W09L12_Population+GeneticsII_post - Feb 3 2009 Quail Ridge...

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Unformatted text preview: Feb 3 2009 Quail Ridge Reserve UC Davis wireless reserve Capuchin monkey Panama Called the Automated Radio Telemetry System, the method relies on seven 130foot-high radio towers scattered across the island that can monitor data from many radio-tagged individuals simultaneously, round the clock, through the calendar. Population Genetics. 1. Multiplicative Rule, Additive Rule 0.5 0.5 0.25 0.25 0.5 0.25 Population Genetics Allele Frequencies, Genotype Frequencies, 0.5 0.25 5 N = 50 individuals 30 A2A2 15 A1A2 What is the probability of drawing: COLOR Package 1 A1A2 Two red: Red 21 (0.123) Green 33 (0.193) Yellow 25 (0.146) Two green: Blue 30 (0.175) Orange 33 (0.193) Brown 29 (0.170) TOTAL (n) 171 Simple conditional probabilities A2A2 A1A1 A1A2 A1A2 A1A2 A1A1 A1A2 A1A2 A1A2 A1A1 A1A2 A1A2 A1A2 A1A2 A1A2 A1A2 A1A1 A1A1 A1A1 **-math problem, not a genetics problem A1A2 A1A2 A1A2 A1A1 A red, green and a blue** p+q=1 A1A1 A2A2 A1A2 A1A2 A1A2 A1A2 A1A2 Just to hammer this home: A1A1 A1A2 A1A2 p= freq of A1= q = freq A2= A1A2 A2A2 A1A2 A1A1 A2A2 Orange and brown: A1A1 A1A1 A1A1 A1A1 Green and yellow: Finding p and q A1A2 A1A2 A1A1 A1A2 A1A2 The probability of a genotype: Population Genetics Allele Frequencies from Genotype Frequencies Population Genetics The Hardy-Weinberg Equilibrium HardyGeneration II An example from the textbook... AA =___________ Aa = ___________ Aa = ___________ p = 0.55 p = _________________ q = _________________ Mix into giant bag (gene pool)... Text Fig 22.7 q = 0.45 0.55(2) = 0.3025; 2*.45*.55 = 0.495; 0.45(2) = 0.2025 Text Fig 22.7 1 Population Genetics Some FUN! Problems FUN! p2 pq pq q2 Population Genetics The Hardy-Weinberg Equilibrium Hardy- IF p = _____, and q = _____ _____, f(AA) = f(Aa) = f(a,a = f(A f(A f(a,a) p2 pq IF p = _____, and q = _____ _____, f(A1A2) = f(A2A2) = f(A1A1) = f(A f(A f(A IF p = _____, and q = _____ _____, f(AA) = f(Aa) = f(aa = f(A f(A f(aa) p p IF p = _____, and q = _____ _____, f(AA) = f(Aa) = f(aa = f(A f(A f(aa) q p2 r p*q p*r p q r p + q + r = _______ p p = q (HW eq) Which populations are at Hardy-Weinberg Equilibrium? Hardy1. 2. 3. 4. 5. 6. 7. p = 0.75; q = 0.25 p = 0.75; q = 0.35 AA = 214; Aa = 428; aa = 214 f(AA) = 0.54; f(Aa) = 0.30; f(aa) = 0.16 f(AA) = 0.35; f(Aa) = 0.70; f(aa) = 0.35 f(AA) = 0.64; f(Aa) = 0.32; f(aa) =0.04 AA = 320; Aa = 160; aa = 20 p*q q2 q*r q q = r IF p = _____, and q = _____ _____, f(AA) = f(Aa) = f(aa = f(A f(A f(aa) pq q2 p*r r2 r r = q*r 3 alleles!!! Population Genetics The Hardy-Weinberg Equilibrium HardyThings that follow from the H-W equilibrium: H1. At H-W equilibrium, genotypic frequencies will be determined Hsolely by allelic frequencies 2. Note that when there are 2 alleles, and p = q = 0.5, the expected ratio of homozygotes to heterozygotes is 1:2:1, as it was for Mendelian inheritance Population Genetics The Hardy-Weinberg Equilibrium Hardy- H-W Equilibrium: the fundamental theorem of population genetics • The H-W theorem makes a set of null predictions about expected allelic and Hgenotypic frequencies • If the observed values of genotypic frequencies do not match those expected those at H-W equilibrium, THEN SOME EVOLUTIONARY PROCESSES MUST BE HACTING ON THE GENE POOL 2 Population Genetics The Hardy-Weinberg Equilibrium Hardy- The Hardy-Weinberg Theorem: In diploid organisms, allele frequencies & Hardygenotypic ratios in large biparental populations reach an equilibrium in one equilibrium generation, and remain constant thereafter, unless disturbed by… by… 1. M 2. G 3. G 4. N 5. N Causes of Evolution A. Mutation, 1. Point Mutations Causes of Evolution A. Mutation • Mutation is the source of all novel genetic variation. • Mutation is any change in DNA – mutations occur ____________ with respect to what might be adaptively beneficial in a particular selective regime – Most mutations are harmful or neutral, but if conditions change, could become advantageous Kinds of mutations 1. Point mutations Substitutions • silent (synonymous) • missense (nonsynonymous) nonsynonymous) • nonsense (nonsynonymous) nonsynonymous) Frameshift mutations • basepair insertion/deletion 2. Chromosomal mutations • Duplications • Deletions • Inversions • Translocations • Transpositions Point Mutations alter a single point in the base sequence a. Substitution: replacement of a single base nucleotide with another nucleotide i. SILENT (synonymous) Some mutations falling on the 3rd position in a codon (the 3-nucleaotide code for an 3AA) have no effect on the AA sequence due to redundancy in the DNA code SILENT Wild-type Wild- ii. MISSENSE (nonsynonymous) nonsynonymous) A change in the DNA code that causes an change in the AA sequence MISSENSE Wild-type Wild- iii. NONSENSE (nonsynonymous) nonsynonymous) A change in the DNA code that creates an unexpected STOP codon. Typically lethal! codon. EXAMPLE Wild-type Wild- NONSENSE Causes of Evolution A. Mutation, 1. Point Mutations Sickle Cell Anemia: Another kind of point mutation is a Frameshift mutation A single nucleotide change of the β-globin gene which codes for hemoglobin This occurs when there is a basepair insertion or deletion, which causes the sequence of codons to be “read” incorrectly... these can read” screw things up really badly! Often lethal. The point mutation is from an 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 Wild-type Wild- Is a missense mutation Is a recessive disorder, so only people who are homozygous recessive express full symptoms (heterozygotes have a few sicklesickleshaped cells, so this is slightly codominant) codominant) Frameshift mutant Causes periods of pain, and a shortened life-span life- 3 Causes of Evolution A. Mutation, 2. Chromosomal Mutations Causes of Evolution A. Mutation, 3. Mutation Rates Chromosomal Mutations Large-scale mutations of whole genes or parts of chromosomes LargeOriginal chromosome Gene Duplication E Deletion Locus D is DELETED Often happens during unequal crossing over; can be beneficial Also often happens during unequal crossing over; usually bad news... Inversion Can reduce recombination, allowing genes to be transmitted as a unit Causes of Evolution A. Mutation, 3. Mutation Rates Spectacular Exceptions Each LOCUS in a gamete has about a 1 in a million chance of mutating each generation Chromosomes form rings leading to high rates of reciprocal translocations and not independently assorting properly. Major radiations of species with different ring forming attributes. • Because of the large number of genes that can mutate, chromosome rearrangements that can change many genes simultaneously, and large large numbers of individuals in a population, mutation can generate substantial variation across the genome and in a population • However: because PER LOCUS mutation rate is low, mutations alone produce small deviations from Hardy-Weinberg equilibrium at a locus. HardyIf there are large deviations from H-W equilibrium at a particular locus, Hother evolutionary processes are likely to be dominating. Tetraploids Camissonia campestris Mojave suncup 1 of ~105 sp, spp, var in genus Causes of Evolution B. Gene Flow GENE FLOW results from the migration of individuals and gametes (or other propagules like seeds or larvae) from one population to another, another, and the incorporation (by successful breeding) of the genes they carry into the novel gene pools Before the brown beetle arrived, the green allele frequency = 1; after, = 0.87 (if all homozygous) 2N 2N gametes 4N These larvae allow gene flow over thousands of kilometers, even though the adults barely move Tetraploidy is common in plants (and some animals). A failure of chromosomal segregation leads to 2N gametes that fuse to form 4N individuals. Often the extra genes can enhance favorable characteristics, such as flower size. Honeybees are important vectors for gene flow – moving pollen over long distances seastar larva 4 Causes of Evolution B. Gene Flow New alleles can be added to the gene pool, OR allele frequencies changed by: ...the _________________ (arrival) of individuals from another population with different gene frequencies into a recipient population population ...the ________________ (departure) of individuals out of a population; this has an especially large effect if the source population is small Causes of Evolution C. Genetic Drift The random change in allele frequencies and loss of alleles, due to chance Genetic drift occurs because populations are not infinitely large: • The larger the population, the LESS the importance of drift • Causes of Evolution B. Gene Flow So, gene flow has important effects on evolutionary change at TWO levels: 1. Within a population • Gene flow can introduce alleles to a population, increasing the genetic variation of that population • Gene flow can change allelic frequencies, causing evolution • Thus it will keep the population out of H-W Hequilibrium as long as it continues 2. Across populations • By moving genes around, gene flow can make distant populations genetically similar to one another, reducing the chance of genetic divergence & speciation. • The less gene flow between two populations, the more likely that two populations will diverge & evolve into two species. Microevolutionary consequences Macroevolutionary consequences Imagine a new habitat is colonized by just a few individuals. Allele frequencies will likely be changed simply by chance events. In addition, rare alleles are likely to be lost (why rare ones?). “New” population Established population The smaller the population, the GREATER the importance of drift Drift happens to some extent in all real populations (though it can be ignored in very large ones), but there are 2 demographic processes that can make drift extremely strong and important: important: 1) 2) Founder effects Population bottlenecks These are becoming more common as we make populations very small! Causes of Evolution C. Genetic Drift, 1. Founder Effects 1890-91 (100 birds) 1890- 2009 (200,000,000 birds) e.g., Founder effect Causes of Evolution C. Genetic Drift, 2. Population Bottlenecks Population bottlenecks are very similar to founder effects, but occur when populations are greatly reduced in size • Bottlenecks occur when species are overharvested by humans, or when when their habitats are reduced or fragmented extensively • European starlings introduced to N. America in 1890 (n=60) & 1891 (n=40) by Eugene Schieffelin, of the Acclimation Society of N. America Schieffelin, • Current population in N. America ≈ 200,000,000 birds • Source population carries >31 alleles at 11 loci • N. American population now carries 18 alleles at the same loci • 42% loss relative to native populations 5 II. Causes of Evolution C. Genetic Drift, 2. Population Bottlenecks Causes of Evolution C. Genetic Drift, 2. Population Bottlenecks Greater prairie chickens in Illinois were reduced by hunting & habitat loss to about habitat 50 birds in the 1990s; they lost an estimated > 75% of allelic diversity they • California fan palms are now restricted to a few oases in southern California due to climate change & habitat destruction, No measurable variation Causes of Evolution Bottleneck Hall of Fame Causes of Evolution Bottleneck Hall of Fame Speke’s Gazelle Causes of Evolution Bottleneck Hall of Fame • Before 1884, populations estimated between 200,000 & 1,000,000 seals • By 1892, hunting reduced the size of the populations to 8-20 individuals 8• In 1991, populations estimated to have recovered to >125,000 individuals Causes of Evolution D. Non-Random Mating NonNonrandom mating occurs when individuals choose mates with particular genotypes or phenotypes; there are 2 types: 1. INBREEDING (or, more correctly, positive assortative mating) occurs when individuals preferentially mate with the same genotype as themselves 2. OUTBREEDING (negative assortative mating) occurs when individuals avoid mating with similar genotypes (or close relatives); relatives); ...we’ll skip this one... ...we’ 3. Sexual Selection also causes non-random mating, but we’ll talk nonwe’ about this as a form of selection later 4. Strong Disparity in mating opportunity Go see them in the winter at Año Nuevo State Park!! 6 Causes of Evolution D. Non-Random Mating, 1. Inbreeding NonInbreeding (positive assortative mating) occurs when individuals preferentially mate with the same genotype as themselves: a. Start with 3 genotypes: A1A1, A1A2, A2A2 • p (A1) = 0.5 • q (A2) = 0.5 • What are the EXPECTED genotype frequencies at H-W equilibrium? H- Causes of Evolution D. Non-Random Mating, 1. Inbreeding NonImagine heterozygote inbred matings... matings... 1st generation: F1’s 2nd generation F2’s b. Mating rule: Each genotype only mates with genotypes like itself (i.e. perfect inbreeding) c. If A1A1 homozygotes only mate with A1A1 homozygotes, & A2A2 homozygotes, homozygotes only mate with A2A2 homozygotes, then neither of these homozygotes, kinds of inbred matings will have any effect on allelic and genotypic genotypic frequencies in the next generation d. What matters is matings between heterozygotes... Causes of Evolution D. Non-Random Mating, 1. Inbreeding Non- : : A1A2 x A1A1(25%) A1A2 A1A2(50%) x A1A1(25%) All hets A1A2 A2A2(25%) A1A2 A1A2(50%) 50% hets All hets A2A2(25%) 50% hets The number of heterozygotes keeps declining by 50% per generation, generation, until they’re gone (not as extreme when inbreeding isn’t “perfect”) they’ isn’ perfect” With perfect inbreeding: 1. allele frequencies __________________ 2. heterozygosity declines dramatically (up to 50% per gen) Causes of Evolution D. Non-Random Mating, 2. Outbreeding Non- Effects of Inbreeding on Fitness: PKU (phenylketonuria) (phenylketonuria) Inbreeding increases the likelihood that deleterious recessive alleles will alleles be present in the homozygous state: ________________________ PKU is caused by a recessive mutation in a gene we’ll we’ call the R-locus (mutant allele = r) RRR and Rr (CARRIER) genotypes can convert phenylalanine to tyrosine rr genotypes cannot do this, so a byproduct of phenylalanine 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 In Ireland, p(r) is also about 0.01, yet until recently, the p(r) incidence of PKU was closer to 1/4500 births. The pin type has a stigma at the top; the thrum type is reversed Insects get pollen on their bodies and transfer it between pin and thrum flowers, or vice versa, to pollinate them Nectar at bottom Fig 22.11 in text How can this be? 7 ...
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This note was uploaded on 10/08/2009 for the course BIS 2 taught by Professor Schwartzandkeen during the Spring '09 term at UC Davis.

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