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Ch. 13 Population genetics

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Ch. 13 Population genetics

  1. 1. Population <br />Genetics<br />
  2. 2. Populations and Variation<br />2<br />Population<br />... Is a group of the same species, living within a particular geographical area, at a given time.<br />Variation exists between members of a population and may be:<br /><ul><li>Structural
  3. 3. Biochemical
  4. 4. Physiological
  5. 5. Developmental
  6. 6. Behavioural</li></li></ul><li>Structural Variation<br />3<br />Eg. Length of hair in dogs<br />
  7. 7. Biochemical Variation<br />4<br />Eg. Coat colour in quolls<br />Eg. Human ABO blood groups<br />Ability to produce enzyme phenylalanine hydroxylase<br />
  8. 8. Physiological Variation<br />Eg. Red-green colourblindness<br />Eg. Ability to taste PTC or other toxins<br />Interestingly, brussel sprouts contain a very similar plant tannin and appear to have the same bitter taste to some people.<br />5<br />
  9. 9. Behavioural Variation<br />6<br />Eg. Horses: trotters vs pacers<br />Eg. What certain dog breeds can be trained to do<br />Eg. Domesticable animals<br />Eg, <br />
  10. 10. Developmental Variation<br />7<br />Eg. Adult vs juvenile appearance<br />Pythons<br />Human proportions<br />
  11. 11. Variation<br />8<br />Geographical variation<br />Not a way in which species will vary, but often a result of one of the aforementioned types of variation occurring in geographically isolated populations<br />
  12. 12. Variations on Variation<br />9<br />How many variants?<br />Monomorphic (only one type, eg. Galahs)<br />Polymorphic (more than 1 type)<br />Continuous or discontinuous<br />Continuous (eg. Height in humans)<br />Discontinuous (eg. ABO blood groups)<br />B<br />O<br />AB<br />A<br />Height in cm<br />
  13. 13. Causes of Variation<br />10<br />Environmental<br />Eg. Identical twins looking different<br />Eg. Bees: caste determination by food<br />Eg. The arrowleaf plant<br />Eg. Hydrangeas<br />Grown in water<br />Grown in soil<br />Alkaline soil<br />Acidic soil<br />
  14. 14. Causes of variation<br />11<br />Genetic<br />Monogenic traits (controlled by one gene)<br />Eg. ABO and Rh blood groups<br />Eg. Cleft chin, detached ear lobes<br />No of alleles and relationship between them determines the number of variations possible<br />Polygenic traits (controlled my more than one gene)<br />Eg. Height and skin tone in humans<br />
  15. 15. Skin tone (simplification)<br />12<br />Hypothetically controlled by two genes each with two alleles (+ / -).<br />(+ = dark, - = light), Incomplete dominance<br />How many possible outcomes?<br />
  16. 16. Genes in populations<br />13<br />Gene pool<br />All the alleles in a given population<br />Allele frequency<br />The proportions of each allele for a given gene in a population<br />Calculating allele frequency<br />Divide number of particular allele by total number of alleles. <br />All allelic frequencies must add up to a total of 1.0<br />
  17. 17. Calculating Allele Frequency<br />Alleles are assigned the letters p and q<br />In this population of sheep<br />Total no. of alleles is 20<br />W = 14, w = 6<br />Allele frequency for W (p)<br />p = 14/20 = 0.7<br />Allele frequency for w (q)<br />q = 6/20 = 0.3<br />14<br />
  18. 18. Calculating Allele Frequency<br />We don’t need to be given both p & q<br />If only given p or q, we know that p + q = 1.0<br />The real world<br />Unfortunately we rarely know the actual genotype for most individuals displaying the dominant phenotype<br />Calculating expected allele frequency<br />We are able to count the number of homozygous recessive individuals and assign them the value q2<br />The Hardy-Weinberg formula predicts that √ q2 will provide us with an approximation of q<br />15<br />
  19. 19. Hardy-Weinberg Equilibrium<br />A population in H-W equilibrium will be expected to maintain near-identical allelic frequencies from one generation to the next.<br />A population is said to be in H-W equilibrium if:<br />The population is large<br />Mating is completely random<br />All matings are fertile<br />The population is closed<br />A population will maintain H-W equilibrium unless an agent of change enacts upon it.<br />16<br />
  20. 20. Agent of change #1 - Selection<br />Selective pressure can be as a result of many things<br />Competition for food, habitat or mates<br />Pressure exerted through predation<br />Death or illness do to parasitic organisms or infectious disease<br />As a result of these pressures, due to genetic variability, some phenotypes may have a selective advantage<br />Greater contribution to next gen = greater fitness<br />No phenotype has a set fitness level – depends on circumstances<br />17<br />
  21. 21. 18<br />It would appear that these beetles are at a distinct disadvantage<br />
  22. 22. 19<br />... and now?<br />
  23. 23. Selection in human populations<br />Case study – Malaria and Sickle Cell Anaemia<br />Sickle cell anaemia is a debilitating genetic disease that causes the red blood cells to take on a sickle shape that is particularly unconducive to carrying oxygen<br />The alleles<br />Haemoglobin A is found in normal RBCs<br />Haemoglobin S is found in sickle cell RBCs<br />The effect<br />Malarial parasites can inhabit only non-sickled RBCs<br />The HA and HS display incomplete dominance<br />20<br />
  24. 24. To whom goes the advantage?<br />Non-malarial environment <br />Most to least successful genotypes<br />HAHA – no sickling, plenty of oxygen<br />HAHS – some sickling, less oxygen<br />HSHS – complete sickling, very little oxygen<br />Malarial environment <br />Most to least successful genotypes<br />HAHS – some sickling, but resistant to malaria<br />HSHS – complete sickling, quite debilitating<br />HAHA – no sickling, high risk of malaria<br />21<br />
  25. 25. Natural Selection<br />When an environmental agent enacts on a wild population causing differential reproduction<br />When one phenotype produces more viable offspring than another<br />Agents of natural selection<br />Same as the sources of selective pressure<br />Results over time<br />In the short term can result in one phenotype being more common than another<br />Over longer periods can result in phenotypically variant groups becoming so different that they can no longer mate = speciation<br />22<br />
  26. 26. Natural Selection<br />When an environmental agent enacts on a wild population causing differential reproduction<br />When one phenotype produces more viable offspring than another<br />Agents of natural selection<br />Same as the sources of selective pressure<br />Results over time<br />In the short term can result in one phenotype being more common than another<br />Over longer periods can result in phenotypically variant groups becoming so different that they can no longer mate = speciation<br />23<br />
  27. 27. Artificial Selection<br />Individuals are selected for desired traits and used as parents for the following generation<br />Often the traits for which these animals have been selected would be disadvantageous in a natural environment.<br />Not even going to go there<br />Masters of predator evasion<br />So what if he can’t breath or smell, he looks so cuuute!<br />24<br />
  28. 28. Artificial selection<br />Further difficulties arise when a species reaches its desired form.<br />In the case of crops, this creates a “monoculture” where each individual has the same advantages and disadvantages.<br />An example of this going wrong was in the case of the great potato famine in Ireland<br />The outbreak of the fungus that causes potato blight decimated the crop of the entire country.<br />Over one million people died of starvation<br />International seed and sperm banks are being created in an effort to maintain genetic diversity<br />25<br />
  29. 29. Migration (aka gene flow)<br />Capable of changing allele frequencies far more rapidly than selection<br />Immigration<br />Disproportionate quantity of certain alleles are brought in to a population <br />Emmigration<br />The departing group do not represent the population as a whole with regard to allelic proportions<br />26<br />
  30. 30. Human Migration<br />The first great migration in hominid history was Homo Erectus’ departure from sub-Saharan Africa approx. 2 million years ago<br />The second was H. Sapiens making the same journey approx. 130,000 years ago<br />Interesting results of human migration<br />People of Celtic ancestry adapted to an environment with far less solar radiation than Australia<br />The HS allele is in drastic decline in US Black populations due to lack of selective pressure.<br />27<br />
  31. 31. Chance events: Genetic Drift<br />When a population experiences a calamitous event that decimates the population indiscriminately, the repercussions can be interesting.<br />Examples of such events are fires, floods, earthquakes, etc.<br />28<br />
  32. 32. Bottleneck Effect<br />Natural disasters do not favour any particular phenotype<br />The resultant reduced population may be unrepresentative of the original population<br />A bottleneck essentially eliminates thousands of years of divergent evolution. <br />The next generation have very few mating options and as a result the growing population will be genetically very simillar<br />Time<br />29<br />
  33. 33. Founder Effect<br />At times members of a population migrate, to another location and become isolated.<br />These new populations may not be representative of the population from which they originated.<br />eg. On the Antarctic peninsula most macaroni penguins have black faces, a very few have white faces.<br />All the macaroni penguins on Macquarie Island have white faces<br />30<br />
  34. 34. Evolution within a species<br />Once there was a population of red circles<br />They were a fairly homogenous population but they used to make fun of the “pinkies”<br />One day the pinkies got sick of this and left<br />31<br />
  35. 35. Evolution within a species<br />A few generations later<br />The pinks met a really nice clan of blues and started having a fling here and there<br />Meanwhile, a dark red had some mutant oval offspring<br />32<br />
  36. 36. Evolution within a species<br />A few generations later<br />The introduced alleles were producing some varying phenotypes in the formerly pink population<br />Meanwhile, skinny was the new black with the reds and the streamline mutants were quite popular<br />33<br />
  37. 37. Evolution within a species<br />A few generations later<br />The green offspring’s photosynthetic abilities gave them a great upper hand and they grew big and strong<br />Meanwhile, skinny was the new black with the reds and the streamline mutants were quite popular<br />34<br />
  38. 38. Evolution within a species<br />A few generations later<br />The most successful greens were the ones with a larger surface area. They could just sit on their ass and photosynthesize all day<br />The reds just kept hooking up with skinny chicks<br />35<br />
  39. 39. Evolution within a species<br />A few generations later<br />One day members of the divided populations decided to check out what sort of action they could get from across the river<br />Apart from the fact that they found each other incredibly<br />Unattractive, their bits didn’t even match any more!<br />36<br />
  40. 40. Species vs Sub-species<br />Two populations that are isolated are often exposed to different agents of change<br />They may stay biologically compatible for thousands of years, but will not be attracted to each other. They are now different sub-species<br />Speciation only occurs once the two populations become reproductively isolated (can no longer produce viable offspring).<br />37<br />
  41. 41. mtDNA<br />Is only maternally inherited<br />Therefore does not recombine<br />Each cell contains hundreds of copies<br />Some regions have a high mutation rate<br />Can be used to trace evolutionary origins<br />38<br />
  42. 42. mtDNA<br />The longer two populations are geographically isolated, the more uniquedifferences they accumulate.<br />mtDNA sequence only found in certain populations are known as haplogroups<br />Haplogroups are compared against the originally sequenced Cambridge Reference Sequence (CRS)<br />Haplogroups can be traced back to their point of origin<br />39<br />
  43. 43. Origin and movement of haplogroups<br />40<br />
  44. 44. Homo neanderthalensis<br />In 1997 it was confirmed via mtDNA that neanderthals were a separate species to modern humans<br />In a sequence of mtDNA 397 base pairs long, there were 27 differences.<br />This is in contrast to the average of 8 differences between human populations<br />41<br />

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