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144 Cards in this Set
- Front
- Back
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Three requirements of evolution... |
1. Phenotype Variation 2. Heritability of phenotypes 3. Differential reproductive fitness |
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Phenotype |
A physical, developmental, or behavioral characteristic of an organism |
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Heritability |
Transmissible from parent to offspring |
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Reproductive fitness |
The passing of genes to the next generation such that they too can pass on genes |
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Early evolution ideas...Methodological Naturalism |
Trying to explain the world based on natural phenomena, using a method or procedure |
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Early evolution ideas....Catastrophism |
The earth's crust during geological history have resulted chiefly from sudden violent and unusual events. - Earth's major geological features arose through sudden catastrophic, large- scale events, rather than through slow gradual change - They believed that natural processes are not observable or subject to manipulative experiments, and they are not expected to occur again in the future |
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***Uniformitarianism |
The world is always changing (E.g., extinction, speciation, climate) - all of the processes that have generated the current geological patterns we see around us can themselves be observed in operation at present, providing with much power to test the hypothesis |
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Where do species come from? Spontaneous generation |
Life arises from non living matter |
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Early Evolution Ideas...Erasmus Darwin |
- Proposed the idea of evolutionary change - Life evolved from a "single living filament" - Humans descended from other primates "struggle for existence" |
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Problems with Erasmus Darwin's ideas |
- Could not connect "struggle" with evolutionary change - Thought traits acquired during life could be passed to offspring |
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Robert Chambers |
-Principle os progressive development-> new species arise from old species |
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Problem...Robert Chambers |
No hypothesis to explain the changes |
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Charles DarwinTwo fundamental insights... |
1. Environment selects on variation in the traits of individual organisms - Some organisms are more successful - Mechanism for this: Natural selection-> filters organisms based on how well the traits of individuals interact with their environment 2. All living species descended from a common ancestor- branching pattern of ancestry for all life |
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Darwin' argument for natural selection... * Darwin published the book, "On the Origin of Species" |
Darwin used artificial selection to argue that natural selection is possible-> humans select some breeds over others |
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Criticisms' to Darwin's Theory |
- How do you account for complex structure with multiple intricate parts? - Why do animals have traits and organs of seemingly little importance? - Why doesn't Natural Selection run out of variation to sort on? |
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Early Evolution Ideas |
Population can not grow linearly because there are not enough resources to support a growing population |
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Artificial selection |
humans systematically breed certain varieties of an organism over others |
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Artificial Selection vs Natural Selection |
- the two impt differences between the processes are the selective agent and the traits being selected - with artificial selection, the selective agent is the human breeder who chooses which traits to modify, and attempts to modify them in a way that is beneficial to the breeder - with natural selection we can think of nature as the selective agent , but it is impt to note that nature is not a conscious agent, in the way that humans are |
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Lamarck vs Natural selection |
Lamarck: Independent progression Darwin: branching tree of life (organisms share a more recent common ancestor) * Transformational (the ensemble changes because each individual member changes) vs Variational processes (the ensemble changes because something sorts among variants in the original ensemble) |
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Alfred Russell Wallace |
- Independently developed a similar theory on Evolution *Species arise from pre existing species "fittest will continue the race" |
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Variation |
Individuals in a population differ from each other |
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Inheritance |
Some of these differences are inherited by offspring from their parents |
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Differential reproductive success |
Individuals with certain traits are more successful than other at reproducing in their environment |
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Given these condition, Natural Selection is inevitable |
variation, inheritance, differential reproductive success |
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Major source of Variation |
Mutation |
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What traits in plants might be affected by drought? |
Things that allow them to reproduce, in low water condition: - Mature quickly into a flower - Water efficient tissue |
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Steven Franks had seeds from wild plants collected in 1997 and 2004. Hypothesis: |
Plants that survived the drought will have a shorter time to flowering than their ancestral population |
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How do genetics and environment affect phenotype? |
Genes do not affect a trait the same way in every environment Ex. Genotype 1 doesn't produce tall or short plants; rather, genotype 1 produces for the norm of reaction "tall at low and high elevations, short at medium elevations" |
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Norm of reaction |
is a curve that relates the contribution of environmental variation to observed phenotypic variation * genes do not affect a trait in just one environment but rather produce a norm of reaction |
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Ex of Natural Selection |
Oldfield mice (peromyscus polionotus) |
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Oldfield Mice Why might they have different coat color morphs? |
Vegetated habitat
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Carl Linnaeus |
Father of Modern Taxonomy |
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Linnaean *spp-> many species |
Hierarchal Classification |
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Hierarchal Classification *Major Problem |
It is not based on evolution |
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Willi Hennig |
Founder of phylogenetic systematics |
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Phylogeny |
Branching relationships of populations as they give rise to multiple descendant populations over time |
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Phylogenetic Systematics |
- Types of organisms are grouped together based on one or more shared unique characteristics - These characteristics are based on common ancestry |
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How is phylogeny different from a pedigree? |
A pedigree looks at an individual whereas a phylogeny looks at populations |
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Character states or traits |
Observable characteristics of organisms |
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Taxon |
group of related organisms at the tip of a branch |
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Clade |
A groups of species that share a common ancestor |
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Phylogenetic Tree |
Uncertainty about evolutionary relationship can be show by polytomy |
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Polyphyletic Group |
disjointed group of taxa |
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Paraphyletic group |
Contains the groups most recent common ancestor but not all of its descendants |
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Rooted vs Unrooted Tree |
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Cladogram |
It is a diagram that depicts evolutionary relationships among groups. |
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Phylogram |
The branch lengths are proportional to the amount of inferred evolutionary change. |
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Chronograms |
explicitly represents evolutionary time through its branch spans |
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Homologous traits |
are shared because of common ancestry Examples: - long legs |
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Analogous |
traits are not shared because of common ancestry Examples: Long tails are an analogous trait |
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Divergent evolution |
occurs when closely related population/ species become different by evolution |
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Convergent evolution |
occurs when species evolve to look more similar |
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Derived Trait |
Trait not present in the ancestor |
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Synapamorphy |
Derived trait shared between taxa due to homology |
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Homoplasy |
An analogous trait * a shared trait not due to common ancestry (analogous trait) |
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symplesiomorphy |
A trait shared due to common ancestry that is not derived |
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How do we know if a trait is ancestral or derived? Outgroups! |
Outgroups are known ancestral taxa that inform us of the ancestral state. They tell us the polarity of traits. |
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Using phylogeny to test hypotheses H: Venomous snakes (Viperidae and Elapidae) evolved from non- venomous ancestors |
Figure 4.31 |
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How do we build trees? |
- Get some species that we can use to test some hypothesis about evolution - Find characters/ traits that are common to some species but not other * Species with lots of characters in common could be closely related - Apply some phylogenetic method and build a tree |
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Phylogenetic methods |
- parsimony - distance |
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Parsimony |
The best phylogeny is the one that both explains the observed character data and posits the fewest evolutionary changes |
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Which is most parsimonious? |
Slide 43- 45 |
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Problem with Parsimony? |
Long branch attraction: is a form of systematic error whereby distantly related lineages are incorrectly inferred to be closely related - When evolutionary rates are different between sister taxa, taxa with similar rates may be incorrectly grouped together |
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What if we wanted to root a tree? |
- We could add an out group - Outgroup * Add a taxon more distantly related to all taxa in the data set that there are to themselves |
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Phylogenetic distance methods... |
- build a distance matrix (DNA) |
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How many potential trees are there? |
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How to find the best tree? |
- UPGMA: Unweighted Pair Group Method with Arithmetic Mean - Neighbor Joining - Bootstrap resampling |
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Bootstrap Resampling |
creates many new data set from the observed data to get a representative distribution of results |
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Independent Contrast |
looks at estimated changes that occur along various branches of the tree in such a way that evolution along each segment can be considered independently of every other segment |
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Blending vs Particular Inheritance |
- Blending would result in the sort of resemblance between parent and offspring that is needed for heditary and thus for evolution . The problem is that blending of this sort also eliminates variation. Blending decreases our color variation from two colors. - The particular theory of inheritance suggested that color filters would be a better metaphor for heredity. While the phenotypic effects of the particles carrying heritable information may blend, the particles themselves remain distinct, and they can be separated again in future event. If a mutation has a positive effect on fitness , its frequency can increase via natural selection |
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Genome |
haploid set of chromosomes in a gamete |
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Chromosomes |
carries genetic information in the form of genes |
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Locus |
location of gene copies on the chromosome |
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Gene |
strand of DNA that codes for something |
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Allele |
Variant of a gene/ variant of the same gene |
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Gametes |
Are haploid, sex cells |
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Transcription |
DNA to RNA |
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Translation |
RNA to proteins |
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genotype |
combination of alleles at a particular locus |
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Homozygotes |
two copies of the same allele at a locus |
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Heterozygote |
two copies of different alleles at the same locus |
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Mendal’sLaws |
1. Law of segregation 2. Law of independent assortment |
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Law of segregation |
alleles segregate into gametes - each individual has two gene copies at each locus and these genes segregate during gamete production so that only one gene copy goes into each gamete |
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Law of independent assortment: |
which alleles get passed on independent of each other (but not always; only hols true for unlinked loci) |
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Point mutation: transition |
changes a purine nucleotide to another purine (A ↔ G) or a pyrimidine nucleotide to another pyrimidine (C ↔ T) |
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Point mutation: transversion |
substitution of a (two ring) purine for a (one ring) pyrimidine or vice versa |
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Synonymous mutations |
mutations don’t change the amino acid |
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Missense mutations |
change the amino acid |
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Nonsense mutations |
result in stop codons |
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frameshift |
Insertions and deletions |
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Inversion |
chromosome sections flip |
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Translocation |
chromosome sections move/swap |
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What effect do mutations have on reproductive fitness? |
Neutral Beneficial Deleterious Mutations happen at random! |
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Hardy-Weinberg Equilibrium |
1.Frequencesof alleles do not change over time without evolutionary processes acting on them 2.We can predict equilibrium genotype frequencies if we knowcurrent allele frequencies 3.A perturbed locus will reach Hardy-Weingbergin a single generation |
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Hardy-Weinberg Equilibrium Important assumptions: |
1.No natural selection 2.Random mating 3.No mutation 4.No migration 5.Infinite population size (genetic drift unimportant) |
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two alleles (A and B) |
Three possible genotypes: AA, AB, BB f[AA] + f[AB] + f[BB] = 1 We can calculate the allele frequency from genotype frequencies: The frequency of allele A is p= f[AA] + f[AB]/2 The frequency of allele B is q= f[BB] + f[AB]/2 Thus p + q = 1 |
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What about genotype frequencies? |
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Selection Coeffecient(s) |
is a parameter indicating the strength of selection. If B is recessive, |
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Natural selection |
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Directional selection: |
One allele is favored over others |
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Overdominance(Heterozygote advantage): |
AB is favored over AA or BB |
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Underdominance: |
AB is disfavored (p 221) |
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Frequency-dependent selection: |
Costs and benefits of a phenotype depends on how common it is in the population -positive: common is better -negative: rare is better |
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Genetic drift |
As sample size decreases, theprobability of mismatch between samples and reality increases. - Same idea with genetic drift. |
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Genetic drift |
the process of random fluctuationin allele frequencies due to sampling effects in finite populations. |
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Genetic Drift Three consequences |
-Allelefrequencies fluctuate over time (even without selection, mutation, etc) -Heterozygositydecreases and alleles go to fixation -Separatepopulations diverge in frequency and presence of alleles |
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Genetic Drift |
Given enough time, every gene in a finite population will achieve a fixed allele * True if there is not any selection |
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Genetic Drift |
Genetic drift reduces heterozygosity and genetic diversity/richness |
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Population bottleneck |
Bottlenecks and founder effects. Genetic drift can cause big losses of genetic variation for small populations. Population bottlenecks occur when a population's size is reduced for at least one generation. - Bottleneck Effect occurs when there is a disaster of some sort that reduces a population to a small handful, which rarely represents the actual genetic makeup of the initial population. This leaves smaller variation among the surviving individuals. |
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Galapagos |
- bigger island you get more diversity - When populations are smaller you get more genetic drift? |
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Coalescent theory |
- Gene trees (phylogenetic tree for one gene) - you get more coalescence with a bigger population - coalescent theory states that all genes or alleles in a given population are ultimately inherited from a single ancestor shared by all members of the population, known as the most recent common ancestor |
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Coalescent theory and geneticvariation |
-We can also infer when alleles arose in the population -Any allelic differences among a set of gene copies at the same locus must havearisen by mutation subsequent to the coalescent point for this set of genecopies - Deepercoalescent point àmore variation in the population |
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Founder effect |
-A subset of individuals found a new population -Reduced diversity in the founders relative to the original population -occurs when a new colony is started by a few members of the original population |
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Genetic drift, mutation, andnatural selection |
-If drift was the only force, then all genes would be homozygous. - Mutation prevents complete fixation - Drift becomes more powerful as population size decreases - Selection dominates if strong (high svalue) and populations are large |
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Neutral Theory |
1.Most of the variation presentwithin a population is selectively neutral 2.Most of the changes in DNA or aminoacid sequence over time – and thus many of the molecular differences betweenrelates species – are selectively neutral. |
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Allelic substitution rate |
the time it takes for a new alleleto reach fixation. -Neutraltheorysays that most substitutions are neutral * Butmost mutations are still deleterious (it’s about the standing variation in apopulation) |
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neutralist-selectionist debate |
is about the importance of driftvs. selection in shaping evolutionary change |
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Evidencefor neutral theory Synonymous substitutions: |
-alleles may code for the same phenotype |
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Nonsynonymous mutations |
often have little or no affect onproteins |
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Evidencefor neutral theory Noncoding regions: |
untranslatedareas of the genome |
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Evidence for neutral theory Pseudogenes: |
-nonfunctionalvariants of a once working gene – many go untranslated -Manyalleles that do code for something have fitness effects so small that they’repractically neutral. |
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Substitution rate = |
2Nkv x 1/2N or Substitution rate = kv - Thus, 1.substitution rate is independent ofpopulation size 2.Neutral substitutions occur in thepopulation at the same rate as in an individual * here allele is going to fixation |
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Molecular clocks |
- Mutation rates can be used to estimate the timing of demographic history and divergence times. - But not all species, and not allparts of the genome, mutate at the same rate. |
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Relaxed clock methods: |
statistical approach to overcome the problem of varying mutation rates. * gets over the mutation rate |
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Nearly neutral theory |
Most alleles are neutral, some areslightly deleterious. * even in neutral theory, genetic drift becomes an impt component |
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Multiple loci Polygenetic traits: |
traits that are affected by morethan one gene Example: winter wheat kernel coloris controlled by three genes |
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Additive genetic effects |
phenotypes can be predicted by thesum of allelic effects |
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Multiple loci Epistasis |
Alleles at two or more lociinteraction in nonaddictive ways - Phenotypic effects arecontext-dependent (the contexts of an allele depends on what the other alleles are doing) |
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Multiple loci Haplotype: |
a combination of alleles E.g., For loci A, B, and C, we have alleles A, a, B, b, C, andc. A genotype might be Aa BB cc and a haplotype might be ABc |
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Multiple loci Linkage disequilibrium : |
occurs when there is a statisticalassociation between alleles. E.g., Ab is more likely to occurtogether than ab or AB Can be caused by physical linkage,where loci are on the same chromosome. |
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Coefficient of linkagedisequilibrium (D): |
the difference between the observedhaplotype frequencies and the expected frequency based on allelic frequencies. LD is no occurring if the haplotypeand allelic frequencies are equal D = hAB – fAfB = 0 Positive value à“coupling” Negative value à“repulsion” |
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Whatcauses LD? |
Mutation and migration: Imagine amonomorphic loci near a polymorphic loci that mutates a new allele. This wouldresult in LD, which will probably dissipate over time (with recombination).(everything is all a and then you get one b but then you do the calculations and a would look like it is with b) Selection: selection for polygenicphenotypes can result in LD Drift: random fluctuations inhaplotype frequencies can result in LD |
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Recombinationdissipates LD Genetic hitchhiking |
occurs when a neutral ordeleterious allele “rides along” with an allele under selection |
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Recombination dissipates LD Background selection |
-occurswhen deleterious alleles carry nearby alleles to extinction |
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Selective sweep: |
strong selection brings the focal alleleand others in LD to fixation |
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Adaptivelandscapes |
Multipeakedlandscapes can limit optimal phenotypes |
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Adaptivelandscapes |
Multipeakedlandscapes can limit optimal phenotypes - Looking at fitness; the globalfitness peak (biggest peak), but you have local peaks |
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Borad-senseHeritability (H2) |
Quantitativegenetics VP = VG + VE Borad-sense Heritability (H2) is the fraction of trait variationattributed to genetics. H2 =VG / VG + VE |
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Narrow-senseHeritability (h2) |
h2 = VA / VA + VD + VI + VE Additive genetics is the componentmost accessableto natural selection |
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E.g., How heritable is nocturnalrestlessness? |
H2 they are comparing offspring andparent genotype. By looking at the slope of the line you can get h^(2). |
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Selection differential (S): |
the difference between the meantrait value of the individuals who successfully contribute to the nextgeneration and the mean trait value of all individual in the population. |
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Selection response (R): |
the difference between the meantrait value of the offspring population and the mean trait value of theparental population. |
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Breeder’s equation |
predicts evolutionary change forquantitative traits R = h^(2)S |
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Breeder’sequation example |
Selectionfor larger fruit has a heritability of h^(2) =0.5, and we select fruit that are 2 grams heavier for breeding R = h^(2)S R =0.5(2) R = 1gram (how big the fruit is going to be in the nextgeneration) We expect offspring to have a meanfruit size 1 gram greater than the parents |
