BIOL380 Lecture Notes II   (Material covered between the first and second tests)

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H/A on Earth age (can write a paper on it); table on the different methods used to estimate the age of the Earth before 1950; RA methods give similar numbers regardless of who/when/how did it.

 
Variation.

Darwin believed that variation existed, Take a look at dogs (we looked at fish before) – face, ears, tales – different types of dogs – we see variation. We can see it from the fossil record as well (mollusks – shells, aperture, # and depth of spiral coils. Notion: variation exist.

Starting point for study. 1.5 million species exist – we can study them.

Q: variation itself. Explain it (science). 2 pages in the book talking about the models. Different types of models (examples: mathematical & more precise examples) – they are used widely in science. Why do we use them? Easier to predict phenomena, make our life easier (1), and, regardless of the model, oversimplification of nature (2) have a high practical value in allowing us to understand things, to make predictions.

(book – chapters 9&10 – but jumping around)

In evolution, they use mathematical models. Read what Futuyma says – why we use them, and don’t panic about them. No great details of the models. Just stay calm.

2 ways in defining bioevolution: historical (descent with modification) and genetic definition (change in allele frequencies). The last perspective is what we use. Populational genetics – the perspective we well be studying it from. Exactly: how the laws of Mandelian genetics apply not to an individual, but to an entire population. How it influences the evolutionary process.

Population: a locally interbreeding group of organisms; a deme (demes). Genotype, phenotype – recall the definitions.

See how the variation arose, and how it occurs over the time (from genetics perspective).

Take a look at gene – a DNA molecule (1953) is composed of phosphate, sugar, base pairs (AGTC). A gene is a piece of DNA (for our purposes), and base pairs are the most important part of it, and how they are arranged. The base pares code for a particular polypeptide - protein. Gene comes in alternative forms – alleles.

2 major classes of genes:

1. Structural genes - genes that are going to code for something. We are more familiar with them.

1. protein encoding genes (transcription-translation, encode polypeptide)
2. RNA-specifying gene (a gene that is just transcribed)

1. Regulatory genes - control where, when, and how much of a particular polypeptide will be produced. We don’t see directly expressed, but very important. Hard to measure them – we don’t see their products. They can mutate, too. What happens if there is a mutation in them? In homeobox genes?

1. replicator genes (control the initiation and termination of DNA replication)
2. recombinator genes (provide a specific recognition sites for recombination enzymes)
3. segregator genes (provide the specific sites for attachment of chromosomes during mitosis and meiosis – segregation machinery)
4. suppressor genes (turn of the production of a particular product)
5. homeobox genes (control an entire region – head, whatever)

Genes 1) come in alternative forms (we’re using a simple model, sexually reproducing organisms, diploid, eucariotes, and it’s DNA); 2) found on chromosomes (linear strands of DNA with associated histones). Individual has a genotype, ½ genes from mom, ½ genes from dad. So, if we look at a particular chromosome, we have two genes (same or different alleles – homozygous/heterozygous). The genes themselves can interact with each other:

1. dominance + recessiveness
2. codominance (both genes are expressed), incomplete dominance.
• all these are how alleles of the same gene interact.
.
3. epistasis – expression of one gene is affected by the expression of another different gene.
4. pleiotropy (pleiotropic genes) – one gene effects more then one characteristic (23 genes control eye color in our eyes).
• all these are how alleles of different genes interact.

Mutations

• the variation we are interested from the perspective of evolution is the variation which is genetically controlled (i.e. different alleles). This type of variation is the subject of evolution.
• variation can also be environmentally controlled. Both of these things interact – keep that in the back of your mind.

A: mutation – the ultimate source of variation in population. Mutation – a heritable (the one that can be passed from one generation to the next) change in DNA. Notice: mutation itself is an ethically neutral term. It’s the effect of a mutation on an organism what is positive, negative, or neutral.

We are going from the lower magnification to the higher one: euploidy - change in chromosome SETs; aneuploidy - change in chromosomes WITHIN a set; deletion, insertion, etc. - changes in PARTS of chromosomes; point mutation - change in a single BASE PAIR (in the simpliest case).  There are two major classes of mutations:

1. a change in karyotype (karyotype is a chromosomal distribution within an organism)

1. Variations in chromosome number (p. 286)

1. Euploidy – the changes which involve the entire set of chomosomes, not a single chromosome. Polyploidy, in particular, is an example 3n, 4n, 5n, whatever. Table on Euploid variations. ABC – AABBCC – AAABBBCCC – etc. In humans, 2n=46. If there was a triploic event, 2n=69. All kinds of fancy names mentioned in the book, don’t worry about that now. In the reality, there are no polyploic humans – the result would be a spontaneous abortion. Then, why bring it up? – you can’t think of everything in terms of humans. In nature, not all the time euploidy is detrimental in other species. Some species have di- triploic number of chromosomes. Plants, polyploidisation occurs relatively frequently. Wheat is polyploic, and we think it evolved from two diploic ancestors. Don’t assume that it’s always negative. In some instances, speciation is directly a result of polyploidisation. We call them instantaneous speciations. Another thing that happens, in some of the polyploic species (esp. triploic) those organisms are partenogenic – reproduce asexually without a male. They are clones. Variation is essentially zero in such populations. They are clones just like two identical twins are. Some of them copulate with a male of other species, and no sperm is involved – it’s a simple fact that they are together. Q for evolutionists: why do we have them?, what are the advantages/disadvantages?
2. Aneuploidy – the type of change that involves only some of the chromosomes in a set – change in the number of a single chromosome within a set. Cells forgot to read the textbook – they don’t know how the mitosis/meiosis occur. Chart (overhead) on aneuploid variations (A -one chromosome; B -another chromosome, etc. AA - two homologous chromosmes): disomic (normal diploid) 2n -AABBCC, monosomic 2n-1 -AABBC, nullsomic 2n-2 -AABB, polysomic – extra chromosomes (trisomic, double trisomic, pentasomic…) – different. Number of chromosomes is different; detremental mutations (yes, Dr. Matson calls them mutations).

1. Variation in the arrangement of chromosome segments. Now we are looking at the parts of a chromosome. Fig. 10.16 – 10.18. Overhead (XXXX-XXX – one chromosome) – deletion: ABCDE-FGH -> AE-FGH, duplication: ABCDE-FGH -> ABSDE-FGHFGH, inversion: ABCDE-FGH -> AEDCB-FGH, reciprocal translocation: AB-CDE NOP-QR -> AB-CON EDP-QR. All these occur in nature, some are more important then others, reciprocal translocations are relatively rare in nature, and from the other hand, we can end up with an instantaneous speciation. Another concept – fission (to brake apart) and fusion (to come together), parts of chromosomes move together (another overhead, and still other overhead – how two goats are related as a result of fusions in their chromosomes –these things are not something we just make up. The goat chromosomes have a lot in common, and they look like they have fused. Point – in a situation like this these kind of fissions may provide a speciation mechanism). Overhead – the karyotype of the "great apes" – humans, gorillas, orangs, chimps. We did not evolve from apes, we have a common ancestor. The sequences of genes are very similar. It’s a monophyletic taxon. Overhead – chromosomes – banding patterns look similar (4, 5, 6), but also some differences (3 – extra dark staining band). In 2 chromosome – a fusion process is hypothetised – gives a long chromosome in humans where the apes have two chromosomes. Point – when we take a look at this data, and more important, when we see the difference, we need to have a mechanism to explain how such event could occur. In terms of evolution, fision/fusion is common and simple, frequently occurs.

1. Point mutations (found at the beginning of chapt. 10, p. 267) – a mutation as I knew it. What happens to a particular piece of DNA, at its one point. Can be as simple as one change in a base pair (molecular level). Point mutations arise by:

• physical or chemical damage to a DNA molecule. E.g. chemicals – mutagens/teratogens/carcinogens (alcohol, thelitamide, agent orange, dioxin – human made; cyanide, uranium – natural. Physical – radiation (sun, RA decay, - also occur naturally).
• errors in replication – a process which has consequences for variation.
• caused by viruses

1. Substitution – a replacement of one nucleotide by another.

1. transition – purine is substituted for purine, or pyrimidine is substituted for pyrimidine
2. transversion – purine for pyrimidine (or vice versa)
3. synonymous (silent) – causes no change in amino acid (when one aminoacid is coded by two different looking codones).
4. nonsynonymous – alters aminoacid sequence

1. Deletion – a removal of one or more nucleotides from a DNA molecule. Causes phase shift because one base pair is inserted, and the whole sequence after it is read differently.
2. Insertion – an addition of one or more nucleotides in a DNA molecule. Causes a phase shift,
3. Stop mutation – a code defining the stop of transcription is inserted.

1. Chromosomal
2. Point
3. Recombination – occurs during crossingover – occurs in phase I of meiosis. It increases the amount of potential variation. A fairly efficient way for variations to occur. Crossingover does not occur every time meiosis occurs.

Inbreeding – decreases the variability (breeding dogs, but increases the frequency of deleterious features).
4. Mobile genetic elements – not all the genetic information stays in nucleus. In some situations the DNA not found in nucleus can have an affect on the organisms. Mitochondria and chloroplasts have their own DNA. Another ways to get DNA from outside the cell are:

1. Plasmids – independently replicating circular pieces of DNA, found in the cytoplasm of some bacteria and some eucaryotes. Can affect the phenotype of the organism where it’s found. E.g., some of the genes responsible for the antibiotic resistance in bacteria are genes found in plasmids. These plasmids can be transmitted from one bacteria to another through the process of conjugation and, sometimes, through a virus. Not only it can be transmitted within individuals of one species, it also can be transmitted between species. That can cause a population to be antibiotic resistant, or can even go to different bacteria. The other way of looking – here is a potential mechanism through which variation can be increased. Evolutionary consequences – DNA transmitted from one species to another – can create a new species.
2. Transposable elements (transons, or "jumping genes"). Crossing over – same piece of the homologous chromosome. Barbara McClintock showed that it is possible for a piece of DNA to move from one chromosome to a non-homologous one. What we’ve done, is inserted a piece of DNA – the linear sequence of base pairs is changed – the way DNA is read is altered – change in phenotype.

The Rates of Mutations.

Mutation – change in DNA, and there are different mechanisms how mutations occur. Now, how often do they occur?

1. In general, rates of mutations tend to be low. Overhead – spontaneous mutation rates of specific genes. There are different rates of mutations. The rates are different – the rates vary by taxa (unicellular/multicellular), the rates also vary within a species. If we average them in general, the rates of mutations occur 1 to 10 mutations per 100,000 cell divisions. The rate is low, but what is the probability that a mutation will show? – If we have 100,000 cells, one of them will be mutant – and it’ll show up. Now it is 5.6 billion people on Earth, and there are 6 billlion careless cells, the probability of a mutation showing up in a population is high. In general, depends on the organism you’re talking about. (Ch. 9&10).
2. Mutations occur at random. Random – no way to predict with mathematical certainty when or where a mutation will occur; nor can we necessarily predicts effect on the organism. But it doesn’t mean that all the mutations are equally likely, and that any imaginable thing can happen in reality. We also don’t know if a particular mutation will persist in a population. Natural selection is a highly non-random process. This adds to the non-randomness of the evolution. Fig. 10.13 (p. 284) and overhead – experiment showing that mutations occur at random.

Polymorphism

Q: How do we partition variation in nature? How do we look at variation, are there different perspectives?
A: Polymorphism within a population
Fig. 9.21 – a group of animals that we consider one species, but they have different forms - they are polymorphic. They are partitioned geographically. They give three instead of two names for them, and they have what some people call "subspecies." There is a practical value for doing it – increases communication preciseness, but also can add more confusion. Maybe (but not necessarily true) we are seeing a speciation in action. But all this is irrelevant, because the point is different .
Fig. 9.23 – geographical variation, the crest is different depending on the location. From South to North, a change from crestless to having a crest. Some are found on islands only – isolated from the rest. Others – something else can be going on. The point – we see a pattern, and you as a biologist have to explain it. Fig. 9.4 – within the same litter (i.e. brothers and sisters) can have white or dark phenotype, or striped/nonstriped phenotypes.
 

Mathematical models to explain variations in populations.

Models how alleles behave in populations.

Electrophoresis (explained).

– – – – – – – – – – – – – – – – monoallelic population – variation = zero.

– – – _ – – – – – – –_ – – – – polyallelic population – there is a variation.

Different forms of enzymes that are controlled by different alleles are called allozymes. The genes have different alleles, and often times they are expressed codominantly. The individual that has ‘–‘ is diploid (homozygous for the fast allele); the one that has ‘_’ also homozygous (for the slow allele) The one that has both ‘_’ and ‘–‘ ( – ) is heterozygous, and it is a codominant inheritance. See handout: F (fast) is –, S (slow) is _, F/F is –, S/S is _; F/S is – in case of codominance. On that, we can calculate genotype frequencies.

Q: what is the frequency of the homozygous fast genotype (F/F)? A: 8/16 = 1/2

Q: what is the frequency of homozygous slow (S/S)? A: 2/16 = 1/8

Q: what’s the frequency of heterozygous (F/S)? A: 6/16 = 3/8

SUM is 1

Q: how many fast alleles (frequency of allele F)? A: 22/32 = 0.6875

Q: how many slow alleles (frequency of allele S)? A: 10/32 = 0.3125

SUM is 1

Percent Polymorphism (P) – the number of loci that contain some variation i.e. they are different allelic forms as compared to the total. Loci containing variants over total. Comparing monoallelic population overhead to the polyallelic population, the percent polymorphism is 50%. Pretend we had 8 more, different %:
.

Quantifies the amount of variation in a population.

Average heterozygocity (another way of measuring variation) – calculated by dividing the number of heterozygous by the total number of individuals for each locus:
.

Look in the textbook table 9.2, numbers in the last two columns – looking at large mammals, 4% of the loci are heterozygous. In Drosophila, this number is 15%. First, variation varies between species. Second, there is so much variation: it is a norm. But, samples were small.
 

Hardy-Weinberg distribution of genotype frequencies

The primary model used to predict the behavior of alleles in populations is the Hardy-Weinberg model/theory/principle/law. Was developed independently by these two scientists. Sometimes third name added – Castle. As any model, Hardy-Weinberg is an oversimplification of the nature, There are some assumptions built into it:

1. we are dealing with Mendelian populations – this is a panmictic population i.e. there is a random mating
2. we have non-overlapping generations (once you reproduce, you die)
3. populations are using sexual reproduction
4. they are diploid organisms
5. the population is infinitely large i.e. there is no genetic drift
6. there is no evolution, i.e.:

1. no mutation
2. no gene flow
3. no genetic drift
4. no natural selection

Let p = frequency of A
Let q = frequency of a
Then p + q = 1 – this is for allele frequencies.

If we have sexually reproducing organisms, we can have AA, Aa, aa.

The genotypic frequencies:

Frequency of AA = p² (product of probabilities that gamete A runs into gamete A)
Frequency of aa = q²
Frequency of Aa = 2pq
 

Hardy-Weinberg distribution
Within a single generationin a randomly mating population the given allele frequencies will conform to a binomial distribution of
.

Hardy-Weinberg equilibrium (HWE)

Example. Q: is this population in Hardy-Weinberg equilibrium (HWE)?
 
 

Phenotypes	Genotypes	Genotype frequencies
M = 298	MM = 298	freq. of MM = 298/1000 = 0.298
MN = 489	MN = 489	freq. of MN = 489/100 = 0.489
N = 213	NN = 213	freq. of NN = 213/100 = 0.213
SUM = 1000	SUM = 1000	SUM = 1

Let p = freq. of M, let q = freq. of N; MM = p² = 0.298; MN = 2pq = 0.489; NN = q² = 0.213

p = p² + ½ 2pq
p = freq. MM + ½ (freq. MN)
p = 0.298 + ½ (0.489)
p = 0.5425
q = 1 - p = 1 - 0.5425 = 0.4575

the frequency of MM under HWE is p² = (0.5425)² = 0.2943
freq. of MN  ~  " ~  = 2pq = 2(0.5425)(0.4575) = 0.4964
freq. of NN  ~  " ~  = q² = (0.4575)² = 0.2093

These numbers are different from what we got above. To estimate how different, we need to run the Chi-square test.

Usage: to estimate the frequencies of alleles in populations, esp. in situations of dominant-recessive relationship in genotype, when phenotype does not convey the genotype.

If a population not in HWE, then the evolution is occurring. If it is in the HWE, can we conclude that the evolution is not occurring? – You cannot prove the negative (like, you cannot prove that purple cows don't exist) - It means that at those particular traits we don’t see evolution.

Estimating genotype frequencies when we have dominance.
 

p = 1 - q = 1 - 0.3768 = 0.6232

Nonrandom mating / Genetic drift

Let’s violate some of the assumptions of HW (ch.11)
Take a look at how alleles might change when we violate these evolutionary forces.

Assumptions:

1. populations are large
2. no genetic drift

• we violate these.

1. Evolutionary force is Genetic Drift - a change in allele frequencies due to a sampling error; due to random chance. Where populations are small, the effect of the sampling error is large. Overhead - change of allele frequency by random genetic drift - sort of like what we saw in the lab III. See fig. 11.3 - with a small sample size, HWE is never reached.
2. Ways drift effect populations:

1. Continuous drift - sooner or later one of the alleles in the population becomes fixed, another becomes lost.
2. Intermittent drift - happens only once in a while. Ex; bottleneck effect - every once in a while a large population gets reduced in size, becomes small, and the effect of genetic drift takes place. A bottle is an analogy, a metaphor. Overhead - beads pouring out of a bottle; if only a few of them fall out, passing through a narrow bottleneck, by chance alone we can come up with a frequency of very different then the frequency in the bottle. As they pass through the bottle neck, beads fall out with a frequency of a chance. On page 304 – 306, read the details. With Northern elephant seal, it was almost hunted to extinction. By the 1800s the population was reduced down to 20 individuals. Then, US, Mexico, and Canada made a treaty not to hunt them. The population size started to rebuild - now is 30 or something thousand. Back in 1974 some scientists sampled tissues on 24 loci, measured variability and found no variation, no heterozygocity, no polymorphism. Even though we had a small sample, we had to have at least 4 loci variable (chart); but they haven’t. Explanation: when they went through the drastic reduction in the population size, that’s when it happened. Which genes were selected - purely by chance.
3. Founder effect - deals with populations that are starting or "founding" a new population. Usually involves colonization and starting a new population. Ex: what happens with islands. Assume that we have regular variability on mainland. For some reason, one individual gets on island. The type of individual which gets there is based on a chance. But once it gets there, it’s going to have a lot of similar to it offsprings. The amount of variation is going to be less. In terms of the alleles we are looking at, the characters chosen are (1) small representation of a total population, and (2) totally random (determined by chance).

Effects of the genetic drift:

• tends to result in a loss of heterozygocity. Esp. in small populations, one allele becomes fixed, and the other allele is lost. Take a look at fig. 11.5 - we can measure the effect of genetic drift. The point - we lose heterozygocity.

• sampling bias (random chance)
• loss of heterozygocity (same overhead as the previous lecture - the smaller the sample, the bigger the extent of the genetic drift.
• the effect of the genetic bottleneck on a population (fig. 11.6) What happens in terms of avg. heterozygocity and how long it takes for the population to rebound.

Positive assortative mating generally increases the frequency of homozygotes at the expense of heterozygotes. AA X AA more frequently then AA X Aa or others (like mates with like):

AAXaa, AAXAa, aaXAa - > freq. of Aa is higher then AA or aa

Inbreeding

• different from + & - assortative matings, where if one gene is selected, it doesn’t affect other genes. All loci, all genes are being affected
• like in the + ass. breeding, inbreeding tends to increase frequency of homozygous genotypes; variation is decreased
• by itself, inbreeding does not alter allele frequencies. It changes genotype frequencies, but not allele frequencies. It does not cause evolution (by itself). So, if it decreases variability, what counterbalances it? Answer: Genetic drift, mutations…
• potential effects; overhead (~fig. 11.9) - table on inbreeding depression in rats - look at a couple of measurements for survivability over time (30 generations). Fecundity (how many offsprings produced per litter) decreased from 7.5 to 3.2 (a decrease of 4 offsprings/litter), nonproductive matings increased from 0% to 41%, mortality rate increased from 4% to 45%. Overhead - effects of inbreeding - in a much wider sample, we see the same general effect. But in four of them (out of 40) nothing happened - it means that inbreeding does not guarantees the decrease of fecundity
• other effects of inbreeding - p. 308-309

Population size - what is a small population size?

Genetic drift and inbreeding more severe in small populations. So, how small is small? Defining is very complicated and depends on different variables. A small population:

• if N (population size) is between 10 and 100 individuals, we see that alleles could be lost at the rate of 0.1 – 0.01 alleles/locus/generation
• if N is between 100 and 10000, alleles are lost at the rate of 10 ^{– 4} alleles/locus/generation
• if N is greater then 10000, the loss of alleles by drift is negligible

Another evolutionary force - mutation.

If we have a population that is a 100% AA, when a mutation occurs (A -> a), we alter the allele frequency. By definition, when this happen, the evolution occur. But it does not necessarily mean that anything will happen, There are other forces (natural selection, genetic drift). But, the other extreme, if a is lethal, it doesn’t go anywhere.
 

How important mutation is? It is an important source of variation, but by itself it’s a relatively weak evolutionary force. This is why:

• mutations occur too infrequently, and it would take too long to account for all the present diversity. A mathematical example to reinforce (~lab):

Q: How many generations would it take to change the allele frequency from 0.50 to 0.49 if mutation is the only evolutionary force acting? (ass. m = 10 ^{– 5})

P_t/P₀ = (1 - m )^t
log (P_t/P₀) = t log(1 - m )
log (0.49/0.50) = t log(1 – 0.00001)
log(0.98) = t log(0.9999)
- 0.00877 = t( - 0.0000043)
t = 2020 (generations)

0.1 -> 0.09, takes 10530 generations

Gene flow is the movement and incorporation of alleles from one population into another.

There are two kinds of the gene flow:

• intraspecific gene flow (within a species, genes move from one population into another)
• interspecific gene flow (interspecific hybridization, movement from one species into another different species)

0. - it can rapidly alter allele frequencies (within one single generation). This is also a potential way to counterbalance the genetic drift
1. - it can homogenize populations (make them similar). Ex: Population 1 - AA, population 2 - BB (@ time 0). Assume free gene flow. At time 1 we get AB/AB and BA/AB - the point is, what was two distinct populations, now became homogeneous. Now it’s one big population.