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Evolutionary Biology in 30 Minutes Dr. Reed A. Cartwright Postdoctoral Research Associate Bioinformatics Research Center North Carolina State University February 6, 2007 Dr. Reed A. Cartwright (NCSU) Evolutionary Biology in 30 Minutes 2/6/07 1 / 41 Introducing Myself Postdoc in Genetics and Bioinformatics at NC State PhD in Genetics from University of Georgia (2006) BS Genetics and AB Latin (UGA, 2000) Computational evolutionary geneticist My current research involves developing, implementing, and applying models of molecular evolution to study mammalian evolution. I am also active in several pro-science citizens organizations And was involved with the Cobb County (GA) Disclaimer case and the Dover Area (PA) Intelligent Design case. Dr. Reed A. Cartwright (NCSU) Evolutionary Biology in 30 Minutes 2/6/07 2 / 41 Evolution Theodosius Dobzhansky, 1973 Nothing in Biology Makes Sense Except in the Light of Evolution. The study of life's variation is the central focus of modern biology. Why do dierent species look dierent? Why do dierent individuals of the same species look dierent? Why do dierent parts of individuals look dierent? Evolution explains the variation and diversity of life. Dr. Reed A. Cartwright (NCSU) Evolutionary Biology in 30 Minutes 2/6/07 3 / 41 Brief History of Evolutionary Biology pre-1850s: Many attempts by early philosophers, authors, and naturalists to apply evolution-like ideas to biology. 1859: Darwin's On the Origin of the Species is rst published. 1860s-1920s: Evolution accepted by the scientic community, but doubts about natural selection abound. 1866: Mendel publishes his laws of inheritance, rediscovered in 1900. 1920s-1940s: Modern synthesis of genetics and evolution, rmly establishing importance of natural selection. 1953: Watson and Crick solve the structure of DNA; molecular biology is born. 1968: Kimura develops the neutral theory of molecular evolution. 1972: Gould and Eldredge develop punctuated equilibrium, applying concepts from evolution and ecology to paleontology. 1982: Kingman develops coalescent theory. 1990s: Genomics and bioinformatics start providing data faster than we can study it. Dr. Reed A. Cartwright (NCSU) Evolutionary Biology in 30 Minutes 2/6/07 4 / 41 What is Evolution? Denition: Evolution Change in the heritable characteristics of a population over time. Populations evolve, not individuals. Think Descent with Modication. Denition: Microevolution Evolution apparent between individuals in the same species. Denition: Macroevolution Evolution apparent between individuals in dierent species. Microevolution and macroevolution are the same process, evolution. They dier by the degree of change typically observed. Dr. Reed A. Cartwright (NCSU) Evolutionary Biology in 30 Minutes 2/6/07 5 / 41 2/6/07 6 / 41 Four Examples of Evolution Peppered Moths as an example from population genetics Whales as an example from paleontology Humans as another example from paleontology HIV as an example from molecular biology Dr. Reed A. Cartwright (NCSU) Evolutionary Biology in 30 Minutes Example: Peppered Moth, Fall of the carbonaria form Biston betularia Source: Cook et al. (1999) Proc. R. Soc. Lond. B. 266:293-297. Dr. Reed A. Cartwright (NCSU) Evolutionary Biology in 30 Minutes 2/6/07 7 / 41 Evolutionary Biology in 30 Minutes 2/6/07 8 / 41 Example: Whales Dr. Reed A. Cartwright (NCSU) Example: Hominins A. Pan troglodytes, chimpanzee, modern H. Homo ergaster, 1.75 My B,C. Australopithecus africanus, 2.6,2.5 My I. Homo heidelbergensis, 300-125 Ky D,E. Homo habilis, 1.9,1.8 My J,K,L. Homo sapiens neanderthalensis, 70,60,45 Ky F. Homo rudolfensis, 1.8 My M. Homo sapiens sapiens, Cro-Magnon I, 30 Ky G. Homo erectus, 1.75 My N. Homo sapiens sapiens, modern http://www.talkorigins.org/faqs/comdesc/hominids.html Dr. Reed A. Cartwright (NCSU) Evolutionary Biology in 30 Minutes 2/6/07 9 / 41 Example: Hominins Source: Nick Matzke (NCSE) Dr. Reed A. Cartwright (NCSU) Evolutionary Biology in 30 Minutes 2/6/07 10 / 41 Example: HIV Alignment: /usr/home/reed/hiv/subset.aln Seaview [blocks=10 fontsize=10 LETTER] on Mon Jan 29 19:46:21 2007 Month 0 Month 24 Month 34 Month 45 Month 51 Month 61 Month 66 Month 68 Month 77 Month 80 Month 87 Month 94 Month 98 Month 105 1 EEEVVIRSEN ........D. .......... .......... .K........ .K........ .K........ .K........ .K........ .K........ .K........ .......... .......... .......... FTDNAKTIIV .......... L......... L......... .......... .......... .......... .......... .......... .......... .......... ..N....... ..N....... ..N....... QLKESVVINC ....P..... .......... ....P..... ..N.P..... ..N....... ..N....... ..N....... ..N....... ..N....... ..N....... ..N....... ..N....... ..N....... TRPNNNTRKS .......... .......... .......... ...S....R. ...S....R. ........R. ...S....R. ...S....R. ...S....R. ...S....R. ...S....R. ...S....R. ...S....R. IQVGPGKAIY ......R... ......R... .P....R... .A....R... .A....R... .A....R... .A....R... .T....R... .A....R.F. .A....R.F. .A....R.F. .A....R.F. .A....R.F. TTGEIIGDIR .......... A......... .......... A.EK...... A.EK...... A.DK...... A.DK...... A.DK...... A.DQ...... A.DQ...... A.DQ...... A.DQ...... A.DQ...... QAHCNLSRAE .......... .......... .......... K........A K........A K........A K........A K........A K........A K........A K........A K........A K....I.K.A Partial sequence of the C2-V5 region of HIV-1 env protein. Subset of samples taken from a single patient during a nine year period. Data Source: Shankarappa et al. (1999) J Virology 73:10489-502. Dr. Reed A. Cartwright (NCSU) Evolutionary Biology in 30 Minutes 2/6/07 11 / 41 What is Evolution Not? ControversialEvolution is the foundation of modern biology and is supported by centuries of scientic research. Just a TheoryEvolution is both a fact and a theory. The Fact of Evolution is that populations of organisms have changed over time. The Theory of Evolution explains the fact of evolution. Calling evolution just a theory is like calling Bush just a president. In science, Theories are well established explanations of natural phenomena. Dr. Reed A. Cartwright (NCSU) Evolutionary Biology in 30 Minutes 2/6/07 12 / 41 What is Evolution Not? DirectionalEvolution has no inherent direction. Species can evolve downwards as well as upwards. There is no such thing as devolution. UniversalThe theory of evolution explains the origin of the diversity of life on Earth. It does not attempt to explain the origin of the universe, or of the Earth, or of life itself. Anti-theisticEvolution, like meteorology or gravity, is an explanation of natural events. It is not part of some atheistic campaign to eliminate religion. Mainstream denominations like United Methodists, Catholics, Episcopalians, Presbyterians (USA), Lutherans, Baptist Joint Committee, etc. have all said that evolution is not in conict with their faith. Dr. Reed A. Cartwright (NCSU) Evolutionary Biology in 30 Minutes 2/6/07 13 / 41 Mechanisms of Evolution There are ve main evolutionary forces. The Generating Force: Mutationincluding recombination, gene duplication, etc. The Choosey Force: Selection The Random Force: Genetic Drift The Uniting Force: Gene Flowincluding isolation. The Genotypic Force: Nonrandom Mating Dr. Reed A. Cartwright (NCSU) Evolutionary Biology in 30 Minutes 2/6/07 14 / 41 Population Genetics A population is a group of interbreeding individuals, like a species or subspecies. Population genetics studies the frequencies of alleles and genotypes in a population. Dr. Reed A. Cartwright (NCSU) Evolutionary Biology in 30 Minutes 2/6/07 15 / 41 Variation: Foundation of Evolution Phenotypic variation is due to the interaction of genotypic variation and environmental variation. Example: Two people can have dierent heights because they have dierent genes and/or dierent diets. Unless there is a relationship between the two. Evolution aects genotypic variation and not environmental variation. If there is no genotypic variation, then there can be no evolution. Where does genotypic variation come from? Dr. Reed A. Cartwright (NCSU) Evolutionary Biology in 30 Minutes 2/6/07 16 / 41 Evolutionary Force: Mutation The Generating Force Genes are copied in order to pass them to ospring. This process is inexact, causing random changesmutationsto the genes to occur. Mutation is the foundation of evolution because it generates the variation that evolution requires. In fact, any species that could reproduce itself awlessly would go extinct because it would be unable to evolve in response to a changing environment. Dr. Reed A. Cartwright (NCSU) Evolutionary Biology in 30 Minutes 2/6/07 17 / 41 Evolutionary Force: Natural Selection Denition: Natural Selection Variation in average reproductive success among phenotypes. If a population has a) variation in a trait and b) a consistent relationship between the trait and reproductive success, Then some variants will consistently have more ospring than other variants. Denition: Evolution by Natural Selection Change in the heritable characteristics of a population due to selection. If the population has c) a heritable component to the trait variation, Then the variants with more ospring will likely become more common in the population in the next generation. Dr. Reed A. Cartwright (NCSU) Evolutionary Biology in 30 Minutes 2/6/07 18 / 41 Natural Selection is Not Random Natural selection is the creative force of evolution. By ltering natural variation, selection is able to extract a signal from the noise. Produces complex adaptations by sequential addition and modication of parts. Natural selection is not random. The tness of a phenotype is a product of the environment and is not determined randomly. Dr. Reed A. Cartwright (NCSU) Evolutionary Biology in 30 Minutes 2/6/07 19 / 41 Selection Example Juveniles 1 Adults 1 Juveniles 2 x Selection Reproduction x x x Juveniles 1 Adults 1 x x x Selection Juveniles 2 Reproduction x x Dr. Reed A. Cartwright (NCSU) x Evolutionary Biology in 30 Minutes 2/6/07 20 / 41 Components of Fitness 5 C y lit bi om pa ia V ti b 1 ili ty Zygotes Gametes Adults S ex ua l tic me a 4 G Fe c 2 3 un di ty Dr. Reed A. Cartwright (NCSU) Parents Evolutionary Biology in 30 Minutes 2/6/07 21 / 41 2/6/07 22 / 41 Adaptation Example Why do we vomit? How is it adaptive? Why do we vomit when we get dizzy? Why do we vomit after other people vomit? Dr. Reed A. Cartwright (NCSU) Evolutionary Biology in 30 Minutes How Evolution Makes Complex Things Mullerian Interlocking Structures Over many generations evolution can produce surprisingly complex adaptations. H. J. Muller, 1918 Most present-day animals are the result of a long process of evolution, in which at least thousands of mutations must have taken place. Each new mutant in turn must have derived its survival value from the eect which it produced upon the reaction system that had been brought into being by the many previously formed factors in coöperation; thus a complicated machine was gradually built up whose eective working was dependent upon the interlocking the characters and factors which, when new, were originally merely an asset nally became necessary because other action of very numerous dierent elementary parts or factors, and many of necessary characters and factors had subsequently become changed so as to be dependent on the former. It must result, in consequence, that a dropping out of, or even a slight change in any one of these parts is very likely to disturb fatally the whole machinery; for this reason we should expect very many, if not most, mutations to result in lethal factors, and of the rest, the majority should be semi-lethal or at least disadvantageous in the struggle for life, and likely to set wrong any delicately balanced system, such as the reproductive system. Dr. Reed A. Cartwright (NCSU) Evolutionary Biology in 30 Minutes 2/6/07 23 / 41 2/6/07 24 / 41 Evolutionary Force: Genetic Drift The Random Force Denition: Genetic Drift The random uctuation of alleles due to sampling error. Dr. Reed A. Cartwright (NCSU) Evolutionary Biology in 30 Minutes Sampling Error 1 in 16 4 in 16 sample 6 in 16 w/ replacement 4 in 16 1 in 16 Dr. Reed A. Cartwright (NCSU) Evolutionary Biology in 30 Minutes 2/6/07 25 / 41 Evolutionary Force: Genetic Drift Denition: Genetic Drift The random uctuation of alleles due to sampling error. Drift is the result of reproduction: all ospring contain a sample of the parents' genes. It is statistically unlikely that ospring will have the same allele frequencies as their parents. Drift occurs in every nite population, i.e. every real population. Drift is stronger in small populations than in large populations. Because of drift, even favored alleles can be lost from a population. Drift is the basis of molecular evolution's neutral theory. Dr. Reed A. Cartwright (NCSU) Evolutionary Biology in 30 Minutes 2/6/07 26 / 41 Interaction of Selection and Drift Evolution is the most mathematical of all the life sciences. It is possible to use math to make predictions about the relative strengths of selection and drift. Probability that a New, Neutral Allele is Fixed. P (xation) = 1/2Ne Probability that a New, Selected Allele is Fixed 1− e −s P (xation) = 1 − e − Ne s 2 Dr. Reed A. Cartwright (NCSU) ≈s Evolutionary Biology in 30 Minutes 2/6/07 27 / 41 Interaction of Selection and Drift Using these equations it is possible to determine how the strengths of selection and drift compare. Selection is Stronger than Drift s 1/2Ne Selection is Weaker than Drift s 1/2Ne Dr. Reed A. Cartwright (NCSU) Evolutionary Biology in 30 Minutes 2/6/07 28 / 41 Evolutionary Forces: Gene Flow and Nonrandom Mating Denition: Gene Flow The migration of alleles from one population to another. Lack of gene ow (isolation) allows populations to evolve independently of one another. Denition: Nonrandom Mating A mating system where partners are not chosen independent of their genotypes, either directly or indirectly. Changes genotype frequencies not allele frequencies. Dr. Reed A. Cartwright (NCSU) Evolutionary Biology in 30 Minutes 2/6/07 29 / 41 Origin of New Genes Duplication and Divergence Sections of a chromosome can be duplicated (a type of mutation) if non-homologous recombination occurs. If a gene happens to be in this duplication, then the organism will have two copies of the same gene. Thus, there is redundancy of function, allowing the duplicated genes to evolve new functions while maintaining the old. Gene families like the globins (hemoglobin, myoglobin, etc.) are examples of duplication and divergence. Dr. Reed A. Cartwright (NCSU) Evolutionary Biology in 30 Minutes 2/6/07 30 / 41 Origin of New Genes Duplication and Divergence Duplication Neofunctionalization Dr. Reed A. Cartwright (NCSU) Subfunctionalization Evolutionary Biology in 30 Minutes 2/6/07 31 / 41 Why Evolution is Important In the culture wars, pundits often regard evolution as unimportant or harmful for our society. Among developed countries, only Turkey has a lower acceptance of evolution than the US. Attacks on the central concept of modern biology have serious consequences, if we want a society that values reality over superstition. A prime example is the case of the Tripoli Six. Dr. Reed A. Cartwright (NCSU) Evolutionary Biology in 30 Minutes 2/6/07 32 / 41 Why Evolution is Important: The Tripoli Six The Tripoli Six are a group of foreign medical workers that worked at Al-Fateh Hospital in Benghazi, Libya. In 1998 they were charged with deliberately spreading HIV and hepatitis to children at the hospital. They've been tortured, raped, and sentenced to death (twice) by the Libyan government. The Libyan government has mostly ignored the pleas of foreign governments to release the Tripoli Six. Libya is using these medical workers to extort money from Europe and to retaliate for the conviction of Libyans in the Lockerbie-Pan-Am-103 bombing. Dr. Reed A. Cartwright (NCSU) Evolutionary Biology in 30 Minutes 2/6/07 33 / 41 What Can Evolution Say? The Tripoli Six Two months ago a team of evolutionary biologists published an analysis of the HIV and hepatitis infections which exonerated the Tripoli Six. Using evolution, the scientists were able to demonstrate that the HIV infections were inconsistent with the accusations. Instead, the infections are consistent with an outbreak caused by bad practices at the hospital before the doctors arrived. Dr. Reed A. Cartwright (NCSU) Evolutionary Biology in 30 Minutes 2/6/07 34 / 41 Evolutionary Origin of the Outbreak Tripoli Six de Oliveira et al. The HIV-1 sequences from the hospital form a well supported monophyletic cluster within the CRF02_AG clade, indicating that the outbreak arose from one CRF02_AG lineage. The cluster is closest to three west African reference sequences (Fig. 1a), the basal location of which suggests that the Al-Fateh Hospital lineage arrived in Libya from there. The branch length leading to the Al-Fateh Hospital cluster is perfectly typical; hence the Al-Fateh Hospital strain is not unusually divergent. Dr. Reed A. Cartwright (NCSU) Evolutionary Biology in 30 Minutes 2/6/07 35 / 41 Evolutionary Origin of the Outbreak Tripoli Six ac, Estimated maximum-likelihood phylogenies for HIV-1 CRF02_AG (a), HCV genotype 4 (b) and HCV genotype 1 (c). Source of sequences used for analysis: AFH, red; Egypt, green; Cameroon, blue. Black circles mark the common ancestor of HCV subtype 4a and 1a; numbers above AFH lineages give clade support values using bootstrap and Bayesian methods, respectively. Scale bar units are nucleotide substitutions per site. For visual clarity, AFH clusters are represented by triangles and some non-informative reference strains are excluded. Dr. Reed A. Cartwright (NCSU) Evolutionary Biology in 30 Minutes 2/6/07 36 / 41 Time of Origin of the Outbreak Tripoli Six de Oliveira et al. We found that, irrespective of which model was used, the estimated date of the most common recent ancestor for each cluster pre-dated March 1998, sometimes by many years (Fig. 2). In most analyses, the probability that the clusters from the Al-Fateh Hospital originated after that time was almost zero (for details, supplementary information). For the three HCV clusters, the percentage of lineages already present before March 1998 was about 70%; the equivalent percentage for the HIV-1 cluster was estimated at about 40%. Dr. Reed A. Cartwright (NCSU) Evolutionary Biology in 30 Minutes 2/6/07 37 / 41 Time of Origin of the Outbreak Tripoli Six Results obtained by using dierent evolutionary models. Vertical lines show the 95% highest posterior density intervals. Red line shows time of arrival of the foreign sta in March 1998. For further details, see supplementary information. 'Const', constant size; 'Expo', exponential growth. Dr. Reed A. Cartwright (NCSU) Evolutionary Biology in 30 Minutes 2/6/07 38 / 41 What has evolution shown? Tripoli Six de Oliveira et al. Our results support the existing nosocomial transmission scenario and suggest that Al-Fateh Hospital had a long-standing infection-control problem. The earlier origin and greater number of HCV clusters than HIV-1 clusters reect the higher transmissibility of HCV compared with HIV-1 by such routes. Crucially, we have shown that the HIV-1 and HCV strains responsible were being spread and transmitted among individuals attending the hospital before March 1998, indicating that many of the transmissions giving rise to the infection clusters must have already occurred before the foreign medical sta arrived. Dr. Reed A. Cartwright (NCSU) Evolutionary Biology in 30 Minutes 2/6/07 39 / 41 What's Next for the Tripoli Six Tripoli Six The work of de Oliveria et al. could not have been done without our understanding of HIV evolution. No intelligent design or biblical creation approach could have even tackled the question. Sadly, the Tripoli Six, although proven innocent by this research, are still on death row. It is unclear whether Libya will even listen to this scientic evidence; they've ignored earlier scientic testimony by the defense. Dr. Reed A. Cartwright (NCSU) Evolutionary Biology in 30 Minutes 2/6/07 40 / 41 Thanks Dr. Reed A. Cartwright (NCSU) Evolutionary Biology in 30 Minutes 2/6/07 41 / 41