Chapter 23: The Evolution of Populations!The Smallest Unit of Evolution!- Natural Selection acts on individuals, but only populations evolve.!- Microevolution - change in allele frequencies in a population over generations !

By natural selection, Genetic drift, or gene flow! only natural selection causes adaptive evolution!

Concept 23.1: Genetic Variation makes evolution possible. - Variation in heritable traits is the prerequisite for evolution!

Evidence provided by Gregor Mendel's work on pea plants!- Genetic Variation - among individuals is caused by differences in genes or other DNA

segments (mutation, gene duplication, rapid reproduction, sexual reproduction). Can be measured as gene variability(heterozygosity) or nucleotide variability(DNA)! Phenotype is the product of inherited genotype and environmental influences (DNA, RNA,

and proteins) physically; what you can see! Homozygous - individual with two identical alleles for a given locus! Heterozygous - individual with two different alleles for a given locus!

- Neutral Variation - differences in DNA sequences that do not confer a selective disadvantage or advantage.!

Concept 23.2: The Hardy-Weinberg equation can be used to test whether a population is evolving. - Population - a localized group of individuals capable of interbreeding and producing fertile

offspring.!- Gene Pool consists of all the alleles for all loci in a population!

A locus is fixed if all individuals in a population are homozygous for the same allele.(only one allele for a particular locus. !- (if there are two or more alleles for a particular locus diploid individuals are heterozygous

or homozygous).!- In order to evolve population must differ genetically, and one of the factors that causes

evolution must be at play (being used by species)!- Hardy-Weinberg Equilibrium: in a population where gametes contribute to the next

generation randomly and Mendelian inheritance occurs, allele and genotype frequencies remain constant from generation to generation without evolution. (constant frequency of alleles in a gene pool).! p+q=1(number of alleles in population)! p = expected frequencies of one homozygous genotype! q = expected frequencies of other homozygous genotype! 2pq = expected frequencies of heterozygous genotype! p+2pq+q=1 frequency of alleles in gene pool!

- Incomplete dominance: each genotype has a distinct phenotype!

- Conditions of Hardy-Weinberg Equilibrium:!! 1. No Mutations!! 2. Random Mating!! 3. No Natural Selection!! 4. Extremely Large Population Size!! 5. No Gene Flow!- Phenylketonuria (PKU) - metabolic disorder that results from homozygosity for a recessive

allele and occurs in about 1 of 10,000 births.!

Concept 23.3: Natural Selection, genetic drift, and gene flow can alter allele frequencies in population. - Adaptive Evolution - an improvement in the match between organisms and their

environment!- Genetic Drift - in smaller populations, describes how allele frequencies fluctuate

unpredictably from one generation to the next. ! Tends to reduce genetic variation through losses of alleles, random allele frequency !

! change, and cause harmful alleles to become fixed.!- Gene Flow - movement of alleles among populations due to movement of fertile individuals or

gametes (Example: Pollen). Gene flow is an important agent of evolutionary change in modern human populations.! Effects: reduce variation among populations over time, decrease/increase the fitness of a

population!

Concept 23.4: Natural selection is the only mechanism that consistently causes adaptive evolution. - Natural selection brings about adaptive evolution by acting on an organisms phenotype!- Relative fitness is the contribution an individual makes to the gene pool of the next

generation, relative to the contributions of other individuals.!- Three modes of selection: (figure 23.13)!

Directional selection favors individuals at one extreme end of the phenotypic range! Disruptive selection favors individuals at both extremes of the phenotypic range! Stabilizing selection favors intermediate variants and acts against extreme phenotypes!

- Why Natural Selection cannot fashion perfect organisms!! 1. Selection can act only on existing variations!! 2. Evolution is limited by historical constraints !! 3. Adaptations are often compromises!! 4. Chance, natural selection, and the environment interact!!Chapter 26: Phylogeny and the Tree of Life!Investigating the Tree of Life!- Phylogeny is the evolutionary history of a species or group of related species!- Systematics classifies organisms and determines their evolutionary relationships!

Concept 26.1: Phylogenies show evolutionary relationships. - Taxonomy: scientific discipline concerned with classifying and naming organisms. !- Binomial Nomenclature: 18th century Carolus Linnaeus published a naming system based

on resemblances (two-part names for species an hierarchical classification).! Binomial: the two-part scientific name of a species! First part of the name is the Genus! Second is Specific Epithet that is unique for each species within the genus !

- Linnaean System: grouping species in increasingly inclusive categories/levels called taxa!- Species, genus, family, order, class, phylum, kingdom, domain!

- Phylogenetic Tree: the branching evolutionary history of a group of organisms!Branch points represents the divergence of two species!Sister taxa are groups that share an immediate common ancestor !Basal taxon diverges early in a groups history and originates near the common ancestor!Polytomy is a branch which more than two groups emerge!Rooted means that a branch point within the tree (often drawn farthest to the left) represents the most recent common ancestor of all taxa in the tree.!-Homologies: phenotypic and genetic (DNA) similarities due to shared ancestry !

- Analogy: similarity due to convergent evolution! Homoplasies: analogous structures or molecular sequences that evolved independently !

-Convergent Evolution: occurs when when similar environmental pressures and natural selection produce similar (analogous) adaptations in organisms from different evolutionary lineages.!

Concept 26.6: Our understanding of the tree of life continues to change based on new data. -From two kingdoms to three domains!

- Now 5 kingdoms: Prokaryotes, Protista, Plantae, Fungi, and Animalia! Three-domain system: Bacteria, Archaea, and Eukarya, --- (B.A.E.)! Analyses of nearly 100 completely sequenced genomes supports

the validity of these Domains.!- The tree of life suggests that eukaryotes and archaea are more closely

related to each other than to bacteria.!- Horizontal Gene Transfer: movement of genes from one genome to

another. occurs by exchange of transposable elements and plasmids, viral infection, and fusion of organisms.! Was so common that the early history of life should be represented as a tangled network of

connected branches! Disparities between gene trees can be explained by the occurrence of horizontal gene

transfer.! !!!!!!Chapter 27: Bacteria and Archaea!!Masters of Adaptation! !- Utah's Great Salt Late can reach a salt concentration of 32%!- Its pink color comes from living prokaryotes!- Prokaryotes thrive almost everywhere, including places too acidic, salty, cold, or hot for most other organisms !- Prokaryotes are divided into two domains: bacteria and archaea!

Concept 27.1: Structural and functional adaptations contribute to prokaryotic success - Most Prokaryotes are unicellular, although some species form colonies, smaller than

eukaryotes, variety of shapes, and were earth's first organisms.! Three most common shapes: Spheres(cocci), rods (bacilli), and spirals.!

Cell-Surface Structures!- Prokaryotic cell walls' maintains cell shape,

protects the cell, and prevents it from bursting in a hypertonic environment! Hypertonic: high concentration! Isotonic: same on both sides! Hypotonic: low concentration!

- Eukaryote cell walls are made of cellulose or chitin!- Bacterial cell wall contain peptidoglycan, a

network of sugar polymers cross-linked by polypeptides! Archaea contains polysaccharides and proteins

but lack peptidoglycan! A polysaccharide or protein layer called a

capsule covers many prokaryotes ! Many antibiotics target peptidoglycan and

damage bacterial cell walls! Gram Stain is used to classify bacteria by call wall composition!

- Gram-positive bacteria have simpler walls with a large amount of peptidoglycan (violet)!- Gram-negative bacteria have less peptidoglycan and an outer membrane that can be

toxic (red)! Gram-negative are more likely to be antibiotic resistant.!

- Many Prokaryotes form metabolically inactive endospores, which can remain viable in harsh conditions for centuries!

- Some prokaryotes have fimbriae, which allow them to stick to their substrate or other individuals in a colony!

- Pili (or sex pili) are longer than fimbriae and allow prokaryotes to exchange DNA!!Mobility!- In a heterozygous environment, many bacteria exhibit taxis, the ability to move toward or

away from a stimulus! Chemotaxis is the movement toward or away from a chemical stimulus!

- Most motile bacteria propel themselves by flagella scattered about the surface or concentrated at on or both ends! Flagella are composed of different proteins and likely evolved independently !!

Evolutionary Origins of Bacterial Flagella!- Bacteria flagella are composed of a motor, hook, and filament!

Are modified proteins from within the bacteria! Exaptation - where existing structures take on new functions through descent with

modification!!Internal organization and DNA!- Prokaryotic cells lack complex compartmentalization!- Some have specialized membranes that perform metabolic functions that are infoldings of the

plasma membrane! Aerobic - respiratory membrane! Photosynthetic - thylakoid membranes!

- Differences between prokaryotes and eukaryotes in DNA replication, transcription, and translation allow people to use some antibiotics to inhibit bacterial growth without harming themselves!!

Reproduction !- Prokaryotes reproduce quickly by binary fission and can divide every 1-3 hours!- Key features of prokaryotic reproduction:!

They are small! They reproduce by binary fission! they have short generation times!

Concept 27.2: Rapid Reproduction, Mutation, and Genetic Recombination promote genetic diversity in prokaryotes. - Three factors that contribute to this genetic variation:!

Rapid reproduction! Mutation! Genetic Recombination!

Concept 27.3: Diverse nutritional and metabolic adaptations have evolved in prokaryotes - Prokaryotes can be categorized by how they obtain energy and carbon:!

Phototrophs obtain energy from light! Chemotrophs obtain from chemicals! Autotrophs require CO2 as a carbon source! Heterotrophs require a organic nutrient to make organic compounds!

- Energy and Carbon sources are combined to give four major modes of nutrition:! Photoautotrophy! Chemoautotrophy! Photoheterotrophy! Chemoheterotrophy!!

Role of Oxygen in Metabolism!- Prokaryotic metabolism varies with respect to O2!

Obligate aerobes require O2 for cellular respiration ! Obligate anaerobes are poisoned by O2 and use fermentation or anaerobic respiration! Facultative anaerobes can survive with or without O2!!

Nitrogen Metabolism!- Nitrogen is essential for the production of animo and nucleic acids!- Nitrogen Fixation some prokaryotes covert atmospheric nitrogen (N2) to ammonia (NH3)!- Metabolic Cooperation occurs between different prokaryotic species in surface-coating

colonies called biofilms!

Concept 27.4: Prokaryotes have radiated into a diverse set of lineages - The use of polymerase chain reaction (PCR) has allowed for more rapid sequencing of

prokaryote genomes!- Horizontal gene transfer between prokaryotes obscures the root of the tree of life!!Bacteria !- Majority of prokaryotic species familiar to people!- Proteobacteria: gram-negative bacteria include photoautotrophs,

chemoautotrophs, and heterotrophs; some are anaerobic and others aerobic! Subgroup Alpha - many species are closely associated with eukaryotic

hosts !- Rhizobium - forms roots nodes in legumes and fixes atmospheric N2 !- Agrobacterium - produces tumors in plants and is used in genetic engineering!

Subgroup Beta: the soil bacteria Nitrosomonas, which converts NH4+ to NO2-! Subgroup Gamma: include sulfur bacteria such as Thiomargarita namibiensis and

pathogens such as Legionella, Salmonella, and Vibrio cholerae!- Escherichia coli resides resides in the intestines of many mammals and is not normally

pathogenic! Subgroup Delta: slime-secreting myxobacteria, which produces drought resistant

myxospores. bdellovibrios mount high-speed attacks on other bacteria! Subgroup Epsilon - contains many pathogens including Campylbacter, which causes

blood poisoning, and Heliocbacter pylori, which causes stomach ulcers!- Chlamydias: are parasites that live within animal cells!

Chlamydias trachomatis causes blindness and nongonococcal urethritis by sexual transmission!

- Spirochetes: are helical heterotrophs. Some are parasites, including Treponema pallidum, which causes syphilis, and Borrelia burgdorferi, which causes Lyme diease!

- Cyanobacteria: are photoautotrphs that generate O2 ! Plant chloroplasts likely evolved from cyanobcateria

by the process of endosymbiosis!- Gram-Positive Bacteria include:!

Actinocetes, which decompose soil! Bacillis anthracis, the cause of anthrax !

- Clostridium botulinum, the cause of botulism!- Some Staphylococcus and Streptococcos, which can

be pathogenic!- Mycoplasms, the smallest known !!Archaea!- Archaea share certain traits with bacteria and other

traits with eukaryotes!- Some archaea live in extreme environments and are

called extremophiles! Extreme halophiles live in highly saline

environments (Great Salt Lake)!

Extreme thermophiles thrive in very hot environments (Yellow Stone Prismatic Spring)!

- Methanogens live in swamps and marshes and produce methane as a waste product (methionine are amino acids)! Methanogens are strict anaerobes and are poisoned by O2 ! Methane contributes to greenhouse gases !

Concept 27.5: Prokaryotes play crucial roles in biosphere - Symbiosis: ecological relationship in which two species live in close contact: a larger host

and smaller symbiont! Mutualism: both organisms benefit! Commensalism: one benefits while neither harming nor helping the other in any significant

way! Parasitism: parasite harms but does not kill its host! Parasites that cause diseases are called pathogens