Test #1 Review 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)
Understanding Earth’s age
Took time to know that earth is older than what we know –> hard to get that persective
Key Developments before Darwin
- Antiquity of the world
- The relationships among organisms
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
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
Lamark’s heredity
Said that traits of organisms match the environment well –> came up with how organisms change over time + how change is transmitted through time
***HAD IDEA OF AQUIRED INHERTIANCE
Lamarkism
Change in organisms brought by natural physical processes Contains:
1. Force of coplefications (Spontenous generation) – increase in complexity through time
2. Force of adaptations (Aquired inheritance) – match body to envirnment – idea of how organisms chang over time
How do we know that Darwin’s conclusion were inevtiable
Becayse Wallace had independentley arrived at the same conlsuions – shows that the conclsuions were inevitable because it actuallt did happen somewhere 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
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
Two models for explaining patterns of biodiversity
- Special Creation
- Descent with Modification
Special Creation
- Species are immutable (unchnaging)
- Lineages fo NOt diverge
- Species are created seperatley
- Species are geniologically independet – not fundementally realted to each other
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
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
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)
Experimental evolution
Take population and expose to new conditions – see change
***SHows that species change over time
Example – Threespine sickle back
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
Law of Succession
Correspondance among fossils and existing fauna and flora in spaces
***Evidence that new forms arise from old -
Example #1 – Australian fossils that are mammals are marsupials BUT asiam mammals are placentals
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
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
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
Evidence that different groups of organisms are related
- Homology
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
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
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
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
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 (overall)
Was one of the first people to really think about teh mathamatic reality of human demography - He realized the remarkable power of unchecked population growth
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
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
Arithmetic growth
Population increase by a constant amount over time
***this does not take into account the density of the population
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
What stops us from being in a state of catastrophe
Mortaloty rates stop us from being in a state of 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
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
NS postulates
NS is simple due to 4 key postulates ***Each postulate is testable BUT tesing is not always easy
1. Populations are variable – variation within populations
2. Traits are heretible
3. Variation in survivorship + reproductive sucess
4. 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
Where can variation be seen?
- Seen in human popultions – Example is disribution of height (
- See genetic variation within popultion – can see varaition in genome
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
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
Why is postulate #2 hard to measure?
Because heretibility is complicated
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
R stadegy
Investment optimized to the number of offspring – faster replication = put more babies hoping to survive Example – octopus
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
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
- 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
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 – 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 test3 – Do all flies continue to the next generation – is there variability in survivorship – YES4 – 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
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 2. 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
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
Darwinian Fitness
The extent to which an individual contributes to future generations
***Need to think of it in terms of LIFETIME reproductive output
Survival + Fitness
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
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
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
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 Molecular homology = extent way beyond closley relate mamales
When can population evolove
If the 4 postulates are trie
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
Misconceptions about evolution
- individuals evolve – REALITY = selection acts on individuals BUT individuals don’t evolove2. Natural sleection can see into the future – it cannot3. Selection adds more varaition – REALITY is that selection acts on existing varaition in popultions4. Selection results in perfection – NOT TRUE 5. Selection favors complexity – NOT TRUE6. 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
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
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
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
Selection + Complexity
Selection DOES NOT favor coplexity – life has increased in complexity iver time BUT NOT because selection is favoring complexity
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 processGet 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
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
Question about mutation in evolution
Is it one rare mutation or is it a build up of many small minor ones (Gradual vs.. SaltationNOW = 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”
Idea of Inheritance during darwins time
Blending inheritance –> - People know that offspring look like parents BUT thought it was a blend of traits - 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
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
Issue in Mednle’s experiments
HE got lucky – the traits that he happened to work with just happened to be discrete traits
OVERALL – people had issues with Mendle’s work because his work failed to epxlain the heredity in continous 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
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
Outcome of Modern Synthesis
Restated the four postulatesin explicitly gebetic terms
MODERN synthesis = explains evoluton as a fundementally genetic process
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
Postulate #2 After Modern Synthesis
Postulate #3 After Modern Synthesis
Through differential survival or reproductive sucess not all individuals contibute the same amount to the following generation
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
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
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
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
Alleles
Variant forms of a genetic locus
Example – can have. a C 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)
