II. Deviations from HWE A. Mutation B. Migration C. Non-Random Mating

II. Deviations from HWE A. Mutation B. Migration C. Non-Random Mating D. Genetic Drift - Sampling Error E. Selection 1. Measuring “fitness” – differential reproductive success

D. Genetic Drift - Sampling Error E. Selection
II. Deviations from HWE A. Mutation B. Migration C. Non-Random Mating D. Genetic Drift - Sampling Error E. Selection 1. Measuring “fitness” – differential reproductive success a. The mean number of reproducing offspring (or females)/female

II. Deviations from HWE A. Mutation B. Migration C. Non-Random Mating D. Genetic Drift - Sampling Error E. Selection 1. Measuring “fitness” – differential reproductive success a. The mean number of reproducing offspring (or females)/female b. Components of fitness:

II. Deviations from HWE A. Mutation B. Migration C. Non-Random Mating D. Genetic Drift - Sampling Error E. Selection 1. Measuring “fitness” – differential reproductive success a. The mean number of reproducing offspring (or females)/female b. Components of fitness - probability of female surviving to reproductive age

II. Deviations from HWE A. Mutation B. Migration C. Non-Random Mating D. Genetic Drift - Sampling Error E. Selection 1. Measuring “fitness” – differential reproductive success a. The mean number of reproducing offspring (or females)/female b. Components of fitness - probability of female surviving to reproductive age - number of offspring the female produces

II. Deviations from HWE A. Mutation B. Migration C. Non-Random Mating D. Genetic Drift - Sampling Error E. Selection 1. Measuring “fitness” – differential reproductive success a. The mean number of reproducing offspring (or females)/female b. Components of fitness - probability of female surviving to reproductive age - number of offspring the female produces - probability that offspring survive to reproductive age

II. Deviations from HWE A. Mutation B. Migration C. Non-Random Mating D. Genetic Drift - Sampling Error E. Selection 1. Measuring “fitness” – differential reproductive success a. The mean number of reproducing offspring (or females)/female b. Components of fitness - probability of female surviving to reproductive age - number of offspring the female produces - probability that offspring survive to reproductive age c. With a limited energy budget, selection cannot maximize all three components… there will necessarily be TRADE-OFFS.

E. Selection 1. Measuring “fitness” – differential reproductive success 2. Relationships with Energy Budgets

1. Measuring “fitness” – differential reproductive success
E. Selection 1. Measuring “fitness” – differential reproductive success 2. Relationships with Energy Budgets GROWTH METABOLISM REPRODUCTION

E. Selection 1. Measuring “fitness” – differential reproductive success 2. Relationships with Energy Budgets Maximize probability of survival Maximize reproduction GROWTH METABOLISM GROWTH REPRODUCTION METABOLISM REPRODUCTION

E. Selection 1. Measuring “fitness” – differential reproductive success 2. Relationships with Energy Budgets Trade-offs within reproduction METABOLISM REPRODUCTION REPRODUCTION METABOLISM A few large, high prob of survival Lots of small, low prob of survival

E. Selection 1. Measuring “fitness” – differential reproductive success 2. Relationships with Energy Budgets 3. Modeling Selection

Selection for a Dominant Allele
3. Modeling Selection Selection for a Dominant Allele p = 0.4, q = 0.6 AA Aa aa Parental "zygotes" 0.16 0.48 0.36 = 1.00

3. Modeling Selection Selection for a Dominant Allele 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 0.2

3. Modeling Selection Selection for a Dominant Allele 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 0.2 Relative Fitness 1 0.25

3. Modeling Selection Selection for a Dominant Allele 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 0.2 Relative Fitness 1 0.25 Survival to Reproduction 0.09

3. Modeling Selection Selection for a Dominant Allele 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 0.2 Relative Fitness 1 0.25 Survival to Reproduction 0.09 = 0.73

3. Modeling Selection Selection for a Dominant Allele 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 0.2 Relative Fitness 1 0.25 Survival to Reproduction 0.09 = 0.73 Geno. Freq., breeders 0.22 0.66 0.12

3. Modeling Selection Selection for a Dominant Allele 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 0.2 Relative Fitness 1 0.25 Survival to Reproduction 0.09 = 0.73 Geno. Freq., breeders 0.22 0.66 0.12 Gene Freq's, gene pool p = 0.55 q = 0.45

3. Modeling Selection Selection for a Dominant Allele 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 0.2 Relative Fitness 1 0.25 Survival to Reproduction 0.09 = 0.73 Geno. Freq., breeders 0.22 0.66 0.12 Gene Freq's, gene pool p = 0.55 q = 0.45 Genotypes, F1 0.3025 0.495 0.2025 = 100

3. Modeling Selection Selection for a Dominant Allele Δp declines with each generation.

3. Modeling Selection Selection for a Dominant Allele Δp declines with each generation. BECAUSE: as q declines, a greater proportion of q alleles are present in heterozygotes (and invisible to selection). As q declines, q2 declines more rapidly...

3. Modeling Selection Selection for a Dominant Allele Δp declines with each generation. So, in large populations, it is hard for selection to completely eliminate a deleterious allele....

3. Modeling Selection Selection for a Dominant Allele Δp declines with each generation. Rate of change depends on the strength of selection; the difference in reproductive success among genotypes. In this case, a new adaptive mutant allele has been produced in the population. The “selection differential”, s, is selection AGAINST the existing allele that had become ‘fixed’ in the population (f = 1.0) So, the “better” the new allele is (represented by the greater selective differential against the old allele), the faster the new mutant accumulates in the population.

3. Modeling Selection Selection for a Dominant Allele Selection for an allele where there is not complete dominance: - Consider incomplete dominance, codominance, or heterosis. In these situations, the heterozygote has a phenotype that differs from either of the homozygotes, and selection can favor one genotype over another: - Selection might favor one homozygote over the heterozygote and other homozygote (first example), or might favor the heterozygote over the homozygotes (second example), or might favor both homozygotes over the heterozygote (not considered here).

Selection for the homozygote of a ‘non-dominant’ allele
(incomplete dominance, codominance, overdominance) 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 0.2 Relative Fitness 1 0.5 0.25 Survival to Reproduction 0.24 0.09 = 0.49 Geno. Freq., breeders 0.33 0..50 0.17 Gene Freq's, gene pool p = 0.58 q = 0.42 Genotypes, F1 0.34 0.18 = 100

Selection for the homozygote of a non-dominant allele
- deleterious alleles can no longer hide in the heterozygote; its presence always causes a reduction in fitness, and so it can be eliminated from a population (if the heterozygote is less ‘fit’ than the AA).

Selection for 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) 0.4 0.8 0.2 Relative Fitness 0.5 (1-s) 1 0.25 (1-t) Survival to Reproduction 0.08 0.09 = 0.65 Geno. Freq., breeders 0.12 0.74 0.14 Gene Freq's, gene pool p = 0.49 q = 0.51 Genotypes, F1 0.24 0.50 0.26 = 100 Maintains both genes in the gene pool peq = t/s+t = 0.75/1.25 = 0.6 AA Aa aa

Maintains both genes in the gene pool
peq = t/s+t = 0.75/1.25 = 0.6

Selection for the Heterozygote
Sickle cell caused by a SNP of valine for glutamic acid at the 6th position in the beta globin protein in hemoglobin (147 amino acids long). The malarial parasite (Plasmodium falciparum) cannot complete development in red blood cells with this hemoglobin, because O2 levels are too low in these cells. NN NS SS

E. Selection 1. Measuring “fitness” – differential reproductive success 2. Relationships with Energy Budgets 3. Modeling Selection 4. Types of Selection - Selection acts on phenotypes, which may be single gene traits, polygenic quantitative traits, and/or effected by epistatic interactions. - The different effects are measured by changes in the mean phenotype over time.

E. Selection 4. Types of Selection - Directional

E. Selection 4. Types of Selection - Stabilizing

4. Types of Selection - Disruptive
E. Selection 4. Types of Selection - Disruptive Lab experiment – “bidirectional selection” – create two lines by directionally selecting for extremes. Populations are ‘isolated’ and don’t reproduce.

4. Types of Selection - Disruptive
E. Selection 4. Types of Selection - Disruptive African Fire-Bellied Seed Crackers

Evolutionary Genetics

Speciation A. Definition: Mayr’s ‘biological species concept’ – “a group of actually or potentially interbreeding organisms that is reproductively isolated from other such groups”.

Speciation A. Definition: Mayr’s ‘biological species concept’ – “a group of actually or potentially interbreeding organisms that is reproductively isolated from other such groups”. - only appropriate for sexually reproducing species - Reproductive isolation will inevitably lead to greater genetic divergence (even just by chance), and an increased likelihood of genetic uniqueness/incompatibility.

Evolutionary Genetics Speciation
II. Making Species - Reproductive Isolation A. Pre-Zygotic Barriers 1. Geographic Isolation (large scale or habitat)

Drosophila speciation on the Hawaiian Islands.
Drosophila speciation on the Hawaiian Islands. As new Hawaiian islands are formed to the east, species from the nearest extant island are able to colonize the new island and become reproductively isolated (gray arrows). This "conveyer belt" speciation process has allowed the Hawaiian members of the Drosophilidae to radiate rapidly, forming a large and speciose group that display extreme morphological and behavioral diversity. This diversity includes the striking but now highly endangered "picture-wing" group (such as D. heteroneura, inset) that have been a major focus of Drosophila evolutionary ecology. The phylogeny (left) illustrates the inferred topology and speciation times of the seven species sampled for this study, with dates derived from model A1 (see main text), which sets speciation dates to the surface emergence of the first volcano of each island. Island dates are given as a span from the time of inferred surface emergence to shield completion for the oldest volcano on the island. Recent divergences involve a specie colonizing a new island (Hawai’i); older divergence occurred in the past, when older islands first crested above the ocean and were made available for colonization. Obbard D J et al. Mol Biol Evol 2012;29: © The Author Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Vicariance – the splitting of a range by a new geographic feature, such as a river or land mass.

Almost all most recent divergence events date to 3 my, and separate species on either side of the isthmus; suggesting that the formation of the isthmus was a cause of speciation in all these species pairs. Snapping ‘Pistol’ Shrimp

Mayr – Peripatric Speciation
Small population in new environment; the effect of drift and selection will cause rapid change, resulting in a speciation event.

Evolutionary Genetics II. Making Species - Reproductive Isolation
A. Pre-Zygotic Barriers 1. Geographic Isolation (large scale or habitat) 2. Temporal Isolation

A. Pre-Zygotic Barriers 1. Geographic Isolation (large scale or habitat) 2. Temporal Isolation 3. Behavior Isolation - don't recognize one another as mates Western Meadowlark Eastern Meadowlark

A. Pre-Zygotic Barriers 1. Geographic Isolation (large scale or habitat) 2. Temporal Isolation 3. Behavior Isolation - don't recognize one another as mates 4. Mechanical isolation - genitalia don't fit; limit pollinators Mimulus cardinalis You’re cute… You’re crazy… Mimulus lewisii

A. Pre-Zygotic Barriers 1. Geographic Isolation (large scale or habitat) 2. Temporal Isolation 3. Behavior Isolation - don't recognize one another as mates 4. Mechanical isolation - genitalia don't fit; limit pollinators 5. Gametic Isolation - gametes transferred but sperm can't fertilize egg; this is a common isolation mechanism in species that spawn at the same time

A. Pre-Zygotic Barriers B. Post-Zygotic Isolation

A. Pre-Zygotic Barriers B. Post-Zygotic Isolation 1. Genomic Incompatibility - zygote dies

A. Pre-Zygotic Barriers B. Post-Zygotic Isolation 1. Genomic Incompatibility - zygote dies 2. Hybrid Inviability - F1 has lower survival Crazy hybrids A ‘zedonk’

A. Pre-Zygotic Barriers B. Post-Zygotic Isolation 1. Genomic Incompatibility - zygote dies 2. Hybrid Inviability - F1 has lower survival 3. Hybrid Sterility - F1 has reduced reproductive success Horse: 64 chromosomes Donkey: 62 chromosomes Mule: 63 non-homologous chromosomes

A. Pre-Zygotic Barriers B. Post-Zygotic Isolation 1. Genomic Incompatibility - zygote dies 2. Hybrid Inviability - F1 has lower survival 3. Hybrid Sterility - F1 has reduced reproductive success 4. F2 breakdown - F1's survive but F2's have incompatible combo's of genes

AABB x aabb F1: AaBb = ok F2: A-B- = ok A-bb = no aaB- = no aabb = ok

A. Pre-Zygotic Barriers 1. Geographic Isolation (large scale or habitat) 2. Temporal Isolation 3. Behavior Isolation - don't recognize one another as mates 4. Mechanical isolation - genitalia don't fit; limit pollinators 5. Gametic Isolation - gametes transferred but sperm can't fertilize egg; this is a common isolation mechanism in species that spawn at the same time B. Post-Zygotic Isolation 1. Genomic Incompatibility - zygote dies 2. Hybrid Inviability - F1 has lower survival 3. Hybrid Sterility - F1 has reduced reproductive success 4. F2 breakdown - F1's survive but F2's have incompatible combo's of genes All of these – except geographic isolation - are fundamentally genetic in nature because physiology (gametic), morphology (mechanical), and behavior (temporal and behavioral) have a genetic component. Obviously, the post-zygotic barriers are entirely genetic. Speciation is the process of creating a genetically distinct population, which maintains its distinction in the face of possible hybridization.

III. Rates of Evolution and Speciation A. Evolution and Speciation - Evolution and speciation are not the same: Evolution is a change in the genetic structure of a population Speciation is the establishment of reproductive isolation between populations.

III. Rates of Evolution and Speciation A. Evolution and Speciation - Evolution and speciation are not the same: Evolution is a change in the genetic structure of a population Speciation is the establishment of reproductive isolation between populations. - Two populations can evolve over time, but maintain gene flow and not speciate. - Two populations can become geographically isolated and be ‘good species’, while being genetically similar.

III. Rates of Evolution and Speciation A. Evolution and Speciation - Evolution and speciation are not the same: Evolution is a change in the genetic structure of a population Speciation is the establishment of reproductive isolation between populations. - Two populations can evolve over time, but maintain gene flow and not speciate. - Two populations can become geographically isolated and be ‘good species’, while being genetically similar. - Small genetic differences can create genomic incompatibility, change in genitalia, or behavioral differences that cause speciation. So, while increasing genetic divergence increases the probability of speciation, small changes can cause reproductive isolation, too.

III. Rates of Evolution and Speciation A. Evolution and Speciation B. Rates of Evolution - depends on: - rate of mutation, introducing new variation (AIDS virus – error-prone reverse transcriptases introduce many mutations each generation, changing the surface proteins and making it very hard for our immune systems to eliminate all of them.)

III. Rates of Evolution and Speciation A. Evolution and Speciation B. Rates of Evolution - depends on: - rate of mutation, introducing new variation - size of the population (freq of new allele = 1/2N; so a mutation in a small population will be at a higher frequency that it would be in a large population)

III. Rates of Evolution and Speciation A. Evolution and Speciation B. Rates of Evolution - depends on: - rate of mutation, introducing new variation - size of the population - effect of this variation (deleterious and adaptive mutations will change frequency rapidly in response to selection; neutral variation will change by drift, alone.)

III. Rates of Evolution and Speciation A. Evolution and Speciation B. Rates of Evolution - depends on: - rate of mutation, introducing new variation - size of the population - effect of this variation - rate of reproduction of the population Populations with high reproductive rates should change faster that populations with low reproduction rates.

III. Rates of Evolution and Speciation A. Evolution and Speciation B. Rates of Evolution C. Using Molecular Clocks - the more differences there are, the more time must have elapsed since a common ancestor for these differences to accumulate. - If we know the rate of change for a given set of genes or proteins, then we can estimate the absolute time since divergence.

Different genes ‘tick’ at different rates; like different radioisotopes with different half-lives. Different genes will give better resolution, then, for different questions…

III. Rates of Evolution and Speciation A. Evolution and Speciation B. Rates of Evolution C. Using Molecular Clocks D. Concordant Phylogenies

D. Concordant Phylogenies
IF species are descended from common ancestors (like people in a family), and IF we know the rate of genetic change (mutation), THEN we should be able to compare genetic similarity and predict when common ancestors lived. AND, if the fossil record is also a product of evolution, THEN the species though to be ancestral to modern groups should exist at this predicted age, too. In other words, we should be able to compare DNA and protein sequences in living species and predict where, in the sedimentary strata of the Earth’s crust, a third different species should be.

Clustering analysis based on amino acid similarity across seven proteins from 17 mammalian species.

Now, we date the oldest mammalian fossil, which our evolution hypothesis dictates should be ancestral to all mammals, both the placentals (species 1-16) and the marsupial kangaroo. …. This dates to 120 million years 16

And, through our protein analysis, we already know how many genetic differences (nitrogenous base substitutions) would be required to account for the differences we see in these proteins - 98. 16

So now we can plot genetic change against time, hypothesizing that this link between placentals and marsupials is ancestral to the other placental mammals our analysis. 16

Now we can test a prediction. IF genetic similarity arises from descent from common ancestors, THEN we can use genetic similarity to predict when common ancestors should have lived... 16

This line represents that prediction. Organisms with more similar protein sequences (requiring fewer changes in DNA to explain these protein differences) should have more recent ancestors... 16

And the prediction here becomes even MORE precise. For example, we can predict that two species, requiring 50 substitutions to explain the differences in their proteins, are predicted to have a common ancestor that lived million years ago... D. Concordant Phylogenies 16

Let’s test that prediction. Rabbits and the rodent differ in protein sequence to a degree requiring a minimum of 50 nucleotide substitutions... Where is the common ancestor in the fossil record?

Just where genetic analysis of two different EXISTING species predicts. 16

OK, but what about all of our 16 "nodes"? Evolution predicts that they should also exist on or near this line.... 16

And they are. Certainly to a degree that supports our hypothesis based on evolution. Concordance between molecular clocks and the geologic record

III. Rates of Evolution and Speciation A. Evolution and Speciation B. Rates of Evolution C. Using Molecular Clocks D. Concordant Phylogenies E. Rates of Speciation - Speciation can be an instantaneous genetic event – through polyploidy, or mutation that affects specific genes important in forming a reproductive isolating barrier.

III. Rates of Evolution and Speciation A. Evolution and Speciation B. Rates of Evolution C. Using Molecular Clocks D. Concordant Phylogenies E. Rates of Speciation - Speciation can be an instantaneous genetic event – through polyploidy, or mutation that affects specific genes important in forming a reproductive isolating barrier. - But speciation can also be a continuous process, reflecting the accumulation of genetic differences. Still, these differences might accumulate at a steady rate or at episodic rates.

- But speciation can also be a continuous process, reflecting the accumulation of genetic differences. Still, these differences might accumulate at a steady rate or at episodic rates.

- 1972 - Eldridge and Gould - Punctuated Equilibrium
1. Consider a large, well-adapted population VARIATION TIME

1. Consider a large, well-adapted population Effects of Selection and Drift are small - little change over time VARIATION TIME

2. There are always small sub-populations "budding off" along the periphery of a species range... VARIATION TIME

X X X - 1972 - Eldridge and Gould - Punctuated Equilibrium
2. Most will go extinct, but some may survive... VARIATION X X X TIME

2. These surviving populations will initially be small, and in a new environment...so the effects of Selection and Drift should be strong... VARIATION X X X TIME

3. These populations will change rapidly in response... VARIATION X X X TIME

3. These populations will change rapidly in response... and as they adapt (in response to selection), their populations should increase in size (because of increasing reproductive success, by definition). VARIATION X X X TIME

3. As population increases in size, effects of drift decline... and as a population becomes better adapted, the effects of selection decline... so the rate of evolutionary change declines... VARIATION X X X TIME

4. And we have large, well-adapted populations that will remain static as long as the environment is stable... VARIATION X X X TIME

5. Since small, short-lived populations are less likely to leave a fossil, the fossil record can appear 'discontinuous' or 'imperfect' VARIATION X X X TIME

5. Large pop's may leave a fossil.... VARIATION X X X TIME

X - 1972 - Eldridge and Gould - Punctuated Equilibrium
TIME VARIATION Eldridge and Gould - Punctuated Equilibrium 5. Small, short-lived populations probably won't...

TIME VARIATION Eldridge and Gould - Punctuated Equilibrium 6. So, the discontinuity in the fossil record is an expected result of our modern understanding of how evolution and speciation occur... X X X

6. both in time (as we see), and in SPACE (as changing populations are probably NOT in same place as ancestral species). VARIATION X X X TIME

Darwin’s Dilemmas: Evolution of Complex Traits: 1. Structures with mutually dependent parts CAN evolve through a stepwise process

Darwin’s Dilemmas: Evolution of Complex Traits: Ornamentation and attraction homeothermy flight 2. Structures may have evolved for other selective reasons than we observe now.

Darwin’s Dilemmas: Evolution of Complex Traits: Source of Heritable Variation: …. Genetics! Nice Job ! You, too!

Darwin’s Dilemmas: Evolution of Complex Traits: Source of Heritable Variation: Discontinuity of Fossil Lineages: Peripatric Speciation and Punctuated Equilibrium TIME VARIATION Genetics has tested and confirmed Darwin’s ideas and solved his dilemmas

II. Deviations from HWE A. Mutation B. Migration C. Non-Random Mating

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II. Deviations from HWE A. Mutation B. Migration C. Non-Random Mating

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