Biology 108: Lectures 1-6

Annotations:

• * variability among living organisms from all sources; includes diversity within species, between species and of ecosystems 

1. Levels of Organization
   1. Biosphere
      1. Ecosystems

         Annotations:

         • * community + physical environment 
         1. Communities

            Annotations:

            • * different species (populations) interacting with each other
            1. Populations

               Annotations:

               • * group of individuals of same species in an area
               1. Organisms
                  1. Organs/Organ systems
                     1. Tissues
                        1. Cells
                           1. Organelles
                              1. Molecules
                                 1. Atoms
   2. Methods of Organization
      1. Nomenclature

         Annotations:

         • system for naming things 
         1. Taxonomy

            Annotations:

            • practice (discipline) of naming and classifying organisms by similarities
            1. Systematics

               Annotations:

               • theory and practice of classifying organisms based on their evolutionary history (phylogeny)
               1. Phylogenetic Trees/Cladogram

                  Annotations:

                  • evolutionary trees/hypotheses that show the evolutionary relationship between organisms (past/present)/common ancestors and descendants
                  1. In-group

                     Annotations:

                     • *group of tree that we are interested in studying
                     1. Out-group

                        Annotations:

                        • * different than in group; distantly related
                  2. character

                     Annotations:

                     • * type of structure, behavior, DNA sequence ex. eye colour
                     1. state

                        Annotations:

                        • *expression of character ex. brown
                     2. synapomorphy

                        Annotations:

                        • shared, derived state
                        1. symplesiomorphy

                           Annotations:

                           • shared, ancestral state (acquired from ancestor)
                     3. homologous

                        Annotations:

                        • look the same and have the same evolutionary origin; result from divergent evolution
                        1. divergent evolution

                           Annotations:

                           • 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)
                     4. analogous

                        Annotations:

                        • structures in different species that look the same but actually developed independently; result of convergent evolution and usually due to similar envrionments
                        1. convergent evolution

                           Annotations:

                           • when unrelated organisms evolve similar characteristics due to similar environmental pressures (same selective pressure)
                     5. vestigial (structures)

                        Annotations:

                        • body structure that is reduced in form and function but may have been useful in ancestor
                  3. principle of parsimony

                     Annotations:

                     • * choose phylogenetic tree/relationships that has the least number of times the character changes states... b/c evolutionary change does not occur so frequently
                  4. clade/monophyletic group

                     Annotations:

                     • has common ancestor and ALL of its descendants and NO other unrelated taxa; use homologous traits
                     1. polyphyletic group

                        Annotations:

                        • 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
                        1. paraphyletic group

                           Annotations:

                           • 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 
                  5. sister taxa

                     Annotations:

                     • two (or more) groups that are each others closest relatives 
            2. Linnean System of Classification
               1. Kingdom
                  1. Phylum
                     1. Class
                        1. Order
                           1. Family
                              1. Genus
                                 1. Species
                  2. Domain
         2. Binomial nomenclature

            Annotations:

            • 2 part name = genus + species * genius = capital * both = italicized ex. Homo sapiens
2. Why do we study it?
   1. Threats

      Annotations:

      • - resource exploitation - conversion of land - pollution  - transport of species -global climate change * As human population increases, extinction increases.
      1. Direct value

         Annotations:

         • * drugs (antibiotics) * agricultural value
         1. Indirect value

            Annotations:

            • 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 ($)
   2. Scientific Method
      1. Observation

         Annotations:

         • * asking and developing question 
         1. Hypothesis

            Annotations:

            • * prediction; purpose = answering question; cause/effect formate * testable and falsifiable * data can support or reject hypothesis but can't prove it
            1. Predictions

               Annotations:

               • * follow the hypothesis * must be testable
               1. Hypothesis testing/experimentation

                  Annotations:

                  • * testing of predictions through observing and experimentation
               2. experiments agree with prediction = process is repeated for more info
            2. results are not consistent with the predictions = new hypothesis
         2. proximate questions

            Annotations:

            • * questions that deal with mechanism and may not require evolutionary explanations
            1. ultimate questions

               Annotations:

               • * questions having to do with evolutionary origins and functions
         3. Questions

            Annotations:

            • * seek to explain observation

Annotations:

• context dependent; increases fitness but does not work towards perfection

1. Organisms produce many more offspring than survive to reproduce themselves.
   1. Resources are limited. (not enough food for all offspring of all individuals)
   2. Most populations = relatively stable
   3. Organisms must compete for limited resources, and not all succeed.
2. 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)
   1. Some variation is heritable.
   2. Some heritable variations are may provide individuals with a competitive advantage.
      1. Individuals with advantageous variations are likely to have more offspring than those without these variations.
         1. 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
   3. Types of Variation
      1. Phenotypic

         Annotations:

         • form, function, behavior
      2. Genotypic

         Annotations:

         • genetic makeup
         1. Genes

            Annotations:

            • combo. of 2 alleles in diploid (2 copies) individuals; one allele per chromosomes 
            1. allele

               Annotations:

               • one of two or + alt. forms of a gene; arise by mutation; found at same place on a chromosome
               1. allele frequency

                  Annotations:

                  • how often an alternative form of a gene occurs
                  1. Evolution

                     Annotations:

                     • change in allele frequency in gene pool between generations
                     1. caused by
                        1. natural selection

                           Annotations:

                           • can affect distribution of allele frequencies via different types of selection
                           1. directional selection

                              Annotations:

                              • 1 extreme phenotype is favored (highest fitness); shift in the mean of population; variance (degree of difference) = same
                           2. disruptive selection

                              Annotations:

                              • both extreme phenotypes are favoured; result = polymorphism (2 or more divergent phenotypes); maintains variation 
                           3. stabilizing selection

                              Annotations:

                              • average/common phenotype(s) favored/ selection against extremes; mean of pop. stays the same = variance (degree of difference) decreases; little or no evolutionary change 
                        2. gene flow

                           Annotations:

                           • 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
                        3. genetic drift

                           Annotations:

                           • change in allele frequency due to *chance*; impact = greater in small pop.; rare alleles are more likely to be lost
                           1. bottleneck effect

                              Annotations:

                              • only few individuals survive; only they reproduce in next generation; allele frequency in next generation is diff. than previous
                           2. founder effect

                              Annotations:

                              • new pop. established by a few colonizers which have diff. allele frequencies than ancestors
                        4. mutations

                           Annotations:

                           • 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
                     2. fitness

                        Annotations:

                        • extent to which an individuals's genotype is represented in the next generation; highest reproductive success
            2. gene pool

               Annotations:

               • total # of genes of every individual in an interbreeding pop.; large = high genetic diversity; small = low genetic diversity
   4. Sources of Variation

      Annotations:

      • - mutation (random changes in DNA) - during meiosis * recombination (crossing-over) * independent assortment (of chromosomes) - fertilization (sexual reproduction; 2 combine to make 1 new genotypes)
   5. Some heritable variations may provide individuals with a competitive advantage.
3. acts on the individuals (causing differential survival and reproduction), but outcome (evolution( is seen at the population level).
4. Selective Agent

   Annotations:

   • something in environment (biotic/abiotic) that is always acting on/applying pressure on organisms/population over generations (ex. climate change, starvation)
   1. selection pressure

      Annotations:

      • intensity with which selective agent acts on a population to evolve
5. Adaptation

   Annotations:

   • * 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.