General Biology 2- First three weeks
General Biology 2- First three weeks EBIO 1220
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This 20 page Class Notes was uploaded by Evan Gallagher on Wednesday January 27, 2016. The Class Notes belongs to EBIO 1220 at University of Colorado taught by Dr. Carol Kearns in Spring 2016. Since its upload, it has received 48 views. For similar materials see General Biology 2 in Science at University of Colorado.
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Thursday, January 28, y Gen Bio 2 Evolution Evolution is a scientific theory, Meaning this can’t be completely proved, but all the evidence supports it The evolution of evolutionary thought • the greek philosopher plato claimed that every organism was an example of a perfect essence or type created by god and that these types were unchanging • Aristotle ordered these types of organisms into a linear scheme called the great chain of being. In this chain species were organized into a sequence based on increasing size and complexity with humans at the top. • Darwin and Wallace proposed that change in species through time does not allow a linear, progressive patten but instead is based on variation among individuals in populations • Darwin and Wallace proposed that evolution occurs because of natural selection The pattern of evolution Darwin describe evolution as descent with modification, meaning that change over time produced modern species from ancestral species. Two big claims 1 species change through time 2 species have a common ancestor Key concepts Populations and species evolve, meaning that their characteristics change through time. More precisely, evolution is defined as changes in allele frequencies over time natural selection occurs when individuals with certain alleles produce the most offspring in a population 1 Thursday, January 28, y natural selection occurs when individuals with certain alleles produce the most offspring in a population an adaptation is a genetically based trait that increases and individuals ability to produce offspring in a particular environment Natural selection depends on four key parameters Overpopulation more babies are produced than can survive. This creates competition between individuals variation in the process of gamete formation, independent assortment of the chromosomes in humans results in 8,388,608 possible genetically different gametes from one person That doesn't take into account crossing over heritability some of the variation among individuals must have genetic basis so offspring can inherit the character trait. differential survival and reproduction individuals that thrive in their environment will survive, reproduce, and pass their traits on to the next generation. Their genes will be represented at a greater frequency in the next generation The process of evolution: fitness and adaption Darwinian fitness; the ability of an individual to produce offspring, relative to that ability in other individuals in the population in biology. an adaption is a heritable trait that increases and individuals darwinian fitness in a particular environment 1/13 fossils are traces of organisms that lived in the past the many fossils that have been found and described in the scientific literature make up the fossil record. 2 Thursday, January 28, y Transitional forms • as the fossil record has become more complete, many transitional forms have been discovered wth traits that are intermediate between earlier and later species • these transitional forms provide strong evidence for change through time • early scientists observed that extinct fossil species are typically succeeded in the same region by similar living species • darwin interpreted this as evidence that extinct forms and living forms are related that they represent ancestors and descendants Evidence for change through time • researchers now have used radioactive isotopes to assign absolute ages to the geologic time scale • geologic data show that the earth is about 4.6 billion years old Extinction many fossils provide evidence for extinct species, those that are no longer alive darwin interpreted extinction as evidence that species are dynamic. He reasoned that if species have gone extinct, then the army of species living on earth has changed through time Vestigial treats a vestigial trait is a reduced or incompletely developed structure in an organism that has o function or reduced fiction, but is clearly similar to function organs or structures in closely related species vestigial thats are evidence that the characteristics of species have changed over time Genetic and developmental homology • Another line of evidence comes from homologies. Homology is a similarly that exists in a species descended form a common ancestor. Homology can be recognized and studied at three interacting levels; genetic, developmental, and structural . 3 Thursday, January 28, y Homology genetic homology is a similarity in the DNA sequences of different species. A main example is the generic code itself developmental homology is a similarity in embryonic traits. An example is the gill riches found during the embryonic developmental in chicks, humans. and cats. Structural Homology refers to similarities in adult morphologies. One example is the common structural plan found in the bones f the limbs in vertebrates (animals with a backbone) in many cases, traits are similar in different species because the species in question were related to each other bt common decent if species were created independently of one another, these types of similarities would not occur Homology is evidence that features do not arise de novo but are built from preexisting structures, indicating decent from a common ancestor Geographic relationships • One line of evidence comes from silicates among island species. For example, darwin collected mockingbirds from the galapagos iskands. The mockingbirds were superficially similar, but different islands and different species 4 Thursday, January 28, y • darwin proposed that mockingbirds were similar because they had defended from a common ancestor Evolution is not goal-directed or progressive • evolution by natural selection is not goal directed. It simply favors individuals that happen to be better adapted to the environment at the time. Adaptions do not occur because organisms want or need them • evolution is also not progressive, meaning producing “better” or more complex organisms. Scientifically, there is no such thing as higher or lower organisms • species are related by a common ancestry and all have evolved equally though time. As evolution continues, species may become simpler or more complex depending on which one is more favorable . Chapter 21 Evolutionary forces • microevolution is a change in allele frequencies in a population over generations • Macroevolution refers to the origin of new groups of organisms, the appearance of major new features in organisms, and the change in diversity associated with mass extinctions Evolution in populations IN population genetics, we consider evolution = a change in allele frequencies in a population over time Forces that can change allele frequencies in populations • Mutation • genetic drift (due to small population size) • migration or gene flow • nonrandom mating • natural selection 5 Thursday, January 28, y mutation Mutations are changes in the nucleotide sequence of DNA Mutations cause new genes and alleles to arise only mutations in cells and gametes can be passed on to children Mutation= the raw material for evolution Mutation rate low on a pergene basis, but organisms have many genes • mutation rates are variable among individuals among species variation among genes Genetic Drift This is unpredictable fluctuations in allele frequencies in small populations due to chance Does not lead to adaption Leads to fixation of alleles important in small population related to the founder effect Fixation Only one allele remains in the population. All others are gone. SO the trait is fixed in that there is only one option Founder effect the founder effect occurs when a small group of individuals establish a new population These individuals are a subset of the original population. Generic traits probably occur at different frequencies in this small subset. They are not entirely representative of the larger, original population Some characteristics may be present at a higher frequency. Others may be entirely missing 6 Thursday, January 28, y Bottleneck effect As a result of genetic drift • Populations lose allele • populations lose genetic diversity • separate populations diverge from each other • genes can become fixed. (that means only one allele still exists in the population Migration, or gene flow movement of alleles between populations \ migration introduces new alleles and changes the frequencies of alleles present If two populations have different selective forces and their gene pool mix through migration, we can expect a change in allele frequencies. 7 Thursday, January 28, y Non-random mating inbreeding outbreeding sexual selection for a particular type positive or negative assortative mating. Inbreeding and conservation Biology endangered species usually exist in small populations. Genetic drift can fix bad genes. Inbreeding can reduce survival and fitness resulting in smaller population size Advantages of Inbreeding it can preserve a fit genotype outbreeding depression When you take an individual from a far away place, and it is more adapted to their environment, you ruin the chance of the offspring being able to survive either environment Sexual selection Sexual selection is natural selection for mating success It can result int sexual dimorphism, marked differences between the sexes in secondary sexual characteristics. Sometimes sexual selection seems to contradict the idea of “survival of the fittest” Female Choice: When the female chooses the male who impresses her most 1/20 Positive assortative mating strong tendency for people to chose traits that are similar to what they have Negative assortative mating: When the individual looks for traits dissimilar to what they have 8 Thursday, January 28, y Natural selection Natural selection is the only one of these forces that can produce adaption The three different modes of selection • Directional selection favors individuals at one end of the phenotypic range • Disruptive selection favors individuals at both extremes of the phenotypic • Stabilizing selection favors intermediate variants and acts against extreme phenotypes Chapter 22 Species and speciation There are different ways to describe species Biological species concept: If they can reproduce with each other, they are part of the same species Prezygoic isolation Occurs when individuals of different species are prevented from mating Postzygotic isolation: Occurs when individuals from different populations do mate, ut the hybrid offspring produce have low fitness and do not survive to produce offspring. Problems with the biological species concept Some species do have distinct forms but hybridize where their ranges overlap (polar bears and grizzlies) Morphospecies concept This emphasizes morphological differences Under this concept, biologists ndenitift evolutionary independent lineages by differences in size, shape, or other morphological features This concept is base on the idea that distinguishing features are most likely to arise if populations are independent and isolated from gene flow The morphospecies concept can be wide;y applied, but the features used to distinguish species under this concept are rather subjective 9 Thursday, January 28, y Problems with this concept Some taxonomists that work in certain groups are splitters and name lots of species for example there are about 200 named species of parthenogenetic british black berry; a vertebrate taxonomist might assign these to 2 or 3 species Cryptic species species that look the same to use, but do not interbreed at all Ecological species concept This looks at how species differ in their interactions with the environment The Phylogenetic species concept this is based on reconstructing the evolutionary history of populations on such a phylogenetic tree, each tip is a phylogenetic species often, this depends looking at the molecular genetics of many individuals Other problems with the species concept Species have different degrees of genetic divergence in different groups For example, there is a disease causing bacteria called legionella pneunophila. Different strains differ by as much as 50% of the nucleotide sequence homologys. That amount of genetic difference s as big as the difference between mammals and fish. Humans and chimps army by 3% 1/22 How do new species form? 1.isolation Founder effect genetic drift 2. Divergence Sympatric Natural Selection The divergence of species happens in the same place 10 Thursday, January 28, y Allopatric Natural selection When the two species diverge in different locations. This is much more common What helps to maintain species? songs/ vocalizations behaviors color patterns breeding season timing mechanical or chemical differences hybrids are not fit Polyploidy A mutation that results in polyploidythe condition of having more than two sets of chromosomes can cause speciation Mistakes in meiosis can result in diploid gametes. If two diploid gametes fuse, the zygote has an even number of chromosomes. Chapter 23 Macroevolution Long term impacts of mass extinctions. Origin of entire new groups of organisms. Major new features or processes. Changes in diversity due to mass extinctions patterns of new evolution on a large time scale Limitations of the Fossil record Biologists think that o.1% of all species that have lived on earth have been discovered though the fossil record. Habitat bias some types of organism are not surrounded by conditions that will fossilize them Taxonomic bias some organisms don’t have have features that help them fossilize. Bony animals will likely be fossilized as opposed to jellyfish Temporal bias The possibility that while an organism was fossilized and some random event either removed it or destroyed it abundance bias some organisms are more plentiful than others 11 Thursday, January 28, y Four eras of fossil records Precambrian from the formation of earth through the appearance of multicellular, soft bodied organisms paleozoic the diversification of animals plants and fungi Mesozoic “Age of reptiles” (Dinosaurs) Cenozoic “Age of mammals” each era ended with a major extinction Mechanisms for macroevolution Continental drift Widely excepted. When two continents get separated leaving separate organisms on both continents. This is because of plates in the earth moving. Pangea was a super continent 1.1 billion years ago Consequences of continental drift: 1. A reduction in shallow water habitat 2. A colder and Drier climate inland 3. Changes in climate as contents moved toward and away from the pole 4. Changes in ocean circulation patterns lading to global cooling Homeotic gene duplication/mutation Hox gene duplication these determine such basic features as where wings and legs will develop on a bird or insect Duplication of these regularity genes allow s more complexity in animal form Genes that program development control the rate, timing, and spatial patten of changes in an organisms form as it develops int an adult Heterochrony An evolutionary change in the rate or timing of developmental events it can have significant impact on body shape The contrasting shapes of human and chimpanzee skulls are the result of small changes in relative growth rates Mass extinctions there have been 5 big mass extinctions. The fossil record shows that most species that have ever lived are new extinct. These happened most likely because of external forces Consequences of mass extinctions 12 Thursday, January 28, y mass extinction can alter ecological communities and the niches available to organisms it can take from 5 to 100 million years for diversity o recover following a mass extinction Adaptive radiation The rapid formation of many species from a single ancestral species. These are not only after mass extinctions, but are often correlated wit morphological innovation. When plants developed a waxy cuticle, they could not live on land. That opened many new opportunities for rapid speciation. When arthropods with their water resistant exoskeletons came onto land, they found many new environments 1/25 exaltation features that arise in one context take on a new role Chapter 24 Prokaryotes The phylogenic tree of life molecular data shows that some organisms previously lumped together as bacteria are more different from each other than plants and animals. Thus we have added an additional layer at the top of the hierarchy, called the domain The domain concept was originally based on rRNA Domain Kingdom Phylum class order Family genus Species Prokaryotes: No nucleus Binary Fission Lateral gene transfer 13 Thursday, January 28, y single celled circular DNA Prokaryotes are the oldest life forms on earth appearing at least 3.5 billon years ago Prokaryotes were the only life forms for almost over a billion years before the appearance of eukaryotes Bacteria Freeliving, Pathogens, Mutualists, and important in ecological cycles Eubacteria have a cell wall of peptidoglycan (a polysaccharide). It prevents the cell form bursting in a hypotonic solution Archaea also have a cell wall, but the chemical composition varies among species Although cells lack membrane bound organelles, they may have imaginations of the plasma membrane. These folds provide large surface areas for enzymes and pigments 14 Thursday, January 28, y 15 Thursday, January 28, y Reproduction of prokaryotes reproduction in prokaryotes is via binary fission which produces clones prokaryotes do not have gametes, zygotes, or sexual reproduction as we know it in animals Mutation: Mutation rate is about 1 x 10^7 per gene/cell/day in E. coli thus a single bacterium can give rise to 6 x 10^6 mutations a day Lateral gene transfer Conjugation transformation transduction Conjugation: DNA is transferred between two cells that are temporarily joined by a plus only cells with the F factor can form a pilus Transformation 16 Thursday, January 28, y Transduction 17 Thursday, January 28, y 1/27 Bacteria 4 broad categories of metabolism based on source of carbon, and source of energy Source of Carbon: Autotrophs carbon derived from CO2 or other inorganic Csource Heterotrophs carbon derived from intake of organic molecules living or dead organisms Source of energy: Photo energy derived from light Chemo energy derived from the break down of chemicals Photoautotrophs Energy from the sun Carbon from CO2 or other inorganic things Photoheterotrophs: Only in certain prokaryotes Get energy from light carbon from consuming organic molecules Chemoautotrophs: Energy from oxidation of chemicals such as NH4, CH4, or H2S oxidation carbon from inorganic source Chemoheterobtrophs: This includes humans and all animals Energy from breakdown of chemicals Carbon from ingestion of organics Archaea They are found in many places that you would find eubacteria. They are common in the ocean and soil Some Archaea are extremophiles, living in conditions of high heat, high salinity, or low pH, and as deep as 2.7 km underground 18 Thursday, January 28, y Methanogens obligate anaerobes which produce methane as a byproduct of metabolism; important in sewage treatment, also found in bogs Halophiles requite hit salt concentrations 1723% Thermoacidophiles require hot, acidic environment such as burning coal deposits Hyperthomophiles tolerate temperatures as high as 106 C In what ways are Archaea like eurobacteria? Archaea look like eubacterial cells Like eubacteria they lack a nucleus They have a circular bacterial chromosome Plasmids are present in cells How do archaea differ from Eubacteria Cell wall alacks peptidoglycan )a normal component of eubacterial cell wall) Lipids are etherlinked(unusual form of lipids) The archaean chromosome contains introns unique ribosomal RNA the DNA is associated with histone proteins in Archaea How are archaea similar to Eukaryotes Archaea have introns in genome DNA is associated with histone proteins Ribosomal proteins are more similar to those of eukaryotes RNA polymerase is more similar to eukaryotes Evolution of the Eukaryotes Major transitions from prokaryotes to eukaryotes Have a nucleus Complex Life cycles 19 Thursday, January 28, y Internal Cell organelles Multicellularity in some Development of cytoskeleton Aerobic metabolism dominates Nucleus Loss of bacterial cell wall Infolding of plasma membrane to surround DNA Greater regulation of generic material within nucleus The nuclear membrane separates transcription from translation. This allows the additional processing of mRNA before it is translated to make proteins. The additional processing includes alternative splicing configurations, which results in additional flexibility in gene expression. Within the nucleus: Formation of distinct chromosomes increase in amount of genetic material evolution of diploid condition evolution of mitosis and meiosis Endosymbiosis Loss of cell wall and development of cytoskeleton permit phagocytosis cells engulf other smaller cells internal cells become endosymbionts Mutualism smaller cel gains a favorable environment larger cell derives benefit from its endosymbiont 20