Lecture 3 genetics and genomic


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Lecture 3 - Genetics and Genomics

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Lecture 3 genetics and genomic

  1. 1. Anthropology 101: Human Biological Evolution Lecture 3: Genetics and Genomics Dr. Leanna Wolfe LAWolfe@aol.com Office AHS 303 Drop In Hours: Thurs. 5:00-6:30 PM
  2. 2. Why are genetics important? • Remember Darwin’s postulate #3: • “Traits are passed from parent to offspring.” • Genetics is the study of how this information is transmitted • Fossil record has limits  New strides in understanding human evolution using genetics! • Genetics and you!
  3. 3. Somatic cells & Gametes both contain DNA nucleus mitochondria DNA in nucleus, mtDNA in mitochondria
  4. 4. DNA Basics • 99.99% of all DNA in the nucleus of a cell • DNA long strands of biochemical information (legos or beads) • Sections of DNA form functional units = genes • Genes are recipes for proteins • Proteins serve functions in the body = traits
  5. 5. Some sections of DNA don’t code for proteins • Structural genes DO code for proteins, affect phenotype • Non-coding sections • Regulatory genes, affect phenotype  On/off regulators  Rate of production  Determine when a gene starts making its protein and stops making its protein • Epigenetic changes, can affect phenotype  Turn genes on or off without changes to the DNA sequence
  6. 6. Phenotype: observable traits The proteins that are built using the recipe. Genotype: the alleles you carry The recipe in your DNA. Genotype / Phenotype
  7. 7. Universal Genetic Code • All living organisms have DNA made of the same material that serves similar functions • The universality of the genetic code implies a common ancestry for all life on the planet • Organisms differ in the amount of DNA • BUT the most important differences are in the arrangement of the DNA.  Different order of nucleotides  different proteins
  8. 8. Chromosomes = packages of DNA Cells have 2 versions of each chromosome – we have 23 homologous pairs, 46 total Homologous Chromosomes
  9. 9. Genes are segments on chromosomes • Genes on chromosomes like beads on a string • Each gene has a specific location = locus  Gene loci • There can be different versions of the same kind of gene: these are called alleles • Homologous alleles work together to produce phenotype
  10. 10. Cell Division: Sharing the recipe • DNA replicates before cell division  Two types of replication: • Mitosis: makes a new somatic (body) cell • Meiosis: makes gametes (sex cells, sperm and eggs) used in sexual reproduction
  11. 11. Mitosis: replication of somatic cells • When somatic cells divide chromosomes are doubled • Doubles are split between two daughter cells • Each daughter cell has an identical set of chromosomes to the original cell
  12. 12. Meiosis: production of gametes • Gametes (eggs and sperm) have only 1 copy of each chromosome • Chromosome pairs duplicate and divide into singles, distributed between 4 gametes • When gametes fuse during sexual reproduction, they create a zygote with full set of chromosomes
  13. 13. To make a new organism Parents make gametes Gametes from two parents fuse to form offspring For each chromosome, offspring carry two copies: one from each parent
  14. 14. Mendel showed simple genetic principles • Segregation • Traits determined jointly by pairs of alleles • Either allele can end up in a gamete • Zygotes get 1 allele from mom, 1 allele from dad • Dominance • Sometimes, when two different versions of alleles at a gene loci (heterozygous) only one is expressed
  15. 15. Genotype  Phenotype • Dominant does not mean better, stronger, more adaptive, or more common!!! • Dominant means that trait gets expressed and hides the other trait Genotype Phenotype AA Yellow Aa Yellow aa Green
  16. 16. Complexity: Organisms inherit many genes • Genes affecting a trait occur at particular sites on chromosome (locus) • Homologous chromosome pairs each have one allele that work together for each gene • Alleles for genes on same chromosome tend to stay together = linked • Allele for seed size linked to allele for seed color • Allele for seed color unlinked to allele for seed texture Seed color Seed texture Chromosome I Homologous pairs Chromosome II Homologous pairs Seed size A a B b dD Independent Assortment
  17. 17. • Recombination  shuffling of alleles during meiosis = unique gametes  Independent assortment of alleles at different gene loci  Mixing of alleles during sexual reproduction = unique offspring • The fate of a new mutation is unrelated to other traits  New traits can spread independently in a population • Novel combinations of traits can appear in offspring  This provides new phenotypes for natural selection to act upon Recombination is important for evolution
  18. 18. Mendel studied discontinuous (discrete) traits Darwin observed continuous variation Before Selectio Frequency of each Beak Depth Beak Depth
  19. 19. MOST traits vary along a continuum Continuous Traits • Height • Weight • Skin color Discontinuous Traits • Finger number • Litter size • Rolling tongue
  20. 20. • Lots of traits are linked and so get inherited as a package deal  Linked (same chromosome) • Lots of alleles for a gene aren’t clearly dominant/recessive  Codominance: Sickle-cell anemia  Complex dominance: ABO blood type • Lots of single genes controls multiple traits  Pleiotropy • Lots of genes work together to affect the same trait = Polygenic inheritance Simple Mendelian inheritance is rare (discontinuous traits)
  21. 21. Linked traits are inherited together
  22. 22. Codominance: Two alleles, three phenotypes Sickle-cell anemia • Normal hemoglobin (A) allele • Sickling hemoglobin (S) allele • Three genotypes and three phenotypes:  AA = normal blood cells  SS = sickled blood cells  AS = slightly impaired blood cells, greater defense against malaria
  23. 23. Complex Dominance: ABO Blood Type • Three alleles: A, B & O • O recessive to A & B • A & B co-dominant Genotype Phenotype Compatibility AA Type A Rec.: A or O Don.: A or AB AO AB Type AB Universal recipient BB Type B Rec.: B or O Don.: B or AB BO OO Type O Universal donor
  24. 24. Pleiotropy: One gene controls two traits • In Darwin’s finches, beak traits are correlated • Depth & width vary together  Deeper & wider  Shallow & narrow • Correlations arise when one gene affects multiple traits
  25. 25. Polygenic Traits: Many genes, continuous variation • Many genes affect each trait • Each one has small effect • Generates a continuous range of variation in the trait • Height  So far approx 10 genes  Affect about 30% of variation in height
  26. 26. All this variation! Where does it come from? • Mutation • Meiosis  Recombination of alleles into unique gametes  increases genetic variation at a faster rate than mutation • Sexual Reproduction  Recombination of alleles from unique gametes into unique offspring  New phenotypes for NS to act upon • Complex genetic inheritance  Polygenic traits  Environment interacts with genotype
  27. 27. Polygenic Traits + Environment: Beak Depth • Multiple genes interact to determine the actual beak phenotype • Environmental effects blur across genetic differences producing a range of phenotypes
  28. 28. Polygenic Traits shaped by many genes + environment Phenotypes are almost ALWAYS the product of genes & environment interacting Adjusted Mean Intelligence Test Scores Across 5 Categories of Breastfeeding Duration 36 37 38 39 40 41 <=1 2 to 3 4 to 6 7 to 9 > 9 Duration of Breastfeeding IQScore 95 100 105 110 BPP Test WAIS Verbal IQ
  29. 29. Variation is maintained in the DNA • Intermediate types common, but genetic variation is maintained  MOST individuals have some + and some – alleles for height • Recessive alleles hidden by dominant alleles  Still passed into gametes & remain in population • Much of the variation is “hidden” from selection  If a trait is affected by genes at many loci  Many different genotypes may have similar selective fate  Some variation is protected • Neutral mutations can be hidden Variation is essential for Natural Selection – without differences in traits, nothing to “select” & survival is random
  30. 30. Speciation: Moving beyond existing variation How can chihuahuas be smaller than the smallest wolves?
  31. 31. Solution: Hidden Variation • Normal sized wolves carry some alleles for small body size (some – alleles, and many + alleles) • As big wolves die (or people prefer small ones), frequency of – alleles increases • Variation is shuffled, some new combinations arise • As – alleles become more common, more – alleles likely to be combined in a single individual • New combinations with more – alleles will be outside initial range of variation
  32. 32. What is the nature of variation? + + • Variation is (usually) continuous • Continuous traits are generated via many genes and environmental effects to produce the phenotype • Variation is generated and extended by:  Mutation  Meiosis  Sexual reproduction  Hidden alleles  Polygenic inheritance + environment
  33. 33. Homozygous vs. Heterozygous Genotypes • Homozygous: the same allele at the same locus on both versions of the chromosome • Heterozygous: a different allele at a particular locus on each chromosome
  34. 34. Dominant & recessive alleles • 2 different alleles (heterozygous) = Aa • Sometimes one of the alleles “overrides” the effects of other: this is called dominance = A > a • A dominant allele overrides the effects of a recessive allele Aa AA or aa
  35. 35. Gregor Mendel discovered the nature of inheritance • Monk • Cultivated pea plants • Focused on traits with 2 forms (allele variants)  Green/yellow seeds  Smooth/wrinkled seeds  Purple/white flowers • Cultivated true breeding lines and then studied results of crosses • Kept careful records
  36. 36. Punnett Square Method Genotypes • 4 Aa Phenotypes • 4 Yellow Aa Aa Aa Aa A a a A
  37. 37. Punnett Square Method Genotypes • 1 AA • 2 Aa • 1 aa Phenotypes • 3 Yellow • 1 Green AA Aa Aa aa A A a a
  38. 38. Heterozygous x Homozygous Dominant Genotypes • 2 AA • 2 Aa Phenotypes • 4 Yellow AA AA Aa Aa A A a A