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Chapter 22: Descent with Modification: A Darwinian View of Life Evolution by natural selection (by Charles Darwin) was 1st proposed (1859) before classical genetics was known (1899) Darwin made 2 important points: 1. modern species were produced by gradual descent by different ancient species 2. natural selection provided the mechanism for the evolutionary change evolution occurs at the level of the population on the gene pool evolution can now be defined as the change in the frequency of alleles of the gene pool natural selection is only one mechanism by which evolution proceeds evolution is a foundational concept of biology that provides a fabric of understanding that no other theory provides History of the Theory of Evolution up to 1750, the Book of Genesis provided the explanation for the origin of life even Aristotle (384-322 BC) believed that species were fixed and unchanging o species could be arranged on a ladder from simple to complex Carolus Linnaeus, 1735, published a taxonomy of all known life o Linnaeus’ classification put species into categories based on similarities that did not imply kinship but instead a creator’s genius Paleontology began with Georges Cuvier (1769-1832) o fossils, remains or traces of past organisms, were uncovered in sedimentary rocks o theories grew on how sedimentary rock was created, through erosion, deposition, accumulation, and then more erosion - to expose the fossils o Cuvier noted that the lower the layer, the more dissimilar the fossils were from present life forms o Cuvier theorized that major catastrophes had occurred at transitions between layers causing extinction of forms ~1750, evidence began to grow that the earth was old and organisms had evolved o James Hutton (1726-1797) theorized that huge geologic changes took place through extremely slow processes of erosion, deposition, and uplift o Charles Lyell (1797-1875) proposed that present geologic processes were common throughout Earth’s history o both ideas presented a slow and gradual change in the landscape of earth, and a much older planet than the bible indicated Jean Baptiste de Lamarck (1744-1829) - French, developed a theory of evolution based on the inheritance of acquired characteristics o in 1809, Lamarck proposed a theory of evolution o organisms could acquire traits that made them better adapted to their environment o as an organism acquired a trait, the new trait would pass information to its germ cells so that the next generation could benefit from the trait o the process occurred slowly so that only over many generations would visible changes occur o organisms had an innate drive to become increasingly more complex o T. D. Lysenko, a Soviet Agriculturalist, proposed Lamarck’s theory would work on agriculture o if humans were given good growth conditions, they should become healthier and more intelligent over time (1930’s) Darwin and Wallace Charles Darwin (1809-1882) and Alfred Russel Wallace both presented natural selection at the Linnaean Society of London in 1858 o both came to the same realization of natural selection through similar experiences Darwin at the age of 16 was sent to study medicine at the University of Edinburgh He left Edinburgh without degree and enrolled at Cambridge, receiving a B. A. in 1831 Darwin was appointed to the H.M.S. Beagle, a British naval survey ship embarking on a 5 year mapping and collecting expedition (left 1831, returned 1837) he was the ship’s naturalist and companion to Captain Robert FitzRoy he had enormous amounts of time for exploration and collection, from rainforest, to pampas, to desert, and mountains he noted that South American temperate regions had flora and fauna dissimilar to Europe, but more similar to the Brazilian tropics South American fossils were more related to modern South American species that to Europe’s o Darwin’s most striking exploration was that of the Galapagos Islands, with species that were distinct and found nowhere else but similar to South American forms in particular, the 13 species of finches he found there resembled South American finch species but each differed in beak shape and size, adaptations for feeding on different food supplies o while sailing, he read Charles Lyell’s book Principles of Geology the book explained the earth was very old, animals and plants have appeared and disappeared over time, giving Darwin a different-than-Biblical view of Earth’s history Darwin’s observations of South American flora and fauna supported this idea o in 1838 Darwin had read Thomas Malthus essay, Essay on the Principle of Population (published in 1879) the essay stated that populations grow geometrically and outgrow their food supplies which grow arithmetically the essay made the phrase “struggle for existence” this planted the idea of “over-reproduction” for many species in Darwin’s mind in 1858, Darwin received Wallace’s manuscript which stated a similar theory to his own Darwin presented his theory and Wallace proposed his at the 1858 Linnaean Society meeting in 1859, Darwin published The Origin of Species by Means of Natural Selection Darwin was painstaking about detail and logic and his ideas were VERY clearly stated, he had a mountain of supporting evidence oddly, blending inheritance was believed at the time the book was published, yet Darwin’s theory required modern genetics within a decade, most biologists believed the theory Origin of Species all organisms descended from a common ancestor through “descent with modification” “adaptations” described the changes that descendants develop in new habitats the theory tied all organisms together by lineage on a “giant tree of life” with closely related organisms as separate twigs and distantly related organisms on separate branches taxonomy was suddenly explained by natural selection - all organisms actually shared a heritage Ernst Mayr analysis of Natural Selection Observation 1: organisms reproduce exponentially Observation 2: despite exponential reproduction, populations remain stable Observation 3: resources are in finite supply inference 1: a struggle for existence occurs because more organisms are produced than resources can support Observation 4: organisms vary in their characteristics Observation 5: variations are inherited o o o inference 2: the struggle for existence is not random; winners have adaptations that made them winners inference 3: differential survival leads to gradual change with favorable adaptations developing over unfavorable ones Darwin’s mountain of evidence included artificial selection - the practice of picking the best of one generation to produce the next generation o if breeders can produce such profound changes in species over short periods of time, nature could do much more in much longer periods of time Natural Selection Important Points: individuals cannot evolve, only populations natural selection cannot work on acquired traits, only inherited ones adaptations that are favorable in one environment may be lethal on the same species in a different environment Natural Selection Theory Explains... the guppy Poecilia reticulata, exists in the Aripo River system in Trinidad o John Endler and David Reznick have studied it in different microhabitats o some pools have different predators than others - killifish or pike-cichlid o killifish eat small guppies, whereas pike-cichlids eat large killifish o guppies reproduce at younger ages in pike-cichlid pools whereas they reproduce at older ages in killifish pools o extensive testing has shown that even when guppies are moved from one habitat to another, their reproductive behavior gradually changes to adapt to their predation pressure o in pike-cichlid pools, guppies that reproduce early have more success than those that don’t get to reproduce at all because they were eaten o in killifish pools, if the guppies survive to adulthood, a long reproductive span is more advantageous HIV has become drug resistant to drugs such as 3TC o 3TC is a cytosine mimic and is used by reverse transcriptase to produce cDNA in host cells o usage of 3TC terminates elongation of the DNA and prevents HIV reproduction o 3TC resistant strains have no selective advantage normally, but in a patient taking 3TC, the drug acts as a powerful selective agent and creates an entire population of 3TC-resistant HIV, which can then be transmitted to the next host In summary: natural selection “edits” the population of vulnerable adaptations and is specific to the habitat where it works; what is beneficial in one area may not be beneficial in others Evidence of Evolution Comparative Anatomy o similar organisms have similar structures o mammals and other animals share similarities - homologies o homologous structures - structures with the same origin but in different species o analogous structures - structures with similar functions but which have different origins o analogous structures exist because different organisms evolved through different lineages and solved their adaptations with different structures; ex: bat and bird wing o vestigial structures - structures useless to an organism but which are homologous to the functional structure of another organism ex: pelvic girdle of a Boa, ear muscles of a human, human appendix Embryology o animal embryology reveals that dissimilar organisms have embryos that possess common structures, mRNA, homeoboxes, and similar mechanisms of pattern formation this suggests that the animal may have evolved from an ancestor where the adult does possess the structure o embryology also reveals that derived characters evolved by the reshaping of ancestral structures Biochemistry o the sequencing of genomes and proteomics shows that dissimilar organisms have important similarities, indicating common ancestry The Evidence from Biogeography o biogeography is the study of the geographic distribution of organisms o Creationism offers no rational explanation why unusual species are present on isolated islands o adaptive radiation - the production of many new species adapted to unique habitats and niches ex: marsupials dominate Australia o evolution will proceed independently on different isolated land masses o biogeographical regions are large land masses characterized by the animal plants they contain ex: Ethiopian Region has African elephant, chimpanzee, gorilla, giraffe, rhinoceros, and antelope ex: Oriental Region has Malay tapir, Indian elephant, and tiger o there are often not clear cut distinction where one region ends an another begins; intermediate regions exist with species of both regions o isolated islands often have unique endemic species found nowhere else ex: 13 species of Galapagos finches, the Galapagos tortoise, and Galapagos iguanas Chapter 23 - The Evolution of Populations Population Genetics Darwin had no knowledge of Mendelian genetics, but held that when the secrets of genetics were finally revealed, they would support his theory blending inheritance would eliminate the variations that natural selection requires Mendel published only a few years later, but the Austrian audience that received his paper (incredibly) did not understand or appreciate it almost 50 years would pass before Mendelian inheritance would apply to natural selection Modern Evolutionary Synthesis at first study, Mendelian inheritance was thought to contradict natural selection theory Darwin’s theory described polygenic traits that varied along a continuum while Mendel described simple “either-or” traits then it was discovered that polygenic traits are based on loci that are each inherited in a Mendelian fashion, and population genetics was born 1940s - the modern synthesis - was developed o integrating paleontology, biogeography, population genetics, and taxonomy o stresses populations as units of evolution and the importance of natural selection as the force that changes them through gradual accumulation of mutations over time Population and Gene Pool population = all members of a given species in a defined area species = all organisms that can naturally interbreed to produce fertile offspring gene pool = all genes present within all members of a population individuals can be heterozygous or homozygous for a gene; if there is only one allele for the gene then the allele is “fixed” at the locus allele frequencies can be calculated: o 500 wildflowers with two alleles, CR (red) and CW (white); the heterozygotes are pink--flowered o 4% (20) are CWCW; 64% (320) are CRCR; 32% (160) are CRCW o with 1000 alleles in 500 plants: o frequency of CW = (20*2 + 160)/1000 = .2 = 20% frequency of CR = (320*2 + 160) = .8 = 80% Hardy-Weinberg Genetics o the Hardy-Weinberg theorem states that allele frequencies will not change (evolution will not occur) despite meiosis and reproduction provided 5 criteria are met: 1. Extremely large population size. 2. No gene flow (no migration). 3. No mutations (new genes). 4. All mating is random (mates are not picked based on any criteria). 5. No natural selection. o from the previous example, the chance of each genotype in the next generation is: CRCR: .8 * .8 = 0.64 = 64% CRCW: .8 * .2 = .16 = 16%; CWCR: .8 * .2 = .16 = 16%; total = 32% CWCW: .2 * .2 = .04 = 4% o thus, meiosis and gene shuffling cannot alter gene frequency in a non-evolving population, they only maintain it o the general Hardy-Weinberg equation starts with alleles of frequency p and q p + q = 1 (the sum of their gene frequencies must be 1) in our previous example, p = frequency of the red allele, q = frequency of the white allele thus p * p = frequency of CRCR = .8 * .8 = .64 = 64% 2pq = frequency of CRCW = 2 * .8 * .2 = .32 = 32% q * q = frequency of CWCW = .2 * .2 = .04 = 4% the Hardy Weinberg equation is written: p2 + 2pq + q2 = 1 .64 + .32 = .04 = 1 o the Hardy-Weinberg equation is not exactly valid for any real population because the 5 conditions cannot be met in reality, but, since most equations evolve VERY slowly, it is a great way to ESTIMATE the allele frequencies of heterozygotes in a population o ex: PKU occurs in 1/10,000 newborns in the US, in aa individuals; Aa are carriers and AA are homozygous normal o the US population is very large, although migration does occur the migrants have approximately the same gene frequencies, mutation rates for PKU are negligible, marriages are not made with regard to PKU, and natural selection operates only against aa individuals o thus: q2 = 1/10000; q = square root of 1/10000 = .01 o p = 1 - q = 1 - .01 = .99 o 2pq = 2 * .01 * .99 = .0198 = .02 = 2% o thus, 2% of the US population are carriers, who can only be identified by pedigree and genetic testing Mutation and Sexual Recombination mutation = change in a nucleotide sequence in a cell’s DNA o somatic mutations die with an organism while germ cell mutations may get passed along to the next generation o point mutations are generally harmless because of codon redundancy and the quantity of noncoding DNA o some point mutations change the amino acid composition of the resulting protein and thus have an effect on the phenotype, altering its selection possibilities o chromosomal mutations are possible, including duplications o tansposons cause gene shuffling and gene duplication, possibly playing a large role in evolution by creating a large copy base of genes that can mutate and carry different functions sexual recombination is more important in the short term than mutation it produces novel combinations of genes that are often very important under changing conditions o although bacteria and viruses lack regular mechanisms for recombination, they can pas DNA between species Natural Selection recombination causes shuffling and variety but cannot change gene frequency natural selection can alter gene frequency o differential reproductive success occurs because individuals vary in reproductive success o successful alleles become more common at the expense of their counterparts genetic drift - random chance fluctuations in allele frequencies o is caused by sampling errors, such as those that occur in small groups o the bottleneck effect occurs when a large population is reduced by disaster o with the massive loss of individuals, some genes are completely lost and others are overrepresented in the small remaining population o the founder effect is when a new population is originated from a small number of individuals o again, some alleles are lost, some are underrepresented, and others are over-represented gene flow - migration of alleles to new populations o tends to reduce the differences between populations o new alleles can have large effects but the same alleles may migrate and alter the existing gene frequencies rather than introduce new ones Natural Selection is the important mechanism of generating adapted organisms o while gene flow and genetic drift alter gene frequency, they don’t adapt organisms o while not all variation is heritable, natural selection maintains favorable adaptations in the population Genetic Variation - the Building Block of Evolution o genetic variation occurs within and between species o quantitative characters vary along a continuum within a population, usually caused by polygenic inheritance; ex: human height o discrete characters are caused by an individual locus with a short list of alleles that cause different phenotypes; ex: Mendel’s pea plant characters phenotypic polymorphism occurs when two ore more phenotypes are represented and maintained in a population not by mutation alone ex: human blood type; not human height (quantitative character) o average heterozygosity measures gene variability, the average percent of gene loci that are heterozygous fruit flies - 14% of their loci are heterozygous o nucleotide variability measures the mean level of difference in nucleotide sequences among individuals of a population fruit flies - about 1% nucleotide variability humans - 0.1% nucleotide variability o geographic variation occurs when phenotype/genotype frequencies differ in populations inhabiting different areas, because of natural selection differential or genetic drift it can occur within an area with subpopulations where the environment is patchy (spatial variation) cline - graded change in a trait along a geographic area, possibly caused by natural selection ex: North American bird body size rises with increasing latitude (conservation of heat) o o Natural Selection - A Closer Look natural selection depends on reproductive success, not physical prowess fitness = contribution of an organism to the next generation gene pool relative to its peers relative fitness compares reproductive success of an individual to the most fit individual in the population o if the most productive organism makes 100 offspring, its fitness is 1; an organism that produces only 40 offspring has a fitness of 0.4 o fitness is 0 if an organism leaves no offspring, even if it survives longer than its counterparts, because it is sterile The 3 modes of selection: 1. directional - a phenotype at one extreme is more fit than the other phenotypes; common during periods of environmental change 2. disruptive selection - extreme phenotypes on either side of the average phenotype are more fit than the average phenotype; has been documented in bird bill size, with large bills crushing large seeds and small bills eating small seeds while the average bill size has no favored seeds; important to early speciation by driving a “wedge” into the population 3. stabilizing selection - where the average phenotype is most fit; both extremes are selected against - ex: human birth weights Diploidy and Balancing Selection diploidy and balanced polymorphism counteract the tendency for natural selection to reduce genetic variation diploidy “hides” recessive alleles in heterozygotes and maintains their frequency in the gene pool; only the homozygous recessive is selected against o the recessive alleles may be favorable in a different future environment balanced polymorphism occurs when natural selection maintains 2 or more phenotypes in a gene pool o can be caused by heterozygote advantage where heterozygotes are more fit than homozygotes o SCA is an example of heterozygote advantage; the maintained balanced polymorphism consists of homozygous normal individuals which are fit in a malaria-free environment, heterozygous individuals which are fit in a malaria environment; and homozygous disease individuals who are selected against o up to 32% of some African populations are heterozygotes (q = .2, p = .8) frequency-dependent selection occurs when the fitness of one phenotype changes with its frequency in the population o ex: predators develop search images of prey, so as a particular morph of prey becomes more common, predators become more successful hunting and killing them o neutral variations have little/no impact on fitness and are not affected by natural selection o ex: human fingerprints; pseudogene inheritance Sexual Selection and Dimorphism o sexual selection produces sexual dimorphism where male and females have different physical phenotypes o intrasexual selection is direct competition among members of the same sex whereas intersexual selection is competition of one sex for the other sex o the selection plays out in males competing amongst one another for access to females for reproduction, and females are choosy about what males they will choose to breed o in most vertebrates, males are larger and showier than females, as as result o males put themselves at considerable risk during times of competition, by injury from opponents and predators o female choice perpetuates specific male phenotypes that were chosen for reproduction o it has been shown that female choosiness may prevent the selection of a diseased mate o Sex is an Evolutionary Enigma o asexual reproduction is much more efficient and rapid than sexual reproduction o if two identical species compete with only mode of reproduction different, the asexual type wins by sheer numbers of offspring in sexual organisms, half of the offspring must be male and cannot bear young, whereas all members of the asexual offspring bear young o disease is believed to play a major reason why sexual reproduction is so common cell surface markers are used by parasites to gain entry to organisms and cells meiosis and gene shuffling ensure that all offspring will have different cell-surface markers and thus not all can be parasitized by pathogens humans have hundreds of alleles for cell-surface markers, an unusually high number for any loci despite the rapid evolution of pathogens, sex produces a massive distribution of cell marker combinations and thus successful offspring o Natural Selection - Perfection? natural selection is limited by the historical context of an adaptation old features cannot be scrapped to build new ones “from scratch” adaptations are often compromises of structure and function ex: human knee is amazing in function, but often weak in structure natural selection is often affected by chance events ex: pregnant female turtle washing ashore a remote island it can only work with the alleles present in the gene pool new alleles cannot be made in response to new environments