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Perspectives of Biology 113 Notes

by: charlotteee

Perspectives of Biology 113 Notes

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Second semester of a two-course introductory sequence for students with a strong background and interest in science. Topics include: evolution, organismal diversity, ecology, and functional biology...
Perspectives in Biology 113
Class Notes
Perspectives of Biology 113, Biology 113, Bio113
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This 6 page Class Notes was uploaded by charlotteee on Wednesday June 1, 2016. The Class Notes belongs to at University of Rochester taught by Bickel in Spring 2016. Since its upload, it has received 6 views. For similar materials see Perspectives in Biology 113 in Biology at University of Rochester.


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Date Created: 06/01/16
Cretaceous Terrestrial Revolution (110-80 MYA): insects and angiosperms diversifying; exponential increase in mammalian diversity Cretaceous- tertiary Paleogene Extinction (65 MYA): dinosaurs’ extinction opens door for more mammalian diversity and diversification into new niches/habitats and for animals to diversify into Stem forms: origin of new groups from early, unspecialized ancestral group Review Session: Life on Earth: physical characteristics on earth (continental drift) 2 plates colliding one plate with slide under the other and form mountain ranges, when plates drift apart, we get formation of ocean basins Pangea Lower half Gondwanan Upper half Africa, SA Australia, llamas Milankovitch cycles: eccentricity, orbital tilt and procession inferring patterns of global movement to infer patterns of climate change Mass Extinctions: Cambrian-glaciation Permian Triassic- volcanism Cretaceous Tertiary-meteor Huge increase in diversity after mass extinction: a lot of space to be filled and opportunities to diversify and speciate Early atmosphere of earth: little to no oxygen, volcanic activity, general chemical reactions, photosynthesis Oxygen Catastrophe: cyanobacteria (first organism to use sunlight) and led to huge massive extinction Three Domains of Life: Eukaryotes, bacteria and archaea Eukaryotes and archaea closely related Gene Duplication: is when region of DNA coded again through recombination and transposable elements Duplicated gene is under less selective pressure so sometimes duplicated gene can acquire so many mutations so different functions Duplicated genes to infer evolutionary Elongation protein in translation EF-TU versus EF-G gene duplication event F1-ATPase and U/V-ATPase LUCA: Because there are no outgroups Ctenophores do not have tissue type and cnidarians do Chordates (notochord, dorsal hollow nerve cord, pharyngeal) Amniotic egg: way to protect the egg Ctenophores: comb jellies Echinoderms: starfish Cephalochordates: Lancets Tunicates: Sea squirts Chordates: US Craniata: hagfish Selective pressure (natural selection): selection still acting in older ancestors and how they catalyze their reactions, natural selection acts on all life and not just complex life Lateral transfer can occur in all three types of bacterial recombination Lateral gene transfer: transfer occurs between bacterial species as opposed to inheritance Often G-C content, higher G-C content = more lateral gene transfer, genes have to find way into organism, so more higher G-C = more stable so likely to withstand the lateral gene transfer Genomic Islands: regions of genome that have evidence of horizontal transfer Transfer via plasmids, vectors, Antibiotic resistance Class Review: Adapting Reptiles are Paraphyletic Feathers (example of exaptation): used in insulation, communication, heat shielding, camouflage, water repellant, defense function Flight arose quite late even though feathers arose quite early Dinosaurs are not monophyletic because birds Geological processes can shape biological life (movement of tectonic plates where land is and where it isn’t.) if plates are pulling apart = new land forming, lava creeping up can create new land, land colliding together = mountain ranges Pacific have a lot of volcanoes because at the edge of the plates and a lot of plates colliding Pangea broke into two big continents (north and south), created barriers to gene flow and started speciation Gondwanan distribution = related species in different continents Milankovitch Cycles: earth’s shape around sun varies throughout time (how elliptical and how circular = glaciation and ice ages) High eccentricity = hotter weather and lower eccentricity = colder weather or ice ages Cambrian Extinction = glaciation and O2 depletion Volcanoes spew out CO2, water vapor and nitrogen and cover the sun = affect photosynthesis Can organic molecules arise from inorganic molecules RNA can store genetic information/self-replicate and catalyze its own reactions We need to replicate more often than degradation and if too much degradation there cannot be consistency so stronger selection for more accurate and quick replication (R= rate of change in the population) If we want a root we need to know something before the species diverged (an outgroup) but all of life there is no outgroup so we use gene duplications (duplicated before last common ancestor of al life). If the gene is present in last common ancestor we look for where the two genes come together Eukaryotes and Archaea have more shared derived traits than bacteria and the three have more shared derived traits Recombination holds bacteria together; more recombine with other individuals more likely to be similar Recombination more likely if you have similar sequences Endosymbiosis (of bacterial species inside in eukaryotic lineage like mitochondria and chloroplasts) Deuterostomes (Echinoderms and Chordates): Echinoderms: starfish; are radically symmetrical adults and bilateral symmetry in larvae; a major group of only marine animals. The name comes from the Greek word for "spiny skin". There are about 7,000 species found usually on the sea floor in every marine habitat from the intertidal zone to the ocean depths. They have a wide variety of colours. There are at least 800 species of echinoderm on the Great Barrier Reef. Echinoderms have radial symmetry, many having five or multiples of five arms. They have a shell, made mainly of calcium carbonate, which is covered by skin. The skin contains cells to help support and maintenance the skeleton, pigment cells, cells to detect motion on the animal's surface, and sometimes gland cells which secrete sticky fluids or even toxins Chordates (a phylum with three subunits Cephalochordata, Urochordata, Craniata of phylum ): animal phylum with which everyone is most intimately familiar, since it includes humans and other vertebrates. However, not all chordates are vertebrates. All chordates have the following features at some point in their life (in the case of humans and many other vertebrates, these features may only be present in the embryo): Pharyngeal slits - a series of openings that connect the inside of the throat to the outside of the "neck". These are often, but not always, used as gills. Opening in digestive tube posterior to mouth, original function was for feeding. dorsal hollow nerve cord - a bundle of nerve fibers which runs down the "back" and becomes the brain and nervous system. It connects the brain with the lateral muscles and other organs, it is the only phylum with a tube and becomes a brain and nervous system. Also forms in the gastrula stage and HAS A ECTODERMAL ORIGIN!! What makes something a Chordates? notochord - cartilaginous rod running underneath, and supporting, the nerve cord, located between the gut and nerve cord in the embryo, functions in support and locomotion in free living forms. The Notochord forms in gastrula stage and has a mesodermal tail AND HAS A MESODERMAL ORIGIN!!! post-anal tail - an extension of the body past the anal opening Urochordates (Tunicates): The body of an adult tunicate is quite simple, being essentially a sack with two siphons through which water enters and exits. Water is filtered inside the sack-shaped body to bring in microscopic organisms. However, many tunicates have a larva that is free- swimming and exhibits all chordate characteristics: it has a notochord, a dorsal nerve cord, pharyngeal slits, and a post-anal tail. Larvae stage pelagic with notochord; larvae have characteristics of chordates, adult sessile like sea squirts (notochord is lost and filter feeders) Cephalochordates (lancelets): found in marine environments, filter feeders, notochord provides structural support; cephalochordates are small, eel-like, unprepossessing animals that spend much of their time buried in sand. However, because of their remarkable morphology, they have proved ccrucial in understanding the morphology and evolution of chordates in general -- including vertebrates. Amphioxus Genome tells us: divergence occurred about 500 MYA, gene loss has not occurred in Amphioxus and gene loss is common in Craniata and Urochordata Craniata : deuterostomes with head; a box of hard tissues (cartilage or bone) which encloses the brain, olfactory organs, eyes and internal ear Neoteny: the retention of juvenile features in the adult animal; retention of juvenile  characters in ancestral group into adult form of descendent group Three branches of Craniata: HagFish: have a cartilinogous skull, body stiffened with large notochord,NO Jaw or vertebra; only have large notochord Lampreys: have vertebra, skull (notochord reduced), are usually parasites of fish Gnathostomes (jawed vertebra): jaw, vertical biting devices, most of the recent vertebrates Jaw did not just form out of nothing; actually similar and homologous to gill arches (common ancestor that did have gill arches but no jaws): gill arches initially used in filter feeding and modified for jaws and respiration Major Innovations leading to Cichilds: have evolved pharyngeal jaws Have a pharyngeal jaw/teleost jaw (food gets vacuumed in). The true jaws capture the food while the pharyngeal jaw processes food. Challenges to Life on Land: -Air breathing: function of lungs (for buoyancy, air sacs), swim bladders. Lungs were already invented by lobe-finned fish -Stable, moving structure: interlocking vertebral column in bony fish, developing a strong, sturdy vertebrae -Limbs/fins: Tiktaalik (transitional form with beginnings of tetrapod limb) -Desiccation (deal with drying out): Some amphibians had scales and impermeable skin amniote egg invented by reptiles Exaptation: a preexisting characteristic that enhances the ability of a species to adapt to a change in its environment or way of living (swim bladder was co-opted to be used as lungs); a feature that performs a function but that was not produced by natural selection for its current use. Perhaps the feature was produced by natural selection for a function other than the one it currently performs and was then co-opted for its current function. For example, feathers might have originally arisen in the context of selection for insulation, and only later were they co-opted for flight. In this case, the general form of feathers is an adaptation for insulation and an exaptation for flight Amniote Egg: extra embryonic tissue that is not involved in the terrestrial life itself such as the amnion: fluid filled cavity to protect embryo, Chorion: exchange gases bet. Embryo and air, Tetrapods: land vertebrates, evolved from lobe-fined fishes, limbs evolved, more robust, skeletal girdle ***WE GO FROM FISH TO TIKTAALIK TO TETRAPOD Adaptive Radiation: the diversification of a group of organisms into forms filling different ecological niches. Must have ecological opportunities to use and results in speciation and adaptive divergence


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