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ANG 6930 Proseminar in Anthropology IIA: Bioanthropology Day 3 ANG 6930 Prof. Connie J. Mulligan Department of Anthropology 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 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 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. Quiz 1 Average – 8.12, two 10s http://www.clas.ufl.edu/users/cmulligan/Webp age/Proseminar.2011/Quiz1answers.htm Difference between Lamark and Darwin, acquired vs inherited variations/adaptations Genetics and the Modern Synthesis 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. 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 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 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 Gregor Mendel (1822-1884) Austrian monk in present-day Slovakia Experiments with truebreeding garden peas, 1856-1863 Published in 1866, but not widely read or understood Rediscovered in 1900 by Hugo de Vries and Carl Correns Green parents Yellow parents GG YY F1 generation: all yellow GY GY F2 generation: 3 yellow 1 green Green parents Yellow parents GG YY F1 generation: all yellow GY GY F2 generation: 3 yellow 1 green GG GY GY YY Mendel’s Insight Organism’s visible characteristics do not always represent heritable qualities Genotype phenotype Hereditary qualities are nonreducible particles, not blended in sexual reproduction Mendelian inheritance Yellow peas can produce green peas 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 Mendel’s Hereditary Principles Principle of particulate heredity Principle of segregation Heredity transmitted by many independent, nonreducible particles that occur in pairs 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 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 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 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 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 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 singlestranded template to synthesize new DNA RNA transcription – Again unzips DNA and uses single-stranded DNA template to synthesize RNA for protein synthesis Types of DNA polymorphisms SNP – single nucleotide polymorphism Large insertion - causes myotonic dystrophy Microsatellite = STR (simple tandem repeat) = STRP (simple tandem repeat polymorpism) = multiple copies of a short (2-6bp) sequence, eg. CACACACA Types of DNA Mitochondrial (mtDNA) no recombination high copy number (but haploid) maternal inheritance high mutation rate studied first large comprehensive database 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 PCR - polymerase chain reaction Kary Mullis – inventor, Nobel prize winner, 1983 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 Mitosis Meiosis (Cell division) (gamete [eggs and sperm] production) Diploid parent cell Diploid daughter cells Diploid parent cell Haploid gametes Blending inheritance (not true) F0 generation Gametes F1 generation Gametes F2 generation Mendelian inheritance (True) 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 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 Meiosis Is Key To Human Variation Second, recombination (crossingover) 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 Assortment and Recombination Inheritance of recombining and nonrecombining segments of the genome Jobling et al. 2004, Fig. 2.18 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) 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 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 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 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 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 Population Genetics Modern synthesis genes in population Four evolutionary mechanisms (phenomena that change frequencies of alleles)??? 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 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 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 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 Bottlenecks and Founder Effects Gene Flow Selection, Drift, Gene Flow, and Variation Evolutionary Force Variation within Populations Variation between Populations Selection Increase or decrease Increase or decrease Genetic drift Decrease Increase Gene flow Increase Decrease Disagree – selection for an advantageous variant will still decrease variation because it decreases the frequencies of all non-selected variants 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 Distribution of Continuous Traits Genotype Genotypes Genotypes Genotypes Genes and Biological Effects Hardy-Weinberg Equilibrium Genotype and allele frequencies remain constant over generations Assumptions Random mating No evolutionary forces No mutation No selection No genetic drift No gene flow Hardy-Weinberg Example Recessive monogenic disorder has incidence of 1 in 2500 - what is frequency of carriers? Frequency of AA genotype = p2 Frequency of Aa genotype = 2pq Frequency of aa genotype = q2 p+q=1 Equations only possible if genotype and allele frequencies remain constant Frequency of recessive allele = q2, therefore q = (0.0004)0.5 = 0.02 Allele frequencies must sum to 1, therefore p = 1-q = 0.98 Frequency of heterozygous genotype, i.e. carriers, is 2(0.02)(0.98) = 0.0392, about 1 in 25 2pq = Significance of Hardy-Weinberg Quantitative demonstration that variation is preserved No inherent tendency for dominant allele to increase frequency Unifies Darwinian evolution with Mendelian inheritance Addresses Darwinian idea that dominant alleles should be most common Springboard for research into evolutionary forces Populations not in Hardy-Weinberg equilibrium are undergoing microevolutionary change Chpt 8 – Serial Homology Serial homologs – structures that arose as repeated series, became differentiated to varying degrees in different animals Huxley (1963) Evidence as to Man’s Place in Nature Vertebrae and ribs, forelimbs and hindlimbs, digits, teeth, etc. Changes in number and kind of serial homologs are key themes in evolution Unique human features result from developmental changes that modified existing primate or great ape structures Chpt 8 - A Brief History of Life Perspectives on Geologic Time The universe is roughly 15 billion years old The earth is about 4.6 billion years old Two major eons: Precambrian eon (4.6 bya to 545 mya) and Phanerozoic eon (545 mya to present) A Brief History of Life The universe is roughly 15 billion years old The earth is about 4.6 billion years old Two major eons: Precambrian eon (4.6 bya to 545 mya) and Phanerozoic eon (545 mya to present) Figure 4.6: Carl Sagan’s Cosmic Calendar. The history of the universe is compressed into a single year, with its origin happening on January 1 and the present day occurring at midnight on the following January 1. A Brief History of Life Precambrian Eon Paleozoic Era 545 to 245 mya Origin of first vertebrates, jawless fish Evolution and diversification of fish, amphibians, and reptiles. Mesozoic Era Beginning of the planet (4.6 billion years ago) to 545 mya Single-celled and multi-celled organisms first appeared 245 to 65 mya Age of reptiles, dominated by dinosaurs First egg-laying mammals (Triassic Period) followed by first placental mammals (Jurassic Period). Cenozoic Era 65 mya to present Age of mammals Evolution of primates and humans Chpt 8 - Dating methods Dating fossil remains Chronometric dating Determines an exact age Relative dating Determines which fossils are older, but not their exact age Relative dating methods Stratigraphy Biostratigraphy Older remains are found deeper in the earth b/c of cumulative build-up of the earth’s surface over time Fossils/sites can be assigned an approximate age based on the similarity of animal remains with those from other dated sites Paleomagnetic reversals Uses the fact that the earth’s magnetic field has shifted back and forth from north to south at irregular intervals Chronometric dating methods Carbon-14 dating Absolute dating of carbon-based remains (organic) based on the half-life of carbon-14 (5,730 yrs), useful over past 50,000 yrs Potassium argon dating Based on half-life of radioactive potassium (1.31 billion yrs), useful for samples older than 100,000 yrs Argon-argon dating Based on half-life of argon, useful for very small samples Dendrochronology Based on tree ring counts of trees in dry climates where trees accumulate one growth ring per year Thermoluminescence Certain heated objects accumulate trapped electrons over time, allowing the date that the object was initially heated to be determined Electron spin resonance Estimates dates from observation of radioactive atoms trapped in calcite crystals present in materials such as bones and shells, useful less then 300,000 yrs altho can be used over a million yrs One more chronometric dating method Molecular dating Use of molecular genetic data to determine genetic distance between species/populations/etc and calibrate a molecular clock to determine # differences = # years divergence Need locus with mutation rate appropriate to question Colonization of the New World Emergence of modern Homo sapiens 100s or 1000s of yrs Divergence of man from non-human primates 10s of 1000s of yrs millions of yrs Example – draw a phylogeny Distance b/t species A and B = 3 (bp changes or some other unit) Distance b/t species A and C = 30 Distance b/t species B and C = 30 Divergence of C from A and B (fossil evidence) = 30 million yrs ago Current hot topics on humans Top 10 mysteries about humans http://www.livescience.com/history/091026-top10origins-mysteries.html Top 10 things that make humans special http://www.livescience.com/culture/091030origins-top10-special.html