1. "HARD" Selection can 'cost' a population individuals:

1. "HARD" Selection can 'cost' a population individuals:
B. Genetic Load 1. "HARD" Selection can 'cost' a population individuals: 2. Why is this a problem? 3. Scenario 4. Solutions a. Selectionists - Suppose we have a population of aa homozygotes initially. All the territories are occupied by aa individuals and 10 individuals die. - Well, If an 'A' allele is produce by mutation and heterozygotes have the highest relative fitness (probability of acquiring a territory), then the allele "A" increase in frequency to equilibrium.... - Selection occurs, BUT THERE ARE STILL ONLY 10 DEATHS PER GENERATION. - In this case there is NO genetic load, as selection is NOT causing ADDITIONAL mortality. It is just changing the probability of who dies. - So, selection across lots of loci does not NECESSARILY lead to impossible loads.... as long as it is SOFT SELECTION

B. Genetic Load 1. "HARD" Selection can 'cost' a population individuals: 2. Why is this a problem? 3. Scenario 4. Solutions a. Selectionists b. Neutralists

B. Genetic Load 1. "HARD" Selection can 'cost' a population individuals: 2. Why is this a problem? 3. Scenario 4. Solutions a. Selectionists b. Neutralists - Maybe MOST of this variation is NEUTRAL, as is simply maintained by drift as new mutant alleles sequentially replace one another.

B. Genetic Load 1. "HARD" Selection can 'cost' a population individuals: 2. Why is this a problem? 3. Scenario 4. Solutions a. Selectionists b. Neutralists - Maybe MOST of this variation is NEUTRAL, as is simply maintained by drift as new mutant alleles sequentially replace one another. c. In a sense, the argument is really about selection.

B. Genetic Load 1. "HARD" Selection can 'cost' a population individuals: 2. Why is this a problem? 3. Scenario 4. Solutions a. Selectionists b. Neutralists - Maybe MOST of this variation is NEUTRAL, as is simply maintained by drift as new mutant alleles sequentially replace one another. c. In a sense, the argument is really about selection. Selectionists state that selection is important for 2 reasons - it eliminates bad alleles and FAVORS advantageous alleles.

B. Genetic Load 1. "HARD" Selection can 'cost' a population individuals: 2. Why is this a problem? 3. Scenario 4. Solutions a. Selectionists b. Neutralists - Maybe MOST of this variation is NEUTRAL, as is simply maintained by drift as new mutant alleles sequentially replace one another. c. In a sense, the argument is really about selection. Selectionists state that selection is important for 2 reasons - it eliminates bad alleles and FAVORS advantageous alleles. Neutralists agree that selection weeds out deleterious alleles, but they claim that this leaves a set of sequences that are functionally equivalent - neutral - in relative value. And changes in these equivalent alleles occur as a consequence of drift.

V. The Neutral Theory C. Neutral Variation

V. The Neutral Theory C. Neutral Variation
- Variation occurs at many levels, from genes to proteins to physical and behavioral characteristics of organisms.

- Variation occurs at many levels, from genes to proteins to physical and behavioral characteristics of organisms. - adaptive phenotypic variation is due to selection.

- Variation occurs at many levels, from genes to proteins to physical and behavioral characteristics of organisms. - adaptive phenotypic variation is due to selection. - But is ALL genetic variation of selective value?

- Variation occurs at many levels, from genes to proteins to physical and behavioral characteristics of organisms. - adaptive phenotypic variation is due to selection. - But is ALL genetic variation of selective value? - "no"; obviously, silent mutations are not maintained by selection

- Variation occurs at many levels, from genes to proteins to physical and behavioral characteristics of organisms. - adaptive phenotypic variation is due to selection. - But is ALL genetic variation of selective value? - "no"; obviously, silent mutations are not maintained by selection - So, Kimura suggested that there is too much variation at the DNA level to be explained by selection... he suggested that MOST of the variation in DNA is of NO selective value - it is NEUTRAL VARIATION.

- Variation occurs at many levels, from genes to proteins to physical and behavioral characteristics of organisms. - adaptive phenotypic variation is due to selection. - But is ALL genetic variation of selective value? - "no"; obviously, silent mutations are not maintained by selection - So, Kimura suggested that there is too much variation at the DNA level to be explained by selection... he suggested that MOST of the variation in DNA is of NO selective value - it is NEUTRAL VARIATION. - Curiously, the rate of substitution by drift, alone = the rate of mutation:

- Variation occurs at many levels, from genes to proteins to physical and behavioral characteristics of organisms. - adaptive phenotypic variation is due to selection. - But is ALL genetic variation of selective value? - "no"; obviously, silent mutations are not maintained by selection - So, Kimura suggested that there is too much variation at the DNA level to be explained by selection... he suggested that MOST of the variation in DNA is of NO selective value - it is NEUTRAL VARIATION. - Curiously, the rate of substitution by drift, alone = the rate of mutation: 1) The number of new alleles produced at a locus = 2N(m), where m is the mutation rate.

- Variation occurs at many levels, from genes to proteins to physical and behavioral characteristics of organisms. - adaptive phenotypic variation is due to selection. - But is ALL genetic variation of selective value? - "no"; obviously, silent mutations are not maintained by selection - So, Kimura suggested that there is too much variation at the DNA level to be explained by selection... he suggested that MOST of the variation in DNA is of NO selective value - it is NEUTRAL VARIATION. - Curiously, the rate of substitution by drift, alone = the rate of mutation: 1) The number of new alleles produced at a locus = 2N(m), where m is the mutation rate. - So, if the average mutation rate is 1 in 10,000, but there are 20,000 individuals (2N = 40,000 alleles), then on average 4 new alleles will be produced by mutation every generation.

- Variation occurs at many levels, from genes to proteins to physical and behavioral characteristics of organisms. - adaptive phenotypic variation is due to selection. - But is ALL genetic variation of selective value? - "no"; obviously, silent mutations are not maintained by selection - So, Kimura suggested that there is too much variation at the DNA level to be explained by selection... he suggested that MOST of the variation in DNA is of NO selective value - it is NEUTRAL VARIATION. - Curiously, the rate of substitution by drift, alone = the rate of mutation: 1) The number of new alleles produced at a locus = 2N(m), where m is the mutation rate. - So, if the average mutation rate is 1 in 10,000, but there are 20,000 individuals (2N = 40,000 alleles), then on average 4 new alleles will be produced by mutation every generation. 2) Each allele has a probability of fixation = 1/2N.

- Variation occurs at many levels, from genes to proteins to physical and behavioral characteristics of organisms. - adaptive phenotypic variation is due to selection. - But is ALL genetic variation of selective value? - "no"; obviously, silent mutations are not maintained by selection - So, Kimura suggested that there is too much variation at the DNA level to be explained by selection... he suggested that MOST of the variation in DNA is of NO selective value - it is NEUTRAL VARIATION. - Curiously, the rate of substitution by drift, alone = the rate of mutation: 1) The number of new alleles produced at a locus = 2N(m), where m is the mutation rate. - So, if the average mutation rate is 1 in 10,000, but there are 20,000 individuals (2N = 40,000 alleles), then on average 4 new alleles will be produced by mutation every generation. 2) Each allele has a probability of fixation = 1/2N. 3) So, the rate of substitution = (number of new alleles formed) x (probability one become fixed) = 2N(m) x 1/2N = m per generation! CRAZY! 4 x 1/40,000 = 1/10,000 = m.

V. The Neutral Theory C. Neutral Variation D. Predictions and Results

D. Predictions and Results
V. The Neutral Theory C. Neutral Variation D. Predictions and Results 1. Rates of molecular evolution should vary in functional and non-functional regions

V. The Neutral Theory C. Neutral Variation D. Predictions and Results 1. Rates of molecular evolution should vary in functional and non-functional regions - Rates should vary in different codon positions. Variation at the third position should be higher, because these are usually silent mutations. Mutations at the first two position change amino acids, and these changes are probably deleterious (selection weeds them out, so the original sequence is maintained; ie., rate of substitution is LOW).

V. The Neutral Theory C. Neutral Variation D. Predictions and Results 1. Rates of molecular evolution should vary in functional and non-functional regions - Rates should vary in different codon positions. Variation at the third position should be higher, because these are usually silent mutations. Mutations at the second position change amino acids, and these changes are deleterious. PATTERN CONFIRMED.

V. The Neutral Theory C. Neutral Variation D. Predictions and Results 1. Rates of molecular evolution should vary in functional and non-functional regions - Rates should vary in different codon positions. Variation at the third position should be higher, because these are usually silent mutations. Mutations at the second position change amino acids, and these changes are deleterious. PATTERN CONFIRMED. - Rates should vary in coding and non-coding regions. Variation in Introns should occur more rapidly than variation in exons, since introns are not transcribed and are also invisible to selection.

V. The Neutral Theory C. Neutral Variation D. Predictions and Results 1. Rates of molecular evolution should vary in functional and non-functional regions - Rates should vary in different codon positions. Variation at the third position should be higher, because these are usually silent mutations. Mutations at the second position change amino acids, and these changes are deleterious. PATTERN CONFIRMED. - Rates should vary in coding and non-coding regions. Variation in Introns should occur more rapidly than variation in exons, since introns are not transcribed and are also invisible to selection. PATTERN CONFIRMED

V. The Neutral Theory C. Neutral Variation D. Predictions and Results 1. Rates of molecular evolution should vary in functional and non-functional regions - Rates should vary in different codon positions. Variation at the third position should be higher, because these are usually silent mutations. Mutations at the second position change amino acids, and these changes are deleterious. PATTERN CONFIRMED. - Rates should vary in coding and non-coding regions. Variation in Introns should occur more rapidly than variation in exons, since introns are not transcribed and are also invisible to selection. PATTERN CONFIRMED - Rates should vary in functional and non-functional regions of proteins.

V. The Neutral Theory C. Neutral Variation D. Predictions and Results 1. Rates of molecular evolution should vary in functional and non-functional regions - Rates should vary in different codon positions. Variation at the third position should be higher, because these are usually silent mutations. Mutations at the second position change amino acids, and these changes are deleterious. PATTERN CONFIRMED. - Rates should vary in coding and non-coding regions. Variation in Introns should occur more rapidly than variation in exons, since introns are not transcribed and are also invisible to selection. PATTERN CONFIRMED - Rates should vary in functional and non-functional regions of proteins. PATTERN CONFIRMED

V. The Neutral Theory C. Neutral Variation D. Predictions and Results 1. Rates of molecular evolution should vary in functional and non-functional regions - Rates should vary in different codon positions. Variation at the third position should be higher, because these are usually silent mutations. Mutations at the second position change amino acids, and these changes are deleterious. PATTERN CONFIRMED. - Rates should vary in coding and non-coding regions. Variation in Introns should occur more rapidly than variation in exons, since introns are not transcribed and are also invisible to selection. PATTERN CONFIRMED - Rates should vary in functional and non-functional regions of proteins. PATTERN CONFIRMED - Rates should vary between vital proteins and less vital proteins.

V. The Neutral Theory C. Neutral Variation D. Predictions and Results 1. Rates of molecular evolution should vary in functional and non-functional regions - Rates should vary in different codon positions. Variation at the third position should be higher, because these are usually silent mutations. Mutations at the second position change amino acids, and these changes are deleterious. PATTERN CONFIRMED. - Rates should vary in coding and non-coding regions. Variation in Introns should occur more rapidly than variation in exons, since introns are not transcribed and are also invisible to selection. PATTERN CONFIRMED - Rates should vary in functional and non-functional regions of proteins. PATTERN CONFIRMED - Rates should vary between vital proteins and less vital proteins. PATTERN CONFIRMED

V. The Neutral Theory C. Neutral Variation D. Predictions and Results 1. Rates of molecular evolution should vary in functional and non-functional regions 2. Rates of replacement (substitution of one fixed allele by another that reaches fixation) should be constant over geologic time.

V. The Neutral Theory C. Neutral Variation D. Predictions and Results 1. Rates of molecular evolution should vary in functional and non-functional regions 2. Rates of replacement (substitution of one fixed allele by another that reaches fixation) should be constant over geologic time. - If changes are random and occur at a given rate, and are selectively neutral, then they should "tick" along like a clock.

V. The Neutral Theory C. Neutral Variation D. Predictions and Results 1. Rates of molecular evolution should vary in functional and non-functional regions 2. Rates of replacement (substitution of one fixed allele by another that reaches fixation) should be constant over geologic time. - If changes are random and occur at a given rate, then they should "tick" along like a clock. - Selection should slow change when an adapted complex becomes abundant, and speed rates when a new adaptive combination occurs, like in obviously adaptive morphological traits. - PATTERNS CONFIRMED (usually).

V. The Neutral Theory C. Neutral Variation D. Predictions and Results 1. Rates of molecular evolution should vary in functional and non-functional regions 2. Rates of replacement (substitution of one fixed allele by another that reaches fixation) should be constant over geologic time. - If changes are random and occur at a given rate, then they should "tick" along like a clock. - Selection should slow change when an adapted complex occurs, and speed rates when a new adaptive combination occurs, like in obviously adaptive morphological traits. - PATTERNS CONFIRMED (usually). - We might even use these predictions to determine which parts of a protein are functional: the functional regions should show the slowest rate of substitutional change.

V. The Neutral Theory C. Neutral Variation D. Predictions and Results 1. Rates of molecular evolution should vary in functional and non-functional regions 2. Rates of replacement (substitution of one fixed allele by another that reaches fixation) should be constant over geologic time. 3. Rates of morphological change should be independent of the rate of molecular change.

V. The Neutral Theory C. Neutral Variation D. Predictions and Results 1. Rates of molecular evolution should vary in functional and non-functional regions 2. Rates of replacement (substitution of one fixed allele by another that reaches fixation) should be constant over geologic time. 3. Rates of morphological change should be independent of the rate of molecular change. - "Living Fossils" show extreme genetic change and variation, yet have remained morphologically unchanged for millenia. And, their rate of genetic change in this morphologically constant species is the same as in hominids, which have changed dramatically in morphology over a short period. PATTERN CONFIRMED

V. The Neutral Theory C. Neutral Variation D. Predictions and Results E. Problems and Resolutions

V. The Neutral Theory C. Neutral Variation D. Predictions and Results E. Problems and Resolutions 1. Selection also explains different mutation rates in functional and non-functional regions

D. Predictions and Results E. Problems and Resolutions
V. The Neutral Theory C. Neutral Variation D. Predictions and Results E. Problems and Resolutions 1. Selection also explains different mutation rates in functional and non-functional regions Essentially, since most adaptive changes should be slight, fewer mutations in functional regions are likely to improve function. So, the rate of change is "constrained" to only those changes that are neutral or ADAPTIVE. Also, a change of one AA is likely to cause a smaller change if it is in a less functional region. "Tweeking" less functional regions are, paradoxically, MORE LIKELY to be adaptive, whereas "tweeking" functional regions are more likely to be deleterious. - Something that is non-functional can’t be hurt by change…it’s already off.

V. The Neutral Theory C. Neutral Variation D. Predictions and Results E. Problems and Resolutions 1. Selection also explains different mutation rates in functional and non-functional regions 2. A truly neutral clock should tick off mutations at a constant rate. But should this ticking occur per unit time, or per generation?

V. The Neutral Theory C. Neutral Variation D. Predictions and Results E. Problems and Resolutions 1. Selection also explains different mutation rates in functional and non-functional regions 2. A truly neutral clock should tick off mutations at a constant rate. But should this ticking occur per unit time, or per generation? - Since mutations produce new alleles (a new "tick"), and mutations only occur during replication of the DNA, it would seem that a truly neutral clock should tick at a rate dependent on the generation time of the organism.

V. The Neutral Theory C. Neutral Variation D. Predictions and Results E. Problems and Resolutions 1. Selection also explains different mutation rates in functional and non-functional regions 2. A truly neutral clock should tick off mutations at a constant rate. But should this ticking occur per unit time, or per generation? - Since mutations produce new alleles (a new "tick"), and mutations only occur during replication of the DNA, it would seem that a truly neutral clock should tick at a rate dependent on the generation time of the organism. - Species with rapid generation times should accumulate mutations at a faster rate than long-lived species with slower generation times.

V. The Neutral Theory C. Neutral Variation D. Predictions and Results E. Problems and Resolutions 1. Selection also explains different mutation rates in functional and non-functional regions 2. A truly neutral clock should tick off mutations at a constant rate. But should this ticking occur per unit time, or per generation? - Since mutations produce new alleles (a new "tick"), and mutations only occur during replication of the DNA, it would seem that a truly neutral clock should tick at a rate dependent on the generation time of the organism. - Species with rapid generation times should accumulate mutations at a faster rate than long-lived species with slower generation times. - This is true of non-coding DNA... but not true for proteins, as we have seen. Proteins accumulate mutations in absolute time, not generational time.

V. The Neutral Theory C. Neutral Variation D. Predictions and Results E. Problems and Resolutions 1. Selection also explains different mutation rates in functional and non-functional regions 2. A truly neutral clock should tick off mutations at a constant rate. But should this ticking occur per unit time, or per generation? - Since mutations produce new alleles (a new "tick"), and mutations only occur during replication of the DNA, it would seem that a truly neutral clock should tick at a rate dependent on the generation time of the organism. - Species with rapid generation times should accumulate mutations at a faster rate than long-lived species with slower generation times. - This is true of non-coding DNA... but not true for proteins, as we have seen. Proteins accumulate mutations in absolute time, not generational time. THIS IS INCONSISTENT WITH THE NEUTRAL MODEL

V. The Neutral Theory C. Neutral Variation D. Predictions and Results E. Problems and Resolutions F. The Nearly Neutral Model (Ohta)

V. The Neutral Theory C. Neutral Variation D. Predictions and Results E. Problems and Resolutions F. The Nearly Neutral Model (Ohta) - Ohta included the very weak effect against slightly deleterious mutations. He found that, if s < 1/2Ne, then alleles are essentially neutral and become fixed as drift would predict.

V. The Neutral Theory C. Neutral Variation D. Predictions and Results E. Problems and Resolutions F. The Nearly Neutral Model (Ohta) - Ohta included the very weak effect against slightly deleterious mutations. He found that, if s < 1/2Ne, then alleles are essentially neutral and become fixed as drift would predict. - In other words, in small populations, drift predominates unless selection is fairly strong (in a population of Ne = 5, drift will predominate unless s > 0.1).

V. The Neutral Theory C. Neutral Variation D. Predictions and Results E. Problems and Resolutions F. The Nearly Neutral Model (Ohta) - Ohta included the very weak effect against slightly deleterious mutations. He found that, if s < 1/2Ne, then alleles are essentially neutral and become fixed as drift would predict. - In other words, in small populations, drift predominates unless selection is fairly strong (in a population of Ne = 5, drift will predominante unless s > 0.1). - In large populations, selection predominates, even if it is fairly weak (if Ne = 10,000, then selection will predominate if s > ).

V. The Neutral Theory C. Neutral Variation D. Predictions and Results E. Problems and Resolutions F. The Nearly Neutral Model (Ohta) SO..... (GET READY FOR THIS!!!!)

F. The Nearly Neutral Model (Ohta)
SO. - We observe a constant AA substitution rate across species, even though we would expect that species with shorter generation times should have FASTER rates of substitution. Sub. Rate OBS. EXP. Short GEN TIME Long

SO. - We observe a constant AA substitution rate across species, even though we would expect that species with shorter generation times should have FASTER rates of substitution. - So, something must be 'slowing down' this rate of substitution in species with short gen. times. What's slowing it down is their large populations size, such that the effects of drift, alone, are reduced, and even very weak selection will reduce the rate of substitution. LARGE POP. SIZE Sub. Rate OBS. EXP. Short GEN TIME Long

SO. - We observe a constant AA substitution rate across species, even though we would expect that species with shorter generation times should have FASTER rates of substitution. - Likewise, species with long generation times have small populations, and substitution by drift and fixation is more rapid than expected based on generation time, alone. And if drift dominates, then substitution rates will occur more rapidly (unless selection is very strong). SMALL POP. SIZE Sub. Rate OBS. EXP. Short GEN TIME Long

SO. - We observe a constant AA substitution rate across species, even though we would expect that species with shorter generation times should have FASTER rates of substitution. SO. - The constant rate of AA substitution across species is due to the balance between generation time and population size …life history trade-offs. SMALL POP. SIZE Sub. Rate OBS. EXP. Short GEN TIME Long

V. The Neutral Theory C. Neutral Variation D. Predictions and Results E. Problems and Resolutions F. The Nearly Neutral Model (Ohta) G. Conclusions

V. The Neutral Theory C. Neutral Variation D. Predictions and Results E. Problems and Resolutions F. The Nearly Neutral Model (Ohta) G. Conclusions - Neutral variability certainly exists; in non-coding DNA, especially.

V. The Neutral Theory C. Neutral Variation D. Predictions and Results E. Problems and Resolutions F. The Nearly Neutral Model (Ohta) G. Conclusions - Neutral variability certainly exists; in non-coding DNA, especially. - However, it is possible that selection maintains molecular variation as well, particularly in coding regions.

V. The Neutral Theory C. Neutral Variation D. Predictions and Results E. Problems and Resolutions F. The Nearly Neutral Model (Ohta) G. Conclusions - Neutral variability certainly exists; in non-coding DNA, especially. - However, it is possible that selection maintains molecular variation as well, particularly in coding regions. It is also possible that selection maintains variability in non-coding regions, as well, if these are "functional" in a structural or regulatory manner.

IV. Selection and Drift A. "Adaptive Landscapes" 1. Single Locus
- consider a locus with selection against the heterozygote p = 0.4, q = 0.6 AA Aa aa Parental "zygotes" 0.16 0.48 0.36 = 1.00 prob. of survival (fitness) 0.8 0.4 0.6 Relative Fitness 1 0.5 0.75 Corrected Fitness 1.0 formulae 1 + s 1 + t peq = t/(s + t) = .25/.75 = 0.33

IV. Selection and Drift A. "Adaptive Landscapes" 1. Single Locus 1.0
- consider a locus with selection against the heterozygote 1.0 0.75 mean fitness 1.0 0.33

- suppose there is random movement up the 'wrong' slope? 1.0 0.75 mean fitness 1.0 0.33

- if this is a large pop with no drift, the population will become fixed on the 'suboptimal' peak, (p = 0, q = 1.0, w = 0.75). 0.75 mean fitness 1.0 0.33

- BUT if it is small, then drift may be important... because only DRIFT can randomly BOUNCE the gene freq's to the other slope! 0.75 mean fitness 1.0 0.33

- And then selection can push the pop up the most adaptive slope! 0.75 mean fitness 1.0 0.33

- The more shallow the 'maladaptive valley', (representing weaker selection differentials) the easier it is for drift to cross it... 0.75 mean fitness 1.0 0.33

2. Two Loci - create a 3-D landscape, with "mean fitness" as the 'topographic relief" Suppose AAbb and aaBB work well, but combinations of the two do not (epistatic, like butterfly mimicry). 1.0 f(A) 1.0 f(B)

2. Two Loci Again, strong selection or weak drift will cause mean fitness to move up nearest slopes. 1.0 f(A) 1.0 f(B)

2. Two Loci Only strong drift or weak selection and some drift (shallow valley) can cause the population to cross the maladaptive valley. 1.0 f(A) 1.0 f(B)

IV. Selection and Drift A. "Adaptive Landscapes" 1. Single Locus 2. Two Loci - so, the interactions between drift and selection are necessary for a population to find the optimal adaptive peak in a given adaptive landscape... think about this in the context of peripatric speciation.... THINK HARD about this...

- so, the interactions between drift and selection are necessary for a population to find the optimal adaptive peak in a given adaptive landscape... think about this in the context of peripatric speciation.... THINK HARD about this... Through peripatric events, an adaptive landscape is “colonized” by small populations with very different gene frequencies… so they ‘placed’ at different places in this adaptive landscape. By chance, one of them is likely to find the optimal adaptive peak for that environment.

1. "HARD" Selection can 'cost' a population individuals:

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1. "HARD" Selection can 'cost' a population individuals:

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