9/10/2012 12:39:00 PM Modern Understanding of Evolution (08/22/12) Charles Darwin Alfred Russell Wallace Biological Evolution Microevolution Any

genetic change in a population over time Macroevolution The process of descent with modification and divergence by which multiple species arise from a common ancestor Research in Evolution Discovering and describing bio diversity How many species are there? How are they similar or different? How are species related to eachother? Understanding the processes that shape biological diversity How do organisms come to fit their environment? Origin of novel traits? What limits biological diversity? Example: HIV Treatment with AZT: short term success but long term failure Origin of HIV? Relevant HIV Facts Retrovirus Genetic material stored as RNA Viral replication requires intermediary DNA phase Retrotranscription AZT Treatment At first, AZT reduces viral load by 50% at small dose 2 years later, 1000X the dose for same effect Selection Thinking HIV is extremely variable=high mutation rate

9/10/2012 12:39:00 PM When AZT treatment is stopped, infection evolves towards susceptibility (that type has faster replication rate=outcompetes) Evolution is short-sighted: there is no end goal, evolution never knows where it is going Natural Selection (08/27/12) A mechanism for evolution (genetic change in a population) Four Postulates (requisite) Individuals within a populations are variable The variations among individuals are, at least in part, passed from parents to offspring (heritable) In every generation, some individuals are more successful at surviving and reproducing than others (competition) Survival and reproduction of individuals are not random; instead they are tied to the heritable variation among individuals. Some phenotypes survive and reproduce more than others (offspring resemble their parents). Example: Darwins Finches of the Galapagos Medium Ground Finch Postulates: Variation in beak size Heritability PROBLEM: Drought causes plants to die back and stop producing new seeds; only seeds remaining are old seeds on the ground and in the soil (seed bank) More energy is expended finding lower quality seeds (harder shells) Finch population crashed Bigger beak size is passed on to next generation Beak size determines fitness (the genetic contribution an individual makes to the next generations), influenced by, Survival Reproduction Quality of offspring

9/10/2012 12:39:00 PM 4 postulates are satisfied, so natural selection occurred! As did evolution (average beak size increased)! Acts on individuals Acts on phenotypes, but evolution is a change in genotypes The Nature of Science and the Scientific Process (08/29/12) An Experiment is often a manipulation of a system, designed to test a hypothesis Fact: data, measurable Theory: A synthetic and coherent proposition that explains some phenomena Key evidence supporting the Theory of Evolution Homology across species Similarity in body structures and function (presumably due to shared, common ancestry) Origin of Modern Evolution Charles Darwin and Alfred Russell Wallace co-publish their ideas on evolution Changes in inorganic and organic world result from operations of natural law, not miraculous intervention Complex organisms evolved from simple organisms; simple organisms usually descended from simple organisms All species descended from one (or a few) original species: Descent with Modification Thomas Malthus on Limiting Resources Essay on the Principles of Population (1798) Food supply increase linearly, population exponentially Population quickly outstrips resources Competition for resources ensues Carl Linneaus Father of modern taxonomy Noted that organisms should be grouped hierarchically based on similarity

9/10/2012 12:39:00 PM Phylogenetics (08/31/12) The science of inferring the historical relationships and evolutionary histories of organisms Tree anatomy Node o Where lineages split; one ancestral lineage divides into two or more derived lineages Branches/Internodes Represent populations through time Terminal Taxa/Tips Populations at the end of the tree Often represent species but can also represent alleles and larger groups such as domains Polytomy The evolutionary relationship is unclear Clade The set of all lineages descended from a common ancestor Monophyletic Monophyletic Describes a group comprised of an ancestor and all of its descendants Paraphyletic Describes a group that contains all but one or a few of the descendants of a last common ancestor Characters The traits or features used to reconstruct Phylogenetics relationships Can include Morphological traits Biochemical traits Behavioral traits Homology Similarity that results from inheritance of characters from a common ancestor

9/10/2012 12:39:00 PM Some homologous characters have more phylogenetic single than others Cladistics Willi Henning Taxa are related by descendent from a common ancestor Relationships can be reflected in a tre Only shared derived traits (synapamorphes) identify Monophyletic groups Derived character state (present in a descendant)= apomorphy Ancestral character state (present in the ancestor)= plesiomorphy Shared traits occur in two or more Taxa (syn/sym) Nonshared traits occur in only one Taxa (auto) Synapamorphy A shared derived character Symplesiomorphy A shared ancestral character Autoapomorphy A derived character found only in one taxon Characters useful for inferring trees Synapomorphes Homoplasy Similarities that result from factors other than common ancestry E.g., convergent evolution Character similarity resulting from independent responses to a similar environment Parsimony Principle Ockham's razor

9/10/2012 12:39:00 PM Complexity should not be posited without complexity Simplest explanation/tree The evolutionary tree that requires the least amount of change is the most likely Taxonomy (09/07/12) The process of biological classification Linnaeus Linnaean classification Hierarchical Kingdom Phylum Class Order Family Genus Species Species is the most fundamental unit of biological classification Nomenclature Latin binomial Canis familiaris Sometimes the genus is abbreviated Genera is the plural of genus The third word in a trinomial name in the subspecies Summarizes diversity, but does not call attention to important evolutionary relationships Phylogenetic classification Every grouping is a clade (Monophyletic) Names involving characters that represent that group Evolutionary transition can be represented Domains Bacteria

9/10/2012 12:39:00 PM Archaea Eukarya Adaptation A trait modified by selection that increases the ability of an individual to survive or reproduce compared to individuals without the trait Molecular clock hypothesis Relation of the divergence of time of two Taxa to the number of molecular

9/10/2012 12:39:00 PM Taxa (09-10-12) Important events in vertebrate evolution Jaws Four limbs Amniotic egg Life Prokaryotes (paraphyletic) Bacteria Archaea (extremeophiles) Eukarya Alveoltes (e.g., malaria) Stramenophiles (e.g., brown algae) Excavates (trypansomes) Plantae Osithokonts Animalia Sponges Eumetazoa Diploblasts Ctenophores Cnidarians Bilaterians Protostomes Dueterostomes Fungi Origin and early diversification of Life (09-12-12) Last Universal Common Ancestor (luca) vs. origin of life Life Bacteria Cyanobacteria Unnamed taxon Proteobacteria Unnamed Taxon Spirochetes Unnamed taxon Archaea

9/10/2012 12:39:00 PM Often extremophiles Eukarya "prokaryote" Bacteria and Archaea Cell wall covered by sticky capsule, peptidoglycan in bacteria Peptidoglycan is a single polymer molecule forms a net around the cell, and antibiotics interfere with the synthesis of this structure "Karyon" means before the nucleus, so no organelles Some attach by means of pili Extremely small, most smaller than most eukaryotes Three common shapes Spherical: coccus, cocci Rods: bacillus, bacilli Helical/spiral Locomotion Flagellum Axial filaments Gas vesicles Reproduction Bacteria reproduce plasmids by binary fission Resistant, dormant stages are called (endo)spores Metabolic diversity Photoautotrophs Photoheterotrophs Chemolithotrophs Chemoheterotrophs Eukaryotes Flexible, loss of cell wall Multiple chromosomes contained in a nucleus Endosymbiotic additions of a proteobacteriium to form a mitochondria and Cyanobacteria to form chloroplasts Protists- not animals, plants or fungi Alveolates Dinoflagellate

9/10/2012 12:39:00 PM Unicellular, marine, often endo symbiotic in corals and other organisms "Blooms" are toxic Ciliates Paramecium Plasmodium Stramenophiles Diatoms Unicellular or filament outs, marine and freshwater, on mosses Secrete top and bottom shells of silica Major component of sedimentary rocks, used in filtering and cleaning Brown Algae Seaweeds with carotenoids in chloroplasts that hide their green Excavates Ventral grove Lack or appear to lack mitochondria Giardia Trypanosomes Euglena Amoebazoans Amoebas Pseudopods Slime molds Macroevolution (09-17-12) The geological record of life The nature of fossils Remains or traces of once living organisms, preserved in the earth's crust Geological objects are the main tool for relative plating Fossils are dead Biological objects are living evidence Fossils as data for studying evolution

9/10/2012 12:39:00 PM Fossils show chronological history of organisms at a fine scale The origin of novelty Phylogenies show branching sequence and relative time of emergence and divergence Pre-modern Natural Philosophy John Woodward The world is only a few thousand years old (1665) The world has always been pretty much as it is today James Ussher Non scientific (scriptural) estimate of the age of earth, ~6000 years old (1650) Nicolaus Steno Head of a shark dissected (1667) Sufficient Similarity 4 principles Superposition Original horizontality Layers are deposited horizontally and then deformed to various attitudes later Lateral continuity Layers are assumed to have continued laterally far from where they presently end Cross cutting Geological things that cut across other things usually post-date (are younger than) them Charles Lyell (1830) Father of geology Uniformitarianism Modern geological processes can explain geological observations Assume that physical law is constant in time and space Use known processes first to explain ancient patterns But modern rates of change may not be representative

9/10/2012 12:39:00 PM Geological chronology Relative dating Numerical dating