Genetics and evolution PDF

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Geneics and evoluion zalas notes: 1) Brief history of geneics - Aristotle - Birth of raionalism and scieniic method - William Harvey- all life comes from eggs - What is an embryo - Pasteur- discovers spontaneous generaion - Hendel- irst law (segregaion), second law (independent assortment), third la...

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Genetics and evolution zalas notes: 1) Brief history of genetics - Aristotle - Birth of rationalism and scientific method - William Harvey- all life comes from eggs - What is an embryo - Pasteur- discovers spontaneous generation - Hendel- first law (segregation), second law (independent assortment), third law (dominance) - Sutton and boveri- explaining laws 1+2 - Alkaptonuria- explaining third law 2) Origin and normal application of medels laws - Cell cycle - Mitosis - Meiosis - Back cross/ testcross - Dihybrid cross - Multiple alleles - Invisible phenotypes - Pleiotropy 3) Dominance- law or guideline - Polygenic inheritance - Epistasis - Co- dominance - Incomplete dominance - Direct vs indirect phenotypes - Underdominance - Overdominance - Variable expressivity - Incomplete penetrance 4) Genetic linkage- breaking the second law - Linkage - Measuring genetic distance - Converting RF to map distance - Three-point test cross 5) When to throw all the laws away - Sex linked inheritance - Cytoplasmic inheritance - Transmission ratio distorters - Zeroth law 6) Medical genetics and disease - Types of genetic disease - Simple gene disorders and pedigrees - Recognising autosomal dominant disorder - Population prevalence - Recognising autosomal recessive disorder - Recognising x- linked recessive disorder

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Recognising x- linked dominant disorders X- chromosome inactivation in females Recognising mitochondrial inheritance Anticipation= increasing severity between generations

Evolution Lecture 1

What is evolution? - A theory, based on scientific evidence, that provides a testable mechanism which can explain the formation of life and the diversification of species

Scientific theory: 1) Make observations and collect facts 2) Make a hypothesis that attempts to explain these 3) Use your hypothesis to make a prediction 4) Test your prediction 5) Reject your hypothesis and repeat - If your hypothesis stands up to rigorous testing it becomes a theory

Moving toward evolutionary theory Caroleus Linnaeus (1707-1778) a Swedish botanist developed the two-part (bi-nomial) format for naming species A century later, Darwin would argue that classification should be based on evolutionary relationships At the beginning. Of the 19th century, people thought that species remained unchanged since their creation, however, scientific process provided testable evidence to show that: - The earth was very old - Creatures appeared, changed and disappear over time - Resources could limit populations The new science of geology- fuel for evolutionary theory The study of fossils was largely developed by French palaeontologist, Georges Cuvier - Noticed that the older the stratum, the more dissimilar the fossils were to current life forms - Noticed that from one layer to the next, life forms appeared and disappearedbelieved that extinctions would account for these absences - Speculated each boundary between the strata represented a catastrophic event such as a flood that destroyed many species living at the time - Suggested that the catastrophise were localised and that the area would be repopulated by species of a different nature from surrounding environments Charles Lyell- incorporated Hutton’s theories into his principle of uniformitarianism, which suggested that processes are constant over time - Proposed that the same geological processes are operating today as in the past, at the same rate

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Hutton and Lyell’s theories greatly influenced Darwin. He agreed that the earth must be older than previously thought and supported the idea that species diversification may also have taken millions of years

Hypothesis- Erasmus Darwin (grandfather of Charles Darwin) Had influence of Charles Darwin’s ideas - Said “would it be too bold to imagine, that all warm-blooded animals have risen from one living filament, with the power of acquiring new parts, sensations, volitions and associations” - Also had the idea that influenced Charles Darwin’s later theory of the survival of the fittest, “the strongest and most active animal should propagate the species, which should thence become improved” Charles Darwin- theory of evolution 1) Document evidence- note variation in domestic animals and plants 2) Test the power of artificial selection He could see that similar observations could be made in nature and drew two inferences from two observations 1) Observation: members of a population often vary in their inherited traits e.g. Asian ladybird beetles- natural selection acts upon: if the variations can be inherited, they affect the beetles ability to survive and reproduce 2) Observation: all species can produce more offspring than the environment can support, and many of these offspring fail to survive and reproduce e.g. puffball fungus can produce billions of offspring, however the majority will not survive to maturity- if they all survived they would carpet the surrounding land surface, they don’t. Inference 2: the unequal ability of individuals to survive and reproduce will lead to the accumulation of favourable traits in the population over generations - Conclusion: natural selection is a driving force for adaption On the origin of species means of natural selection- 1859 Darwin explained three broad observations: 1) The unity of life 2) The diversity of life 3) The match between organisms and their environment modern scientific study of evolutionary biology: innovations:

How to advances in molecular biology help us to study evolution today? Example 1: Darwin’s finches - The Galapagos finches all evolved from a single species commonly found along the pacific coast of South America - Once on the Galapagos islands the finches adapted to their habitat and the size and shape of the bills reflect their specializations; - - the ground finch eats ticks they remove with their crushing beaks from the Galapagos tortoises, and the Galapagos iguanas - On Isla wolf the sharp beaked found finch is known as the ‘vampire finch’ as it jumps on the backs of masked boobies and red-footed boobies pecking at their flesh and feeding on their blood Example 2: tracking evolving diseases - Flu caused by a virus Spread around the world in seasonal epidemics, kill more than 100,000 people each year, pandemic occur when a new strain spreads- can kill millions - Evolution in action: Biologists collect information about the virus year round from all over the world, they have developed a way to map the characteristics of the flu virus in 2d- they call it an antigenic map, they use it to visualise the virus’ evolution and help predict the evolutionary direction of the virus to choose the most effective vaccine Example 3: human evolution: - We can now isolate DNA from many sources, even from fossils, and examine how particular gene families have evolved. - E.g. we now know that homo sapiens did interbreed with Neanderthal after they left the African continent, and so all modern non-African humans are in fact part Neanderthal

Lecture 2evidence for evolution

What’s the evidence that evolution by natural selection happens? - Comes from many sources, e.g. the fossil record, observations of. Living populations, the DNA record - Evidence that supports a theory of adaption from common ancestry comes in many forms, e.g. all modern organisms use DNA to encode their genetic information, which is then transcribed into RNA and translated into protein, ‘THE CENTRAL DOGMA’ this shared relationship strongly supports the notion that life on our planet has a common and ancient origin. Homology Homology is similiarity resulting from common ancestry Homologous structures are anatomical resemblances that represent variations on a structural theme present in a common ancestor- homology can be anatomical or molecular Mammalian Forelimbs: Although adapted for different functions, the forelimbs of all mammals are constructed from the same basic skeletal elements; 1 large bone is attached to 2 smaller bones which are attached to. Several smaller bones attached to several metacarpals which attach to approx. 5 digits

Convergent evolution: - Distantly related organisms can resemble each other for another reasonconvergent evolution - Convergent evolution is the evolution of similar, or analogous, features in distantly related groups - Analogous traits arise when groups independently adapt to similar environments in similar ways - Convergent evolution does not provide information about ancestry example of convergent evolution- Marsupials and Eutherians: - Marsupials are born as embryos and complete their development in an external pouch (e.g. kangaroos) - Some Australian marsupials have eutherian look-alikes with superficially similar adaptations, e.g. the sugar glider is a forest dwelling marsupial that is superficially similar to the flying squirrel found in north American forests - This is an example of convergent evolution, where a similar habitat drives the appearance of a similar phenotype that confers a survival or reproductive advantage. - Such superficial similarities are referred to as ‘analogous’, not homologous. Analogous features share a similar function but not a common ancestry. In contrast homologous features share a common ancestry but not necessarily a common function.

How can we test ancestry, adaption and evolution using the scientific process? - Examine the fossil record: The fossil record provides evidence of the extinction of species, the origin of new groups and the changes within groups over time - Observe changes within the fossil records: Fossils can document important transitions: e.g. the transition from land to sea in the ancestors of cetaceans - Using fossil evidence, DNA sequence analysis and observations of modern-day animals, we can predict the evolutionary line that led, for example, to the loss of hind limb bone development in modern day cetaceans Evidence for evolution that can support fossil evidence comes from biogeography - Biogeography, the geographic distribution of species provides evidence of evolution - Earths continents were formerly united in a single large continent called Pangaea, but have since separated by continental drift - An understanding of continent movement and modern distribution of species allows us to predict when and where different groups evolved

Direct observations of evolutionary change: Natural selection in response to introduced plant species- Scott Carrol Soapberry bugs use their beak to feed on seeds in fruits In southern Florida soapberry bugs feed on balloon vines with larger fruit; they have long beaks - In central Florida they feed in the introduced golden rain tree which has smaller, flatter fruit. The bugs that feed on these have smaller beaks - They then compared beak size between the bugs feeding on the different fruit with examples held in museum collections that were made before the introduction of the non-native species A very significant difference was found in bugs feeding on the introduced fruit, this significant alteration, a result selection of mutant bugs that could feed on the introduced fruit had taken 35 years -

Host pathogen interaction- example of drug resistance in infectious disease - The bacterium staphylococcus aureus is commonly found on people, about 1 in 3 people harbour it on their skin, nasal passages with no negative side effect - S. aureus can cause a range of illnesses from minor skin infections, such as pimples, impetigo, boils, to life threatening diseases such as pneumonia, meningitis, etc

It can survive on domesticated animals and can cause bumblefoot in chickens. It can survive for hours to weeks or even months, on dry surfaces The treatment of choice for s. aureus infection is penicillin; in most countries, penicillin resistance is extremely common. - In 1928 alexander Fleming of imperial college London observed the antibacterial activity of penicillium fungus when he was growing a culture of s. aureus - Antibiotic resistance in s. aureus was at first uncommon but in 1950, 40% of hospital aureus isolates were penicillin- resistant; and by 1960 this had risen to 80& - Today s. aureus has become resistant to many commonly used antibiotics - Methicillin was then used as it had a different target to penicillin (both inhibit cell wall formation but target different enzymes) but only two years later, the first case of MRSA was reported in England. – MRSA: Methicillin resistant s. aureus -

How does MRSA arise? It is a direct observation of evolutionary change: - the selection pressure, in this case the antibiotic, favours those bacteria within the population that already exist, and which carry a mutation that makes them resistant. These individuals can then replicate while the others perish, giving rise to a new ‘evolved’ strain of the same species - MRSA highlights an important point: Natural selection does not create new traits, but edits or selects for traits already present in the population The local environment determines which traits will be selected for or against in any specific population However, what is beneficial in one situation may not be so in another, it may reduce the chance of survival Molecular homology- Homeobox (HOX) genes as an example To control the formation of a complex organism, you need to be able to organise the development of an embryo in a precise way so that body parts are manufactured at the right place The geneticist Ed Lewis discovered that single genes were in control of the organisation of distinct parts of the organism Later, Basel identified the gene that controlled eye development, he found that the same gene could be found in mice and that it could replace the function of the fly gene- these were HOX genes What are HOX genes? - regulatory genes that control the timing and route of development. - Hox proteins are transcription factors, as they are capable of binding to specific nucleotide sequences on the DNA called enhancers where they either activate or repress genes. - Hox genes cluster together on the genome and play a major role in the development of animal segments with different hox genes being expressed in different segments

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Expression of a hox gene in the wrong place at the wrong time can engage the wrong programme and make the wrong limb, or more than the usual number for example

Evolution of hox genes Hox genes are presented in many different animals, it is possible to track their evolution. The number of hox genes has actually expanded during animal evolution. This means when the DNA was being copied in the sex cells of our ancestors’ mistakes were made, and instead of copying the hox gene once, they were copied twice. When the hox gene was duplicated, the function of the two copies diverged and each evolved a special role in the development of the animal. However, some sections of the gene remained the same- they were conserved- these allow us to see how the genes are related.

Lecture 3 allele frequency and evolution

Micro evolution: the smallest unit of evolution - It describes a change in allele frequencies in a population over generations An allele is one of a number of alternative forms of the same gene or same genetic locus (generally a group of genes) Changes in allele frequent are due to four different processes: 1) Mutation 2) Selection 3) Gene flow 4) Genetic drift Mutation and sources of genetic variation Formation of new alleles - A mutation is a change in the nucleotide sequence of DNA - Only mutations in cells that produce gametes or can be passed to offspring - Mutations could be point mutations, deletions, reversions, recombination’s, duplication events - Mutations can arise as a result of mistakes during DNA synthesis or repair following DNA damage

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Cells have evolved mechanisms to protect against mutations, but they are inevitable

Variation within a population - Both discrete and quantitative characters contribute to variation within a population - Discrete characters can be classified on an either-or basis Discrete characters e.g. anthocyanin production in the flowers of Mendel’s peas is controlled by a single gene - Quantitative characters vary along a continuum within a population, these are visible as the range of differences we see in a population. E.g. different symptoms that two people exhibit when infected with the same virus- they react differently because of the cumulative effect of their genetic makeup

Three mechanisms cause allele frequency change: 1) Natural/artificial selection 2) Gene flow 3) Genetic drift Only natural selection causes adaptive evolution

Average beak depth (mm)

1) Natural selection- case study Differential success in reproduction- results in certain alleles being passed to the next generation in greater proportions - A population of medium ground finches on daphne major island in the Galapagos - In 1977 there was a long period of drought and only about 10% of birds survived - This was because during the drought small soft fruit disappeared and largebeaked birds, which were more likely to crack large seeds, were able to survive 10

In the graph we can see that after the drought the average beak depth had increased The finch population evolved by natural selection.

9 8 0 1976 (similar to the prior 3 years)

1978 (after drought)

2) Gene flow gene flow- consists of the movement of alleles among population - Alleles can be transferred through the movement of fertile individuals or gametes - Gene flow tends to reduce variation among populations over time - Gene flow has the potential to modulate the fitness of a population Gene flow- case study - Consider the great tit (parus major) on the Dutch island of vineland - Mating causes gene flow between the central and eastern populations - Immigration from the mainland introduces alleles that decrease fitness - Natural selection selects for alleles that increase fitness - Birds in the central region with high immigration have lower fitness; birds in the east with low immigration have higher fitness

3) Genetic drift Chance has a role in determining whether a given individual survives and reproduces -

Genetic drift therefore describes how allele frequencies fluctuate unpredictably from one generation to the next

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Genetic drift tends to reduce genetic variation through losses of alleles

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The smaller a sample, the greater the chance of deviation from the predicted result

Genetic drift can lead to the random loss of phenotype

5 2 CRCR CWCW CRCR CRCR plants plants leave leave CRCR CRCW CRCW CRCR offoffspring spring CWCW CRCR CRCR CRCR CWCW CRCR

CRCR

CRCW CRCR

CRCW CRCW

CRCR CRCW Generation 1 p (frequency of CR) = 0.7 q (frequency of CW) = 0.3

CRCR

CWCW CRCR CRCW

CRCW

Generation 2 p = 0.5 q = 0.5

CRCR CRCR

CRCR CRCR Generation 3 p = 1.0 q = 0.0

Example- this small wildflower population has 10 individuals. - By chance only those in the white boxes produce fertile offspring - By chance the offspring of these plants have only two plants that can reproduce and by chance these are the ones in the white boxes. - The result of this genetic drift has been that the Cr allele has been lost from the population

Geographic variation between populations is caused by genetic drift -

Most species exhibit geographic variation, differences between gene pools of separate populations For example, madeira is home to several isolated populations of mice. Chromosomal variation among populations is due to drift, not natural selection

Ldh-Bb allele frequency

The formation of a cline is a common event: - some examples of geographic variation occur as a cline, which is a graded change in a trait along a geographic axis - for example, mummichog fish vary in a cold-adaptive allele along a temperature gradient this variation results from natural selection an allele of 1....