Biology 108: Lectures 1-6

Biology 108: Lectures 1-6

1. BIOLOGICAL DIVERSITY

   • * variability among living organisms from all sources; includes diversity within species, between species and of ecosystems 
   • Levels of Organization
     • Biosphere
       • Ecosystems
         • * community + physical environment 
         • Communities
           • * different species (populations) interacting with each other
           • Populations
             • * group of individuals of same species in an area
             • Organisms
               • Organs/Organ systems
                 • Tissues
                   • Cells
                     • Organelles
                       • Molecules
                         • Atoms
     • Methods of Organization
       • Nomenclature
         • system for naming things 
         • Taxonomy
           • practice (discipline) of naming and classifying organisms by similarities
           • Systematics
             • theory and practice of classifying organisms based on their evolutionary history (phylogeny)
             • Phylogenetic Trees/Cladogram
               • evolutionary trees/hypotheses that show the evolutionary relationship between organisms (past/present)/common ancestors and descendants
               • In-group
                 • *group of tree that we are interested in studying
                 • Out-group
                   • * different than in group; distantly related
               • character
                 • * type of structure, behavior, DNA sequence ex. eye colour
                 • state
                   • *expression of character ex. brown
                 • synapomorphy
                   • shared, derived state
                   • symplesiomorphy
                     • shared, ancestral state (acquired from ancestor)
                 • homologous
                   • look the same and have the same evolutionary origin; result from divergent evolution
                   • divergent evolution
                     • process by which members of a species become more and more different, resulting in 2 different species; usually due to different environments (unique selective pressures)
                 • analogous
                   • structures in different species that look the same but actually developed independently; result of convergent evolution and usually due to similar envrionments
                   • convergent evolution
                     • when unrelated organisms evolve similar characteristics due to similar environmental pressures (same selective pressure)
                 • vestigial (structures)
                   • body structure that is reduced in form and function but may have been useful in ancestor
               • principle of parsimony
                 • * choose phylogenetic tree/relationships that has the least number of times the character changes states... b/c evolutionary change does not occur so frequently
               • clade/monophyletic group
                 • has common ancestor and ALL of its descendants and NO other unrelated taxa; use homologous traits
                 • polyphyletic group
                   • more than one common ancestor or lacking common ancestor/taxa is grouped together although they do not share recent ancestors; or grouped by superficial similarities instead of common ancestory
                   • paraphyletic group
                     • groups that do not contain ALL descendants of a common ancestor; usually happens when most divergent group (group that looks the most different) is removed 
               • sister taxa
                 • two (or more) groups that are each others closest relatives 
           • Linnean System of Classification
             • Kingdom
               • Phylum
                 • Class
                   • Order
                     • Family
                       • Genus
                         • Species
               • Domain
         • Binomial nomenclature
           • 2 part name = genus + species * genius = capital * both = italicized ex. Homo sapiens
   • Why do we study it?
     • Threats
       • - resource exploitation - conversion of land - pollution  - transport of species -global climate change * As human population increases, extinction increases.
       • Direct value
         • * drugs (antibiotics) * agricultural value
         • Indirect value
           • allows us to have info to use for  * recycling biological and geochemical matter * nutrient-cycling decomposers * water cyclings (transpiration of trees) * prevents soil erosions  * regulates climate-carbon cycle * ecotourism ($)
     • Scientific Method
       • Observation
         • * asking and developing question 
         • Hypothesis
           • * prediction; purpose = answering question; cause/effect formate * testable and falsifiable * data can support or reject hypothesis but can't prove it
           • Predictions
             • * follow the hypothesis * must be testable
             • Hypothesis testing/experimentation
               • * testing of predictions through observing and experimentation
             • experiments agree with prediction = process is repeated for more info
           • results are not consistent with the predictions = new hypothesis
         • proximate questions
           • * questions that deal with mechanism and may not require evolutionary explanations
           • ultimate questions
             • * questions having to do with evolutionary origins and functions
         • Questions
           • * seek to explain observation

2. Natural Selection

   • context dependent; increases fitness but does not work towards perfection
   • Organisms produce many more offspring than survive to reproduce themselves.
     • Resources are limited. (not enough food for all offspring of all individuals)
     • Most populations = relatively stable
     • Organisms must compete for limited resources, and not all succeed.
   • Variation among individuals within species; for natural selection to act on variation, must be seen by environment (expressed in phenotype) and be heritable (caused by genotype)
     • Some variation is heritable.
     • Some heritable variations are may provide individuals with a competitive advantage.
       • Individuals with advantageous variations are likely to have more offspring than those without these variations.
         • Next generation will have more individuals with that variation than were present in previous generation = adaptive changes over generation = "descent with modification"; refer to lecture 4 pg 7
     • Types of Variation
       • Phenotypic
         • form, function, behavior
       • Genotypic
         • genetic makeup
         • Genes
           • combo. of 2 alleles in diploid (2 copies) individuals; one allele per chromosomes 
           • allele
             • one of two or + alt. forms of a gene; arise by mutation; found at same place on a chromosome
             • allele frequency
               • how often an alternative form of a gene occurs
               • Evolution
                 • change in allele frequency in gene pool between generations
                 • caused by
                   • natural selection
                     • can affect distribution of allele frequencies via different types of selection
                     • directional selection
                       • 1 extreme phenotype is favored (highest fitness); shift in the mean of population; variance (degree of difference) = same
                     • disruptive selection
                       • both extreme phenotypes are favoured; result = polymorphism (2 or more divergent phenotypes); maintains variation 
                     • stabilizing selection
                       • average/common phenotype(s) favored/ selection against extremes; mean of pop. stays the same = variance (degree of difference) decreases; little or no evolutionary change 
                   • gene flow
                     • transfer of genes (alleles) between pop.s; ex. interbreeding, migration; variation = increases within pop but decreases between pop.s b/c allele frequency between pop.s = more similar
                   • genetic drift
                     • change in allele frequency due to *chance*; impact = greater in small pop.; rare alleles are more likely to be lost
                     • bottleneck effect
                       • only few individuals survive; only they reproduce in next generation; allele frequency in next generation is diff. than previous
                     • founder effect
                       • new pop. established by a few colonizers which have diff. allele frequencies than ancestors
                   • mutations
                     • change in DNA caused by error in DNA replication or by structural damage to DNA; random process; can be good, bad, or neutral depending on environment
                 • fitness
                   • extent to which an individuals's genotype is represented in the next generation; highest reproductive success
           • gene pool
             • total # of genes of every individual in an interbreeding pop.; large = high genetic diversity; small = low genetic diversity
     • Sources of Variation
       • - mutation (random changes in DNA) - during meiosis * recombination (crossing-over) * independent assortment (of chromosomes) - fertilization (sexual reproduction; 2 combine to make 1 new genotypes)
     • Some heritable variations may provide individuals with a competitive advantage.
   • acts on the individuals (causing differential survival and reproduction), but outcome (evolution( is seen at the population level).
   • Selective Agent
     • something in environment (biotic/abiotic) that is always acting on/applying pressure on organisms/population over generations (ex. climate change, starvation)
     • selection pressure
       • intensity with which selective agent acts on a population to evolve
   • Adaptation
     • * heritable variation; individuals vary in their characteristics (phenotype) due to varied genetic makeup (genotype) * limited resources = pop. produces more offspring than environment can sustain * phenotypes with favorable traits = better suited to survive and reproduce; genetic contribution to next gen. = greater = increased fitness * characteristics (and genes coding for them) of fit individuals = increase in pop.