1. Phylogenetic Trees: Common Ancestry and Divergence 1B1: Organisms share many conserved core processes and features that evolved and are widely distributed among organisms today. 1B2: Phylogenetic tress and cladograms are graphical representations (models) of evolutionary history that can be tested. 2D2: Homeostatic mechanisms reflect both common ancestry and divergence due to adaptations in different environments

2. Shared Characteristics of Life Three main domains: Bacteria – prokaryotic – single celled, no nucleus Archaea – prokaryotic – single celled, no nucleus – closer relation to eukaryotes – determined by looking at the rRNA (ribosomal RNA) Eukaryotes – contain a nucleus and other membrane bound organelles All three domains share: Same type of genetic material: DNA and or RNA Central Dogma: DNA  mRNA  chain of amino acids (aka protein) Metabolic pathways: ATP is the energy coinage for all three domains Cellular Respiration: Glycolysis, Kreb Cycle, Oxidative Phosphorylation (aka Electron Transport Chain)

3. Shared Characteristics of Eukaryotes Endomembranes: Nucleus: contains the genetic material (DNA) Endoplasmic Reticulum: transports proteins to Golgi Complex Golgi Complex: packages, sorts, transports proteins Organelles: Mitochondria Ribosomes Chloroplast (only in plant cells) Linear Chromosomes

4. Phylogeny The evolutionary history of a species or group of species To construct a phylogeny biologists use systematics A discipline focused on classifying organisms and determining their evolutionary relationships Systematists use data ranging from fossils, molecules (proteins), and genes (DNA, mDNA, rRNA) to infer evolutionary relationships Info is used to construct a tree of life Tree continues to be refined as additions information becomes available Phylogenetic Tree: a branching diagram that shows the evolutionary history of a group of organisms; represents a hypothesis

5. Terminology of a Phylogenetic Tree Branch point: represents the divergence of two evolutionary lineages from a common ancestor Taxon (plural, taxa): think of it as describing the species level on a phylogenetic tree Sister taxa: group of organisms that share an immediate common ancestor and hence are each other’s closest relatives Rooted: brand point represents the last common ancestor of all the taxa in the three Polytomy: branch point from which more than two descendant group emerge; indicates the evolutionary relationships among the descendant taxa are not yet clear Clade: is a group of organisms that consists of a common ancestor and all its lineal descendants

6. How to read a phylogenetic tree

7. What We Can and Cannot Learn from Phylogenetic Trees Sequence of branching in a tree does not indicate actual ages of the particular species No assumptions should be made about when particular species evolved or how much genetic change occurred in each evolutionary lineage Cannot assume a taxon on a phylogenetic tree evolved from the taxon next to it  we can only infer sister taxa shared a common ancestor

8. Morphological and Molecular Homologies Similarities due to shared ancestry are called homologies Two main types: Morphological homology – similar structures due to a common ancestor Genetic homology – similar DNA sequences due to a common ancestor

9. Partner Share Will the morphological homologies match the genetic homologies? In other words – if there is a structural change will there be a genetic change and vice versa? If the morphological homology and genetic homology do not match then which one is more reliable when constructing a phylogenetic tree?

10. Sorting Homology from Analogy Morphological divergences between related species can be great and their genetic divergences small (or vice versa) Analogy – similarity due to convergent evolution Convergent evolution – occurs when similar environmental pressures and natural selection produce similar (analogous) adaptations in organisms from different evolutionary lineages Ex: Bat wing is analogous, not homologous, to a bird’s wing Both organisms evolved wings; however, they came from different common ancestors

11. Pair Share Explain the difference between homology and analogy. Explain why distinguishing between the two is critical when constructing an Phylogenetic Tree

12. Shared characters are used to construct phylogenetic trees In constructing a tree the first step is to distinguish homologous features from analogous features Second biologist place species into groups of clades Clade: an ancestor species and all of its descendants Monophyletic – consists of an ancestral species and ALL of its descendants Paraphyletic – consists of an ancestral species and SOME of its descendants Polyphyletic – consists of taxa with more than one ancestral species

14. Shared Ancestral and Shared Derived Characters Shared ancestral character – characteristic that is shared by ALL the ancestors in the taxon including the shared common ancestor Shared derived character – characteristic that is not shared by the common ancestor but appeared later in the evolutionary sequence

15. Inferring Phylogenies Using Derived Characters Outgroup: a species from and evolutionary lineage that is known to have diverged before the lineage being studied Ingroup: a group of species whose evolutionary relationship we seek to determine By comparing members of the ingroup to each other and to the outgroup, we can determine which were derived at the various branch points

16. Let’s Practice With the person sitting next to you use the data table to construct a phylogenetic tree

18. 2D2: Homeostatic mechanisms reflect both common ancestry and divergence due to adaptations in different environments Homeostatic mechanisms: Osmoregulation: process by which organisms control solute concentrations and balance water gain and loss For physiological systems to function properly, the relative concentrations of water and solutes must be kept within fairly narrow limits Ions such as sodium and calcium must be maintained at concentrations that permit normal activity of muscles, neurons, and other body cells Excretion: breakdown of nitrogenous molecules releases ammonia, a very toxic compound, the process of eliminating the nitrogenous waste Thermoregulation Digestive Mechanisms Circulatory