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OBJECTIVES Chapter 22: Descent with Modification, A Darwinian View of Life 1.

He proposed the mechanism he termed natural selection, which is the idea that a population can change over generations if individuals that possess certain heritable traits leave more offspring than other individuals. He also presented evidence that the many species of organisms presently inhabiting Earth are descendants of ancestral species that were different from the modern species (focused attention on the great diversity of organisms origins and relationships, similarities vs. differences, geographic distribution, adaptations to environment). Evolution is defined as a change over time in the genetic composition of a population; gradual appearance of all biological life-formspopulation accumulates enough change to become a new species. Evolutionary adaptation is the accumulation of inherited characteristics that enhance an organisms ability to survive and reproduce in specific environments. Aristotle thought species were fixed and unchanging; recognized certain affinities among living things, arranged life-forms in a ladder/scale of increasing complexity (scala naturae or scale of nature). Each form of life is perfect and permanent, and has its own rung on this ladder. Carolus Linnaeus, however, was the founder of taxonomy, believing in a classification system that grouped similar species into increasingly general categories instead. He developed the binomial system of naming organisms according to genus and species. Catastrophism: Georges Cuvier, paleontology, strata in fossils, each boundary between strata represents a catastrophe that destroyed many of the species living at that time; periodic, usually confined to local geographic regions, which are repopulated by species immigrating from other areas Gradualism: profound change takes place through the cumulative effect of slow but continuous processes; James Hutton, Earths geologic features Uniformitarianism: incorporated Huttons thinking; same geologic processes are operating today as in the past and at the same rate Lamarck proposed use and disuse, or the idea that parts of the body that are used more become larger and stronger, while those that arent deteriorate, and inheritance of acquired characteristics which says that an organism can pass on these modifications to its offspring; evolution happens because organism have an innate drive to become more complex. Darwin observed and collected thousands of South American plants and animals and their adaptations to the environments they inhabited; geologic observations. Darwin read Lyells Principles of Geology while aboard the Beagle, experienced geologic change during a violent earthquake, and saw the coastline rise by several feet; fossils on Andes Mountains rose up. Descent with modification: unity in life, all organisms related through descent from an ancestor that lived in the remote past; various habitats over millions of years accumulate diverse modifications/adaptations that fit them to specific ways of life; TREE; most branches are dead ends (99% of all species that ever lived are now extinct); categorized on anatomy, order of appearance in strata, and geographic distribution Galapagos finches that were unique to individual islands, while others were distributed on two or more adjacent islands; all species had strayed from South America and diversified; beaks and behaviors adapted to specific foods available on their home islands Linnaeus realized that some organisms resemble each other more closely than others; groups subordinate to groups to fit taxonomy into Darwins theory Inference1: Production of more individuals than the environment can support leads to a struggle for existence among individuals of a population with only a fraction of their offspring surviving each generation. Inference2: Survival depends in part on inherited traits. Individuals whose inherited traits give them a high probability of surviving and reproducing in a given environment have higher fitness and are likely to leave more offspring than less fit individuals. Inference3: This unequal ability of individuals to survive and reproduce will lead to a gradual change in a population, with favorable characteristics accumulating over generations. Malthus thought much of human suffering (disease, famine, homelessness, and war) was the inescapable consequence of the human populations potential to increase faster than food and other resources; capacity to over reproduce rest eaten starved diseased unmated; favored traits will be represented in the next generation; EVOLUTIONARY MODIFICATION Artificial selection: selecting and breeding individuals that possess desired traits to modify species over many generations; domesticating plants and animals. Natural selection: differential success in reproduction among

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individuals that vary in their heritable traits; individual interacts with its environment; can increase adaptation of organisms to their environment. Individuals do not evolve; only populations can; evolution is measured as changes in relative proportions of heritable variation in a population over a succession of generations. (can only amplify/diminish heritable traits Wild guppy populations in pools in Aripo River system on Caribbean island of Trinidad (small freshwater fish); differences between population sin average age and size which reach sexual maturity correlates with type of predator most active on that population. Killifish: juvenile guppies; pike-cichlids pretty on sexually mature individuals; guppies by PC reproduce younger&smaller. Introduced fish from pools into other; changes to the time/size of that pools fish. Natural selection! omology: underlying similarity resulting from common ancestry. Homologous structures: variations on a structural theme that was present in a common ancestor (aka forelimbs); comparative embryology=tail posterior to anus, pharyngeal pouches. Vestigial organs: structures of little importance to organism; remnants of structures that were important to ancestors. Darwin common ancestor through modifications (check)! Even genes (DNA) and proteins resemble each other. Biogeography: Darwins observations of geographic distribution of species; closely related species tend to be found in the same geographic region. Although two mammals adapt to similar environments in similar ways, evolved independently from different ancestors. Form new species. Endemic: species of plants and animals are found nowhere else in the world; islands are especially.

Chapter 23: The Evolution of Populations 1. Natural selection acts on individuals; each organisms combination of traits affects its survival and reproductive success to other individuals; but evolutionary impact of natural selection is only apparent in changes in a population of organisms over time. Microevolution: evolutionary change on its smallest scale; in the genetic makeup for a population from generation to generation; Darwin did not define it this way. Did not know the heritable variations or how organisms transmitted them to offspring; how inherited variations are maintained in populations. first blending hypothesis, but then eliminate. Gregor Mendel: particulate hypothesis of inheritance, parents pass on discrete heritable units (genes) that retain their identities in offspring. Discrete traits: either-or meaning Mendels purple or white flowers in pea plants; versus quantitative characters (vary along a continuum in population, aka fur length or running speed). Discovered that quantitative characters are influenced by multiple genetic loci and that the alleles at each of these loci follow Mendelian patterns of inheritance population genetics! Study of how populations change genetically over time. Modern synthesis: mid-20th century comprehensive theory of evolution that integrates ideas from many other fields; statistics (Mendelian characters are inherited) and biologist (rules of natural selection, geneticists, biogeographer, paleontologist, botanist; is still expanding to integrate new ideas, focus on populations has shaped much of our current thinking about evolutionary processes. Population: localized group of individuals that are capable of interbreeding and producing fertile offspring; may be isolated from one another, rarely exchange genetic material. Gene pool: the collection of genes in a population at any one time; consists of all alleles at all gene loci in all individuals of the population (fixed in gene pool means only one allele exists at a particular locus in a population and all individuals are homozygous for that allele; 2+ alleles in a particular locus means may be homozygous or heterozygous individuals; frequency of allele=proportion in gene pool) In order to alter the frequency of alleles some form of evolution must be introduced into a population. Random fertilization and meiosis is not such a form. Hardy-Weinberg equilibrium: all male-female mating are equally likely and population has same allele frequencies from one generation to the next; genotype frequencies can be predicted from allele frequencies. 1) Extremely large population size (smaller=greater chance fluctuations in allele frequencies form one generation to the next=genetic drift). 2) No gene flow (transfer of alleles between populations; can alter allele frequencies). 3) No mutations (mutations modify gene pool). 4) Random mating (if dont have, including inbreeding, random mixing of gametes does not occur). 5) No natural selection (differential survival and reproductive success of different genotypes alters allele frequencies). POPULATION MUST NOT EVOLVE

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8. Hardy-Weinberg equation: p^2+2pq+q^2=1. For a locus with two alleles and three genotypes. If then

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Q =.5 and P =.5; The probability of QQ=.25 ; PQ =.5 ; PP =.25

9. Much of DNA in eukaryotic genomes does not code for protein products. Genetic code is redundant, dont alter amino acid composition. 10. Most mutations are not heritable because they do not affect any cell line leading to gametes and are thus preserved solely in the individual. 11. Transposons are a result of gene duplication when small bits of DNA are introduced into a genome. This increases the number of loci and can lead to further mutations or new functions. This can be beneficial or detrimental depending on what happens. 12. Sexual recombination is more important than mutation on generational scale in producing variations that make adaptation in sexually reproducing populations. Shuffling of existing alleles in the gene pool creates nearly all phenotypic variations. Mating combinations and fertilization with different genetic backgrounds; rearranges alleles into fresh combination every generation. 13. While there are many mechanisms for evolution, genetic drift and gene flow work in a random manner. Natural selection, on the other hand, preserves favorable traits to any specific environment, and passes those traits down. Thus, while all can evolve a species, only natural selection does so according to what is best for a given environment. 14. The smaller the sample population, the greater chance of deviation from the predicted result (genetic drift); explain how allele frequencies can fluctuate unpredictably from one generation to the next. This is because, speaking in percentages, a single random change in a small population affects a greater percentage of the total population compared to a large population. Drift tends to reduce genetic variation thorough losses of alleles from gene pool. 15. Bottleneck effect: sudden change in the environment drastically reduces the size of a population so certain alleles are overrepresented/underrepresented/eliminated among the survivors; genetic drift. Founder effect: few individuals become isolated from larger population; new gene pool is not reflective of the source population; isolation bottleneck; accounts for high frequency of certain inherited disorders among isolated human populations. 16. Gene flow: genetic additions to and/or subtractions from a population resulting from the movement of fertile individuals or gametes; population may gain or lose alleles; reduces differences between populations; evolutionary change in populations that were previously isolated. Gene flow takes place when alleles transfer between populations. This, in essence, blends the two populations together (over the generations) and reduces the genetic difference between them. 17. Both discrete and quantitative characters contribute to variation within a population. Discrete characters vary members within a population through definite categories; are determined by a single gene locus with different alleles that produce distinct phenotypes; either or genes. Morphs=different forms of a discrete character. Phenotypic polymorphism=character with 2+ distinct morphs each represented in high enough frequencies to be noticeable. Quantitative characters vary members through a continuum. That is, there are no discrete categories. This continuum is formed when more than one gene contributes to a phenotype; heritable quantitative variation results from the influence of two+ genes on a single phenotypic character. Height variation =genetic polymorphisms for alleles at the several loci that influence height. 18. Average heterozygosity is the average percent of loci that have heterozygous alleles. Nucleotide variability is an average computed by comparing the nucleotide sequence in two individuals of the same population many times over with many pairs. Average heterozygosity tends to be greater because a single nucleotide sequence change can affect two alleles for that loci. 19. A cline is a gradual change of some phenotype of a species across a geographic line or plane; type of geographic variation or difference between gene pools of separate populations/subgroups (genetic variation and environment play a role in differences of phenotype). 20. Fitness: Relative fitness is the relative chance of successful reproduction for any particular variant in the population. The basis for comparison is the most successful variant which is given a relative fitness of one. Relative fitness is zero for any sterile organism because, no matter how well adapted they are for the environment, they will never be able to reproduce. Even short lived organisms, if they reach maturity at a young age, can have a good reproductive success rate. 21. Directional selection occurs when natural selection favors individuals deviated in some direction away from the average. This is usually the case when the environment changes suddenly. An example is larger bears being favored when the climate gets colder. Disruptive selection occurs when natural selection favors individuals on both ends of the deviation of any particular phenotype from the average. This can cause speciation to occur as well. An example is both light and dark mice (living in grass with light and dark patches) being favored over the

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average, middle-shaded mouse. Stabilizing selection occurs when natural selection favors the average, and the individuals who deviate too far on either end do not survive as well. An example is the weight of human babies. A too light or too heavy baby will have complications, whereas one in the middle is considered healthy (as far as weight is concerned). Diploidy assures that recessive alleles are maintained even if they are harmful for the given environment. This is because, in heterozygotes, it is the dominate allele that effects the phenotype, not the recessive. Therefore, these non-apparent variations are passed from generation to generation and can increase in frequency later on if the environment changes to favor them. However, since they do not affect the phenotype in heterozygotes with the other, dominate, allele, natural selection has no effect on them. If natural selection favors heterozygotes, then the possibility of any one allele being eliminated because of complete homozygosity is decreased. Since having both alleles preserves both of the morphs, heterozygote advantage promotes balanced polymorphism. The same is true for frequency-dependent selection. If too many of any one morph appear in the population, natural selection will make the other morph favorable. Thus, natural selection would keep the two in some kind of balance promoting balanced polymorphism. Neutral variations are variations that have no positive or negative effects on the individual. Since there is no advantage or disadvantage, the variation would not effect reproductive success rate. However, what is considered a neutral variation in one environment might not be a neutral variation in another environment. Intrasexual selection is competition within a single sex. For example a male competing against other males for mating privileges by fighting off other potential mates for a specific female. Intersexual selection occurs between different sexes. This is, in essence, mate choosing. Females often choose to mate with the flashiest or showiest males, for example. The female gains advantage by picking mates that are strong to produce strong offspring. In species with bright or showy traits, an individual with dull appearance may be carrying a disease or parasite that impedes its health. By preferring the showy male, a female may be able to avoid mating with this diseased individual. Sexual reproduction allows only one half of the individuals to actually produce offspring. This means that species that reproduce sexually will have exponentially less offspring than those who reproduce asexually. Sexual reproduction produces the most genetic variation (on a generational time scale) because of sexual recombination. These variations can help especially against disease by varying resistance to different diseases instead of having the same resistance as per asexual reproduction. Natural selection cannot produce perfect organisms for several reasons. First, evolution is limited by what has happened in the past. Genes that once produced favorable phenotypes, but now produce unfavorable ones, are most of the time still in the genetic code. Since the environment is always changing, the genetic code does not have time to completely change itself to perfectly adapt before the environment changes again. Second, adaptations that help in one area often hinder another forcing a compromise. As per natural selection, the overall most fit individuals will have a proportionally higher reproductive success rate than others. The key word here is overall. Sometimes a hindrance in one area is outweighed by that same genes positive effect in another area. Third, a major part of evolutionary change and natural selection is chance. Chance moves in every direction, not always toward the betterment of the species. Chance changes in an environment completely change what is naturally selected. These are both impossible to predict and very influential. Finally, natural selection can only preserve the most favorable traits, but cannot create new alleles to perfectly adapt to an environment. Thus, it is the best out there that survives, even if the best isnt that great.

Chapter 24: The Origin of Species Anagenesis: phyletic evolution; accumulation of changes that gradually transform a given species into a specie with different characteristics. Cladogenesis: branching evolution; splitting of a gene pool into two or more separate pools, which each give rise to one or more new species; only this can promote biological diversity by increasing the number of species. both patterns of evolutionary change 2. Mayrs biological species concept: defines 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 viable, fertile offspring with members of other populations. 3. Prezygotic: impede mating between species or hinder fertilization of ova if members of different species attempt to mate. Postzygotic: prevent hybrid zygote from developing into a viable, fertile adult. 4. 1) habitat isolation: two species occupy different habitats in the same area and encounter each other rarely even though not isolated by obvious physical barriers like mountains (e.g. garter snakes, one lives in water, one lives on 1.

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land). 2) temporal isolation: species that breed during different times of the day, seasons or years and cant mix their gametes (e.g. skunks mating in late winter versus late summer). 3) behavioral isolation: courtship rituals that attract mates and are unique to a species (e.g. highfeet of blue-footed boobies). 4) mechanical isolation: morphological differences (e.g. flowers with different appearances attracting different pollinators so no crosspollination in between the two). 5) gametic isolation: sperm of one species cant fertilize eggs of another, biochemical (e.g. sea urchins release sperm and eggs into surrounding water, cant inter-fuse). Reduced hybrid vitality may be caused by genes of different parent species interacting and impairing hybrid development. Hybrid breakdown: first-generation hybrids are viable and fertile, but when mate with one another or with either parent species, offspring of next generation are feeble or sterile. Biological species concepts emphasis on reproductive isolation has influenced evolutionary theory but number of species that it can be applied to is limited; asexual organisms, and reproduction between species. Ecological species concept: views a species in terms of its ecological niche, role in big community; can accommodate asexual as well as sexual species. Paleontological species concept: focuses on morphologically discrete species known only from fossil record; forced because little or no info on their mating capability. Phylogenetic species concept: defines species as set of organisms with a unique genetic history; compare physical characteristics or molecular sequences; sibling species so similar cant be distinguished on morphological grounds. Morphological species concept: characterizes species by body shape, size and structural features; asexual and sexual; dont need extent of gene flow, heavily subjective however. Allopatric speciation: gene flow is interrupted when population is divided into geographically isolated subpopulations; also without geologic remodeling, aka when individuals colonize a remote area; how big geographic barrier must be to keep populations apart depends on ability of organisms to move about; new species=potential to interbreed and produce fertile offspring? Sympatric speciation: takes place in geographically overlapping populations; chromosomal changes and nonrandom mating reduces gene flow; polyploidy (extra sets of chromosomes). Allopatric speciation model: geographic separation, separated gene pools diverge; mutations, sexual selection, selective pressures, genetic drift, new species. ] Adaptive radiation: evolution of many diversely adapted species from a common ancestor upon introduction to various new environments; often occurs when few organisms make way to new, distant areas/extinctions. Hawaiian archipelago and Galapagos have multiple islands gradually populated by stray organisms; physical diversity of each island provides many chances for evolutionary divergence by natural selection. Reproductive barriers: INCOMPLETE Sympatric speciation: takes place in geographically overlapping populations; failure of cell division causes double chromosome sets; unpaired chromosomes result in abnormal meiosis; sterile offspring, reproductive isolation. Autopolyploid: individual with more than two chromosome sets all from a single species. Allpolyploid: fertile hybrids that are polyploidy; cant interbreed with either parental species however. Cichlids: mate choice based on coloration is main reproductive barrier; different colored tails, behavioral barrier; can no longer mate. Adaptive radiation: evolution of many species from a common ancestor because of different environments; may occur during extinctions or founder effect. In speciation in Mimulus two gene loci are lewisii pollinated by bees and cardinalis pollinated by hummingbirds, keeping gene pools separate; 2 gene loci responsible for pollinator choice (one flower color and other amount of nectar flowers make). Natural selection adapts to environment, differences that help survival accumulate until become evolution and change the entire species; simpler versions complex structures. Exaptation: structure that evolved in one context became co-opted for another function. Slight genetic divergences may lead to major morphological differences between species because accumulates in a population to become macroevolutionary changes. INCOMPLETE Temporal developmental dynamics: organisms shape depends on relative growth rates of different body parts during development; can change adult form substantially; timing of reproductive development. Spatial developmental dynamics: can have profound impact on morphology; appendages/orientation. Evo-devo: interface between evolutionary biology and developmental biology; illuminates how slight genetic divergences can be magnified into major morphological differences between species; genes that program development control rate, timing and spatial pattern of changes in organisms form as develops form zygote to

adult. Heterochrony: evolutionary change in the rate or timing of developmental events. Allometric growth: proportioning that helps give a body its specific form. Paedomorphosis: sexually mature stage of species retains juvenile body features in an ancestral species when reproductive development accelerates compared to somatic development. 23. Extracting a single evolutionary progression from the fossil record can be misleading because by selecting certain species from available fossils; can arrange intermediate between extinct and current species that vanishes if include all fossil horses; branching evolution! 24. Species selection: species that endure longest an degenerate most new offspring determines direction of major evolutionary trends; differential speciation success plays role in macroevolution (evolutionary change above species level)=to role of differential reproductive success in microevolution (changes confined to a single gene pool, in a population). 25. Evolution is not goal-directed because it is merely a result of the interactions between organisms and their current environments; even though there appear to be trends in evolution, often it is merely by chance, no intrinsic drive toward a particular phenotype. Chapter 25: Phylogeny and Systematics 1. Phylogeny: evolutionary history of a species or group of species; fossil record. Systematics: analytical approach to understanding the diversity and relationships of organisms, both present-day and extinct; morphological and biochemical resemblances. Formation of fossils: sand and silt eroded form land carried by rivers to seas where minerals settle to bottom with remains of organisms, deposits pile up and compress older sediments into strata (sedimentation); usually hard shells, skeletons that are fossilized. Distinguishing between homology and analogy is critical in reconstructing phylogenies because closer examinations can reveal that complex structures are highly different (ancestors). Analogy: convergent evolution. Homology: shared ancestry. Bird and bat wings are homologous as vertebrate forelimbs because both similar to other mammals; analogous in function because both let them fly. Molecular systematic: uses comparisons of DNA, RNA, and other molecules to infer evolutionary relationships between individual genes and entire genomes; can construct universal tree of all life. Comparing nucleic acid sequences: likely differ at only one or a few sites if closely related; longer periods of time insertions and deletions alter length of gene sequences; must align comparable nucleic acid sequences from two species. a) binomial nomenclature: scientific name (binomial); two-part; first is genus to which species belongs, second is specific epithet. b) hierarchical classification: species, genus, family, order, class, phylum, kingdom, domain; classifying. Domain, kingdom, phylum, class, order, family, genus, species. Clade: a group of species that includes an ancestral species and all its descendants. Monophyletic: valid; consists of ancestral species and all its descendants. Paraphyletic: lack info about some members, ancestral species and some but not all of descendants. Polyphyletic: several species that lack a common ancestor. Shared primitive character: shared beyond taxon we are trying to define. Shared derived character: evolutionary novelty unique to a particular clade. Analyzing distribution of share derived characters can provide insight into vertebrate phylogeny. Outgroup: species or group of species that is closely related to ingroup (species we are studying) but not as closely related as any ingroup members are to each other; homologies between two = primitive characters that predate the divergence of both groups from a common ancestor. Ingroup: species we are studying. Phylogram: length of branch reflects number of changes that have taken place in a particular DNA sequence in that lineage. Ultrameric tree: equal amounts of chronological time even through branches in phylogram have different lengths; diff lineages descend from common ancestor survive same time; does not contain info about diff evolutionary rates; in order of geologic time. Maximum parsimony: first investigate simplest explanation that is consistent with the facts. Maximum likelihood: given certain rules about how DNA changes over time, a tree can be found that reflects the most likely sequence of evolutionary events; complex and incorporate as much info as possible. Distance methods minimize total of all percentage diff among all sequences. Character-state methods minimize total number of base changes or search for most likely pattern among all sequences.

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15. A phylogenetic hypothesis may be modified when new evidence compels systematists to revise their trees. 16. Orthologous genes: homologous genes that are passed in a straight line from one generation to the next but have ended up in diff gene pools because of speciation; can only diverge after speciation has taken place. Paralogous genes: result from gene duplication; found in more than one copy in same genome; diverge while in same gene pool, specify many different proteins now. 17. Molecular clocks: measures absolute time of evolutionary change based on observation that some genes and other regions of genomes appear to evolve at constant rates; number of nucleotide substitutions in orthologous genes is proportional to the time that has elapsed since the species branched form their common ancestor. Calibrate molecular clock of a gene that has reliable average rate of evolution by graphing number of nucleotide diff against times of series of evolutionary branch points that are known from fossil record. 18. Limitations: does not run as smoothly as neutral theory predicts; irregularities caused by natural selection; fluctuations; estimate with high degree of uncertainty. 19. Neutral theory of evolutionary change: much evolutionary change in genes and proteins has no effect ton fitness and so is not influenced by Darwinian selection; many new mutations are harmful and have little or no effect on fitness. Differences in rate of clock in different genes are a function of how important each is; is essential, genes change slowly since mutational changes are harmful. 20. Researchers compared samples of the virus from various times during the epidemic; showed that virus evolved in a clocklike fashion; discovered first HIV-1 M invasion into humans in 1930s. 21. Genetic code is universal in all forms of life; so all present-day organisms must therefore have a common ancestor; systematic.