Evolution

I. Types A. Macroevolution - changes in a gene pool that cause evolution of entirely new species B. Microevolution - changes in a gene pool that do not necessarily involve the development of new species C. Divergent Evolution - occurs when a population becomes isolated (for any reason) from the rest of the species, becomes exposed to new selective pressures, and evolves into a new species - homologous structures D. Convergent Evolution - when unrelated species occupy the same environment, are subjected to the same environmental pressures, and show similar adaptations; natural selection acts in the same way, in different parts of the world - analogous structures -ex. the whale, a mammal, and any fish both have evolved the same streamlined appearance with lateral and posterior fins. They look similar because they evolved in the same environment; however, they do not share a recent common ancestor -ex. Ocotillo cactus (SW USA), and Allaudia euphorbia (Madagascar) -ex. bird wings and bat wings (expanding niches) E. Parallel Evolution - describes two related species that have made similar evolutionary adaptations after their divergence from a common ancestor -ex. the marsupial mammals of Australia and the placental mammals of North America have striking similarities; they share a common ancestor and evolved in similar environments, but they evolved great distances from each other F. Coevolution - a reciprocal set of evolutionary adaptations of two interacting species -ex. all predator-prey relationships; if the population of prey develops a new way to protect itself, the predator population must change in the same way in order to feed on the prey and survive II. Hypotheses A. Origin of Life on Earth i. Organic Compounds Possible locations for the synthesis of the organic compounds needed for the origin of life: 1. Atmosphere and in water, on the surface of the earth - Miller and Ureys experiments 2. Hydrothermal vents deep in the oceans - chemicals welling up from the rocks below - very unusual chemical conditions around these vents, which might have allowed the spontaneous synthesis of the organic compounds from which the first organisms evolved 3. Outer space; Extraterrestrial origin - NASA experiments have shown that organic compounds and proto-cells could have formed in cold interstellar space - heavy bombardment of earth by meteorites 4,000 million years ago - meteorites, comets, or interplanetary dust ii. Cells Four processes necessary for first cells to form: 1. chemical reactions to produce simple organic molecules -ex. amino acids, from organic molecules (water, carbon dioxide, ammonia) 2. assembling of these simple organic molecules into polymers -ex. amino acids to polypeptides 3. formation of self-replicating polymers, allowing for inheritance of characteristics 4. development of membranes to form spherical droplets, with an internal chemistry different from the surroundings, including the polymers that held the genetic information * Product could have been cell-like structures; natural selection could have acted on them, beginning evolution Membranes and Protobionts * to form first cells, membranes were needed to separate cytoplasm and metabolism from surrounding fluid * phospholipids naturally form bilayers in water, which form spherical structures enclosing a droplet of fluid, similar to the vesicles now found in cells * water containing these membrane-bound microspheres is called coacervate and is viscous and cloudy * protobionts: primitive cell-like structures that may have preceded living cells * to become cells, they would have had to develop genetic mechanisms to allow reproduction and the transmission of characteristics to offspring Endosymbiotic theory * both mitochondria and chloroplasts have evolved from independent prokaryotic cells, which were taken into a larger heterotrophic cell by endocytosis * instead of being digested, the cells were kept alive and continued to carry out aerobic respiration and photosynthesis * characteristics of mitochondria and chloroplasts support the endosymbiotic theory: i. they grow and divide like cells ii. naked loop of DNA, like prokaryotes iii. synthesize some of their own proteins using 70s ribosomes, like prokaryotes iv. double membranes, as expected when cells are taken into a vesicle by endocytosis Prokaryotes and the atmosphere * prokaryotes were first organisms on earth to use photosynthesis of the synthesis of organic compounds * when these organisms started using water as a source of hydrogen in photosynthesis, oxygen started being released as a waste product into the atmosphere * there is evidence that before this there was little oxygen in the atmosphere * concentrations of increased over a relatively short periodabout 100 million years

* probably due to the activity of photosynthetic prokaryotes * other prokaryotic organisms were able to use aerobic cell respiration, once the atmosphere contained oxygen * The banded iron formation (rocks) in Greenland dating from 3.7-3.8 million years ago, give evidence of oxygen in the atmosphere, which suggests that prokaryotic cells had evolved and were producing oxygen by then * among existing organisms, photosynthetic bacteria in ho springs and other extreme environments are probably most similar to these early prokaryotes Heterotroph Hypothesis - the first cells on Earth were anaerobic, heterotrophic prokaryotes - they probably arose about 3.5 billion years ago - eukaryotes arose about 1.6 billion years ago gene pools and allele frequencies - if there is random mating, any two individuals in an interbreeding population could be the two parents, so the individual could inherit any of the genes in the interbreeding population, the genes being the gene pool - gene pool: all the genes in an interbreeding population - many genes have different alleles. In a typical interbreeding population, some alleles will be commoner than others. How common an allele is can be assessed using allele frequency - allele frequency: the frequency of an allele, as a proportion of all alleles of the gene in the population * can range from 0.0 to 1.0 * evolution always involves a change in allele frequency in a populations gene pool, over a number of generations iii. Role of RNA various parts of genetic mechanism in prokaryotes cannot function without each other whole mechanism evolved at once because gradual evolution would have required simpler intermediate stages possibility is the use of RNA instead of both DNA and enzymes Properties that could have allowed for this: 1. Catalysis - RNA catalyzes a broad range of chemical reactions and could therefore have taken the role that is carried out by proteins (enzymes) in the organisms that now exist on Earth - RNA still catalyzes some reactions -ex. peptide bond formation during protein synthesis in the ribosome 2. Self-replication - one molecule can form a template for the production of another molecule, following the rules of complementary base pairing - if the newly synthesized molecule is then used as a template, a replicate of the original molecule will be produced RNA molecules can no longer self-replicate, as it has been superseded billions of years ago by DNA and proteins as the genetic material and catalysts of life. One possibility for the DNA-protein world replacing the RNA world is that the maximum length of RNA molecules is about 1,500 nucleotidesthis places a severe restriction on the amount of genetic information that can be held RNA viruses, for example, have a very small genome. iv. Humans A. Origins i. Humans as Primates grasping limbs, with long fingers and a separated opposable thumb mobile arms, with shoulder joints allowing movement in three planes and the bones of the shoulder girdle allowing weight to be transferred via the arms stereoscopic vision, with forward facing eyes on a flattened face, giving overlapping fields of view skull modified for upright posture Notable feature of family Hominidae is bipedalism ii. Trends in Hominid Fossils increasing adaptation to bipedalism increasing brain size in relation to body size skull differences - Australopithecus afarensis - Australopithecus africanus - Homo habilis - Homo erectus - Homo neanderthalensis - Homo sapiens B. Evolution i. Tracing Human Evolution - Not unusual for fossil record to be incomplete. Only a tiny proportion of animal bodies become fossilized; theyre usually eaten by detritivores, decomposed by bacteria, or broken down with alkali in bones and teeth - Because hominid fossil record is incomplete, its far from clear how different species of hominid are related. ii. Hominid Diets and Brain Size a. Diets - mainly vegetarian diet of early hominids, indicated by powerful jaws and teeth - 2.5 million years ago Africa became much cooler and drier. Savannah grassland replaced forest, prompting the evolution of the first species of Homo, with the development of increasingly sophisticated tools and a change to a diet that included meat obtained by hunting and killing large animals - change in diet corresponds to brain size b. Brain size - brains of early hominids were only slightly larger in relation to body size than the brains of apes

- change in diet corresponds to increase in brain size, due to continued rapid brain growth after birth - in apes and earlier hominids, brain growth slows after birth - the correlation between the change in diet and the increases in brain size can be explained in two ways: 1. eating meat increases the supply of protein, fat, and energy in the diet, making it possible for the growth of larger brains 2. catching and killing prey on the savannas is more difficult than gathering plant foods, so natural selection will have favored hominids with larger brains and greater intelligence iii. Genetic and cultural evolution - cultural evolution: the passing on of new methods, inventions, or customs related to language, toolmaking skills, hunting techniques, methods of agriculture, religion, art, and many other forms of behavior are passed on by teaching and learning * NO changes in allele frequencies in the gene pool * much more rapid; can happen in one lifetime * involves characteristics acquired during a persons life (nurture) * one aspect, the development of medicine, has reduced natural selection between different genetic types and therefore, genetic evolution - genetic evolution: involves natural selection between inherited differences * involves characteristics that are inherited (nature) * 1,000 years too short to cause much change B. Scientists * Pre-evolution i. Aristotle (384-322 BC) - species were created and could never change - could be ordered in ladder of increasing complexity - coincided with Old Testament ii. Carolus Linneaus (1707-1778) - similar to Aristotle iii. George Cuvier (1769- 1832) - paleontology: study of fossils - fossils: remains or traces of organisms from the past - Types of rock a. igneous b. metamorphic (granite) c. sedimentary (particulates; mud has solidified by pressure) - evolution by catastrophe (vs. gradualism) 1. Darwins Theories (late 18th century) a. Who? - naturalist who traveled on the HMS Beagle to the Galapagos Islands (540 miles, or 900 km, west of S. America); finches and common location, finches began spreading out and adapting - On the Origin of Species in 1859 - influenced by Charles Lyell * uniformitarianism (same geological processes important in past are important today; same rate) Two major points (unity and diversity; adaptive nature and radiation): 1. Descent w/ modificationorganisms living now had ancestors that were different 2. Natural Selectiondifferential reproduction and survival of the evolutionary adaptation b. Theory of Natural Selection (Wallace had also come up with this idea; published together) i. What - differential survival and reproduction of the genotypes - Populations grow exponentially and exceed their resources (Malthus 1798) - Overpopulation results in competition and struggle for survival - In every population, variation among individuals leads to an unequal chance for survival and reproduction - only the best-fit individuals survive and can pass their traits on to offspring - evolution occurs in a population as advantageous traits accumulate or as disadvantageous ones disappear from a population ii. Types Stabilizing selection - eliminates extremes from a population - weeds out many mutants -ex. human baby survival rate is higher for babies that are 6-8 lbs; for larger or smaller babies, survival rates are lower Diversifying (disruptive) selection - extremes in a population are favored at the expense of intermediate forms - may result in formation of 2 or more new species (sympatric speciation) -ex. Coho male salmon maintain two strategies to fertilize eggs: large hooknoses fight for proximity to the nests, while small jacks sneak into the nests; the largest and smallest salmon achieve their goals, while in-between sizes seldom do Directional selection - changing environmental conditions cause one population to replace another - can be very rapid, as in the following examples -ex. industrial melanism or peppered moths * In preindustrial England, most peppered moths were light-colored because they were camouflaged by the bucolic countryside; therefore, they had the advantage over dark moths * Industrialization changed the environment, making it soot-covered and dark.

Light moths were no longer camouflaged and were preyed upon by birds. Their numbers declined, leaving dark moths with the advantage * Dark moths survived and passed on their genes. Over a short time, the population changed and most peppered moths were dark * No single moth became dark. The light ones in the population died out, leaving a population of dark moths -ex. development of antibiotic resistance * bacterial resistance to antibiotics is carried on plasmids that can be transferred from one bacterium to another; exposure to a particular antibiotic kills only those bacteria not carrying resistance to it. Resistant bacteria then reproduce without competition, producing an entire population that is resistant to the antibiotic * no individual bacterium becomes resistant; exposure to the antibiotic causes a change in the population -ex. dark fur in mice being superior (absorb more light, stay warm), population bell curve will shift to the right Sexual selection - selection based on variation in secondary sexual characteristics - the fittest male gets to mate -ex. elk males having the largest antlers may achieve supremacy over other males and will inseminate all the females in a harem, thus successfully passing on their genes iii. Principles Giraffes long neck - some giraffes had long necks, some short - short-necked giraffes could not survive because they would not reach enough leaves for adequate nutrition - long-necked animals lived to reproduce and pass on genes for long necks - eventually, all had long necks - no single giraffe changed the length of its neck; the population changed Resource Partitioning - one species evolves, through natural selection, to exploit different resources in order to survive - does not necessarily involve the formation of a new species Artificial Selection - humans breed plants and animals by seeking individuals with desired traits for breeding stock - humans have bred cabbage, cauliflower, and broccoli by selecting different traits from one plant: the wild mustard plant Frequency-Dependent selection (minority advantage) - decreases the frequency of the more common phenotypes and increases the frequency of the less common ones - unusual-looking individuals have the selective advantage and will thus become more common over time -ex. if prey individuals differ in their appearance, the most common type will be preyed upon disproportionately while the less common ones will escape predation because they may not be recognized as prey c. Gradualism (vs. Catastrophesasteroid and dinosaur extinction) - currently not in fashion - organisms descend from a common ancestor over a long period of time, in a linear and branching fashion - according to this theory, fossils should exist at every stage in the evolution of a species with no missing links 2. Miller and Ureys Experiment to determine how organic materials arose on ancient Earth tested Oparin-Haldane hypothesis - hypothesized separately that organic molecules could have formed on the early Earth - without corrosively reactive molecular oxygen present to react with and degrade them, organic molecules could persist proved that almost any energy source would have converted the first molecules to a variety of organic molecules, including amino acids 3. Lamarcks Theory (1809) Abandoned theories did believe in gradualism, but looked at how organisms adapted to environment (use/disuse) supposes: - Inheritance of acquired characteristics -ex. Giraffes long neck * the giraffe grew a longer neck because it repeatedly stretched its neck to reach leaves from tall acacia trees, resulting in offspring with longer necks - Use and disuse: if an organ is not used, it will disappear 4. Lynn Margulis Endosymbiosis Theory - mitochondria, chloroplasts, and possibly nuclei were once free-living prokaryotes that took up residence inside larger prokaryotic cells; this mutually beneficial symbiotic relationship became permanent 5. Niles Eldridge and Stephen J. Gould Punctuated Equilibrium - modern theory - proposes that new species appear suddenly after long periods of stasis; a new species arises and replaces the ancestral species after it becomes extinct 6. Pasteur

 Spontaneous generation does NOT take place - oldest undisputed bacterial fossils are in the Gunflint cherts of Ontario, dating from 1.9 billion years ago III. Causes 1. Genetic Drift - a change in the gene pool due to chance -ex. bottleneck effect * natural disasters reduce the size of a population unselectively and cause the loss of genetic variation * the resulting population is much smaller and not representative of the original population, with some alleles that are under- or overrepresented compared with the original population -ex. founder effect * when a small population breaks away from a larger one to colonize a new area, this small group is not representative of the original population; rare alleles may be overrepresented in the new population -ex. the Amish community was founded by people who happened to have a high incidence of the rare trait polydactyly; due to the isolation of this closed community in America, the Amish of today have a very high incidence of polydactyly 2. Gene flow - the movement of alleles into or out of a population - occurs as a result of the migration of fertile individuals or gametes among populations -ex. pollen from one valley can be carried by the wind across a mountain to another valley 3. Mutations - any change in genetic material - raw material for evolutionary change - a major source of variation - mutations rarely occur, but their cumulative effect at all loci in a population can be significant - can occur in the DNA (gene mutation) or at the chromosome level (chromosome mutation) - chromosome mutations can be seen on a karyotype 4. Nonrandom mating - individuals choose mates that are best adapted - serves to eliminate less-fit individuals or genes from a gene pool 5. Natural selection IV. Evidence A. Fossil Record provides evidence that organisms have evolved over 4.6 billion years from prokaryotes to multicelled organism of every variety fossils dated using radioisotopesradioactive isotopes of chemical elements. When an atom of a radioisotope decays, it changes into another isotope and gives off radiation. The rate of decay varies between different radioisotopes and is the half-life half-life: the time taken for the radioactivity to fall to half of its original level - two most common radioisotopes used are 14C and 40K. In radiocarbon dating, the percentage of surviving 14C atoms is measured. * the half-life of 14C is 5730 years so its useful for dating samples between 1,000 and 100,000 years old - in potassium-argon dating, the proportions of parent 40K atoms and daughter 40Ar atoms are measured * the half-life of 40K is 1250 million years so it is useful for dating samples older than 100,000 years 97% of the organisms that ever lived have become extinct because they were no longer adapted to an environment that changed found mostly in sedimentary rocks - rivers bring sediment to ocean, covering animals, additional strata are added, adding fossils form different periods - trilobites: extinct arthropod absolute dating of fossils uses radioactive decay and half-life relative dating compares an unknown fossil to a known, index fossil transition fossils - fossils that link older fossils to modern species -ex. Eohippus, an ancient horse = fossil link to the modern horse, Equus -ex. Archaeopteryx = fossil link between reptiles and birds two geologists, Lyell and Hutton, strongly influenced Darwin B. Comparative anatomy homologous structures - demonstrate common origin and ancestry - result from divergent evolution - have similar underlying structure, although the function may be different -ex. bats wing, humans arm, tails in vertebrate embryos, pharyngeal pouches analogous structures - Do NOT provide evidence of common ancestryexample of convergent evolution - same function but different internal structure -ex. flys wing and bats wing study of homologous structures helps us understand which organism are related and share a common ancestry vestigial structures are evidence that structures have evolved -ex. the appendix in humans, pelvic bones in snakes and whales C. Comparative embryology related organisms go through similar stages in their embryonic development in fish, gill pouches develop into gills; in humans, they develop into eustachian tubes D. Molecular biology a comparison of the amino acid sequence of cytochrome c, a protein present in the electron transport chain of all aerobic organisms, shows how organism are related Cytochrome c in humans is almost identical to that of chimpanzees and gorillas, which increasing variation when compared with lobsters and hydra E. Biogeography the theory of continental drift states that about 200 million years ago, there was one continent, Pangaea, which slowly separated into 7 continents geographic distribution of marsupial fossils provides evidence for this theory

 marsupials migrated by land from South America to Australia before these two continents separated 50 million years ago F. Patterns 1. Divergent evolution 2. Convergent evolution 3. Parallel evolution 4. Coevolution 5. Adaptive radiation - the emergence of numerous species from one common ancestor introduced into the environment - evolution of many diversely adapted species form a common ancestor upon introduction to various new environmental opportunities and challenges -ex. all 13 species of Darwins finches that live on the Galapagos Islands today diverged from a single ancestral species perhaps 10,000 years ago. Each different species of finch fills a different niche; there are 6 ground finches, 6 tree finches, and 1 warbler finch -ex. 65 million years ago, mammals went through explosion of adaptive radiation after demise of dinosaurs 6. Transient polymorphisms - polymorphic: population in which there are two alleles of a gene in the gene pool - transient polymorphisms: population when one allele is gradually replacing the other -ex. peppered both, Biston betularia 7. Balanced polymorphisms - balanced polymorphism: when two alleles of a gene can persist indefinitely in the gene pool of a population -ex. sickle cell anemia * individuals with genotype Hb^A Hb^A do NOT develop sickle cell anemia but are susceptible to malaria * individuals with the genotype Hb^S Hb^S are resistant to malaria, but develop severe sickle cell anemia * heterozygous individuals (Hb^A Hb S) are resistant to both and are therefore best adapted in areas where malaria is found * both of the alleles of the hemoglobin gene therefore tend to persist in malarial areas. The sickle cell allele has increased in frequency to high levels in some of these areas. * In parts of Africa, as many as 40% of the population are carriers of the sickle cell allele, so show resistance to malaria V. Principles 1. Population Variation - tremendous variation is hidden in any gene pool and can be expressed by selective pressures -ex. there is tremendous variation among dog breeds although they all belong to the same species - Causes: a. Sexual dimorphism - differences in appearance between the males and females of one species - in many species of birds the males have bright conspicuous plumage while the females are plain; the males, not the females, compete to pass on their genes successfully - the fittest male gets to pass on his genes to the next generation b. Balanced polymorphism - the presence of two or more phenotypically distinct forms of a trait in a single population of a species - each morph is better adapted for a different area -ex. the shells of one species of land snail exhibit a wide range of colors and banding patterns; each is adapted for a particular area within its range c. North-south cline Rabbits - one species of rabbit exists in two different regions in North America - rabbits in the cold, snowy northern regions are camouflaged with white fur and have short ears to conserve body heat - rabbits living in warm, southern regions have mottled fur that blends in with woodsy areas and long ears that radiate off excess body heat Trouts d. Mutation - any change in genetic material raw material for evolutionary change a major source of variation mutations rarely occur, but their cumulative effect at all loci in a population can be significant can occur in the DNA (gene mutation) or at the chromosome level (chromosome mutation) chromosome mutations can be seen on a karyotype e. Outbreeding - the mating of organisms of the same species that are not closely related maintains variation within a species and a strong gene pool -ex. to prevent self-pollination (inbreeding), some flowering plants have male and female structures that do not mature at the same time -ex. the dominant male lion of a pride chases away young maturing males before they become sexually mature; this ensures that these males do not inbreed with their female siblings f. Diploidy the normal condition of sexually reproducing organisms two copies of every gene (except on the Y chromosome) the 2n condition maintains and shelters a hidden pool of alleles that may not be suitable for present conditions but that could be advantageous if conditions change g. Heterozygote superiority (hybrid advantage) the hybrid state is selected because it has a greater survival rate and reproductive success preserves diversity in a population -ex. people in West Africa who are hybrid for sickle cell anemia (Ss) have an advantage because they are resistant to malaria h. Frequency-dependent selection (minority advantage)

- decreases the frequency of the more common phenotypes; increases the frequency of the less common ones - unusual-looking individuals have the selective advantage and will thus become more common over time -ex. if prey individuals differ in their appearance, the most common type will be preyed upon disproportionately while the less common ones will escape predation because they may not be recognized as prey 2. Species and Speciation A. Species - population whose members have the potential to breed in nature and produce fertile offspring B. Speciation - formation of new species, caused by anything that fragments a population and isolates small groups of individuals - Types a. Allopatric Speciation - caused by geographic isolation: mountains, rivers, canyons, lakes, and so on b. Sympatric Speciation - caused by something other than geographic isolation: Polyploidy * having more than two complete sets of chromosomes (3n, 4n) * results from nondisjunction * common in plants, naturally or artificially * polyploid plants are isolated because they cannot exchange genes with plants that are normal (2n) Habitat isolation * two organisms of the same species that live in the same area but encounter each other rarely * individuals are isolated form each other and cannot exchange genes Behavioral isolation * mating often depends on an elaborate mating ritual; if one partner does not enact the proper ritual, no mating occurs and genes cannot be exchanged Temporal isolation * a flowering plant colonizes a region with areas that are warm and sunny and areas that are cool and shady; flowers in the warmer regions mature sooner than those in the cooler areas. Thus the flowers are isolated by the time of maturation, and genes cannot be exchanged Reproductive isolation * organisms of the same species are unable to mate because of anatomical or biochemical incompatibility * prezygotic barrier: prevents mating -ex. habitat isolation, behavioral isolation (little/no sexual attraction), temporal isolation (different mating/flowering seasons), different number of chromosomes (cell division wont function correctly), mechanical isolation (differences in genitalia), gametic isolation (because of mechanical or chemical forces) * postzygotic barrier: prevents production of fertile offspring once mating has occurred -ex. reduced hybrid viability (hybrid zygotes fail to develop or fail to reach sexual maturity), reduced hybrid fertility (hybrids fail to produce functional gametes) hybrid breakdown (offspring of hybrids have reduced viability or fertility; mules) 3. Hardy-Weinberg a. Equilibrium - describes a stable, nonevolving population; allelic frequencies do not change. If a certain allele is 0.5 and the population is not evolving, after 1,000 years the frequency of that allele will still be 0.5 - for the population to be stable-nonevolving, the following must be true: the population must be large the population must be isolated no mutations mating must be random no natural selection b. Equation p + q = 1 or p + 2pq + q = 1 p = dominant allele; q = recessive allele 2pq = hybrid condition (carriers) If 9% of a population has blue eyes, the H-W equation can be used to determine the percentages of genotypes in the population If q = 9%, then q = .09 and q = 0.3 Since p + q = 1, if q = 0.3, then p = 0.7 Homozygous brown = p = 0.7 x 0.7 = 49% Hybrid = 2pq = 2 x 0.3 x 0.7 = 42% 4. Character Displacement - competing organisms of similar species evolve different characteristics to coexist in an environment -ex. Galapagos finches evolved different beak sizes to avoid competing for food 5. Classification and phylogeny A. Advantages species identification- easier to find out which species an organism belongs with organisms classified rather than forming a disorganized catalogue predictive value- if several members of a group have a characteristic, another species in this group will probably also

have this characteristic evolutionary links- species in the same group probably share characteristics because they have evolved from a common ancestor, so the classification of groups can be used to predict how they evolved B. Artificial vs. Natural Artificial classification based on analogous structuresstructures with a common function, but different evolutionary origin -ex. putting insects, birds, and bats into one group because they fly Natural classification based on homologous structuresstructures that have a common evolutionary origin, even if their function is different. Organisms with homologous structures should be classified in the same group because they must have common ancestry, even if they look superficially -ex. the peradactyl limb C. Biochemistry and Common Ancestry All use DNA (or RNA) as their genetic material All use the same universal genetic code, with only a few insignificant variations All use the same 20 amino acids in their proteins All use left, and not right-handed amino acids - Strongly suggest that all organisms have evolved from a common ancestor, which had all of these characteristics D. Phylogeny and Biochemistry phylogeny: tracing evolutionary links and origins - phylogeny of many groups has been studied by comparing the structure of a protein or other biochemical that they contain. Usually the results match the existing classification of the group -ex. chimpanzees and gorillas are currently in a family with orangutans, but should probably be placed in the same family as humans, according to this DNA evidence E. Variation and Evolutionary Clocks differences in the base sequence of DNA and therefore, in the amino acid sequence of proteins, accumulate gradually over long periods of time evidence that differences accumulate at a roughly constant rate; can be used as an evolutionary clock the number of differences in amino acid sequence can be used to deduce how long ago species split from a common ancestor -ex. mitochondrial DNA from three humans and four related primates has been completely sequenced. From the differences in base sequence, a hypothetical phylogeny has been constructed. Using the numbers of differences in base sequence as an evolutionary clock, these approximate dates for splits between groups have been deduced: * 70,000 years ago, Europeans-Japanese split * 140,000 years ago, African-European/Japanese split * ~5 million years ago, human-chimpanzees split F. Cladistics i. Definitions nodes: branding points used by diagrams to show groups of organisms that evolved from a common ancestor clades: a group of organisms that evolved from a common ancestor - can be large groups, with a common ancestor far back in evolution, or smaller groups with a more recent common ancestor cladograms: tree diagrams showing clades - have been used to re-evaluate the classification of many groups of organisms. The methods used are very different from procedures traditionally used by taxonomists, so a new name has been given to this type of classificationcladistics cladistics: a method of classification of living organisms based on the construction and analysis of cladograms ii. Cladograms and Classification - The classification of many groups has been re-examined using cladograms. In many cases, cladograms have confirmed existing classifications, which isnt surprising, as both traditional classification and cladistics are attempting to reflect phylogenetic relationshipsthe evolutionary origins of groups of living organisms - Cladograms can be difficult to reconcile with traditional classifications, because the nodes can occur at any point. It can therefore seem rather arbitrary how the hierarchy of taxa is fitted to the clades - In some cases, cladistics suggests radically different phylogenies. - The strength of cladistics is that the comparisons between organisms are objective, based, as they are, on molecular differences. - The weakness is that these molecular differences are analyzed on the basis of probabilities. Occasionally, improbably events occur, making the analyses wrong. So, although cladistics should not be treated as infallible, in many cases it can stimulate a reinterpretation of the data on which traditional classification have been based