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Unformatted text preview: I. The Hardy-Weinberg Equilibrium I.
In lab this week, you will compare the expected genotype frequencies (calculated In from the H-W equation) to the observed genotype frequencies (obtained by counting actual genotypes) to see if the population is in H-W equilibrium actual If not, then you reject the null hypothesis and conclude that one of the assumptions If is not met, and something interesting may be happening... interesting Populations are only in H-W equilibrium when no evolution is Populations happening, so the assumptions of the H-W equilibrium theorem can also be thought of as a list of ___the causes of evolution_____: ___the A. Mutations B. Gene flow from other populations C. Genetic drift/chance D. Nonrandom mating E. Natural selection (including sexual selection and kin selection) In the next lectures, we will examine each item on the list... II. Causes of Evolution A. Mutation
• Mutation is the source of all novel genetic variation. • Mutation is any change in DNA
– mutations occur randomly with respect to what might be mutations randomly adaptively beneficial in a particular selective regime adaptively – Most mutations are harmful or neutral, but occasionally a Most beneficial mutation will happen beneficial Kinds of mutations
1. ___point mutations_______ Substitutions • silent (synonymous) • missense (nonsynonymous) • nonsense (nonsynonymous) Frameshift mutations • basepair insertion/deletion 1. _chromosomal mutations___ • Duplications • Deletions • Inversions • Translocations • Transpositions II. Causes of Evolution II. A. Mutation, 1. Point Mutations
__point mutations___ alter a single point in the base sequence _substitution___: replacement of a single base nucleotide with another nucleotide of the genetic material, DNA or RNA
_SILENT (synonymous)_ _SILENT Some mutations falling on the 3rd position in a codon (the 3-nucleotide code for an AA) have no effect (neutral mutation) on the AA sequence due to redundancy in the DNA code to _MISSENSE (nonsynonymous)_ A change in the DNA code that causes a change change in the AA sequence (effect on amino acid inserted on the protein. In cases these can be disastrous to the organism) disastrous ___NONSENSE (nonsynonymous)__ A change in the DNA code that creates an change unexpected STOP codon. Typically lethal/disastrous! (enzyme ends up not being produced.
Wild-type SILENT Wild-type Wild-type MISSENSE Wild-type NONSENSE II. Causes of Evolution A. Mutation, 1. Point Mutations
Sickle Cell Anemia: Sickle A single nucleotide change of the single β-globin gene which codes for hemoglobin hemoglobin The substitution mutation is from an The substitution A to a T, causing a codon change from GAG to GTG, which results in the substitution of valine instead of glutamic acid in Hemoglobin glutamic Is a _MISSENSE__mutation Is _MISSENSE__ Is a recessive disorder, so only people who are homozygous Is recessive express full symptoms (heterozygotes have a few sicklerecessive shaped cells, so this is _codominant_(is expressed slightly, the little shaped r allele_)) allele_) Causes periods of pain, and a shortened life-span II. Causes of Evolution A. Mutation, 1. Point Mutations
Another kind of point mutation is a ___frameshift mutation_ ___frameshift This occurs when there is a basepair insertion or deletion, which This or causes the _entire sequence___ of codons to be “read” _entire incorrectly... these can screw things up really badly! Often lethal. these Wild-type Frameshift Frameshift mutant mutant II. Causes of Evolution A. Mutation, 2. Chromosomal Mutations
__chromosomal mutations__ Large-scale mutations of whole genes or parts of chromosomes
Original chromosome Gene Duplication Gene
Often happens during unequal Often crossing over; can be beneficial crossing critical in evolutionary history
Locus D is DELETED Deletion Also often happens during unequal Also crossing over; usually bad news... crossing Inversion
Can reduce recombination, allowing Can genes to be transmitted as a unit genes Can be good or bad for organism. II. Causes of Evolution A. Mutation, 3. Mutation Rates
__mutation rates are usually low____—about one per locus in a million __mutation —about zygotes zygotes – i.e., each nucleotide LOCUS in a gamete has about a 1 in a million ., LOCUS chance of having a mutation each generation chance • Because of the large number of genes that can mutate, chromosome Because rearrangements that can change many genes simultaneously, and large numbers of individuals in a population, mutation can generate substantial variation across the genome and in a population across • But... 1. Because PER LOCUS mutation rate is low, mutations alone produce Because __only minor deviations from Hardy Weinberg equilibrium__at a locus __only 2. If there are large deviations from H-W equilibrium at a particular locus, If other evolutionary processes are likely to be acting other II. Causes of Evolution B. Gene Flow
_gene flow__ results from the migration of individuals and gametes (or _gene other propagules like seeds or larvae) _between populations__, and _between and the incorporation (by successful breeding) of the genes they carry into the novel gene pools the
Before the brown beetle Before arrived, the green allele frequency = 1; after, = 0.87 (if all homozygous) (if These larvae allow gene flow over These thousands of kilometers, even though the adults barely move though Honeybees are important vectors Honeybees for gene flow – moving pollen over long distances long seastar larva II. Causes of Evolution B. Gene Flow
New alleles can be added to the gene pool, OR allele frequencies changed by: changed
...the _immigration___(arrival) of individuals from another population with ...the _immigration___(arrival) different gene frequencies into a recipient population different • If many immigrants arrive in a population carrying an allele that is rare If (or absent), then allele frequencies will change, thus so will genotypic frequencies expected at H-W equilibrium (if many arrive with rate allele frequency, he gene frequency will change and HW is will knocked out of equil.) of ...the _emmigration___(departure) of individuals out of a population; this has ...the _emmigration___(departure) an especially large effect if the source population is small (small popul and many leave, then likely allele frequency will change. • If you started with a population of only 6 M&Ms, 3 red and 3 blue, and If a red ones leaves, the allele frequency changes quite a bit (from 0.5 red to 0.4 red). If the population is 100 M&Ms, then not as big of an effect. (important is relavent to how big the amount of emigrants in comparison to popul.) comparison II. Causes of Evolution B. Gene Flow
So, gene flow has several important effects on evolutionary change at So, 2 levels: levels:
1. _within a population____ 1. • iit can introduce or reintroduce alleles to a population, t increasing the genetic variation of that population (typically good for popul) (typically • it can change allelic frequencies, causing evolution • Thus it will keep the population out of H-W equilibrium as Thus long as it continues long 1. __across populations__ • By moving genes around, gene flow can make distant By populations genetically similar to one another, reducing the chance of genetic divergence & speciation. (the less gene flow, the more likely species will diverge and created new species. And vice versa) created • The less gene flow between two populations, the more The likely that two populations will diverge & evolve into two species. species. _microevolution_ macroevolution II. Causes of Evolution C. Genetic Drift Genetic drift__ is the random change in allele Genetic frequencies and loss of alleles, due to chance (by chance alone, onlly a subset of the genotype will be represented, the larger the occurance, the more times the gene frequency will show up will Genetic drift occurs because populations are not infinitely large: • The larger the population, the LESS the importance of drift o _large_: > 1000-10,000 breeding individuals The smaller the population, the GREATER the importance of drift o small_: <100 - 1,000 breeding individuals (the size of our M&M populations) • Drift happens to some extent in all real populations (though it can be ignored in very large ones), but Drift there are 2 demographic processes that can make drift extremely strong and important: there 1) 2) Founder effects Population bottlenecks Population populations large) populations (These two are becoming more common as we make the II. Causes of Evolution C. Genetic Drift, 1. Founder Effects
Imagine that a new habitat is colonized by just a few breeding individuals: • Simply by chance, the _allele frequencies_ at many loci will differ Simply _allele from what they were in the source population from • And, the _# of alleles___ (allelic diversity) will also be reduced by _# chance alone. chance The probability of allelic loss will be greatest for rare alleles The (WHY?) because there are less likely chance that they will migrate, less likely one of them will appear in your founder population (ie mnm popul and choosing a less frequent color. ) population II. Causes of Evolution II. C. Genetic Drift, 1. Founder Effects
COLOR COLOR Red Green Yellow Blue Orange Brown TOTAL (n) Package 1 21 (0.123) 33 (0.193) 25 (0.146) 30 (0.175) 33 (0.193) 29 (0.170) 171 171 Package 2 14 (0.081) 47 (0.273) 25 (0.145) 37 (0.215) 24 (0.139) 15 (0.087) 172 We can see evidence We of genetic drift in the two bags of M&Ms that were used to get allele frequencies No alleles were lost in this case (populations are reasonably large, No with only 6 alleles), but the allele frequencies in the 2 new populations (the bags) are different than the founder population (where presumably they’re all equal), so the bags _evolved_ presumably _evolved_ II. Causes of Evolution C. Genetic Drift, 1. Founder Effects
1890-91 (100 birds) 2006 (200,000,000 birds) • European starlings introduced to N. America in 1890 (n=60) & 1891 (n=40) European to central park in New York, by one complete idiot, Eugene Schieffelin, of the Acclimation Society of N. America the Current population in N. America ≈ 200,000,000 birds Current Source population carries >31 alleles at 11 loci N. American population now carries 18 alleles at the same loci (42% loss of allelic diversity because of that founder event. ) allelic • • • II. Causes of Evolution II. C. Genetic Drift, 2. Population Bottlenecks
Population bottlenecks are very similar to founder effects, but occur when populations are greatly reduced in size populations • Bottlenecks almost always cause allelic frequencies to change and Bottlenecks almost alleles to be lost compared to the pre-bottleneck population. alleles • When populations remain small for multiple (i.e., >5-10 generations), When the loss of allelic diversity may be extreme the • Bottlenecks occur when species are overharvested by humans, or when Bottlenecks their habitats are reduced or fragmented (cut up in diff, sections, might not allow interbreeding) extensively allow
• This is a major concern in _conservation biology!, Why do we care? A diverse population allows This for variability to survive against diseases for example. and more individuals can survive. II. Causes of Evolution II. C. Genetic Drift, 2. Population Bottlenecks
Greater prairie chickens in Illinois were reduced by hunting & habitat loss to about 50 birds in the 1990s; they lost __> 75% of their original allelic diversity. 50 II. Causes of Evolution C. Genetic Drift, 2. Population Bottlenecks
• California fan palms are now restricted to a few oases in southern California California due to climate change & habitat destruction due • There is _virtually no genetic variation___ in any population There _virtually II. Causes of Evolution C. Genetic Drift, 2. Population Bottlenecks
Elephant seals Elephant • Before 1884, populations estimated Before between 200,000 & 1,000,000 seals between • By 1892, hunting reduced the size of By the populations to 8-20 individuals the • In 1991, populations estimated to In have recovered to >125,000 individuals individuals • Now populations growing 20-30% per Now year year • There is still virtually no detectable There genetic variations, only a little at the most variable loci most Go see them in the winter at Año Nuevo Go State Park!! Make appt. , this is during breeding season breeding II. Causes of Evolution D. Non-Random Mating
Nonrandom mating occurs when individuals choose mates with Nonrandom particular genotypes or phenotypes; there are 3 types: 1. _inbreeding_(or, more correctly, positive assortative mating) (or, positive occurs when individuals preferentially mate with the same genotype as themselves (often close relatives) genotype 1. _outbreeding__(negative assortative mating) opposite of (negative inbreeding, occurs when individuals avoid mating with similar genotypes (or close relatives); ...we’ll skip this one... Causes deviation from HW equilibrium deviation 1. _sexual selection__ also causes non-random mating, but we’ll also but talk about this as a form of _natural selection__selection _natural II. Causes of Evolution D. Non-Random Mating, 1. Inbreeding
Inbreeding (positive assortative mating) occurs when individuals Inbreeding preferentially mate with the same genotype as themselves: preferentially
a. Start with 3 genotypes: A1A1, A1A2, A2A2 • • • p (A1) = 0.5 (A q (A2) = 0.5 (A What are the EXPECTED genotype frequencies at H-W equilibrium? b. Mating rule for completely inbred population: Each genotype only b. only mates with genotypes like itself (i.e. perfect inbreeding) most extreme scenario. extreme c. If A1A1 homozygotes only mate with A1A1 homozygotes, & A2A2 c. If homozygotes homozygotes only mate with A2A2 homozygotes, then neither of these homozygotes kinds of inbred matings will have any effect on allelic and genotypic frequencies in the next generation, just propagating their own kind. d. What matters is matings between heterozygotes... d. What between II. Causes of Evolution D. Non-Random Mating, 1. Inbreeding
Here we just look at the heterozygote matings...
1st generation: F1’s : A1A2 x A1A2(50%) A1A2
all hets A1A1(25%) A2A2(25%) 50% hetz 2nd generation F2’s : A1A2 x A1A2(50%) A1A2 all hetz A1A1(25%) A2A2(25%) 50% hetz The number of heterozygotes keeps declining by 50% per generation, until The they’re gone (not as extreme when inbreeding isn’t “perfect”) they’re With perfect inbreeding: With 1. allele frequencies _do NOT change____ allele _do 2. __heterozygosity declines_ dramatically (up to 50% per gen) II. Causes of Evolution D. Non-Random Mating, 1. Inbreeding
Effects of Inbreeding on Fitness: PKU (phenylketonuria) kills kids when young., Inbreeding increases the likelihood that deleterious recessive alleles will be present in the homozygous state: _inbreeding depression_(not good be for popul) for
PKU is caused by a recessive mutation in a gene we’ll call the PKU R-locus (mutant allele = r) R-locus RR and Rr (CARRIER) genotypes can convert phenylalanine RR to tyrosine to rr genotypes cannot do this, so a byproduct of phenylalanine rr accumulates in nervous tissue and causes severe brain damage The observed frequency of the r allele is about 0.01 in human populations, so the EXPECTED frequency of rr homozygotes (diseased) is (0.01)2 = 1/10,000 (diseased) In Ireland, p(r) is also about 0.01, yet until recently, the In incidence of PKU was closer to 1/4500 births. incidence How can this be? Inbreeding. Some amount of it, small areas How with ppl in small towns so incidence of pku went up. Even though that allele frequency wasn't higher, the rate of expression was higher showing that more inbreeding is going on. II. Causes of Evolution II. D. Non-Random Mating, 2. Outbreeding
_______________________________ _______________________________ The pin type has a stigma at the The top; the thrum type is reversed top; Insects get pollen on their bodies Insects and transfer it between pin and thrum flowers, or vice versa, to pollinate them pollinate Nectar at Nectar bottom bottom Fig 22.11 in Fig text text Outbreeding causes fewer than expected crosses between _________________ Outbreeding _________________ ...
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This note was uploaded on 11/29/2010 for the course BIOLOGY 1211 taught by Professor Patricelli during the Spring '10 term at UC Davis.
- Spring '10