Speciation the formation of new and distinct species in the course of evolution. Species A group of similar organisms that can breed and produce fertile offspring. Microevolution Change in allele frequencies in a population over generations. Macroevolution the broad pattern of evolution above the species level What is the bridge between micro and marco evolution? speciation What do changes in morphology result from? changes in regulation of genes; expression How do we define a species? biological species concept biological species concept a population that can

1. interbred in nature

2. produce viable, fertile offspring

3. don't breed successfully with other popoulations what holds populations together genetically? gene flow What are the limitations to the biological species concept? - organisms in asexual reproduction

• fossils

• emphasizes an absence of gene flow where they are morphologically and ecologically distinct morphological species concept characterizes a species by body shape and other structural features, very subjective ecological species concept views a species in terms of its ecological niche; emphasizes disruptive selection phylogenetic species concept A definition of species as the smallest group of individuals that share a common ancestor, forming one branch on the tree of life. reproductive isolation biological barriers that impede members of different species from interbreeding and producing viable, fertile offspring Barriers to hybridization prezygotic and postzygotic barriers hybrids Offspring of crosses between parents with different traits prezygotic barriers Barriers that impede mating or hinder fertilization. postzygotic barriers Barriers that prevent the hybrid zygote from becoming a fertile adult. types of postzygotic barriers - reduced hybrid viability

• reduced ferility

• hybrid breakdown types of prezygotic barriers 1. habitat isolation

2. temporal isolation

3. behavioral isolation

4. mechanical isolation

5. gametic isolation habitat isolation Two species encounter each other rarely, or not at all, because they occupy different habitats, even though not isolated by physical barriers temporal isolation form of reproductive isolation in which two populations reproduce at different times; seasons, days, years but can live in the same area behavioral isolation Form of reproductive isolation in which two populations have differences in courtship rituals or other types of behavior that prevent them from interbreeding; attraction mechanical isolation Morphological differences can prevent successful mating due to genotypes gametic isolation Sperm of one species may not be able to fertilize eggs of another species reduced hybrid fertility Even if hybrids are vigorous, they may be sterile reduced hybrid viability When the genes of different species interact and impair hybrid development. hybrid breakdown Hybrid is fertile, but when they breed the next generation is sterile. allopatric speciation The formation of new species in populations that are geographically isolated from one another. Separated populations may evolve independently through -Mutations are random -Selective pressures for natural selection -Genetic drift can do odd things to a population sympatric speciation The formation of new species in populations that live in the same geographic area What is sympatric speciation driven by? sexual selection factors reducing gene flow polyploidy, habitat differentiation, sexual selection Polyploidy condition in which an organism has extra sets of chromosomes habitat differentiation sympatric speciation can also result from the appearance of new ecological niches; when a subpopulations exploits a habitat or resources not used by the parental population sexual selection A form of natural selection in which individuals with certain inherited characteristics are more likely than other individuals to obtain mates. Autopolyploidy The state of having more than two full sets of chromosomes due to a mutation that doubled the chromosome number allopolyploidy a species with multiple sets of chromosomes derived from different species hybrid zone a geographic region in which members of different species meet and mate, producing at least some offspring of mixed ancestry what can hybrid zones tells us over time? if the population has gene flow within then the isolated population diverges and a barrier to gene flow form outcomes of hybrid zones 1. Reinforcement

6. Fusion

7. Stability Reinforcement barriers that occur when hybrids are less fit than the parent species fusion weakening of reproductive barriers- the two species fuse stabiility continued formation of hybrid individuals What is the pace of speciation/evolution? polyplodies Marcoevolution components mutation, gene flow, genetic drift and natural selection stasis lineages don't change much over time with a puncunated equilibria character change lineages can change quickly or slowly; in a single direction or in reverse; within a single lineage or across several lineages Lineage splitting (speciation) may vary in frequency, timing extinction frequent or rare event within a lineage or it can occur simulaneously across many lineages does evolution tend to proceeded slowly or steadily or in quick jumps slowly and steadily how does evolution produce new and complex features? So evolution is a continuous process taking place in every population. Individuals in a species who are well adapted to an environment will pass their genes to the offspring, and after generations passed by natural selection acts upon each connect rates, and natural selection acts upon its structure within an organ, like the eye, producing incremental improvements in the process. Each tiny change in the structure is dependent upon changes in all of the other structures. Are there trends in evolution, and if so, what processes generate them? local trends and not directional Elderedge and Gould Geographical isolation can cause fairly rapid evolution if a relatively small portion of the species becomes isolated on the fringes of the species' range changes in gene regulation Changes in morphology likely result from changes in the regulation of developmental genes rather than changes in the sequence of developmental genes chemical and physical processes on early earth produced simple cells in 4 steps 1. Abiotic synthesis of small organic molecules

8. Joining of these small molecules into marcomolecules

9. Packaging of molecules in protocells 4.Origin of self-replicating molecules abiotic synthesis formation of organic molecules from inorganic material; monomers what compounds made up the atmosphere on early earth? released by volanic eruptions: nitrogen carbon dioxide NH3 methane hydrogen Stanley Miller *An American Scientist who experimented in Harold Urey's laboratory at the University of Chicago in 1953 to see if the gases hypothesized to exist on early earth could really create organic compounds. *He filled a flash with all of the proposed gases early earth had, heated it, and gave it occasional electric charges, and after a week, he discovered amino acids had formed in the mixture. Protocells spontaneously formed from fluid-filled vesicles with a membrane like structure; Self-replicative; Have RNA molecules that can polymerize Origin of self-replicating molecules RNA-- it worked like an enzyme; single strandred and self-replicated Ribozymes RNA molecules that function as enzymes DNA mode of genetic material that is passed to further generations because it is more stable and can be replicated more accurately what documents the history of life? sedimentary rocks and fossils When did the earth begin? 4.6 billion years ago when did seas begin to form? 4 billion years ago organisms that were common are now extinct Nicholas Steno First to recognize fossils were remains of organisms; in a sequence of rocks, any layer is older than the layer above it Principle of Superposition When artifacts are found in rock or earth that is layered, the deeper layers hold the older artifacts. sedimentary strata reveal the relative ages of fossils radiometric dating the process of measuring the absolute age of geologic material by measuring the concentrations of radioactive isotopes and their decay products how old can strata be for radiometric dating? 75000 what happens during radiometric dating? parent isotope decays into a daughter isotope Biostratigraphy a relative dating technique based on the regular changes seen in evolving groups of animals as well as the presence or absence of particular species absolute dating A technique used to determine the actual age of a fossil half life length of time required for half of the radioactive atoms in a sample to decay Carbon-14 a long-lived naturally occurring radioactive carbon isotope of mass 14, used in carbon dating and as a tracer in biochemistry. what isotopes can be used for older fossils K-AR What are the eras in order? Neo-proertozic, Paleozoic, Mesozoic, Cenozoic geologic record The division of Earth's history into time periods, grouped into three eons—Archaean, Proterozoic, and Phanerozoic—and further subdivided into eras, periods, and epochs. Periods in the Geological Time Scale edicaran, cambrian, ordovician, slurian, devoniran, carboniferous, permian, trassic, jurassic, createous, paleogene, neogene, quarternary Epochs of the Cenozoic Era Paleocene, Eocene, Oligocene, Miocene, Pliocene, Pleistocene, Holocene Eons Hadean, Archean, Proterozoic, Phanerozoic Hadean Eon The oldest of the Precambrian eons; the time between Earth's origin and the formation of the first rocks that have been preserved. Archaen Eon - prokaryotic cells

• stromatolites

• oxygen revolution oxygen revolution--when did it occur? 2.7-2.2 BYA Cyanobacteria Bacteria that can carry out photosynthesis Stromatolites Oldest known fossils formed from many layers of bacteria and sediment. oxygen revolution the accumulation of oxygen released by cyanobacteria beginning 2.6 billion years ago Proterozoic Eon - mutlicellularity (eukaroytes)

• endosymbiotic theory

• snowball earth endosymbiotic theory proposes that mitochondria and plastids were formerly small prokaryotes living within larger host cells and they were formed from cells engulfing other prokaryote evidence of endosymbiotic theory - Inner membranes are similar to plasma membranes of prokaryotes

• Division and DNA structure is similar in these organisms and prokaryotes

• These organelles transcribe and translate their DNA

• The organelles' ribosomes are more similar to eukaryotic ribosomes Snowball Earth Hypothesis the hypothesis that glaciers covered the planet's landmasses from pole to pole 750-570 million years ago, confining life to very limited areas; deep sea vents and equatoiral regions The Phanerozic Eon is divided into what eras? Paleozoic, Mesozoic, Cenozoic Cambrian explosion A burst of evolutionary origins when most of the major body plans of animals appeared in a relatively brief time in geologic history; recorded in the fossil record about 545 to 525 million years ago. ( predator/prey interactions) Phanerozic colonization photosynthesis (less water) mass extinction event during which many species become extinct during a relatively short period of time (50% or more) Permain extinction "the great dying", 96% of marine life, 70% of land animals went extinct, only known mass extinction of insects Cretaceous Extinction -65 million years ago -asteroid in Yucatan peninsula Mexico -debris block sun -extinction of many marine and land mammals, dinosaurs, birds spared plate tectonics A theory stating that the earth's surface is broken into floating plates that move on a fluid core tectonic plates move through contiential drift causing the formation of moutains and islands tectonic plates shape climate and allopatric speciation adaptive radiation An evolutionary pattern in which many species evolve from a single ancestral species adaptive radiation may follow - Mass extinctions

• The evolution of novel characteristics

• The colonization of new regions mechanisms of radiation heterochrony and paedomorphosis heterochrony Evolutionary change in the timing or rate of an organism's development; alter the timing of non reproductive organs example of heterochrony the contrasting shapes of human and chimpanzee skulls are the result of small changes in relative growth rates Paedomorphosis the rate of reproductive development accelerates compared with somatic development which may retain body features that were juvenile in ancestral species Changes in Spatial Pattern Substantial evolutionary change can also result from alterations in genes that control the placement and organization of body parts homeotic genes (hox genes) Genes that determine basic features of where a body part is. changes in genes New morphological forms likely come from gene duplication events that produce new developmental genes changes in gene regulation (radiation) Changes in morphology likely result from changes in the regulation of developmental genes, rather than changes in the sequence of developmental genes Phylogeny Evolutionary history of a species Taxonomy The scientific study of how living things are classified who developed taxonomy Carolus Linnaeus Format of taxonomy (Binomial nomenclature) and Hierarchical classification system (e.g., Kingdom, Phylum, Class, Order, Family, Genus, Species) convergent evolution Process by which unrelated organisms independently evolve similarities when adapting to similar environments binomial nomenclature Classification system in which each species is assigned a two-part scientific name

• first letter of genus is captailized

• the entire binomial is italizcied phylogenetic systematics classification of organisms by their order of branching on an evolutionary tree branch point represents the divergence of two species sister taxa Groups of organisms that share an immediate common ancestor and hence are each other's closest relatives. basal taxa a lineage that diverges early in the history of a group polytonomy a branch point from which more than two descendant groups emerge monophyletic groups ALL descendants came from one common ancestor paraphyletic group composed of some but not all members descending from a common ancestor polyphyletic group A taxonomic grouping consisting of several species that lack a common ancestor (more work is needed to uncover species that tie them together into a monophyletic clade). Cladistics A phylogenetic classification system that uses shared derived characters and ancestry as the sole criterion for grouping taxa. maximum parsimony fewest evolutionary events maximum likelihood A principle that states that when considering multiple phylogenetic hypotheses, one should take into account the one that reflects the most likely sequence of evolutionary events, given certain rules about how DNA changes over time. what are the alternative principles to cladistics maximum parsimony and maximum likelihood Clade A group of species that includes an ancestral species and all its descendants. How to read a phylogenetic tree Oldest species is at the base of the tree with the most recent at the ends of the branches. The closer the branches, the closer the evolutionary relationship Phylogenies are inferred from morphological and molecular data Morphology similar structures molecular DNA sequences types of homologous genes orthologous genes and paralogous genes orthologous genes originates from an ancestor and due to the speciation within a species paralogous genes occurs within the same species due to duplications of the genes over many generations Analogous structures (convergent evolution) various structures in different species having the same function but have evolved separately, thus do not share common ancestor homoplasies Analogous structures and molecular structures that have evolved independently. molecular evolution statistical tools have been developed to determine whether DNA sequences that share more than 25% of their bases do so because they are homologous molecular clock a yardstick for measuring the absolute time of evolutionary change based on the observation that some genes and other regions of genomes appear to evolve at constant rates mutations are proportional to... divergence of time Neutral Theory a majority of mutations are neutral, neither advantageous or deleterious genes and regions that accumulate mutations quickly are good for tracing recent change Why is it bad to have frequent changes in molecular clocks? - Ribosomes can't handle it who was the neutral theory proposed by motoo kimaura Origin of Viruses - may have originated from host cells

• viruses are more closely related to their host than other viruses

• nucleic acids that break away from the host cell and maintain the ability to replicate inside the host cell Viruses tiny particles, smaller than bacteria and other pathogens, which must invade living cells in order to reproduce; when they invade, the cells are damaged or destroyed in the process releasing new particles to infect other cells Sources of viral genomes - Plasmids

• Circular DNA in bacteria and yeast

• Transposons characteristics of viruses - cant reproduce or metabolize independently, but can direct living cells to do it for them

• Obligate interacellular parasites

• not a cell

• don't contain DNA

• lipid membranes to faciliate contact with cells selfish elements genes that are transmitted more than other genes. May be neutral or harmful to the organism Viruses consist of nucleic acid surrounded by a protein coat, host cells for replication and metabolism tobacco mosaic disease stunts growth of tobacco plants and gives their leaves a mosaic coloration Tobacco mosaic diseases in the 1800's researchers hypothesized that a particle smaller than bacteria that caused the disease Tobacco mosaic diseases in 1935 W. Stanley confirmed this by crystallizing the infectious particle: the virus Viral genomes can be DNA or RNA, single or double stranded, linear or circular RNA viruses Usually single stranded, may be double stranded, may be segmented into separate RNA pieces, easier to mutate Glycoproteins Membrane carbohydrates that are covalently bonded to proteins. capsids protein coats that enclose and protect their nucleic acid (viral genome) caposomeres caposomeres DNA viruses Usually double stranded (ds) but may be single stranded (ss) Circular or linear Replication transcription and translation can cause the viral infections to be blocked or intervened Bacteriophage A virus that infects bacteria Most information about viruses studies of bacterial infections-- easy to reproduce and prokaryotic infections don't harm eukaroytes complex capital structure - Elongated capsid head encloses their dna

• Protein tail piece attaches to the phage to the host and injects the phage DNA inside obligate intracellular parasites Viruses will only replicate within a host cell Each virus has a host range, a limited number of host cells that it can infect broad host range rabies virus infects various cells of all mammals; west nile river virus narrow host range can infect only humans; measles what do viruses make use of? - host enzymes

• ribosomes

• tRNA

• amino acids

• ATP what can self-assemble themselves into new viruses? viral nucleic acids molecules and capsomeres Cycles of Phages lytic cycle and lysogenic cycle lytic cycle a viral reproductive cycle in which copies of a virus are made within a host cell, which then bursts open, releasing new viruses virulent phage A phage that reproduces only by a lytic cycle. lysogenic cycle a viral reproductive cycle in which the viral DNA is added to the host cell's DNA and is copied along with the host cell's DNA animal viruses viruses that infect animals and humans virus cycle in animals Infect animals that have a membranous envelope Many viruses that infect animals have a membranous envelope (helps with attaching to host cells) Viral glycoproteins on the envelope bind to specific receptor molecules on the surface of a host cell viral envelopes A membrane that cloaks the capsid that in turn encloses a viral genome. glycoproteins roteins that allow this particular virus to attach to the target cells → determines the host range because these are the proteins that interact with the receptors of the target cell, determines which cells it will be able to infect RNA as viral genetic material broadest variety of RNA genomes are found in animal viruses. Retroviruses use reverse transcriptase to copy their RNA genome into DNA provirus Viral DNA that inserts into a host genome. prophage A phage genome that has been inserted into a specific site on the bacterial chromosome. vaccines harmless derivates of pathogenic microbes that stimulate immune system in mount defense against the harmful pathogen disease causing organisms can lead to infections which can create a immune response of recovery death disability immune memoery herd immunity The resistance of a group to an attack by a disease to which a large proportion of the members of the group are immune what needs to be done to achieve immunity? certain thresholds Challenges to herd immunity - pathogen changes

• antigenic drift

• antigenic shift antigenic drift molecules on the surface changing due to mutations in the genes encoding them antigenic shift molecules on the surface changing due to recombination of genes of existing pathogens emerging viruses viruses that appear suddenly or are new to medical scientists How do emerging viruses arise? - mutations

• dissemintation of viral disease from small isolated populations

• spread of exisitng viruses from other animals Where do prokaryotes thrive? almost everywhere, including places too acidic, salty, cold, or hot for most other organisms What are the two domains of prokaryotes? Bacteria and Archaea structural and functional adaptations of prokaryotes - unicellular

• smaller

• variety of shapes (cell wall) Most common shapes of prokaryotes spherical (cocci), rod-shaped (bacilli), spiral bacteria groupings Diplo - means paired; strepto - means arranged in chains; staphylo - means arranged in clusters. what is the most important feature for prokaryotic cells and why cell wall

• maintains shape

• protects the cell

• prevents from bursting into a hypotonic environment eukaryotic cell wall plants= cellulose fungi= chitin what do bacterial cell walls contain peptidoglycan peptidoglycan a network of sugar polymers cross-linked by polypeptides what do archaean cell walls contain polysaccharides gram stain A staining method that distinguishes between two different kinds of bacterial cell walls. Gram-positive bacteria Bacteria that have simple cell walls with much thick layer of peptidoglycan; spherical Gram-negative bacteria Bacteria that have a thin peptidoglycan cell wall covered by an outer plasma membrane. They stain very lightly (pink) in Gram stain. Gram-negative bacteria are typically more resistant to antibiotics than Gram-positive bacteria. what is the cell wall covered by in prokaryotes? capsule capsule A sticky layer of a polysaccharide that surrounds the cell walls of some bacteria, protecting the cell surface and sometimes helping to glue the cell to surfaces. Biofilm A surface-coating colony of one or more species of prokaryotes that engage in metabolic cooperation. capsule layer functions - Attachment aid (either to substrate or other cells to form a biofilm)

• Desiccation protection

• Protection from the host immune system in pathogenic bacteria Fimbriae attachment structures on the surface of some prokaryotes Pili Appendages that allow bacteria to attach to each other and to transfer DNA sex pili longer than fimbriae and allow prokaryotes to exchange DNA how does pilli work? connects with the cytoplasm of two different prokaryotes endospores metabolically inactive, can remain viable in harsh conditions for centuries taxi movement towards of away from a stimulus; in a heterogenous environment chemotaxis Cell movement that occurs in response to chemical stimulus Phototaxis movement in response to light Flagellum A long, hairlike structure that grows out of a cell and enables the cell to move. exaptation the process in which existing structures take on new functions through descent with modification internal organization of prokaryotes no nucleus or other membrane-enclosed organelles; usually no complex compartmentalization How do prokaryotes reproduce? binary fission key features of binary fission - small

• short generation times why do prokaryotes have considerable genetic variation? - rapid reproduction

• mutations

• genetic recombination genetic recombination the combining of DNA from two sources, contributes to diversity horizontal gene transfer The transfer of genes from one genome to another through mechanisms such as transposable elements, plasmid exchange, viral activity, and perhaps fusions of different organisms. prokaryotic DNA from different individuals can be brought together by: - transformation

• transduction

• conjugation transformation process in which one strain of bacteria is changed by a gene or genes from another strain of bacteria transduction movement of genes between bacteria by bacteriophages conjugation the process where genetic material is transferred between prokaryotic cells F factor A piece of DNA that confers the ability form a sex pili. F factor plasmid - Mating bridge forms, one strand of plasmid breaks. New strand synthesized in F+, broken strand enters F- cell.

• Synthesis of complementary strand begins in F- cell.

• DNA replication continues; transfer of strand continues

• Plasmids circulize; both F+ R plasmid A bacterial plasmid carrying genes that confer resistance to certain antibiotics. R Plasmids and Antibiotic Resistance - R plasmids carry genes for antibiotic resistance

• Antibiotics kill sensitive bacteria, but not bacteria with specific R plasmids

• through natural selection, the fraction of bacteria with genes for resistance increases in a population exposed to antibiotics

• Antibiotic-resistant strains of bacteria are becoming more common Phototrophs obtain energy from light chemotrophs obtain energy from chemicals Autotroph requires CO2 as carbon source heterotroph requires an organic nutrient to make organic compounsd Photoautotrophs Organisms that use light as a source of energy to synthesize organic substances. Photoheterotrophs An organism that uses light to generate ATP but that must obtain carbon in organic form. Chemoheterotrophs An organism that must consume organic molecules for both energy and carbon. Chemoautotrophs Organisms that use hydrogen sulfide or other chemicals as energy source instead of light. The Role of Oxygen in Metabolism Prokaryotic metabolism varies with respect to O2 obligate aerobic bacteria require oxygen Obligate anaerobic bacteria can only live without oxygen; fermentation or anaerboic respiration facutative anaerobes can survive in environments with or without oxygen and toggle metabolic processes accordingly Nitrogen Metabolism in Prokaryotes - Nitrogen is essential for the production of amino acids and nucleic acids

• Prokaryotes can metabolize nutrogen in a variety of ways

• In nitrogen fixing, some prokaryotes convert into atmospheric nitrogen to ammonia (NH3) host cell structures are viral membranous envelopes derived? plasma membrane, ER, and Golgi appartus Virus-first hypothesis Potentially relics of the pre-cellular world and products of the first protocells because they have RNA genomes Progressive hypothesis Evolved as mobile pieces of nucleic acid that could move between cells since they can only replicate within cells regressive hypothesis Originated as intracellular parasites that lost the ability to live Independently plasmids small circular DNA molecules that replicate separately from the bacterial chromosome Transposons (jumping genes) short strands of DNA capable of moving from one location to another within a cell's genetic material mobile genetic elements plasmids, transposons, and viruses helical viruses hollow, cylindrical capsid Adenovirus respiratory infections Icosahedral 20-sided with 12 corners when do viral infections begin binds to a host cell and the viral genome makes it way inside the cell temperate phage A phage that is capable of reproducing by either the lytic or lysogenic cycle. viral diseases in plants -More than 2,000 types of viral diseases of plants are known and cause spots on leaves and fruits, stunted growth, and damaged flowers or roots -Most plant viruses have an RNA genome -Many have a helical capsid, while others have an icosahedral capsid horizontal transmission disease is spread through a population from one infected individual to another vertical transmission from parent to child prions infectious proteins characteristics of prions Act slowly Can't be destroyed or deactivated Misfolded protein how do plants spread viruses? vertical and horizonal transmission Frequency dependent selection the fitness of a phenotype depends on how common it is in the population Miller-Urey Experiment A: NH3 (ammonia),H2 (hydrogen),CH4(methane),H2O Represented the atmosphere B: Electric current- lightning C: Water, represents the ocean D: Organic compounds- amino acids; They used blotting techniques whose hypothesis was the MIller-Urey experiment based off of Oparin-Haldane Hypothesis: life arose gradually from inorganic building blocks regulatory regions of DNA They are the promoter and upstream regions of DNA (non-coding regions) where transcription elements bind. Live attenuated vaccines Weakened pathogen Closely mimic an actual infection Confers lifelong cellular and humoral immunity Inactivated vaccines dead organisms injected into patient to build immunity binary fission - Can divide every 1-3 hours

• Bacterial growth: an increase in the number of cells which occurs by cell division

1. Mother or parent cell doubles in size a. Enlarges it cell wall, cell membrane, and overall volume and DNA replication starts B. Septum begins to grow and DNA move towards opposite ends of the cell c. Septum is synthesize completely through the cell center creating two separate cell chambers

2. Divides into two daugther cells a. Some species separate completely others remain attached forming chains, doublets, and grape-like cluster Hfr bacterium High frequency of recombination bacterium An F+ bacterium that has the fertility factor integrated into its chromosome. When conjugation takes place, it is able to transfer not only the F factor, but also its genomic DNA.