1. Phylogeny and the Tree of Life Chapter 26

2. Systematics: Discipline focused on classification of organisms

3. Taxonomy: naming organisms. Linnaeus - hierarchy of increasingly inclusive categories. Taxon: Taxonomic unit at any level of hierarchy Species Panthera pardus Panthera Genus Family Felidae Carnivora Order Mammalia Class Phylum Chordata Kingdom Animalia Eukarya Domain

4. Binomial nomenclature: genus & specific epithet. Homo sapiens

5. Phylogeny: evolutionary history of a group of species. Phylogenetic tree: evolutionary relationship between species represented in a branching diagram. Drosophila Lancelet Fish Amphibian Bird Human Rat Mouse

6. Phylogenetic tree represents a hypothesis about evolutionary relationships relationships are represented by a series of dichotomies (branch points) sister taxa: group of organisms that share an immediate common ancestor (branch point) branch points within the tree represents the last common ancestor of all taxa in the tree

7. Polytomy: branch point with more than 2 descendant groups.

8. Limitations of phylogenetic tree: Does not tell us when a species arose How much genetic change occurred in each evolutionary step May not tell us the exact ancestral species

9. Application of phylogeny: Agriculture and plant breeding Investigation of poaching Forensic and bioterrorism

10. Homology: similarities due to shared ancestry

11. Analogy: similarity due to convergent evolution Homoplasies: Analogous structures; similarities arose independently

12. What is the relationship between  wings of birds,  wings of bats and  forelimbs of cats?

13. Morphological and molecular homologies: Organisms that share very similar morphologies or similar DNA sequences are likely to be more closely related than organisms with vastly different structures or sequences.

14. Molecular systematics: Using molecular data to determine evolutionary relationships.

15.  Genes: sequences of thousands of nucleotides.  If genes in two organisms share many portions of their nucleotide sequences, it is highly likely that the genes are homologous. 1 2 1 2 Deletion Insertion 1 2 1 2

16. Cladistics: Systematics using common ancestry as the primary criterion. Clades: groups of species that have been sorted according to common ancestry.  Like taxa clades reside within larger clades.

17. Shared ancestral character: character that originated in an ancestor of the group Shared derived character: evolutionary novelty unique to a particular group.

18. Outgroup: species or a group of species from an evolutionary lineage that is known to have diverged before the lineage that is being studied. Ingroup: species included in the group being studied.

19. Outgroups and ingroups are determined on the basis of  morphology,  paleontology,  embryonic development,  gene sequences To determine various branch points in a phylogenetic tree we compare members of ingroups to each other and to members of outgroups as well.

20. Using derived character to infer phylogeny

21. Hair Amniotic (shelled) egg Four walking legs Hinged jaws Vertebral column (backbone) Character table CHARACTERS TAXA Lancelet (outgroup) LampreyTunaSalamander TurtleLeopard

22. Turtle Leopard Hair Amniotic egg Four walking legs Hinged jaws Vertebral column Salamander Tuna Lamprey Lancelet (outgroup) Cladogram

23. Principle of maximum parsimony: first investigate the simplest explanation that is consistent with the facts  Occam’s razor: shaving away unnecessary complications – minimalist problem solving approach. Maximum likelihood: the phylogenetic tree that reflects the simplest explanation of DNA change

24. Gene families and gene duplication: Gene families: groups of related genes within an organisms genome resulting from repeated duplication. Orthologous genes: homologous genes found in different species due to speciation. Paralogous genes: more than one copy of a gene in the same genome

25. Ancestral gene Speciation Orthologous genes Ancestral gene Gene duplication Paralogous genes

26. Three domain system: All organisms are classified into three domains –  Bacteria: currently known prokaryotes  Archaea: very diverse group of prokaryotes, variety of habitats including extreme ones  Eukarya: All organisms that have cells with true nuclei (single-celled or multicellular)

27. Eukarya

28. CharacteristicsBacteriaArcheaEukarya Nuclear envelopeabsent present Membrane bound organelles absent present Circular chromosomes present absent Peptidoglycans in cell walls presentabsent Sensitivity to antibiotics like streptomycin, chloramphenicol yesno Growth at exterme conditions (temperature, salt) no most species no

29. Horizontal gene transfer: genes are transferred through transposable elements, viral infection, plasmids. According to some scientists – to represent extensive horizontal gene transfer in early organisms, a ring is a better representation than a dichotomous tree Archaea Bacteria Eukarya