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http://www.cdc.gov/swineflu/ Evolution and Population Genetics SCBI 113 Essential Biology Nuttaphon Onparn, PhD. 28 April 2009 Swine Flu (Influenza A: H1N1) Outbreak 2009 Source: WHO 2 hemagglutinin , neuraminidase Swine Influenza Virus (SIV) Hybridziation, antigenic shift 3 http://en.wikipedia.org/wiki/File:Symptoms_of_swine_flu.svg 4 http://en.wikipedia.org/wiki/File:Flu_und_legende_color_c.jpg Outline • Evolution and population genetics – Introduction • National Science Museum – Sue and Thai Dinosaurs Exhibition – Evolution, species and speciation – Population genetics 5 6 1 Sue the Tyrannosaurus rex (67-65 MYA) 7 Siamotyrannus isanensis (130 MYA) 9 8 Lucy the Australopithecus afarensis (3.2 MYA) 10 Bio-Geo Path at Mahidol, Payathai 11 Cenozoic Era display in Natural History Museum 12 2 13 14 Mechanisms of Evolution • Hawaiian Drosophila Nothing makes sense in biology, except in the light of evolution. – 500 described species – One fertilized female, a single founder – More species than islands (T. Dobzhansky, 1973) • Island within island – Keneshiro hypothesis • Mating behaviour plays role in speciation. 15 Introduction Kenneth Kaneshiro, Evolutionary biologist 16 Introduction • Darwin introduces a revolutionary theory • Natural selection as evolutionary process – On the Origin of Species by Means of Natural Selection (November 24, 1859) – Population changes over time, certain heritable traits can help organism leave offspring than other. • Species are descendants of ancestral species • Natural selection as evolutionary process • Evolutionary adaptation – An accumulation of inherited characteristics that enhance organisms’ ability to survive and reproduce in specific environment. 17 18 3 Introduction • Evolution – Descent with modification – A change over time in the genetic composition of a population • Speciation: new species – A gradual appearance of all of biological diversity. 19 A marine iguana, well-suited to its rocky habitat in the Galapagos Islands. Historical Context 20 Scala Naturae • Darwinism • The sacle of nature and classification of species – Timing and logic – Resistance to the idea of evolution – Aristotle (384-322 B.C.) → • Western culture: Earth is a few thousand years old, populated by unchanging organisms. • Scala naturae (scale of nature) • (linear) – Carolus Linnaeus (1707-1778) → • classify life’s diversity for the greater glory of God. • (nested) 21 22 Catastrophism • Fossils, Cuvier and catastrophism – Fossils • Remains or traces of organisms from the past. The historical context of Darwin’s life and ideas. 23 24 4 Catastrophism • Fossils, Cuvier and catastrophism – Paleontology • The study of fossils developed by Georges Cuvier (1769-1832) • Catastrophism – Not believe in gradual evolution, strata boundaries came from catastrophism. – Sudden and violent changes (flood or drought) that can destropy many species. 25 26 Gradualism and Uniformitarianism • Theories of Gradualism – Change can take place by the cumulative effect of slow, but continuous process. Fossils from strata of sedimentary rock: The Colorado river and the Grand Canyon. 27 28 Lamarck’s Theory of Evolution Gradualism and Uniformitarianism • Jean-Baptiste de Lmarck • Uniformitarianism – Evolutionary change explains the fossil record and organisms’ adaptations to their environments. – James Hutton and Charles Lyell → – Geological processes are operating today as in the past, at the same rate. • Darwin thought that similar slow process could act on organism and produce changes as well. • Changes occur, but no extinction. Species only transformed. – How does evolution occur? • Use and disuse • Inheritance of acquired characteristics – Innate drive 29 30 5 Darwin’s Research • The Origin of Species – Species change through natural selection • Darwin – Shrewsbury (western England) – University of Edinbrugh (medicine) – Cambridge University (clergyman) • John Henslow (botanist) • Robert FitzRoy (captain of HMS Beagle) Acquired traits cannot be inherited: the bonsai. 31 The Voyage of the Beagle 32 The Voyage of the Beagle • What did Darwin find? • What did Darwin find? – Various adaptation of plants and animals – Fossils were distinct, but resemble those living species of the continent. – Ecological diversity, from grassland to high mountain – Geologic processes can change the landscape • Principles of Geology (Chales Lyell, 1830) – South America temperate species are resembled species in the tropic, rather than Europe temperate species. – Galapagos island species 33 34 35 36 The voyage of HMS Beagle 6 Darwin’s Focus on Adaptation Darwin’s Focus on Adaptation • Adaptation and speciation • The origin of species – 1840s – Could a new species arise from an ancestral form by the gradual accumulation of adaptations to a different environment? • major features done, Darwin was in poor health. – 1844 • the long essay was written but unpublished. • Galapagos finches – 1858 – Their beaks and behaviours are adapted to specific food found on their specific islands. • Alfred Russel Wallace wrote to Darwin – 1859 • Darwin published “The Origin of Species” 37 38 The Origin of Species • Descent with modification – Darwin’s view of life – Tree of life • Elephant evolution – Linnaeus taxonomy • Reflect the branching history of the tree of life as species descended from their common ancestors. Beak variation in Galapagos finches 40 41 42 Descent with modification: evolutionary tree of elephant 39 7 Observations and Inferences • Observations Observations and Inferences • Inference • Population would increase exponentially if all individual reproduced successfully. (after Thomas Malthus, 1798) • But, populations tend to remain stable. • Resources are limited – Only a fraction survive as many struggled for existence. • Members of species vary • Much of variations can be inherited (artificial selection in agriculture) 43 44 Observations and Inferences • Inference – Some traits give more fitness to organism (survive and reproduce) – Unequal fitness lead to gradual change in a population. 45 Overproduction of offspring 46 Variation in population 47 48 Artificail selection 8 Natural Selection Natural Selection • Definition • Effects – Natural selection is the differential success in reproduction that results from the interaction between individuals that vary in heritable traits and their environment. – Over time, natural selection can increase the adaptation of organisms to their environment. • If the environment change or individual move to new habitat, natural selection could sometimes give rise to new species. • Differential success in reproduction – The unequal ability of individuals to survive and reproduce. 49 50 Natural Selection • Unit of evolution – A population is the smallest unit that can evolve. • Natural selection occurs through interaction between individual and environment, but individual do not evolve. • Population Camouflage as an example of evolutionary adaptation – A group of interbreeding individuals belonging to a particular species and sharing a common geographic area. 51 Natural Selection 52 Natural Selection • Measuring evolution • Life as Darwin see it – Relative proportions of heritable variations in a population over a succession of generations. 53 – Life evolve through gradual accumulation of small changes. • Natural selection operates in various contexts over time as can be seen in geological evidence and the entire diversity of life. 54 9 Differential Predation and Guppy Population Differential Predation and Guppy Population • Guppies (Poecilia reticulata) • Guppies (Poecilia reticulata) – Observation – Experimentation • Different average age and size at sexual maturity. • Correlation with type of active predator. • Transplantation experiment – Move guppies from pike-cichlid pool to killifish pool (has no guppy prior the experiment) – Small killifish → prey on juvenile guppies – Pike-cichlid fish → prey on mature guppies » Guppies with pike-cichlid reproduce at younger age and are smaller at maturity. 55 56 57 58 The Evolution of Drug-Resistant HIV • Human Immunodeficiency Virus (HIV) – The drug 3TC interfere with reverse transcriptase. 3TC is cytosine analog. – Some virus has reverse transcriptase that can distinguish 3TC and normal C. • This variation replicate slower than normal virus. • With 3TC, this variant replicate bettern than normal virus. 59 60 10 The Evolution of Drug-Resistant HIV • Human Immunodeficiency Virus (HIV) Natural Selection • Two key points – Drug-resistant pathogen can spread quickly in the present of strong selective force. – Natural selection is a process of edition not creation. – Natural selection depends on time and place. • Adaptive in one situation become maladaptive in other situations. 61 62 Evidence of Evolution • Evolution can help answer questions – Why certain characteristics in related species have an underlying similarity even though they may have very different function. • Homology – Anatomical homologies • Comparative embryology – Molecular homologies • Biogeography • The fossil record 63 64 Evolution of drug resistance in HIV. Homology Homology • Homology • Homology • Homologous structure – Similarity resulting from common ancestry. – Anatomical homologies (comparative anatomy) – Variation on a structural theme that was present in their common ancestor. – Vestigial organs » Remnants of structures that served important functions in the organism’s ancestors. • Comparison of body structures between species. • Comparative embryology – The comparison of early stages of animal development, not visible in adult organisms. 65 66 11 Homology • Homology – Molecular homologies • Similarity at the molecular level. All forms of life use the same genetic machinery of DNA and RNA. • Many share genes (bacteria vs human) – Homologies and the tree of life • Molecular homology can date back to the ancestral past. • Some homologies evolved just recently (tetrapods), 5-digit limbs → nested pattern. • Organisms evolved from a common ancestor. 67 Mammalian forelimbs: homologous structure 68 Anatomical similarities in vertebrate embryos 69 Comparision of a protein found in diverse vertebrates 70 Biogeography • Biogeography – The geographic distribution of species. • Closely related species tend to be found in the same geographic region. • Distant region with same ecological niche occupied by different species (sometimes look similar). 71 72 12 Biogeography • Biogeography • Australia – Australian marsupials have eutherian lookalike. (i.e. sugar glider and flying squirrel). – Convergent evolution (not homologous) • Endemic – Species that found no where else (Galapagos, Hawaii) Different geographic regions, different mammalian brands 73 74 75 76 The Fossil Record • The fossil record – The Darwinian view of life predicts that evolutionary transitions should leave signs in the fossil record. • • • • Ape and Human fossils Dinosaur and bird fossils Terrestrail mammal and whale fossils Not so fossil: prokaryote and eukaryote A transitional fossil linking past and present 77 78 13 Darwin’s Theory of Evolution Fact or Theory? • Does Darwinian view of lfie a fact or a theory? • It can explains so many different kinds of observations. – As can be seen from various evidence, it is a fact. – Homologies match patterns in space (biogeography) and time (the fossil record). • The different between theory and fact or hypothesis. – With many observation and data, hypothesis become theory. – Natural selection can explain how similar adaptations can evolve independently (convergent evolution, e.g. sugar glider and flying squirrels) • Is natural selection the only evolutionary mechansim? 79 – No. Other factors have been found to play important roles. 80 Outline • Key concepts – Biological species concept – Reproductive isolation – Speciation The Origin of Species • Allopatric speciation • Sympatric speciation The definition of species and speciation process – Macroevolution and many speciation events 82 Mystery of Mysteries Mystery of Mysteries • Darwin’s diary • Evolutionary changes – Galápagos Island • “Both in space and time, we seem to be brought somewhat near to that great fact – that mystery of mysteries – the first appearance of new beings on this earth.” • Speciation – The origin of new species – The source of biological diversity (species diversity) 83 – Microevolution • Changes confined to single gene pool (at species level) – Macroevolution • Evolutionary changes above species level – Evolutionary novelties (e.g. feathers separate birds from dinosaurs) 84 14 Two patterns of evolutionary change How would you explain the origin of flightless birds? The flightless cormorant (Nannopterum harrisi), one of many new species 85 that have originated on the isolated Galápagos Islands. 86 What is Species? Patterns of Evolutionary Changes • Anagenesis • Species – Ana=new, genos=race (new race) – One species transform to another species. – Number of species not increase – Latin word, species=kind or appearance • Real or artificial? • Cladogenesis – Klados=branch, genos=race (branching evolution) – Gene pool split, give rise to one or more new species – Number of species increase • Biological diversity – Real entity as species can recognize its own species. – Higher taxonomic levels are artificial. • Continuous or discrete – Discrete (morphologically distinct species) – Cladogenesis 87 The Biological Species Concept • Biological species concept (BSC) 88 The Biological Species Concept • Limitations of the BSC – Ernst Mayr (1942) – Members of the same species are reproductively compatible. • A species as a population or group of populations whose members have the potential to interbreed in nature and produce viable, fertile offspring, but are unable to produce fertile offspring with other populations. 89 – Fossil (extinct species) – Asexual organisms – No information of reproduction = inconclusive – Has no potential to interbreed (geographically isolated) 90 15 Reproductive Isolation • Reproductive isolation • Factors that prevent members of two species producing viable, fertile hybrid offspring. Similarity between different species (Left) The eastern meadowlark (Sturnella magna) (Right) The western meadowlark (Sturnella neglecta) Both are distinct species, their song and behaviour are different prevent interbreeding if they meet in the wild. – Many barriers can work together. – Gene flow restriction Diversity within a species All human (Homo sapiens) can interbreed. 92 91 Reproductive Isolation Reproductive Isolation – Prezygotic barriers (before the hybrid zygotes are formed) – Postzygotic barriers (after the hybrid zygotes are formed) • • • • • Habitat isolation Temporal isolation Behavioural isolation Mechanical isolation Gametic isolation • Reduced hybrid viability • Reduced hybrid fertility • Hybrid breakdown 93 94 Postzygotic isolation Prezygotic isolation (cont) Prezygotic isolation 95 96 16 Other Species Concepts Other Species Concepts • Morphological species concept • Paleontological species concept – Similarity between members of species is greater than with other species. – Morphological discrete characters found from fossils. • Good for both sexual and asexual species; taxonomists use this for ages. • Bad for its subjectivity, lack of reproductive isolation data • Good for fossil identification • Bad for its lack of reproductive isolation data 97 Other Species Concepts 98 Other Species Concepts • Ecological species concept • Phylogenetic species concept – Similar ecological niche (what they eat, how they live, etc.) – Same species with a unique genetic history (belong to the same clade; appear as monophyletic group) • Good for both sexual and asexual organisms • Bad for lack of reproductive data and different species could have similar niche. • Good for both sexual and asexual, even fossils; can distinguish sibling species (then confirmed with BSC) • Bad for its requirement of extensive information (time and money as well as man hours) 99 100 Other Species Concepts Speciation • Conclusion: • Speciation – Each species concept provides framework to work with in its respective research areas. – The origin of new species. – There are two ways gene flow between subpopulations can be interrupted. • Allopatric speciation • Sympatric speciation 101 102 17 Allopatric Speciation • Allopatric speciation Two main modes of speciation – Greek allos=other, patra=homeland – Gene flow interruption 103 Allopatric Speciation 104 Allopatric Speciation – When subpopulation divided with geographic barrier (or distance) – Small populations diverge from large population • Barriers’ effectiveness depending on mobility of organisms (birds vs turtle vs plants). • Genetic differences accumulate over time (mutations) • Allele frequencies altered by selection, drift • Just 2 million years plants and animals from S.America evolved to new species on Galápagos. • Small populations also proned to extinction. 105 Harris’s antelope squirrel (Ammospermophilus harrisi) of the southern rim of the Grand Canyon. 106 Can divergence of allopatric fruit fly populations lead to reproductive isolation? White-tailed antelope squirrel (Ammospermophilus leucurus) of the northern rim of the Grand Canyon. Starch Population Starch flies tend to mate with other starch flies. Allopatric speciation of antelope squirrels on opposite rims of the Grand Canyon. Birds and other organisms that can disperse across the Grand Canyon have not diverged into different species on opposite rims. 107 The barrier is not absolute, some flies mate with other flies from different population. Maltose Population Maltose flies tend to mate with other maltose flies. 108 18 109 110 111 112 113 114 Allopatric Speciation • Allopatric speciation – Geospiza difficilis • Females respond to song of same island males, but ignore songs from other island males. – Prezygotic barrier (behavioural isolation) – Geographic barrier • Not a reproductive barrier by itself. – Female’s mate choice (mating song discrimination) • A reproductive barrier in this finch species. 19 Sympatric Speciation Polyploidy • Sympatric speciation • Polyploidy – Greek syn=together, patra=homeland – Mutation that increase extra set of chromosomes. – Rare in animals, but more common in plants. • How can reproductive barriers (reduction in gene flow) between sympatric populations evolve when members remain in contact? – Chromosomal mutation » Polyploidy – Nonrandom mating » Habitat differentiation » Sexual selection • Autoploidy – Extra set of chromosome originate from a single species (Greek: autos=self) 115 116 Polyploidy • Mechanism – Nondisjunction in cell division (2n→4n) • Results – 2nx4n→3n which is sterile – 4n can self and mate with other 4n – In ONE generation, autoploidy generates isolation without any geographic barrier. Sympatric speciation by autopolyploidy in plants 117 Sympatric Speciation 118 Sympatric Speciation • Allopolyploid • Allopolyploid – Greek allos=other – Mechanism – Result • When 2 species interbreed and produce sterile hybrids → this hybrid can asexually reproduce • Or, with some events, allopolyploid will emerge (see figure) 119 • Allopolyploid that can interbreed with each other, but not with its both parent species. • Allopolyploid plant represents a new biological species. • Speciation without geographic barrier. 120 20 One mechanism for allopolyploid speciation in plants 121 122 Sympatric Speciation • Polyploid species – The goatbeard plants (genus Tragopogon) • Diploid species – T. dubius, T. pratensis and T. porrifolius • Tetraploid species – T miscellus (T. dubiusxT. pratensis) • Allopolyploid species http://ftp.funet.fi 123 – T mirus (T. dubiusxT.porrifolius) – With ongoing hybridization with its parent species. 124 Sympatric Speciation • Agricultural crops are polyploid – Oats, cotton, potatoes, tobacco and wheat – The bread wheat (Triticum aestivum) • Allohexaploid – Six sets of chromosomes, two sets from 3 different species – First polyploid might occur naturally in the Middle East, approximately 8,000 years ago. – Breeding program can be used to create allopolyploid species. • Chemical can be used to induce meiotic and mitotic errors. http://www.littletree.com.au/bread.htm 125/239 126 21 Sympatric Speciation • Habitat Differentiation and Sexual Selection – The North American apple maggot fly (Rhagoletis pmonella) • Reproductive isolation occurs as subpopulation prefer different food than parent population (native hawthorn trees). 127 128 Sympatric Speciation • The lake Victoria – Only 12,000 years old, but there are 500 species of cichlid fishes. Similar genetically, suggested that they diverged just recently, probably from food preferences. http://www.pbase.com/crocodile/image/32253695 129 Sympatric Speciation 130 Does sexual selection in cichlids result in reproductive isolation? • Pundamilia pundamilia and P. nyererei Under normal light, females of both species mate with male of the same species. – Sexual selection → females select males from appearance. – Nonrandom mating, but pollution is clouding the water. Under monochromatic orange light, females of both species mate indiscriminately resulting in hybrid and viable hybrids. Males and females of Pundamilia pundamilia and P. nyererei 131 Mate choice based on male colouration by females is reproductive barrier. As prezygotic become breached in the lab it suggests that genetic different is small and the speciation occur just recently. 132 22 Adaptive Radiation • Adaptive radiation – Evolution of many diverse species • In new environment with many ecological niches to occupy. • Same habitat, but after mass extinction (just what thought to happen 65 MYA, when dinosaurs gave way to mammals to diversify. Seeds – Hawaii archipelago – Australia 133 Long-distance dispersal: seeds of Pisonia plant on black noddy tern and Velcro invention. 134 The Genetic of Speciation • The monkey flowers (Mimulus lewisii and M. cardinalis) Dubautia laxa Argyroxiphium sandwicense Dubautia linearis – Mechanism • Prezygotic isolation (different pollinators) • Postzygotic isolation (none; hybrid is viable and fertile) – Genetic level Dubautia waialealae • Mutations at two loci; one for flower colour, another for nectar availibility. Dubautia scabra Adaptive radiation of the silversword alliance came from only one species of tarweed about 5 million years ago (molecular analysis). 135 136 http://www.nsf.gov/od/lpa/news/03/images/mimulus_cardinalis_lewisii.jpg 137 138 http://www.stauder.net/bildearkiv/Mimulus%20lewisii%205.jpg 23 http://visionlab.bio.unc.edu/images/mimulus.image.png The Tempo of Speciation • Gradualism – Descent with gradual modification (Darwin) – Little changes accumulate over time. – Species continuously adapted to the environment. • Real evidence or just incomplete data? – Not all of the changes can be fossilized (physiological or biochemical changes) 139 140 The Tempo of Speciation • Punctuated equilibrium Two models for the tempo of speciation – Niles Eldredge and Stephen Jay Gould – Long stasis, punctuated by sudden change. Gradualism model Punctuated equilibrium model • Real evidence or just incomplete data? – Incomplete fossil data set appears to be punctuated. • Both tempo is possible. 142 141 Macroevolution Macroevolution • Macroevolution – Evolutionary changes above species levels. – As small differences accumulated, it would become clear and more pronounced. 143 • Evolutionary novelties – Descent with modification • Complex structure evolved from something thing with same basic function. – How would human eyes have evolved in gradual increments? – How would simple eyes be any use to the ancestors? » Only complicate eyes are useful? Certainly not. 144 24 A range of eye complexity among molluscs Macroevolution Patch of pigmented cells in limpet (mollusc) Eyecup in another mollusc • Evolutionary novelties – Exaptation Pinhole camera-type eye (no lens) in Nautilus (mollusc) • Structures that evolve for one thing, but have another function sometime later (feather and flying). Eye with primitive lens (transparent epithelium) in Murex (mollusc) 145 Evolution and Development Complex camera-type eye in squid (mollusc), similar to vertebrate eyes, but evolve independently 146 Evolution and Development • Genes that control development • Genes that control development – How slight genetic divergences can be magnified into major differences between species? • Genes that control development: rate, timing and spatial patterns; from zygote to adult. – Allometric growth • Greek: allos=other + metron=measure • Different growth rate and pattern during development alters body proportions. – Human body and limbs – Human and chimp skulls – Salamander feet – Heterochrony • Greek: hetero=different + chronos=time • Change in rate and timing of development events. 147 148 Different Time Allometric growth Heterochrony Differential growth rates in human. Legs and arms lengthen more than head and trunk. Comparison of chimpanzee and human skull growth. Salamanders that live on tree have their digit development end sooner, giving more webbing to developed for tree climbing. Similar for both chimpanzee and human in fetus. In adult, human skull become rounded with little sloping whereas chimp skull become elongated wilth sloping face. 149 Short, but more webbing 150 25 Changes in Spatial Pattern Different regions of Hox genes expression in chicken and fish. Homeotic genes Determine where basic structures (a pair of wings or legs) will develop. Paedomorphosis – retaining larval characteristics even in adult form (full size, sexually mature). 151 152 Grazers Hox mutations and the origin of vertebrates Invertebrate with one copy of Hox complex First duplication occurred 520 MYA New set of genes with new role of backbone development. Second duplication 425 MYA yielding 4 set of Hox complexes made jaws and limbs development possible. 153 Browsers Yellow line indicates the evolution of modern horse with trend toward increasing size, reduced number of toes and grazing adaptations. Evolution is not goal-oriented. 154 Modern Synthesis • The modern synthesis – Darwin Population Genetics • Quantitative characters (continuous) → multiple genes with Mendelian inhertitance – Mendel The study of allele frequencies dynamic in a population. • “Either or” (red or white flower) – Modern synthesis • Integrated theory of evolution from Darwin, Mendel and mathematics. 156 26 Modern Synthesis Modern Synthesis • The modern synthesis • The modern synthesis – Theodosius Dobzhansky (1900-1975) a geneticist – R.A. Fisher (1890-1962) – Ernst Mayr (1904-2005) a biogeographer – J.B.S. Haldane (1892-1975) – George Gaylord Simpson (1902-1984) a paleontologist – Sewall Wright (1889-1988) a geneticist – George Ledyard Stebbins (1906-2000) a botanist 157 158 Introduction • Population genetics – The study of allele frequency distribution at the population level. Sir Ronald Aylmer Fisher John Burdon Sanderson Haldane Sewall Green Wright – Gene pool • All the genes present in breeding population at a given period. – Allele frequency George Ledyard Stebbins George Gaylord Simpson Ernst Mayr Theodosius Dobzhansky • Proportion of a given allele to the total allele of that locus in a population. 159 Allele Frequency 160 Allele Frequency • Allele • Allele frequency (gene frequency) – Alternate version of a gene at a given locus on a chromosome. – For diploid organism, there are two alleles (A or a) at a locus on homologous chromosomes. – Diploid organism • There are two alleles on the homologous locus on each chromosome. • Frequency of allele A is p. • Frequency of allele a is q. – There could be more than two alleles as well, called multiple alleles (i.e. ABO bloodtype; IA, IB and i). 161 162 27 Total Alleles Randomly Pick a Gamete • Total alleles • Probability – At a particular time, a total of all genes in the population is called gene pool. – Probability of getting gamete containing allele A is p. • The total alleles at a locus is 2N in diploid organism because there are two set of chromosomes in the nucleus. – However, in Y-linked genes, there is only 1 Ychromosome per nucleus. Eventhough the organism is diploid, there is only one copy of Y-linked gene in the cell. » The total of alleles on any loci on Y-chormosome is only N. – Probability of getting gamete containing allele a is q. • The probability of getting either gamete containing allele (A) or (a) is p+q=1. 163 164 Fertilization of Gametes Random Zygote • Zygote • Fertilization of gametes – After fertilization of two gametes, one from male and another from female. – Zygote = fertilization of 2 gametes. • Probability of getting one gamete containing allele (A) and another gamete containing allele (A) is pxp = p2. • Probability of getting one gamete containing allele (a) and another gamete containing allele (a) is qxq = q2. • Probability of getting zygote (AA) is pxp = p2. • Probability of getting zygote (aa) is qxq = q2. • Proability of getting zygote (Aa) is pxq = pq. • Proability of getting zygote (aA) is qxp =qp. • Probability of getting heterozygotes (Aa) or (aA) is pq+qp = 2pq. 165 Total Possible Zygotes 166 Allele and Genotype Frequencies • Total possible zygotes • Allele frequency – Homozygous zygotes (AA) or (aa) is p2 or q2. – Heterozygous zygotes (Aa) is 2pq. – p+q = 1 • Genotype frequency – p2+2pq+q2 = 1 • Probability of getting zygotes (AA) or (aa) or (Aa) is p2+2pq+q2=1 • Binomial expansion – (p+q)2 = p2+2pq+q2 = 1 167 168 28 Polyploidy Genotypic and Allelic Frequencies • Haploid – (p+q)1 = p+q = 1 • Diploid – (p+q)2 = p2+2pq+q2 = 1 • Triploid – (p+q)3 = p3+3p2q+3pq2+q3 = 1 • Tetraploid Heterozygote frequency will be at maximum in a diploid two-allelic population when allelic frequencies p and q are equal at 0.5. – (p+q)4 = p4+4p3q+6p2q2+4pq3+q4 = 1 169 Pascal’s Triangle 170 Multiple Alleles • Multiple alleles n= – There are more than two alleles at a gene locus. 0 1 1 11 2 121 3 1331 4 14641 5 1 5 10 10 5 1 6 1 6 15 20 15 6 1 7 1 7 21 35 35 21 7 1 8 1 8 28 56 70 56 28 8 1 • Example: ABO bloodtype – Three alleles IA, IB, and i – Allele frequencies p, q, and r – p+q+r = 1 – (p+q+r)2 = p2+q2+r2+2pq+2pr+2qr = 1 – Trinomial expansion 171 Obtaining Allele Frequencies • Techniques for obtaining gene frequencies 172 Numerical Gene Counts • Numerical gene counts – There are 400 genes in 200 diploid individuals. – Diploid population of 200 individuals • There are 90 TT, 60Tt and 50tt (200 indv.) • Using numerical gene counts • Using genotype frequencies – T = 180 (TT) + 60 (Tt) = 240/400 = 0.6 – t = 100 (tt) + 60 (Tt) = 160/400 = 0.4 173 174 29 Using Genotype Frequencies • Using genotype frequencies Conclusion • Two parental populations – From 90(TT), 60(Tt), and 50(tt) (200 indv.) – Genotype frequencies – Genotype frequencies • TT = 0.45, Tt = 0.30, and tt = 0.25 • TT = 0.40, Tt = 0.40, and tt = 0.20 • 90/200 = 0.45 (TT) • 60/200 = 0.30 (Tt) • 50/200 = 0.25 (tt) • Two offspring populations – Genotype frequencies • TT = 0.36, Tt = 0.48, and tt = 0.16 • T = 0.45 (TT) + 1/2(0.30)Tt = 0.45+0.15 = 0.60 • t = 0.25 (TT) + 1/2(0.30)Tt = 0.25+0.15 = 0.40 – Allele frequencies • T = 0.6 and t = 0.4 175 Conclusion 176 Conservation of Gene Frequency • Random mating • Conservation of gene frequency – In large populationg with random mating – After rediscovery of Mendelian genetics • Genotypic frequencies could be altered by random mating. – As can be seen by genotypic frequencies differences between parental generation vs offspring generation. • However, random mating does not change allele frequencies of the population from one generation to the next. • Frequency of dominant allele will reach equilibrium frequency, ratio of 3:1 (3 dominants to 1 recessive individual). – Not true for dominant allele that occurs at low frequency of “brachydactyly” (short fingers). – Hardy and Weinberg disproved it in 1908. 177 178 The Hardy-Weinberg Theorem The Hardy-Weinberg Theorem • Hardy-Weinberg theorem (1908) Godfrey Harold Hardy – Frequencies of alleles and genotypes remain constant from generation to generation. • Allele frequencies preservation Godfrey Harold Hardy – Genetic variations are preserved that natural selection can act over many generations. • Not evolving gene pool • Only Mendelian segregation and recombination occur. 179/239 Wilhelm Weinberg (1862 — 1937) 180/239 Wilhelm Weinberg (1862 — 1937) 30 Hardy and Weinberg Hardy-Weinberg Equilibrium • Equilibrium frequencies • Conservation of gene frequency – Population that has no change in allele and genotype frequencies over generations. – Gene frequencies do not depend upon dominance or recessiveness, but remain essentially unchanged from one generation to the next under certain conditions. • Random mating in large population (no drift) • No selection, mutation and gene flow. – Gene frequencies remain constant over generations. 181 Equilibrium at Multiple Loci 182 Sex Linkage • Sex-linked genes • Equilibrium at one locus – Genes on sex chromosomes (X,Y in human) – Only one generation is needed for the population to reach equilibrium. • Equilibrium at multiple loci • There are 5 genotypes for X-linked genes, for allele A and a on gene locus A. – If genes are linked and not segregated independently, equilibrium cannot be reached in one generation. – In female: AA, Aa, and aa (two X chromosomes). – In male: A and a (only one X chromosome; hemizygous) » Allele frequencies are the same in both sexes, whereas genotype frequencies are different. • Given more time, it could reach equilibrium. 183 184 Equilibrium in Natural Populations • How to study equilibrium in real populations? – This can be done if all segregants can be scored. • Observed phenotypes reflect genotypes. – Codominant alleles » MN blood group 185 186 31 American Ute Indians American Ute Indians • Is this population at HWE? • MN blood groups – Phenotype/genotype frequencies – Population size, n, 104 individuals – Phenotype/genotype frequencies • 0.59 MM, 0.34 MN, 0.07 NN – Observed allele frequencies • 0.59 MM, 0.34 MN, 0.07 NN • M = 0.59 + (0.34/2) = 0.76 • N = 0.07 + (0.34/2) = 0.24 – Allele frequencies • M = 0.59 + (0.34/2) = 0.76 • N = 0.07 + (0.34/2) = 0.24 – Calculated allele frequencies • MM = (0.76)2 = 0.58 • MN = 2(0.76)(0.24) = 0.36 • NN = (0.24)2 = 0.06 187 Albinism 188 HWE at Multiple Loci • Albinism • HWE at multiple loci – Albinism affects 1 in 20,000 individuals. – HWE can also be studied, for example of three alleles system: p, q, and r. • q2 = 1/20,000 = 0.00005 • q = 0.007 2( A1A1) + ( A1A2) + ( A1A3) 2N 2( A2 A2) + ( A1A2) + ( A2 A3) q= 2N 2( A3 A3) + ( A1A3) + ( A2 A3) r= 2N p= • p = 1-q • p = 0.993 • Heterozygotes (carriers) = 2pq = 0.014 189 Inbreeding 190 Factors Affecting Allele Frequencies • Inbreeding • Population can deviate from HWE – Related individuals of similar genotype mated preferentially with each other. • Selfing (self breeding, self fertilization) – Two gametes from a single individual fertilized to form zygote. • Consequences – Mutation – Selection – Migration – Random genetic drift (small population size) – Not alter allele frequencies. – But inbreeding will lead to excess of homozygotes. 191 192 32 Mutation Mutation • Mutation • Mutation – Changes in the nucleotide sequence of DNA. – Difficult to predict what mutation will bring. – Mutation in somatic will be lost, only in germ cell line will be passed on to next generation. • Point mutation – Change only one base. – Most of the point mutation has little to no effect. • Mutation rate is low in animals and plants (1 mutation in 100,000 genes per generation) • Gene duplication – Increase gene number (1000 olfactory genes in human (60% inactive), 1300 in mice (20% inactive)) 193 194 195 Diverse colour pattern of these mustangs are the product of past mutations.196 Mutation • Mutation • Chromosomal mutations –Deletion, insertion, inversion, translocation (change expression level) Recombination Recombination • Recombination • Sexual reproduction – Interchromosomal recombination – Rearrange alleles into fresh combinations every generations. • Independent assortment • Sexual reproduced organisms lack recombination, has little genetic variations. – Intrachromosomal recombination • Crossing over – No new genetic variations – Reshuffling existing genetic variations • Bacteria and virus also have different version of recombination, plus their high mutation make them very dangerous. 197 198 33 Natural Selection Natural Selection • Natural selection • On HWE – Better individuals (fitter; better surviving and reproduction) will leave more offspring than less fit. – Differences in survial and reproductive success would disturb HWE. • Red flowers (CRCR) – would produce more offspring (set more seeds) as they attract more pollinators. » Frequency of CR would increase whereas CW decline. 199 Genetic Drift 200 Genetic Drift • Genetic drift • The bottleneck effect – Fluctuation of allele frequency from generation to generation. – Drift tend to reduce genetic variation, lead to fixation of genes. – A population is forced through a restrictive “bottleneck” such as disasters (storm, flood, drought). • Gene pool of this surviving population would be different from the original. – Small population is the most affected by drift. 201 202 Genetic Drift • The founder effect – A small population (or even one fertilised female) becomes isolated from its large population, and establish new population, possibly in the new location. • Isolation bottleneck 203 204 34 205 206 Gene Flow • Gene flow – Movement of the gene from one population to another. • Movement of individuals for animals, or plants’ seeds • Movement of gametes for plants as in pollen via pollinators 207 208 Gene Flow • On HWE, – Immigration and emigration would increase or decrease allele frequencies in populations. 209 210 35 Adaptive Evolution • Adaptation – Something that increase fitness of the organisms, compared to those that don’t. • Adaptive evolution – Evolution that occurs to increase fitness of the organisms. • Adaptive traits • Maladaptive traits • Natural selection – Only natural selection can lead to adaptation. 211 Genetic Variation 212 Genetic Variation • Genetic Variation • Genetic Variation – Variation within a population – Variation between populations • Polymorphism (as oppose to monomorphic) • Geographic variation – More than one morph can be detected (>0.01) » Phenotypic polymorphism » Genetic polymorphism – Cline = a graded change in trait along a geograhpic axis. • Measuring genetic variation – Average heterozygosity (e.g. it is 14% in Drosophila) » Of all its 13,000 loci → 1,800 loci are heterozygous. 213 214 Geographic variation in chromosomal mutations Fusion of chromosomes (2.4 is between chromosome 2 and chromosome 4) Nonheritable variation within a population European map butterflies (Araschnia levana) have 2 seasonal forms. If one of these form have better fitness, there would be no change in colouration alleles as they are identical genetically. This fusion appear to be neutral. These two patterns (yellow vs red dots) are different. 215 216 36 cline Does geographic variation in yarrow plants (Achillea) have a genetic component? Collecting seeds to grow in the common garden (same elevation). Plants’ height reflect both genetic variation and environmental effects. 217 218 Fitness Fitness • Fitness • Fitness – How well the organism survive and reproduce. • Inclusive fitness – Inclusive fitness = direct fitness + indirect fitness • The contribution an individual makes to the pool of the next generation, relative to the constribution of other individuals. – Relative fitness • The contribution of a genotype to the next generation compared to the contributions of alternative genotypes for the same locus. – Range from 1 to 0. 219 Mode of Selection 220 Mode of Selection • Disruptive selection • Mode of selection – Selection that favour extreme traits, but against intermediate traits. This mode could lead to speciation. (finch’s beak) – Natural selection can alter phenotypic distribution in 3 ways. • Stabilizing selection • Directional selection – Selection that favours intermediate traits, but against extreme traits. This mode reduces variation. (human birth weight) – Selection that deviate from average to one of the directions. (fossil bears) 221 222 37 223 224 225 226 227 228 38 The Preservation of Genetic Variation The Preservation of Genetic Variation • Why recessive alleles remain in the population? • Why recessive alleles remain in the population? – Diplody – Neutral variation • Dominant alleles conceal recessive alleles in heterozygote. • Neutral mutations, pseudogenes → no effect on fitness – Balancing selection (balanced polymorphism) – Sexual selection • Heterozygote advantage (malaria-sickle-cell anemia) • Frequency-dependent selection (the rarer, the better) 229 • Selection for showy trait (reduce fitness of male), but could reflect that the showy male has better genes. 230 Frequency-Dependent Selection • Frequency-dependent selection – Fitness of the organism depending on its own frequency. • Example – Predator-pray relationship » Batesian mimicry » Search images 231 232 Phenotypic variation Generation time Frequency independent selection Using a virtual population to study the effects of selection Blue jay recieves a food reward it can peck a screen with virtual moths. Patterned digital moths are harder to detect 233 234 39 Evolution of Sex Evolution of Sex • Evolution of sex • Evolution of sex – How did sex evolve in the first place? – To increase population expansion? (asexual is better) • Reproductive handicap of sex – Majority of eukaryotes reproduce sexually. – What advantage does sex provide? • Despite sex’s reproductive drawback, sexual reproduction is favoured by natural selection because sex generates genetic variations enable future adaptation to ever-changing environment. – Asexual population increase rapidly compared to sexual population (assuming that 2 surviving offspring per female). 235 236 Evolution of Sex • Evolution of sex • Coevolution between species and its pathogen –(Red Queen race: Alice to run as fast as she could just to stay in the same place) 237 Sexual dimorhism and sexual selecion in peacocks and peahens. 238 Perfect Oranism • Why could natural selection not create “perfect organism”? – Evolution is limited by historical constraints. – Adaptations are often compromises. – Chance and natural selection interact. – Selection can only edit existing variations. The reproductive handicap of sex 239 240 40 Perfect Oranism References • Better than… • Textbooks – Natural selection can select better trait, compared to other – Campbell, N. A. (2008). Biology. San Francisco, Pearson Benjamin Cummings. – Starr, C. (2006), Basic Concepts in Biology (the 6th edition). Thomson Brooks/Cole. USA. 241 242 41