alleles and know the phenotype - Interaction among alleles at different loci - More than one gene affecting a trait
***Can’t predict the effects of the genotype at one locus without knowing the genotype at another locus (If the answer for the phenotype is IT DEPENDS = know its epistasis)
***Common in nature
Epistasis + Evolution
Epistasis is a constraint on evolution
Complication of Epistasis on inheritance
Affects the straightfoward parent phenotype to offspring phenotype relationship
Type of interaction in Epistasis
Statistical interaction
Statistical interaction example – Plant experiment
IF looking at plant growth – you are tesing the effect of temerature and of fertailizer Nitrogen level (Looking at low vs. high temp AND looking at Low N vs. High N)
If the results = graph with two parrael lines = there is no interaction and there is an additive effect
If the results = graoh with intersectiong lines then there is an interaction and there is NO additive effect
No Interaction Result
Have two parallel lines (the slope of the lines are the same) = no interactions + have an additive affect
- Means that the affect of one things (N fertlizer) is independnt of the increase of the other things (The affect of the N is indepent of the increase in temperature)
In Example:
No matter the temperture this is alwats an increase in height when there is an increase in temperature
- No matter what temperture the N will always increase the height and no matter what N level the temperature will increase the height
ALSO the temperature increases the height no matter the NItrogen level
MEANS – that there is an additive affect and they ARE indepent
- The effect of temperture does not affect the affect of Nitrogen
- As the temperture incerases plant height increases AND as N increases plant height increases BUT at either tempertures the plant height will incerases because of teh increases in N and at either N the plant height will increase because of temperture (Means that the affect of N is not dependnet on the N level = means they are indepentdent)
When is no interaction not additive
If they have the same slope but they are flat
Result when you have an interaction
NO parralele (the slopes are different) = not additive
Result when you have an interaction
NO parralele – they intersect (the slopes are different) = not additive
- Since the slops are different there is an interaction
Example –
you can’t predict the efefct of one. ofthe variuables without knwoing the state. ofteh other (The effect of teh temperature depends on the state of teh N – The temperature oncerase plant height but ONLY in high N condition)
- At high N the higher temperture decreases height
But at low N the higher temperature increases height
HERE = need to specify teh state of nitrogen – if you asked how does tempertaure affect plant growth - you would need to say IT DEPENDS – because the way that temperaure affects plant groiwth depends on teh state of N
Since you say IT DEPENDS = you know you have an interaction (because the state. ofone affects teh other)
- Effect of Temperature depends on teh state of N
How do you know you have an interaction
On a graph – if the slopes are different = the lines interact
On a question – If the answer contains “It depends”
Statistical interactions
When you can’t predict one varaible without knowing the state of another
Example – can’t know the effect of temperature without knowing the state of N
Example of No epistasis
Scenrio: Have 3 Loci controlling plant height with 2 alleles for each loci
HERE = if the alles have indepent affect (have no interaction) then you would know the genotype by adding up the effect of each genotype for each allele to get the plant height
Example – A1A1B1B1C1C1 → +1 + +1 + +4 + +4 + +6 + +6 = 22
IF have NO epistasis = they are all indepent –> Then they have an additive affect (each alelle contributes seperatley to the overall height of the plant based on the genotype)
Can know the height of the plant by just adding all fo the effects of each genotype
How to know if there is no epistasis
Know there is no epistasis if there is no interaction – know if all of the alleles for the locus are additive to give the phenotype
Example – if the plant height is just the sum of the allels for each locus
- We can on there is no interaction of we can predict plant height by just counting the number of the allele for each genotype and adding the individual effect
No epistasis
There is an additive eefct + there is no interactions – the controbution of each allele is indepent of teh other genotypes
- Indepent contribution of effects of alelle
AABBCC – AA is indepentdent from BB and CC
- A will add an amount no matter the genotype of B (A1 will add + 1 NO matter what the genotype is at B – will add +1 if have B1 or have B2)
Changing genotype when have no epistasis
If you have a plant. andknow the genotype and then chnage the chantype we will know the different in height between the two genotypes IF there is no epistasis
Example
- We know that the height different between the 2 is 5 inches because we know that the effects of each genotype is additive and. sowe know the height of teh first will be. 22and the second will be 27
***SINCE THERE IS THIS ADDITIVE AFFECT AMONG LOCI = WE KNOW THAT THERE IS NO EPISTASIS
Example WITH epistasis
In plant example – if we added a new locus D that is part of the hormone pathways
- Locus D does not add height it just affects the hormone production
- IF hace D = have no height in plant
NOW – when you change D to D- you have no stem at all and have no height (have no elongation – stop ability for the plant to grow upwards –> means that since that since the plant is not growing upwards at all so the efefcts. ofthe other allleles. donot matter (no matter what the other alleles are there will be no height – whther is A1 or A2 it would be the same height because there woudl be no height)
MEANS – the other Loci now depend on the state of D (Now if you asked a question of how the height would change if we swicth B1 to B2 you could have to say IT DEPENDS – because now it depends on the state of D)
- Since IT DEPEDSN = means that ther us an interaction = means that there is epistasis
Question to know if there is epistasis
Question = can you predct the affect. ofan allele based ONLY on that allele itself
IF the effect of the allele depends on the state of another of another allele = then you have episatsis
- If “it depends” = means that there is an interactuon = you have epistasius
Plant heigh exmaple of epistasis
ONce add in D = we can’t prediect the effect of the other alleles without knwoing the stats of D
- If D+ then they will hadd height BUT if D- then they will not change teh height because there will be no height (Since it depends = have epsistasis)
INteraction = epistasis
Sources of variation in a population
- Genetic
- Environmental
Phenotype
The measurable properties of an organism manifested throughout its life
- Any trait that you can measure
Includes: Morphologocal + Phsyicological + biochemical + behavioral
What is contained in a phenotype
The phenotype contains everything but usually we just kook at a subset of that
- Includes the TOTAl set of these properties or traits but we’re usually just conceced with a given subset of traits for a gievn question
What determines phenotypic varaition – ways that phenotypic variation can come about
- Genetic variation
- Environmental variation
- Gene X Envirnment interaction
Genetic variation
Because we know someone’s genotype we can predict the phenotype
MEANS that phenotypic differences among individuals are epxlained by allelic differences (explained by genotypic differents)
- Phenotypic differences are a direct result of genotypic differences
- Straight fowards DNA –> Gene product = genetic variation
Example – varaition in human taste sensitivity
Example of genetic varaition
Human tests sensitivity
Have PAV and AVI allele – the ability to detect compund = varies strongly with genotyoes
- The distribution of detecting the compound depends on the genotype
Looking for which allele is homozygous
IMAGE
Answer: PAV because the heterozgous is more like the PAV that PTC homozygous
- Means that PAV is the driving phenotype
Variation within each genotype (when looking at a trait that is genetic varaition)
Might still have more varaition within each genotype (same genetype and still different phenotypes – there is varaition that can’t be explained by genotype because they all have the same genotype)
Reason = might be that other genes affect the traut OR maybe have envirnmental variation too
Genetic varaition inheritance
Genetic varaition = straightfoward inheritance between parents and offspring
- If you know the offsrping’s genotype then we can make a strong prediction about phenotypes
Phenotype
Direct molecular product of the genome
- Straight fowards DNA –> Gene product
Other examples of Genetic variation
- Eye color – likley predictable genotype
- Blood type –> only affected by genotype
(very little possible effect of envirnment)- Purley genetic phenotypic varaitions (phenotype is the same regardless of envirnment)
Common form of molecular phenotypes
Purpley genetoc phenotypic varaition (the phenotype is the same regardless of envirnment = often teh form of molecular phenotype)
Environmental variation
Phenotypic differences among individuals are explained by difefrences in conditions
- Some envirnmnetal variable explains the differences in phenotypes
- Phenotypic differences exist due to differences in the conditions experinced by organisms
- Here – organisms can have the same genes BUT different phenotypes
Phenotype = dtermined by external condition (by extrinsic factor)
Ex. determined by diet or drug in an experiment
How to know if it is envirnmental varaition
Hard to know:
- IF all the same genotype (like they atre clonal organsisms) but they are in different envirnemnst and have different phenotypes THEN it is likley an emvirnmental effect
IF they have the same genes BUT different phenotypes = based on envirnmnet
Example of environmental variation
Daphnia – organism that reproduces by cloning (same genotype)
IF they are exposed to different environments THEN they look different
- Of they are reared around predators = they have a point and hard outside
- HERE – have different phenotyopes based on predator cues (based on envirnmental cues)
***They have the same gnotype BUT have different phenotyoes based on the envirnment
Envirnmental varaition in humans
We have envirnmnetal varaitions in humans
Example – very muscular person –> based on diet + excersize
Phenotypuc plasticity
Changes in the phenotype exhibited by the same genotype due to envirnmental differences
- Phenotype can be shaped by the envirnmnet BUT the genotype stays the same
- Envirnmental variation effects phenotype
- Envirnmental determines the phenotype
What leads to phenotypic plascity
Envirnmental varaition
Polyphenosim
Discerete phenotypic varaition arising from the same genotype in different envirnments (SAME GENOTYPE)
- Type of phenotypic plasticity
- Get catagorical varaition (one phenotype or the other) because of of different envirnments
Example – Daphnia (get either with body armore OR without – two discrete values)
Polyphenisms vs. Non-polyphenism example
BOTH types of Phenotypoic PLasticity BUT only one is Polyphenism
Example #1 – Ants – Workers can be a range of body sizes based on theior diets as larva (continous gradient)
- Same genotype BUT different sizes depedning on how fed as larvae
Example #2 – Workers vs. soldier ants
- Depends on larval nutrition - ONLY have 2 forms = polyphenism
Examples of Polyphenism
1 – Space toads
- Have 2 forms –> individuals will go one way or the other
- Have chnage in body size + change in trophic ecology (eating ecology)
2 – Tiger Salamnder
- Have two forms – some will go on land and some with stay in the pond
***Depends on the population density of the salamders in the pond (if there are many then they will leave the pond BUT if there are few then they will stay in the pond)
Gene X Envirnment interactions
Means that the phenotypic differences that are caused by alleleic differences depends on. aparticular condition and vica versa (the differences cause my envirnment depends on a particular genotype)
- Effect of the allele depends on the envirnment or effct of envirnment depends on allele
- Phenotypic differences are driven by differnt intercations between alelleic varaitions and envirnmnetal conditions
- Genes have different effects in different envirnmnets
MEANS we don’t know the contribution of an allele to the phenotype without knowing the envirnment
Means of interactions in GXE interaction
One thing depends on the other – effect of the genotype depends on envirnmnet and effect of envirnment depends on genotype
IS A statistical interaction – can’t predict the effect of the allele without knowing the envirnment
Reaction norm
The mathematical relationship between environmental variable and the values at the phenotypic plastic trait (relationship between envirnment and phenotype)
In example – there is a linear relationship ebtween chemical and physiological response to pollutants (As the chemical concentarion increases the enzyme production increases)
Example of phenotypic plastic trait
Phenotypically plastic ability to detoxify pollutants in environment
- Ability to produce detoxifying enzymes = costly (costs to up regulate those systems) = cost
- can be beneficual for the trait to be phenotypically plastic (if there is less pollutant then you dont upregaulte and if there is an increase in pollutant then you upregulate and shift to put more resources in)
In chart – as chemical concentration increases the enzyme production increases = phenotypic plasticty
GXE interaction example
IMAGE – the two genotypes have different reaction norms = know that it is GXE because the effect of the envirnment depends on the genotyoe that you have
- The two lines intersect = means that they are not paraellel = means that the relatsionship between the envirnment and the phenotype depends on the genotype
In example – the slopes of the lines are different = they intersect –> we know that the relationship between phenotype and envirnment for one genotype is diferent form the other = know that the relstionship between the phenotype and envirnment depends on the genotype
- The envirnment afefcts each genotype differentlye = the affect of the envirnment depends on the genotype (DEPENDS = GXE)
***GXE because the two genotypes have different reaction norms
How to know if there is a GXE interaction
In GXE = have different genotypes have different reaction norms
- The different reaction norms = evidence for GXE
How to know if there is a GXE interaction
In GXE = have different genotypes have different reaction norms
- The different reaction norms = evidence for GXE
Real world example of GXE
Seratonin Transporter gene:
- Based on variation in the transporter gene
SEEMS like the genotype affects depressive episodes BUT they found that the importance of the gene varies based on external conditions
- ALL of the genotypes have different reaction norms = the effect of the envirnment depends on the genotype = GXE (the affect of the allele depends on the envirnment that you are in – LIKE the affect of SS depends on the envirnment that you are in – all SS have different traits dependning on environment)
- ll = has very little effect on increasing probability BUT once have an S allele = increases the chance of a depressive episodes
- Increased chance depends on the genotype BUT the effect of that genotype depends on the envirnment
BOTH the genotype and the envirnment matters
OVERALL: genotypes have different reaction norms (all have different slopes) = GXE – because the effect of the gebnotype depends on the emnvirnment and each genotype is affected by the envirnment differentley
Reaction norms + NS
Reaction norms = often the target of NS
- NS = acts on the reaction norm itself –> Act on the same enivrnments interaction with the phenotype
- Somtimes this can give the apperance of Lamarkian Phenomanon – because the change in evnirnment causes change in phenotype that is then pased down = seems genetic
How do phenotyoically plastic traits evolove
By acting on the reaction norm
Example of NS acting on reaction Norm
Mandica – Black worms can turn green after a heat shock treatment
- There are differences in the degrees of response of the catipillars = inidcate different reaction norms (because they each have have different leevls in plasticity – they turn different colors)
- The amount that temperature affects phenotype varies
- Have different phenotypic effects (some stay black + some go a little green and some go very green) –> IN ALL of the same temperatures they all they all respond differentley – they all trun different colors)
THEY ALL have different reaction norms because they all have different responses to the envirnment
Researchers made:
1. A high plastcity line
2. A control line
3. A low plasticty line (Stay black)
Results: The low plasticity line lost ability to turn green and the high plasticity line increased in plasticity
HOW – selection is acting on the reaction norm itself
- Low plsticity line = ends with lower RN
- High plasticity = ends with a higher reaction norm (means that it takes less temperature change in color)
***By selecting for envirnment determined traits = evolove because the reaction norm is chnaging
OVERALL – a selection experimnet on this GXE varaition not only chnages the phenotype but it does so by altering the reaction norm
Reaction norm + plasticty
Low plasticty = lower reaction norm
High plasticity = Stronger reaction norm
Normal reaction norms
Reaction norms are not usually linear
What in reaction norm differs
Slope + shape + position of the reaction norm can differ by genotype
***The shape and the position can be under selection – that selection can change the reaction norm (can change the shape and the slope)
Selection + reaction norm
The shape and the position can be under selection – that selection can change the shape and the slope
Selection = can change the shape – can go from being contibous to having only two options (from more gently sloping line to being either the value at the top or the bottom)
Continous to polyphenism
Selection - can change the shape – can going from continous to only two options (from gently sloping tp being either value)
***Goes from continuous phenotypic plasticity to polyphenism – change the phenotypic outcome (because still phenotypic plasticity because change in phenotype based on environment but genotype isn;t change BUT only now have two phenotyoez
Making a plastic trait fixed in a population
Selection on reaction norms can also take a plastic trait and make it fixed in a popultion (no longer repsonive to envirnment)
To make a genetically engrained chnage BY changing the sensity needed to be plastic
Ex. making calacous without needed any friction – At the start you need friction (need environmental change) to get them BUT can shift the amount of friction that is needed to be practically no friction needed = make an environmental variable into a fixed trait
Genetic Assimiliation
The evolution of a fixed trait from phenotypic plastic varaition
***Was an envirnmental trait and is now hardwired
What is needed to mkae it a fixed trait
To make it genetically engrained = changed by chnaging the sensity needed to be plastic
How does Genetic Assimilation occurs
Occurs if you lower the limit of envirnmental condition needed
- If you make it so that you have the trait at. avery low limit of envirnmental condition then you will have the trait in all envirnmnets – in the end you have a varaible trait going to a genetically fixed trait
SINCE – lowered the limit and selection acted on the reaction norm – by pushing the infelction point of the reaction norm below the threshold – the trait will now appear under any set of realistic conditions
Example of changing reaction norms
Salamander – reaction norm evoloved from something that was senistive to the envirnmnet to no longer behaving in a phanotypically plastic way
- IF you are in a big body of water then the salamnders don’t have to run away (because there is plemnty of space for them all to be in the water = can shift the reaction norm to make it less sensitive to chnage in phenotype)
NOW in all envirnments they stay in the wayer – a shirft in reaction nowm = no longer sensitive to change in envirnment
NOW they have the capacity to become terrestrial BUT they don’t because there was a chnage in reaction norm
***Increased envirnmental standards – it needs to be very dense for them to change = they are less sensiitive to change in envinrmnet = they won’t leave the water
Range of mutations
Goes from small scale to large scale
Small Scale mutations
Mutations that make a new allele at a locus in that gene
Large Scale mutations
New variations that generate new loci
- Large scale or change in genome structure
Example Small scale mutations
- Point mutations
- SNPS
- Indels
SNPS
Change in one nucleotide to another
Like a C → T – now have an A-T BP instead of a C-G BP
- Could change a codon = can change AA - Sequence length stays the same
Worse case = 1 AA change
Worse case SNP vs. Worse case Indel
Worse Case SNP = change in 1 AA
Worse canse Indel = screw up really bad
Indels
Small inseration and deletions of base pairs
- Hard to know if mutation is an inseration or deletion - Some number of nucleotides are added or subtracted - Chnage in length of sequnce
When do Indels usually occurs
Usually occurs because you have a slip in the template – teh polymerases skip over = loss or gain BP
Indels in the coding region
Shifts the reading frame –> Affects all. ofthe code downstream
- If in the coding region = all of the downstream is affected unless it is a 3 BP indel
***Causes severe change to protein
Indels in Introns
Can affect splicing
***Indels almost anywhere can have an affect
Mutations that we are concerned about
Most mutations that we are concerned with are mutations that are. inthe germ line (not somatic)
BECAUSE – somatic mutations are not inherited
Germ line mutations vs. Somatic mutations
Somatic mutations ate not passed down but germiline are
DNA damage = drives germline and somatic but usually need error in the DNA repair mechanisms to have a germline mutations
- Damage in repair mechanisms = passed on
Which type of mutations is more important for evolution? Point mutations in Exons (coding genes) Or Introns Or regulatory regions (promoters or suppressors – including cis and trans)
Debate = was debated for a while
Many say exons + some say regulatory regions (because then you might not make the protein)
ANSWER: ALL OF THEM ARE IMPOORTANT FOR EVOLUTION
Important alterations on small scale mutations can have an important effect
Mutation is regulatory region
Might not make a protein at all
Larger mutations
Might affect whole arm of a chromosomes OR might affect long noncoding RNA that is important in regulation
Importance of long non-coding RNA
Important in regulation
Small scale mutations make
Small scale muttaions make new alles within a locus
Large scale mutations make
Large scale mutations generate new genes (New loci)
Gene duplications are due to
- Unequal crossover (Meiotic error)
- retroposition
Retroposition
mRNA processed by viral or retransponson machinery and integrated back into the genome
***More common that we think
- Often occurs after the RNA has been spliced then it is reverse transcribed into the genome
- Transcribed RNA gets picked up and gets reverse transcribed to DNA and integrated into the genome
Retroposition process
Transcribed RNA gets picked up and gets reverse transcribed to DNA and integrated into the genome
***Can be inserted into the genome through DNA repair mechanisms
Example of Unequal Cross over
Charlie- ____ Shark tooth disease –> Disease satte - due to liklihood of unequal crossover
- Because the CMT1A repeats on the sides can cause. tehchromsomes to not align correcvtley – crossover occurs so that you have 2 copies of a locus in one cell and no copies of the locus in the other celll
Issue in Unequal Crossover
Crosover occurs so that you have 2 copies of a locus in one cell and no copies of that locus in teh other cell
NOW – get a longer and a shorter part
- Have too much ofa locus in 1 cell + Lose a copy of teh locus in the otehr cell
***Can cause phenotype – if the longer chromsome stays THEN new offspring might have extra copies of loci = the new loci can have new functions
IMAGE – start with all haveing 2 copies of exon 1 and 2 –> in the end one chromome that have 3 copies and 1 chdomsome with 1 copy
Affect of Unequal Crossover
Can cause phenotype – if the longer chromsome stays THEN new offspring might have extra copies of loci = the new loci can have new functions
Result of gene duplication events
Get novel Loci – Start with one loci and end with 2 loci (the 2 loci can have identical sequences)
- get new region of the genome
THESE 2 loci = now 2 genes because they are inherited independently of each other
Where can Retrponson be inserted
Can be inserted into a copy fo. afunctioning gene
NOW – have 2 levels of affect
1. Get new gene
2. Break up another gene
How do you identify Retroposition
Indeitified by one copy having exons and introns and the oyer copy somewhere else without the introns –> tells us it was inegrates again after splicing
SHOWS us that retroposition occured
Retroposition + Expression
Might have a fully functional copy but it isn’t assocated with regulatory region of the gene that it came from – mighyt not be expressed at all of might be expressed differentley
Trend in retroposition
New gene typically does not have introns – inserted after mRNA is spliced
Where can gene jump to in retroposition
Can jump to new chromsome
Chromosomal rearrangements
- Inversions
- Fissions/fussions
***Occur often
Inversions
Change in the order of genes due to double stranded breaks and misaligned repairs – chang in the order of genes on chromsome
Why does inversion occur
Due to mistake in DNA repair – if you have 2 breaks and the chromsome is twisted –> when the break is repaired = it can be attched back in a new way
Importance of inversions
- They were some of the first “genes” studied in natural populations – Could study them because they are visible in the karytotype
- They were studied before they could sequence DNA and just look in the micropscope –> teh inversions stood out – the two chromsoomes were no longer aligned = can be identofied in microscope
- One of the first markers in molecular biology (looking at frequncey that this occurs)
- They are important for reconbination
Inversion + Recombination
Inversions = important for recombination – chromsomes no longer can have recombinations
- Protects the region from recombinations – Makes genes linked –> if the genes are linked then Natural selection acts on them more. =acts on inversions more
Natural selection + inversion
natural selection = acts on linked inversions – natural selection. =acts faster than individual genes inherited independeltley
NS = acts faster on linked genes than genes than genes that are inherited independetley. =NS acts on the inversion event because the genes are linked
***Inversions might play a strong role in evolutionary processes by keeping sets of genes together
NS + linked genes
NS = acts faster on linked genes than genes than genes that are inherited independetley
***Seen in rapid evolution + Speciation
Natural selection acting on Inversion
Having difefrent chromsomes based on the latitude – Natural selection acts on inversions in colder vs. warmer
- Example of a pattern of chromosomal adaptation
- NS = acts faster because multiple genes under selection together
Importance of Fissions. +Fusions
Drives Karyotype diversity (Haploid chrsomosome counts)
- Number of chromsomes (haploid)
Fission
1 Chromosome –> 2 chromosomes
Fussion
2 chromosomes –> 1 chrossome
Number of Chrosmome diversity
Organisms have a wide range of the amount of chrosmomes they have in one set (wide range in N)
Example – there are some organsims that have one gene per chromsomes. –have 16,000 chrosmomes
How did we get 23 chromosomes
Our closest ancestor has 24 chromsomes – our 23 is bevcause of a fussion event
**Fusion event gave us our 23 chrosmomes
**Shows that fussions/fissions drive karyotype diversity
Whole genome duplication
Typically due to meitotic erros
Very common in some groups of organims (Particulaly plants)
May play a role in speciation and adaptation
May have been very important in early history of life – providing fodder for protein diveristy
Whole genome diplication (process)
Have zygotes that end up with extra copy of genome (usually have diploid + diploid that are sually two haploids –> creates a tetraploid) –> That tetraploid individual acts like a dioploid with X2 chromsomes
Importance of whole genome duplication
- May play a role in speciation
- Important for speciation. inplamnts – makes sexually incomptaible plants)
- May have been very important in early history of life – providing a fodder for protein diveristy
- Likley important for the biochemical paths that we have – the extra set of chromsomes due to duplication can mutate and evolve and take on new forms = important for developing complexity in Eukaryotic organisms
- Think it was important for developinhg the complexity of Eukaryotic organisms
- Likley important for the biochemical paths that we have – the extra set of chromsomes due to duplication can mutate and evolve and take on new forms = important for developing complexity in Eukaryotic organisms
How often do mutations occur
Occur pretty often – muttaions occuring in the germ line occur all of the time –> the DNA of the parents is different than the DNA of teh offspring
Because occur pretty often the fact that the DNA of the parents is almost always different that the DNA of the offspring is almost always true
***We can measure mutations rates by tracking lines of model organisms in the lab
How do we know how often mutations occur
We can measure mutation rates by tracking lab lines of model organisms OR whole genome sequncing of known pedigree
Example Experimnet – Looked at the genome of parents vs. offspring (Sequnceing)
- RESULTS: had 49 ghermline mutations in one family and 35 germline mutations in another family
- The two families differeed because in one the mutations mostly came from father and in one the mutations mostly came from the mother
SHOWS – mutations almost always occur but how it ends up differs from person to person (Ex. in some cases the mutations might come from the mother and in some the mutations might come from the father)
What mutations are of interst
Germline mutations – because those of able to be passed down (those are heretible)
Mutations rates across organisms
Differs from organism to organism
Mutation rate at. asingle locus Vs. mutation rate in organism
The chance of a mutation at a single locus is low BUT if you scale that up to account for all of the loci in a genome get a liklihood of having of 30 mutations
The chance of a mutations at a singel nucleotide is low but when you scale the chance of a mutation up to genome level = epxevct to see around 30 mutations in the genome level
IMAGE – shows mutations rates for a single locus
Mutation rates within the genome
Different regions of the genome have different mutation rates
Example – mitocondria mutation rate is higher than the nuclear genome
Variability in mutation rate
Mutation rates are very variable BOTh acrosses organisms + within organisms but between regions of the genome
What do most mutations do to fitness
The majority are either bad or neutral (no effect on fitness) BUT some can imporve fitness
- beneficiual miutations are rare but do occur
SEEN IN bacteria + Yeast
- Studies look at the fitness of clonal indivioduals vs. the fitness of the ancestral strain
- Most common = nuetral
- In the chart most of the mutations. are<1.0 – means that they lower fitness or at 1.0 which means that they are neutral
- The chart also shows that some of the mutatinos were lethal (biggest decrease in fitness)
- YEAST = mostly nuetral with some distribution of deleterious + have lethal
- BUT in both organisms there are sine numbers >1.0 – means that there is. anincrease in fitness = have 3-4 mutations that impirved fitness over ancestral
Consequence of mutations
The mixture of bad BUT also some good mutations still provides enough fodder for NS
***Can see in a mutation Accumilation experiment
Mutation Accumilation Exeperiment
IF mutation just acted by itself (doing a mutation accumulation experiment) – allow mutations to build up but take selection out of the picture by babying the warms as much as possible – the warms are not completing at all
RESULTS – After genertaions the fitness. ofthis line decreases A LOT
- When there is No natural selection (because took out any competition) + have a lot of mutations the fitness decreases –> the new mutations are deleterious – as they accumilate theu hurt fitness
IF intriduce natural selection (increase NS – Increase competition) –> The Naturak selection can sort through allelic varaition
- NS = can pick out the good mutations and take out. thebad mutations and return the popultion to orginal fitness
- returns very quickly to normal fitness
OVERALL – is NS is not acting then mutations lead to decrease in fitness BUT when NS is restored it can act efficiently and restore the fitness alsmot instantaneously
Mutations + fitness
In the absence of selection, deleterious mutations
accumulate and drive fitness down
Return of selection: rapidly sort out the good from the
bad and fitness bounces back
Textbook definition of Pop Gen
The branch of evolutionary biology responsible for investigating process that cause changes in allele and genotype frequencies in populations
ISSUE with definition – Evolution = the change in allele frequncey = all of evolutionary biology should look. atchnage in allele frequcney BUT this syas that Pop gen. isa branch of Evolutionary Biology = not a good definition
- Incorrect in saying that it. isa subset of evolutionary biology because it is really all of evolutionary biology – all of Evolutionary biology needs to look through this lense
- Really all of evolutionary biology needs to boil down to pop gen
Population Genetics (good definition)
The mathematical and empirical study of allelic variation
within and among populations, including the dynamics of changes in allelic variation through time
***All about understanding allele frequcney
Why is it important to study Pop Gen
Understand population geentics = impotant applied applications + important for looking at postulates forms
Example – Affects forensics – need to know gentics and allele frequencies to do forensics
Important because:
1. Mechanistic underpinnings of evolutionary change (or stasis)
2. Understanding Pop Gen is essential to a number of applied fields and it has strong implications for fields outside of evolutionary biology
Allele
Varaint forms at a genetic locus
Frequency
Looking at something in terms of the proportion
Looking at the counts relative to the whole
- Looking at the proportion of varaition for a locus represented by as ingle allele
Count of an allele/WHOLE (count of all alleles in population)
Example frequency (using phenotype) – 21 Students with glasses and a total of 157 students – What is the Frequency of students with glasses and without glasses
Frequencey of students with glasses = 21/157 = 0.134
Frequency of studnets without glasses = 1- 0.134 = 0.866
**Can just subtract from one because we know that the two possible Frequency need to add up to one
Adding up frequencies
All of the individual frequencies will ALWAYS add up to one (IF have FReq 1 and Freq 2)
Freq 1 + Freq2 = 1.0
OR if have two alleles A and a
Frequencey of A + freq of a = 1.0
NO MATTER HOW MANY ALLELES THERE ARE – ALL OF THE ALLLES NEED TO ADD UP TO 1.0
- Same is true for genotype frequencey
Finding allele Frequency
Work the same way as phenotype Frequency – need to count up all of the allele in question and determine the proportion it makes up of all of the copies of that locus in the population
- Look at allle and determine the proportion that they make up of all of the alleles
Example – Finding allele Frequency
of homozygous Indv + 1/2(# of heterozygous Invd)/Total number of individuals
Have two alleles A and a
Can count – we know that the total number of individuals is 147 (can just add up all of the individuals in the chart)
Need to find the frequencey of A:
– Might want to do 47/147 –> THAT IS WRONG – because these are not allele counts they are genotype frequnceies – need allele count + need to account for how alleles are distrubuted into the genotypes
Focusing on A:
47 AA –> 47 A and 47A –> 94 A
88 Aa –> 88 A and 88 a
12 aa –> 12 a and 12 a –> 24 a
***Need to double to account for being diploid + need to adjust for heterozygous
Total A = 94 + 88 = 182 A
Total A/ Total Alleles = 182/294 = 0.619
OTHER WAY:
***Instead of counting alleles we can count genotyoes and adjust accordingly
# of homozygous Indv + 1/2(# of heterozygous Invd)/Total number of individuals
47 + 1/2(88) / 147 = 0.619 –> get. thesame answer
OR – can use genotype frequencies
Freq of A = Freq of AA + 1/2(Freq Aa)
0.319 + 1/2 (0.599) = 0.619
***Here = don’t divide by anything because already in frequencies
Looking at a:
12 + 1/2(88) = 0.381
OR
1.0 - 0.619 = 0.381
- can do this because freq of A + Freq of a (because the sum of all of the frequencies of all of. thealleles in a popultion = 1.0) = 1.0 (need to sum up to one)
Finding the total number of indoviduals
Just add up all of the genotype frequencies – because each individual has one genotype
AA - 47
Aa - 88
aa - 12
of indiviudals = 47 + 88 + 12
Why is genotype freqincey not allele frequencey
Allle count is NOT the genotype frequincey becasue each genotype has two alelles (because these are diploid organisms) – have two alleles per locus (two alleles per genotype)
- When you have diploid individuals – total # of alelles = X2 the number of indivoduals
Example. –147 indiviuals –> there are 294 copies of the locus
NEED TO ACCOUNT FOR HOW ALLELES ARE DISTRIBUTED IN THE GENOYTYPES (need to account for heterozygotes) + Need to account for diploid nature
Equation for calculating allele frequency from genotypes
of homozygous Indv + 1/2(# of heterozygous Invd)/Total number of individuals
- Use 1/2 because only 1/2 of the heterozygous are each of the alleles (1/2 A and 1/2 a)
Instead of counting alleles we can count genotyoes and adjust accordingly
OR
You can work directley with genotype frequnceies
***Genotype frequncies also all have to sum to 1.0
Freq A = Freq of AA + 1/(Freq of Aa) – here you don’t divide by total individuals becvaue you ate already using frequnceies
- By dealing with genotype frequencies we have already accounted for the proportion of the whole = no need to divide anymore
Finding allele frequencey from genotype freunecey
Freq A = FreqAA + 1/2Freq of Aa
Example
AA –> 47/147 = 0.314
Aa -> 88/147 = 0.599
aa –> 12/147 = 0.082
Freq A = 0.314 + 1/(0.599) = 0.619
***Don’t divide by anything here because they are already in frequcneies
Sum of all of the frequencies of all the different alleles in a population
Equals 1.0
How to get genotype frequencey
of indioviual with genotype/ Total # of individuals
***No need to double here (Just number/total)
Ex.
#AA/Total # of individuklas
Practice –
Freq H+ = 0.8
Freq H- = 0.2
Genotype Freq:
HH = 0.63
Hh = 0.34
hh = 0.03
Freq H+ = Freq of HH + 1/2 Freq of Hh
0.63 + 1/2(0.34) = 0.8
Freq of h = 1.0 - 0.8 = 0.2
Population
A group of interbreeding individuals and their offspring (for sexually reproducing organisms)
- Hard to define
More generally:
Perhaps more generally: a group of conspecific
organisms occupying a more or less well defined
geographic area that exhibit reproductive continuity from generation to generation
- Conspecific = members of the same species
- We model reproductive continuity –> potential for allle frequncey to change from one generation to the next (parent genotype to offspring genotype without the input from other groups)
What are we modelling in Pop Gen
We model reproductive continuity –> potential for allle frequncey to change from one generation to the next (parent genotype to offspring genotype without the input from other groups)
Mendle’s laws in populations
We need to think about how Mendle’s Laws operate at the population level from one generation to the next
- Sclaing up Mendle’s laws of segregation and independent assortment up to the popultion level
KEY = thinkning about reproductive continuity (offspring genotypes)
What is needed when scaling up mendelian principals up to populations
- We have to define the specific life cycle of our populations
- Examine the points at which allele frequencies might be subject to change
NEED to think how allele frequncies might chnage from one genration to the next – need. tothink about this chnage in a life cycle
General Life cylce that we use
1 – ADults –> Sdults make gametes – make up the gene pool (2) –> Gametes form the gene pool combine to make zygotes (3) –> Zygotes mature to offspring (these new offspring make up. thepopulation) (4) –> Offspring become adults (1)
- Parental genertaion
- Gametes pool derived from the parental generation
- Combination of gametes from pool of zygotes
- Offspring generation
Allle Frequncies within life cylce
What types of populations do we use in our models
We use “idealized populations” – a simplified model of a population that meets certain criteria assumptions –> allowing us to islate the effects of interst
REAL groups of organisms might not meet this BUT this allows us to islate the effects of interst
DOING SO = gives us a NULL model –> Shows. us the way we think the world works and then compare that to hwat actually happens
- We can compare data from real populations to expectation from idealized populations to test hypothesis
Example – Scaling up mendelian Principlas in populations
1 – Start with our parental popultions –> genotype the indoviuals – get the genotype frequencies for parental generation
GET Parents popultion genotype frequencey
Example:
AA =0.36
Aa = 0.48
aa = 0.16
2 - Generate the gamete pool – based on. theintial parental genotypes
- Get the frequencey of the alleles in the gamete pool
- Assuming Mendle’s kaws = take a diploid genotype and make all of the possible gametes
Frequncey of gametes = Frequncey of alleles on the parental generation
Freq A = Freq AA + 1/2(Freq of Aa) = 0.36 + 1/2(0.24) = 0.6
Freq A = 0.6
Frq a = 0.4
Freq in gametes = 0.6 and 0.4
- means that 60% of sperm is A and 40% of sperm. is a and 60% of eggs are A and 40% of eggs are a
Can call Freq of A “p”; Frequncey of a “q”
P + q = 1.0 (Freq of A + Freq of a) = 1.0
q = 1 - 0.4 –> q = 0.4
NOW = we know that the gamete pool is 60% A and 40% a
3 – Geenrate Zygotes
- use basic probability – choosing one sperm and one egg at random from the gamete pool
- Porbability of getting a gamete with a particular allele is simply equal to the allele frequncey
- probability of choosing a gamete with A = freq of Ain gemete pool
P(A sperm) = p = 0.6
P( a sperm) = q = 0.4
P(A egg) = p = = 0.6
P(a Egg) = q = 0.4
P(A sperm) And P(A egg) = 0.6 X 0.6 = 0.35 –> P(AA) = 0.36
SAME AS p X p = 0.36
P(aa) = 0.4 X 0.4 = 0.16
q X q = 0.16
P(Aa) = P(A sperm) AND P(a Egg) OR P(a sperm) AND P(A Egg)
- There. aretwo ways that this can happen = need to account for both
P(Aa) = [0.6 X 0.4] + [0.4 X 0.6] = 2[0.4 X 0.6] = 0.48
[p X q] + [q X p]
4 – Assuming that all of the zygotes survive and develope – the genotype frequncies of. tehnew generation are
AA = 0.36
Aa = 0.48
aa = 0.16
NOTICE: NO CHANGE – the same frequncey as the parental generation
- Genotype -> gamete frequncey –> Probability events in teh gamete pool –> zygoites –> if all of the zygotes surivive to be offspring = the genotyp[e frequnceies don’t chnage in the offspring
How do you get the frequncey of gametes in gamete pool?
You can asusme mendles laws – take a diploid genotype and make all of the possible gametes
- Get the gamete pool from the parental genotypes
- Want the alleles frequncey on the gamete pool – this is equal to teh allele frequncey in parental generation
END – frequencey of gametes = frequncey of alleles in the parental generation
- If we make the assumption that all individuals in the parent population contribute evenly to the next population –applying Mendel’s law of segregation
to the population as a whole –> Frequency of gametes equals allele frequency of the parental population
P
The allele frequncey of the alelle that we are focused on
***Could be an allele that doesn’t even make a phenotype
- Doesn’t say anything about dominant vs. recessive
***In an idelaized biallelec system = we can call the frequncey of the other allele “q”
Generating zygotes from the gamete pool
Use Basic probability – choosing one sperm
and one egg at random from the gamete
pool
- probability of choosing a gamete with A = freq of A in gemete pool
Probability of getting a gamete with a particular allele is simply equal to the allele frequncey in gamete pool
Probability of two independent events
Probability of two independent events
occurring together is the product of their
individual probabilities
AND statement = multiply
Probability of two ME events
Probability of either of two mutually
exclusive events occurring is the sum of
their individual probabilities
OR statement = ADD
Looking at Punnet square for a population Vs. for two individuals
Started – punnet square of two individuals (just looked at male and female)
- Here – the frequency of each of the gametes is 50% (50% chnace they will give A and 50% chance they will give a)
- HERE – P and Q = 50%
- If only two inidviuals then p and q = 50%
THEN – just change cross to have different frequency of p and q to account for all indivdiuals in the population (NOW just chnaging the cross to have different requencey of p and q)
NOW – instead of a gamete pool of two indoviduals – gamete pool is of the entire idealized popultion
- Have new p. and q values to account for allele frequencey. inthe gamete pool
THEN – can use p and q in. thepunnet square –> The frequncey of each genotype in each square is equal to the pdorct of the gamate (allele) frequencies
- Have AA = p X P
- Have aa = q X q
- Have Aa = p Xq OR q X P = 2pq
END – know that p^2 + q^2 + 2pq = accounts for all indovoduals in the popultions = p^2 + 2pq + q^2 = 1.0
Looking at Punnet square for a population Vs. for two individuals
Started – punnet square of two individuals (just looked at male and female)
- Here – the frequency of each of the gametes is 50% (50% chnace they will give A and 50% chance they will give a)
- HERE – P and Q = 50%
- If only two inidviuals then p and q = 50%
THEN – just change cross to have different frequency of p and q to account for all indivdiuals in the population (NOW just chnaging the cross to have different requencey of p and q)
NOW – instead of a gamete pool of two indoviduals – gamete pool is of the entire idealized popultion
- Have new p. and q values to account for allele frequencey. inthe gamete pool
THEN – can use p and q in. thepunnet square –> The frequncey of each genotype in each square is equal to the pdorct of the gamate (allele) frequencies
- Have AA = p X P
- Have aa = q X q
- Have Aa = p Xq OR q X P = 2pq
END – know that p^2 + q^2 + 2pq = accounts for all indovoduals in the popultions = p^2 + 2pq + q^2 = 1.0
Hardy-Weinburg Equillibrium
P^2 + 2pq + q^2 = 1.0
- Sum need to always equal 1.0 – accounts for all genotypes
- Looks at allele frequencey and the porbability of an allele in the gamete pool
CAN BE SEEN IN PUNNET SQUARE – look at image
- They ALL have to equal the whole rectangle = no matter what they always add up to 1
How do we know if a population is in equilibrium
Look if the genotype frequnceies matches the allele frequncies
NO MATTER WHAT – the sum of genotype frequncies should still add to 1
Getting H-W from Punnet Square
You can make the punnet square with the allele frequncey of each allele – include p and q
THEN you can see that:
Freq AA – PXP = p^2
Freq Aa – P X q OR Q X P = 2PQ
Freq aa = q X q
***Can do frequnceies in this way because the frequncie of AA = Freq of A AND the Freq of A = P X P
ALL OF THESE NEED TO ACCOUNT FOR GENOTYPES OF ALL INDIVUDALS IN POPULTIONS = ALL ADD UP TO 1
GET EQUATION – P^2 + 2pq + q^2 = 1.0
Assumptions of the H-W model
- No selection
- No mutation
- No migration (in or out)
- Infinate popultion size
- Mating choice occurs at random
Violating 1-4 = changes allele frequncies = generates evolution
What happens if violate random mating
Violating random mating assumtion DOES NOT change allele frequencies – only changes genotype frequencies
=
Purpose of infinate population size assumtion
Important assumtion that genetic drift is based on
SMALLER populations = have inevitability of chnage in allele frequency
***Makes this an idealized model
Where can we examine for fitness in life cycle
We can look at different points in the life cycle fir fitness – can exmaine fitness at many time points
- Can consider each point individuals
One can model the seperarte components. offutness at different points along our generlized life cycle
- ALL of the seperate fitnesses these typically all sum together to one value of overall fitness that we would use to adjust our HW model
Examples = in image
WE will just look at survival for fitness BUT you can incorporate other metrics of fitness into the models – it’s generally easier to think about, we’re also going to stick with examples where fitness is driven by differential survival rates
- All of the ways to look at fitness sum together but we will look at one alone
- We will just look at different survival rates
- Assign fitness value to genotyoes based on differential survival
Selection
Essentially unequal rate. ofsurvival and reproductive success acriss genotypes
Quantifying seleectin
Requires Quantifying unequal survival and reproduction
w
Generalized fitness value
p and q in non-dominent/recessive relationships
You can still use p and q – doesn’t matter which you call p and which you call q
- p and q say nothing about dom/rec
p = just the one that we are ficusing on
Assigning fitness. inour class
We will just asisgn fitness value to genotypes based on different survival
- Looking at survival rates and assign fitness
WE look at juvinile to adult hood part of life cycle (differences in survival to reproduction)
Quantifying fitness
Example – we have moved mice to. a location were coat color matters
Moved 1000 mice from a population in HW to a new location
We are looking to see if coat color is under selection (looking at ciat color)
Total = have 1000 mice –> tracking their survival in nature
- Intital population is in H-W (gene frequenceies match expenctations –> NOW putting mice in new envirnment)
Here
AA = 0.36
Aa = 0.48
aa = 0.16
THEN before reproduction a number of mice are eaten
AA Survivnng = 288
Aa Surviving. =288
aa Suriving = 64
OVERALL – need to compare the observed survival rate vs. the expected survival rate (expected = that each have equal survival rates)
Steps:
1. Need to calculate the survival rate for each geneotype
- Ratio of mice survivors in each genotype vs. the expected number of survival if Survival is uniform
- Need to calulatue NULL – that survival rate is uniform
- To find – take total suvivors in population/ total in populations
288 + 288 + 64 = 640 –> 640/1000
P(survival) = 0.64 – if it is unifrm
THEN need. to find teh expected NUmber of survivors per genotypes (if survival rate is equal)
Expected number = Number of genotype X P(survival in unofrm)
- Exoect 64% survival in each genotype IF survival is uniform (expect 64% of each genotype to survive to reproduction)
0.64 X 360 = 230.4 – expected numbver of survivors
0.64 X 480 = 307.2
0.64 X 160 = 102.4
NOW have expected survivors
- Comprare observed vs. Expected survicors
AA – 288/230.4 = 1.25
Aa – 288/307.2 = 0.9375
64/102/4 = 0.625
THESE numbers = represent the deviation form uniform suvrival for each genotype –> Theyre propeortional over or under the representation of that genotypoes in the next geenration = they are fitness
- They show the deveioation from unoform surivale (If uniform survivale is 1 then AA has slightly higher survival and Aa has slightly lower survival)
THIS GIVES ABSOLUTE FITNESS BUT we want theor relationships to each other –>. wecan rescale them (we don’t want to use the raw fitnes svalue we want them on a relationship scale– want relative fitness)
THEN TO GET RELATIVE FITNESS – We can do this by simply setting the value of the highest
fitness genotype to 1 and dividing the others by that value to adjust them accordingly
Mke your highest values = 1 and dvide. therest by that value
Here :
1.25 is highest –> 1.25/1.25 = 1
0.9375/1.25 = 0.75
0.625/1.25 = 0.5
NOW have relative fitness
Adjusting H-W model
Before = we used an idealized model 00 no differentail survival or reproduction (just random events) –> This kept frequencey the same
- Mice were not evolving
- They were NOT under selection
NOW – we are putting them under selection
Mice + coat color studies
This system has been studies a lot
Mice = get eatne by Hawks and hawks are visual predators – coat colro allows some mice to blend = allows for differential survival
- Look at survival of mice. inreal studies in nature + done with fake mice and looking at attack rates
What is needed to quantify survival
Need to see if the survival is uniformly or not uniformly distributed for each
- Need to see if the survival rate for each as a null model that each have equal survival
Need to compare expected to observed survival
- Need to look at the ratio of mice surviving in each genotype compared to expected number. ifthe survival rate is uniform
Calculating Null for quantofying survival rate
Null = that survival rate is uniform
- That they all have
Do total amont of surivvors in populations (regardless of genotypes)/Total populations
Meaning of survival rates
If over 1 = means that that genotype is slightly more liley to survive
If less than. 1= means that genotypes is lsightly less likley tp survive
Ex. 0.625 – means thaty you have a 0.625 chnace. ofsurvival relative top everyone else in the same popultion
Why go from absolute fitness to relative fitness
Because we care about their relationships to each other
DO this. byseeting the highest fitnes sto 1 and rescaling everything relative to that
How to predict effect of NAtural selection from. onegeneration to another
You need =fitness BUT you also need to think about it in the context of teh current popultion – need to know the starting point of the popultion for alelleic variation
- The effect of natural selection doesn’t just
depend on these values alone, it depends on
the context of the allelic variation in the
population too
NEED
1. Relative fitness
2. Need starting alelelic frequncey
Need to know fitness + allele frequncey THEN you can know if Natural selection is acting by itself
THEn you need to know the avergage fitness. ofthe populations as a whole – how high or below avergae fitness are you if you are carrying a certain phenotype
What effects whether an allele will increase or decrease
Depends on the genotype fitness values and. the current allele frequnceies in the popularions
NEED – to calculate for avergage fitness across the popultions – the avergae fitness takes both alelleic frequencey and fitness into account
What alleles will do depends on Avergage fitness (w/)
Average fitmess in populations
Takes into account allelic frequencey and and realtive fitness
YOU COULD – add all of. thefitness of all of the indivuduals in populations and divide by the total BUT you can just use genotype or allele frequncey
- If you know allele frequncey and fitness = know Avergage fitness
w/ = P^2wAA + 2pqwAa + q^2waa
In example – w/ = 0.8
Calculating effect of natural selection
NEED:
1. Avergage fitness
2. Starting allele frequnceies
Using w/ and relative fitness and allele frequncey = can calulate what alleles frequncey will be from. onegeneration to the next
LOOK AT THE CHANGE in allelE FREQUNCEY
dP = p/w/ X [(PXwAA) + (q X wAa) - w/]
Example – (0.6 X1) – means that you have a fitness of 1 60% of the time – are above w/ 60% of the time
(0.4 X 0.75) – means that you have a fitness of 0.74 40% of the time
IF dp = 0.075 – tell us that teh allele frequncey will be slightly higher in the next generation
p’ (p in next generation) = 0.675 – alelle frequncey in the next generation
Effect of natural selection
The change in allele frequceney between the parental and offspring generation
Avergage excess
[(PXwAA) + (q X wAa) - w/] – average fitness effect of a gamete carrying allele A – that can combine at random with either A or a gametes in the population at their given frequencies
A gamete can either combine with another A – then get AA OR can combine with a and get Aa –> depedning on which happens have diffrent affects on fitness (if AA – has certain fitness + if Aa has different fitness then subtrcat that from the avergae fitness)
- If you have A in the gamete pool = can form zygote with. Aor a – look. atthe probability that you will get AA or Aa – done by multiplying by. p and q
THEN once you have the expected amount of AA or Aa you can see if on avergaege You will be above or below w/ by subtracting from w/
- SHows tha orbability of A combining with A and the fitness that the resulting zygote would have
WHETHER AN ELLE GOES UP OR DOWN IS BASED ON AVERAGE EXCESS
Relationship between p and q change
If p increases by a certain amount q will decrease by that same amount
If p increases by 0.075 then q decreased by 0.075
LOGICAL - because p and q always add to 1
How should the lowest fitness allele change
The lowest fitness allele should go down because its the lowest fitness
Highest fitness alelle should go up
Selection coeffeciants
Sometimes it is easier to keep track of the strength of selection directley rather than relative fitness
- Look at selection directley
s = 0 – no sleection aganist it
s (selection coefficient) = 1 - Relative fitness
Graphing popultion fitness
Preidcting the outcome of NS
LOOKING at mean popultion fitness vs. allele frequncey (w/ as a function of alle frequcey for a particular set of fitness values)
- Tells you w/ at a certain allele frequncey
When picking points always pick p = 0 and p = 1
Example:
1 Point – p = 0 –> w/ = 0.5 (because at p = 0 then ONLY have q –> W at aa = 0.5)
2 point – p=1 –> w/= 1 (AA = 1)
- If the entire popul;atioon is A then p=1 –> Then everyone has w = 1 –> then w/ = 1
- If fixed for A then w/ = 1
3 point – p= 0.5
CAN use equal;toon to find w/ at p=0.5 BUT here since Homozygous is Dom is. 1and Homozygous rec is 0.5 THEN you know that w/ of 0.5 would be in the middle of them = w/ would be 0.75 (Can’t always do it this way but can always use the equation)
How many points do you need in graphing population fitness
Need 3 points in plot (shows if the graph is a staight line or has curves)
Effect of Adaptive topography on a population
Efefct of NS = always to push the graoh uphill
- Want the max w/ based on ale;les in popultion – NS push popultion uphill
- w/ will increase uphill as much. aspossible
- Shows how adaptation will occur over adapative Topograohy
NS will always push the population uphill along the topography
Example (from the calculations earlier)
If have p = 0.6 –> w/ = 0.8 – in teh next geenration when p = 0.675 w/ becaomes 0.8375 (Shows that NS is pushing AT uphill)
Graphs of fitness vs. alelle frequncey
Adaptive topograohy
USE the graogs to define an adaptive topography for the popultion
Linear Adaptive topography
If linear slope – affect in w/ for a give chnage in dP – rate of increase is the same
Example graphing Adaptive topography
Solving for the middle point:
Pick p=0.5 –> and the plug in to w/ –> get w/
HERE – NOT a styraight line
- w/ will still always go up hill BUT here NS is pushing P to decrease
- Curvature = affectes the rate at which this happens
Lower slope = smaller chnage in fitmess (lower investment)
Steeper slope = small chnage in P leads to bigger chnage in w/ (higher investment)
Steepness in Adaptive topography
Steepness of the slope determines. thestrenbgth of affect of Anatural selection
Lower slope = lower investment (Making less of a change when putting. ineffort)
Steeper slope = small chnage in P leads to bigger chnage in w/ (higher investment)
Fitness differential + NS
NS can work on any fitness differential – in the absence of other evolutionary forceses
Weaker fitness differences just lead to slower rates of change
ALL = end with fixing for one allele and gegtting rid of the ither – occurs in any case of selection even if diffrence in fitness is not as big
No matter the strebgth. ofNS = still change alleles – The strength of selection just alters the rate (just takes different amounts of time)
ALSO no matter the diffreential – the slopes of the lines (the fastest rate of chnage) = al;ways when p=0.5 – when the genetic varaition in fitness is at its highest
Effect of NS
Directional selection – always pushes to get rid of one and have only the other
Where does allele frequencey change the fastest
Looking. atthe slop of chnage in alelle frequncey over time – where it chnages the fastest = always in the middle
- rate. ofchnage os fastest at 0.5 – because at 0.5 is where you have the most varaition
RATE OF CHNAGE IS PROPORTIONAL TO THE AMOUNT OF VARIATION
Fisher’s Fundamental Theorem of Natural Selection
Change in population fitness is proportional to
the variance in fitness
Rate of chnage = the fatsest at p=0.5 – fastest when there is the most variation
Natural Selection is a…
Natural Selection is a deterministic force – if we know what the conditions are, we know what the outcome will be
- Natural selection by itself is driven by straight forward mathematics towards a predictable outcome
