LS1 Lecture

1/9/2014 10:23:00 AM

1/9/2014 Thursday Fixed Syllabus Time for February Midterm 6-7:50 PM No Chapter one jus know scientific method Evolution and Natural Selection Evolution explains similarities/differences (Molecules to Species) Geology shows evolution signs Buffon Noticed many similarities in items commonly thought different (Bones) Lamarck Use or disuse altered traits over life time (Giraffe Necks) And could be inherited by offspring Old Common Thought Immutable traits Wallace and Bates Wallaces Line States Naturalist should look beyond what we see Darwin very wealthy/respectable Goes on trip to Islands Capt. FitzRoy allows Darwin to be Naturalist on the ship Recent Pink Iguana Discovery on Galapagos Darwins Theory Observations All populations have the ability to grow exponentially o Growth without limits then reaches Carrying Capacity Carry Capacity (K) many factors Exponential J curve Logistics sigmoidal curve A Population cannot grow exponentially o Shows the struggle for existence only some offspring prosper Variation exists within a population o Polymorphism (Many forms) o Therefore those that are better able to adapt will survive

Variation must be heritable o Survivors pass on favorable traits to their offspring Evolution it happens over time Natural selection happens on a individual basis o Individuals do not evolve Populations evolve Evolution Occurred? Examples on Tuberculosis and Finches (READ) Was there variation? Was the variation heritable? Was there variation in reproductive success? Did natural selection occur? Evidence for Evolution Fossils, Homologies, Fossils any trace of the past Evidence from the Past Fossil Record Patterns of extinction explain a lot about current biodiversity explanations Carbon dating Extinction Five extinctions Darwin interpreted extinction as evidence of dynamic species Transitional Forms Law of Succession (Small Asian Kids = Natural Selection!?!?!) Transitions happen in small steps (Terrestrial animals become more aquatic) Your Inner Fish Book Phylogenetic Trees Show common ancestry by comparing homologies Structural Homologies different modified parts from common ancestors Vestigial Traits Homologous structures that no longer have function Traits that are not adaptive Developmental Homologies Small changes in bone structure

Genetic Homologies reflects common ancestors Homeotic Genes housekeeping genes o Control body part development Look at sequences Descendant sequences will have mutations Species Distributions Galapagos Finches Similar species in the same area Homology describe things that come from common ancestor Analogy structure with similar function but do not share ancestry Convergent Evolution (Dolphin and Shark) Things to remember Not all traits are adaptive Evolution has no road map no conscience No Predictions of future conditions Next Week sources of variation 1/14/2014 Tuesday Week 2 Changes in Allele Frequencies: Mechanisms of Evolution This Week Lab Horses Macro evolutionary change Mechanisms of micro evolutionary Change Meiosis Reduction division for reproduction (haploid gametes) o Homologous chromosomes separate first o Meiosis promotes genetic variation individual fitness Fitness = number of offspring Only two alleles for diploid individuals One from dad and the other from mom Chromosomes assort independently Source of variation Cross-over: homologous chromosomes can cross over New combination more variation Unit of evolution = population o Populations evolve change in allele frequency Allele frequency: number of alleles desired / number of alleles in population Hardy-Weinberg Principle (Null Hypothesis)

o No change in allele frequency no evolution o Allele frequency will remain same value throughout generations o Punnett Square Shows genotype frequency o p^2 + 2pq + q^2 = 1 : genotype frequencies o p + q = 1 : allele frequencies Assumptions of Hard-Weinberg o Random Mating Not that easy to achieve Every individual has equal chance of mating with individual of other gender o No Natural Selection HAS to be ideal conditions (Few predators, temp.) Natural Selection increases traits that enhance reproduction How is variation maintained? Balancing Selection No chance, exactly the same variation Heterozygous advantage Has two different alleles for variation Frequency-dependent selection Why arent deleterious alleles simply removed from the population? Dominant and recessive alleles Recessive alleles survive in heterozygous individuals Natural Selection acts on phenotype Heterozygote expresses dominant trait and has better fitness Ex) Sickle Cell Anemia Disruptive Selection increase variation Favors extreme stereotypes Directional Selection favor one extreme in one direction Genetic variation reduction

Sexual Selection DOES NOT result in adaptation Good for reproductive success, but not that useful for other things such as survival Bateman-Trivers Theory Asymmetry of sex o Sperm are cheap and eggs are expensive o Females have larger gamete o Females make LARGER investment

Sexual Selection acts more strongly on males Competition for mates Investment or competition? o No Genetic Drift Random fluctuations of genetic frequency Small populations more likely to drift because higher chance of allele loss/fixation o No Gene Flow Gene Flow homogenizes allele frequencies between populations Gene flow is random in respect to fitness of individuals o No Mutations Harmful, beneficial, neutral No effect on fitness what so ever Single mutation does very little to change allele frequency very slow process towards evolution Mutation and recombination is a source of genetic variation o o o o o EXAMPLE Left side: A1 = 1, 50 individuals Middle: A1 = 0.4 and A2 = 0.3, 150 individuals Right side: A4 = 1, 50 individuals Allele frequencies for the entire population? 250 total diploid individuals

1/16/2014 Thursday

Lab Quiz video is fair game for quiz Reading quiz extended to Tuesday 8am Lots of variation in populations (quantitative and qualitative) o Qualitative polymorphism Norm of reaction: represents genotype performance in respect to environment o Natural selection does not act on individuals with flat norm of reactions (flat = perform the same regardless of environment) Breeding experiments to show the genetic basis of phenotypic variation Processes that generate genetic variation o Mutation produce new alleles Not all mutations are bad Spontaneous/Heritable change in DNA Mutations change the genotype but not the phenotype because these are never seen by natural selection Exons are coded for protein, introns are not Selection is concerned with what is seen Most variations are neutral (Neutral evolution) Transversion purine to pyrimidine Transitions change within class of bases o Rearrangement of existing alleles Hardy-Weinberg Principle o P+q=1 Divergent Evolution: Bones and digits are homologous but can see divergence Chromosomal Change Same genes but different arrangement o (Like Humans vs. Chimpanzees) Do we care what species are similar or different? a species? Do they look alike? Can the interbreed? Are they evolutionarily distinct?

What is

Species are: Evolutionarily independent populations Subspecies: No reproductive isolation = no evolution = no separate species Remember: Even with Natural Selection the original species may still be alive New species arise when two populations diverge from one another What processes actually produce new species ? Dobzhansky Muller Model o Single ancestral population is divided into two o Different genetic changes accumulate in different lineages Genetic Divergence in Isolated Populatiosn o Extent of divergence is a function of time Anagenesis vs. Cladogenesis o Anagenesis: evolution involving an entire population o Cladogenesis: process of differentiation Branching off Generate new clades/organisms Molecular Clocks get idea of time since divergence o Some genes act as molecular clocks Meaning the genes change in regular intervals Histone Proteins: Allow DNA to compact into cell o Clocks gives us genetic time of divergence o Fossil Records give us physical evidence of divergence o Reproductive Isolation: Gene flow homogenizes populations Isolation Mechanisms: Pre-zygotic and Post-zygotic Pre-zygotic Behavioral Isolation: mating behavior Mechanical Isolation: genital differences Post-zygotic Hybrid inviability- zygotes do not survive Hybrid sterility hybrid are sterile due to weird chromosome number cannot form appropriate gametes Hybrid breakdown with reduced fitness of the F2 hybrid-hybrid offspring are inadequate Hybridization

o Horse + donkey = mule o Occurs when two divergent species interbreed o Causes of Hybridization:

o Hybrid Zone: common ground for interbreeding to produce hybrid offspring Hybrid zones are not static Sometimes hybrid offspring are more fit Outcomes of secondary contact: o Interbreeding o Reinforcement: selection against individuals that hybridize when hybrids have lower fitness

Week 3 1/21/2014 Tuesdays LS1 Midterm Review Thursday Allopatric Speciation based on subpopulation subdivision o Dispersal, Colonization, Vicariance o Isolation limits gene flow more likely for genetic drift to occur o Vicariance: physical separation of population genetic isolation leads to genetic divergence by mutation, selection, and genetic drift Sympatric Speciation selection on individuals of same species and residing in the same area o Selection, Polyploidy o Ex) Soapberry bugs beak length correlates with fruit size Long beak for large fruit, etc o Polyploidy: polyploidy individuals cannot mate with other parent species individuals triploids are unable to split evenly when combined with another gamete (common in plants) Occurs when sister chromatids fail to separate in meiosis stops gene flow o Chromosomal arrangements are different no longer mate with parent even though same genes

o What prevents speciation from occurring in sympatric populations? (Gene Flow) Dispersal vs. Vicariance o Vicariance has something acting as physical barrier o Dispersal is simply migration s How are speciation events represented in phylogenies? o Shown through the branching/forks What criteria do researchers use to derive evolutionary relationships? o Phylogenetic tree serves as testable hypothesis Outgroup: used as a comparison to compare with other species polarizes all the ingroup/taxa Monophyletic Group: descendants of the same ancestor Parsimony: means cheap Parsimony tree has the least number of changes Trees made for species, orders, DNA Trees help us look at speciation and patterns o Which trait is most useful? Trait 2 had A,A,B,B shows two sister taxa groups o The whole tree with common ancestor can count as one monophyletic group o Which tree is the better phylogeny, when given two tree? Map out and pick the one that is parsimonious o Fossil Record: Determine names and morphology Adaptive Radiation: adaptation through ecological opportunity and morphological innovations RAPID o New resources/niches available o Exploit new food, occupy new area

1/23/2014 Week 3 Thursday Adaptive Radiation By Ecological opportunity and morphological innovations Cambrian Explosion Higher Oxygen levels

Evolution of Predation New niches produce more niches New genes and new bodies o Hox genes: segments express genes for certain body part development Important for early development Biodiversity: allow speciation we see today BIODIVERSITY SECTION DO NOT MEMORIZE THOSE DIFFERENT SPECIES Just Know General Characteristics given Prokaryotes: abundant (a lot of diversity in belly button bacteria) Eukarya and Archaea are closely related, sister taxa Bacteria Cell wall of peptidoglycan, single circular chromosome Plasmids, no membrane bound nuclei, no energy producing organelles, no sex, haploid SUPER high mutation rates that can lead to antibiotic resistance Gram stain identification: Gram Positive or Gram negative o Measures peptidoglycan on cell wall Why are bacteria small? For efficient rate of diffusion How can they be so diverse when single cell and small? Morphologic and metabolism diversity Metabolic diversity: autotrophs, chemoorganotrophs, chemolithotrophs (Rock-Feeders) Cellular Respiration Electron donor and Electron acceptor convert different amounts of usable energy in ATP How does genetic diversity occur? Conjugation (Share plasmid DNA), Transformation (DNA is taking up by a cell), Transduction (Genetics is inserted into a cell), Mutation (INCREASE VARIATION/DIVERSITY) Bacteria is haploid so phenotype is the genotype Lateral Gene Transfer: movement of DNA between lineages Characteristics of three domain DO NOT MEMORIZE Just note: there are actually many similarities

How do prokaryotes help humans? Oxygen production, Biogeochemical cycles, Bioremediation (Fertilizing and Seeding) Bacteria and their environment Do not memorize processes But know that bacteria are important for crop health How do we study these lineages? Meta-genomic Analysis (Environmental sequencing) Why are Archaea important? Their morphology make them interesting Unique lipids in cell membranes these lipids are related to the environment Why study Archaea? Ancient life forms provide insight onto evolution

EXAM INFO Exam room info: Emailed Origin of Species Lizards in an evolutionary tree (hhmi) Twig lizard short legs Ground lizard long legs faster Different niches in the level of the tree in which they reside

1/9/2014 10:23:00 AM Week 4 1/28/2013 Tuesday Eukaryotes Protists all have nucleus Membrane organelles allow internal compartments o Alternate between sexual to asexual life cycles o Alternate between diploid to haploid phases Gametophyte (Haploid) Generation makes gametes o Mitosis to make haploid gametes fusion of gametes to 2n growth by mitosis to sporophytes Sporophyte (Diploid) Generation makes spores o Meiosis to make haploid spores then mitosis growth to gametophyte Eukaryote Features: Larger, cytoskeleton, nuclear envelope, Whats the big deal about sex? Hermaphrodites contain both sex organs Unisexual species chromosomes duplicate in the egg What are some disadvantages to sex? Asexual can reproduce rapidly, but sexual males cannot reproduce alone More energy and offspring are less related What are advantages of sex? New allele combinations, new genotypes, more variation, clear deleterious mutations What is recombination? Allows fast adaptation. On the other hand, asexual is slow to adapt since multiple mutations are required to get the same new allele combination as recombination. What is Mullers Ratchet? Sexual reproduction can get rid of deleterious combinations quickly. Asexual reproduction can only accumulate more deleterious mutations. Does this mean all eukaryotes are diploid? Alternation of Generations

Understand the general gametophyte and sporophyte one, not the other stuff. What are the hypothesis on the origin of eukaryotic cells? What is What is What is the evolution of the mitochondria? Primary endosymbiosis the evolution of the chloroplasts? Same idea as mitochondria endosymbiosis Chloroplast genome closely related to photosynthetic bacteria the role of secondary endosymbiosis?

Prokayote engulfs a photosynthetic protists that has already gone through endosymbiosis results in 4 internal membranes Are symbiotic interactions really that likely? The organisms live in close proximity so the idea is not too crazy(?) When did protists arise? Molecular Phylogenies Two major protists groups: Unikonta and Bikonta Amoebozoa plasmodial slime molds o Carbon cycle decomposers o Produce haploid spores and fuse and form diploid organisms o Form aggregates, and each organisms has different functions Excavata o Can be parasitic or symbiotic or even free-living o Cytoskeleton and flagella (Not like bacteria flagellum) Plantae o Cell walls of cellulose, photosynthetic, agar Rhizaria o Pseudopod for feeding o CaCO3 shells Alveolates o Diverse group of organisms o Represent different movement, feeding, and reproduction for protists Stramenopiles

Week 4 1/30/2013 Thursday Ecological impacts by protist Primary producers Outer shell contribute to petroleum formation Iron Fertilization increases photosynthesis by enhancing the electron transport chain mechanism Protists are small, but have a huge role!! Green Plants General Plant structure: Stem, Roots, Photosynthesis Green Algae, Land Plants, Before plants only unicellular bacteria, archaea, and single-celled protists Land Plants Evolved from green algae Primary land producers Major Roles of Plants o Produce oxygen, build/hold soil, stop erosion, buffer local climate Human Uses of Plants via artificial selection o Agriculture, wood, coal (Wood that was not decomposed), bioprospecting (Medicine) , aesthetic flowers Agriculture Plant based fuels Sphagnum much of biomass Forestry wood Pharmaceutical Value biorpospecting What can we say about plants? a,b chlorophyll and beta-carotene, thylakoids, cellulose cell walls, starch, sperm, peroxisomes (degrade fatty and amino acids) How can we study plants ? Fossil Record of Plants Molecular Phylogeny of Green Plants Sporophyte pine tree diploid Gametophyte haploid

Some of the issues: How to transition to land safely Early on gametophyte live in moist areas UV radiation Major adaptations: Sporopollenin: helps prevent dessication Cuticle: first layer against dessication Stomata pores o Cells swell up with water and the pores open o To allow CO2 to come in and excess water vapor to be lost Vascular Tissue to move water Adaptations Two groups for land plants o Bryophytes (mosses) nonvascular Lignin support weight Apical Meristems allow vertical growth Embryophytes embryos form in tissues Liverworts: Hornworts: o Tracheophytes Tracheids cells that contain lignin for support Water movement Water potential is the pressure potential + solute potential Vascular Tissue o Xylem carries water o Phloem carries food sugars from photosynthesis The evolution of leaves

Major innovations: Trends: o Heterospory make two different spores Lycophyta Pterophyta Week 5 2/4/2014 Tuesday Gymnosperms seed plants

Flagellated sperms are lost as plants transitions to land Gymnosperm life cycle NOT EXPECTED TO DRAW OUT o Male cones are smaller than female cones Angiosperms flowers Great radiation possible de to vessels, flowers, and fruits o Innovation: dispersal of seeds Divided into Monocots and Dicots The role of genome duplication diversification Monocots and Dicots differ Same function, but different arrangement of vascular tissue Flowers require some sort of sugar water production Have pollinators Sexual Production: Getting gametes to different places Fertilization: Embryo develops in flower carpel Fruits ripened ovaries Fungus what are they? How do we characterize them? Heterotrophic and extracellular digestion Close to animas related trait: chitin

Week 5 2/6/2014 Thursday The plant carbon transfer questions Answer: B Week 6 2/11/2014 Tuesday Office Hours: Thursday 11-1, Friday 8 9:30 Reproduction sexual and asexual Choanoflagellates Bring food by beating Usually resides in colonies Porifera suspension feeders Benthic: Cnidaria radially symmetrical

Ctenophora Cone jellies

Week 7 2/18/2014 Tuesday Fins assist locomotion and act as stabilizers Protosome coelom evolved just once

Week 7 2/20/2014 Thursday Ecology The Planet is covered in water Levels of Study Organismal Population Community Ecosystem Global Determinants of Distribution Abiotic o Organisms interaction with the environment Biotic o Interaction with other organisms History and Distribution Plate Tectonics o Formation of mountain ranges o Large Rivers Climate Patterns Why rainforests and deserts only on certain regions? o Hadley Cell Causes the climate patterns 30 degrees south and north of the equator Example smaller scale Hadley cell effect seen on mountains

Terrestrial Biomes Need to know different types of biomes Do not need to know what defines them and such Aquatic Biome o Benthic Zone: bottom area o Different wavelengths of light can penetrate the water depending on the shallowness o Lack Turnover: Behavioral Ecology Genes and behaviors Prairie voles are monogamous male and female stay with each other till death Learning from experience FAP fixed action patter n o Genetically controlled o Species specific o Once the pattern starts, it goes all the way to completion Conditional Strategies o Changing Sex Huge hormonal and morphological changes

Week 9 3/4/2014 Tuesday Study hint early on in podcast Species Diversity Grizzly Bear From each chapter Most interesting point and worst points in each chapter Complete 90% of the sheet to get the points Explanations have to be thorough Upload excel file on myucla Due 8am day of final

1/9/2014 10:23:00 AM