ANG 6930 Proseminar in Anthropology IIA: Bioanthropology

1. ANG 6930Proseminar in Anthropology IIA: Bioanthropology Day 3 ANG 6930 Prof. Connie J. Mulligan Department of Anthropology

2. Next week • Genetics and the development of evolutionary theory • Mendelian and molecular genetics • Population genetics • Evolutionary development biology (Evo Devo) • Reading • The Human Species, Chpts 2 (Human genetics), 3 (Evolutionary forces), 8 (Paleoanthropology) • Course packet • Tattersall I. 2000. Paleoanthropology: The last half-century. Evolutionary Anthropology 9:2-16 • Foley R. 2001. In the shadow of the modern synthesis? Alternative perspectives on the last fifty years of paleoanthropology. Evolutionary Anthropology 10:5-14 • Carroll SB. 2003. Genetics and the making of Homo sapiens. Nature. 422:849-857 • “Beyond Stones and Bones”, Newsweek, March 19, 2007. • Topic and abstract for journal analysis is due • First set of questions/comments is due

3. Next week • Primate evolution, ecology and behavior • Primatology as anthropology • Diversity of living primates • Primate models for human evolution and behavior • Comparison of humans and other primates • Reading • The Human Species, Chpts 5 (Primates), 6 (Primate behavior and ecology), 7 (The human species) • Course packet • Martin RD. 2002. Primatology as an essential basis for biological anthropology. Evolutionary Anthropology 11:3-6. • Strier KB. 2003. Primate behavioral ecology: From ethnography to ethology and back. American Anthropologist 105:16-27. • Rieseberg LH and Livingstone K. 2003. Chromosomal speciation in primates. Science 300:267-268. • Khaitovich P et al. 2005. Parallel patterns of evolution in the genomes and transcriptomes of humans and chimpanzees. Science 309:1850-1854. • Amici et al. 2010. Monkeys and apes: Are their cognitive skills really so different? American Journal of Physical Anthropology 143: 188-197. • Judson O. 2008. Wanted: Intelligent aliens, for a research project, New York Times blog

4. Journal analysis • Once you choose your topic, you will write a paper (~10 pages, double-spaced) that discusses how your topic was addressed in the five journals over that past 15 years • An important point will be to examine how bioanthropology and another subfield of anthropology cover your topic, e.g. what are the important questions being addressed/hypotheses being tested, what are the interpretations and conclusions, are there major differences in interpretations/conclusions? • Compare coverage of your topic in three ways: 1) across five journals, 2) through time, and 3) between two subfields. Be EXPLICIT in your comparisons. This is not an explanation of your topic or a review of the literature, but an explicit comparison of coverage/treatment of your topic in the three ways listed above. Provide # articles/journal, talk about how the questions addressed differ through time, by subfield, etc • The final paper is due at our last class, Feb 18.

5. Quiz 1 • Average – 8.12, two 10s • http://www.clas.ufl.edu/users/cmulligan/Webpage/Proseminar.2011/Quiz1answers.htm • Difference between Lamark and Darwin, acquired vs inherited variations/adaptations

6. Genetics and the Modern Synthesis

7. Timeline of Key Developments 1859 Darwin lays out the theory of natural selection in his On the Origin of Species. 1866 Mendel publishes findings on laws of inheritance; posits “Elementes” as unit of heredity. 1882 German biologist Walter Fleming, by staining cells with dyes, discovers rod-shaped bodies he calls "chromosomes." 1902 American biologist Walter Sutton shows that chromosomes exist in pairs that are similar in structure. In light of Mendel's theory that genetic "factors" segregate, he concludes that hereditary factors must lie on chromosomes.

8. Timeline of Key Developments 1915 Thomas Hunt Morgan, an American geneticist, presents results from experiments with fruit flies that prove genes are lined up along chromosomes. He also describes the principle of “linkage” and lays the groundwork for gene mapping. 1944 Avery, MacLeod, and McCarty report that the molecule that carries genetic information is deoxyribonucleic acid (DNA) 1953 Crick and Watson determine that the structure of the DNA molecule is a double helix formed by strands of sugar and phosphate molecules joined by the bonding of four bases

9. Darwin’s Postulates • Infinite ability of populations to grow, but finite ability of environments to support growth • Within populations, organisms vary in ways that affect ability to survive and reproduce • Variations are transmitted from parents to offspring • Natural selection – evolution by variation and selective retention

10. Darwin’s Difficulties • Blending inheritance • Cannot explain how variation is maintained • Favors selection of discontinuous traits, not accumulation of small changes • Natural selection removes variation • Natural selection cannot explain variation beyond original range

11. Gregor Mendel (1822-1884) • Austrian monk in present-day Slovakia • Experiments with true-breeding garden peas, 1856-1863 • Published in 1866, but not widely read or understood • Rediscovered in 1900 by Hugo de Vries and Carl Correns

12. Green parents Yellow parents GG YY F1 generation: all yellow GY GY F2 generation: 3 yellow 1 green

13. Green parents Yellow parents GG YY F1 generation: all yellow GY GY F2 generation: 3 yellow 1 green GG GY GY YY

14. Mendel’s Insight • Organism’s visible characteristics do not always represent heritable qualities • Genotype  phenotype • Yellow peas can produce green peas • Hereditary qualities are nonreducible particles, not blended in sexual reproduction • Mendelian inheritance • Each ‘particle’ retains its characteristic though it may not manifest in an individual, i.e. a green gene is still a green gene even if the plant is not green • Hereditary particles generally function as pairs • Transmission of pea characteristics only works if he has two ‘particles’ to work with in each individual, i.e. recessive and dominant traits

15. Mendel’s Hereditary Principles • Principle of particulate heredity • Heredity transmitted by many independent, nonreducible particles that occur in pairs • Principle of segregation • Each hereditary pair is split during production of sex cells, and new pairs are formed by fertilization • Principle of independent assortment • Hereditary particles for different traits generally inherited independently

16. Rediscovery of Mendel • Hugo De Vries (1848-1935), Dutch botanist • Suspected mutations as source of new variation • Replicated Mendel’s insight in experiments with evening primrose De Vries

17. Chromosomes • In 1902, Sutton made connection between chromosomes and Mendel’s principles of heredity • Long strands of DNA in cell nucleus, 23 pairs in humans

18. Genes • Genetic equivalent of atom: fundamental unit of heredity • DNA is organized into chromosomes • A locus is a particular site on chromosome • An allele is one of several forms of a DNA sequence • Gene is a locus that encodes a protein • The genome is all genes on all chromosomes in an organisms

19. DNA • Invariant sugar-phosphate backbone • Variable chemical bases that make up the ladder ‘rungs’ • Four complementary bases • Adenine (A) bonds with thymine (T) • Guanine (G) bonds with cytosine (C) • Complementary bases are key to DNA function, i.e. provide variation • Sequence of bases code for amino acids that form proteins

20. DNA Structure Uniquely Suited for Inheritance • Nearly infinite variety of messages from four-base structure • Structure implies how inheritance works • Two strands held together by weak hydrogen bonds, i.e. can be unzipped for DNA replication or RNA transcription • DNA replication - Reliably replicates message by unzipping and using single-stranded template to synthesize new DNA • RNA transcription – Again unzips DNA and uses single-stranded DNA template to synthesize RNA for protein synthesis

21. Types of DNA polymorphisms

22. SNP – single nucleotide polymorphism

23. Large insertion- causes myotonic dystrophy

24. Microsatellite = STR (simple tandem repeat) = STRP (simple tandem repeat polymorpism) = multiple copies of a short (2-6bp) sequence, eg. CACACACA

25. Nuclear DNA (nDNA = autosomes + sex chromosomes) homologous recombination single genome/diploid cell biparental inheritance variable mutation rate studied more recently multiple studied loci make comparisons more difficult Types of DNA • Mitochondrial (mtDNA) • no recombination • high copy number (but haploid) • maternal inheritance • high mutation rate • studied first • large comprehensive database

26. PCR - polymerase chain reaction Kary Mullis – inventor, Nobel prize winner, 1983

27. 1 copy of DNA sequence Polymerase chain reaction = PCR, the exponential, synthetic amplification of nucleic acid from a targeted region of the genome Billions of copies of DNA sequence

28. Meiosis (gamete [eggs and sperm] production) Mitosis (Cell division) Diploid parent cell Diploid daughter cells Diploid parent cell Haploid gametes

29. Blending inheritance (not true) Mendelian inheritance (True) F0 generation Gametes F1 generation Gametes F2 generation

30. Predicting Offspring Distributions • Mendel’s principles explain ratio of genotypes in the offspring of particular parents • A given allele of each parent has 50 percent chance of transmittal

31. Meiosis Is Key To Human Variation • First, independent assortment leads to differences among gametes • Haploid cells (egg or sperm) produced by meiosis are all genetically different • Requires selection of either paternal or maternal copy of each chromosome • Number of possible combinations of haploid chromosome subsets is 223 (8,388,608) • Assuming no recombination

32. Meiosis Is Key To Human Variation • Second, recombination (crossing-over) creates new combinations of genetic material • During meiosis, chromosomes physically line up • At certain places, strands join together and exchange pieces • Process reshuffles genetic material in creation of new gametes (egg or sperm) Meiotic recombination Jobling et al. 2004, Fig. 2.17

33. Assortment and Recombination Inheritance of recombining and nonrecombining segments of the genome Jobling et al. 2004, Fig. 2.18

34. Genotypes and Phenotypes • One of Mendel’s insights was that phenotype does not necessarily reflect genotype • Phenotype – observable trait of individual • Genotype – set of two alleles at a particular locus • Homozygous if both alleles are the same (AA or aa) • Heterozygous if the two alleles are different (Aa)

35. Genotypes and Phenotypes • Phenotype determined by relationship between two alleles at a given locus • Dominant alleles mask effect of other allele • Phenotype of AA = phenotype of Aa • If selection favors dominant phenotype, AA and Aa genotypes are equally favored • Recessive alleles are masked by other allele • Recessive phenotype only expressed in aa genotype

36. Molecular Basis of Recessiveness • Most recessive disorders result in absence or severe reduction of gene product • Example – cystic fibrosis • Present in homozygous recessive genotype • Sufferers lack protein that helps transport water across cell membranes → thick and sticky mucus • Heterozygotes are carriers, but do not have disease

37. Emergence of the Modern Synthesis • Modern synthesis – a movement to unify evolutionary biology under a single conceptual umbrella (1930s-1940s) • Biologists first thought Mendelian inheritance was incompatible with Darwinian evolution • Mendel suggests inheritance fundamentally discontinuous, i.e. two discrete heritable units • Darwin emphasize accumulation of small changes • Fisher, Wright, and Haldane worked out mathematical theory to show how Mendelian inheritance could explain continuous variation • Complex vs monogenic phenotypes

38. Individual Selection • Selection arises from competition among individuals, not among populations or species • Example – individual reproductive success and species’ survival • Selection may favor high individual fertility, even if population growth threatens survival of species

39. Evolution and Population • Evolution involves change in genetic makeup of populations • Two scales of evolutionary change • Macroevolution – evolution of new species • Microevolution – evolution at level of population, within species • Evolution = change in frequency of alleles in a population from one generation to the next

40. Population Genetics • Modern synthesis  genes in population • Four evolutionary mechanisms (phenomena that change frequencies of alleles)???

41. Population Genetics • Modern synthesis  genes in population • Four evolutionary mechanisms (phenomena that change frequencies of alleles) • Mutation • Natural selection • Gene flow • Genetic drift • Microevolutionary mechanisms also underlie macroevolution

42. Evolutionary Forces • Mutation • Ultimate source of all new genetic variation • Other evolutionary forces alter frequency of new alleles • Natural selection • Filters new variation • Analysis focuses on fitness – proportion of individuals with given genotype who survive to reproduce

43. Evolutionary Forces • Genetic drift • Random change in allele frequency from one generation to next • Occurs each generation, reduces variation over time • Gene flow • Movement of alleles from one population to another • Makes populations more similar over time

44. Genetic Drift • Genetic drift causes fixation and elimination of new alleles • Magnitude of genetic drift depends on size of population • Present day variation depends on past small population sizes Genetic drift in populations of different sizes

45. Bottlenecks and Founder Effects

46. Gene Flow

47. Evolutionary Force Variation within Populations Variation between Populations Selection Increase or decrease Increase or decrease Genetic drift Decrease Increase Gene flow Increase Decrease Selection, Drift, Gene Flow, and Variation Disagree – selection for an advantageous variant will still decrease variation because it decreases the frequencies of all non-selected variants

48. Monogenic and Complex Traits • Mendel’s experiments involved discrete traits shaped by single locus • Single-gene (monogenic) traits are not typical of human variation • Many traits of interest to us are complex • Involve multiple genes • Influenced by environment • Follow complex mode of inheritance

49. Distribution of Continuous Traits

50. Genotype