Phylogenetics: Classification Notes

Phylogenetics: Classification

1. Phylogenetics : Classification of Life p pt. by Robin D. Seamon 1 HOOK VIDEO: COSMOS- “Some Things Molecules do”

2. 2 TYPES OF CELLS Prokaryotes Oldest life forms Cell wall Cell membrane cytoplasm single chromosome: circular strand of DNA Reproduction: binary fission Eukaryotes (Plants, fungi, some protists have cell wall) Cell membrane Cytoplasm DNA inside a membrane-bound nucleus Organelles to perform metabolic and reproductive processes Reproduction: asexual or sexual reproduction 2 VIDEO: How we think complex organisms evolved endosymbiosis (5:40) REVIEW

3. 3 Domains: Prokaryote: no nucleus or organelles Eukaryotes : nucleus & membrane-bound organelles VIDEO: How we think complex cells evolved (5:30) 3

4. NEW There are 3 Domains K C O F S G P RANKING SYSTEM 4

5. 5 CC video: comparative anatomy (10 min) Kingdom Archae -bacteria

6. H I S T O R Y Aristotle: (Greek philosopher 384-322 CE) classified animals based on method of reproduction 6

7. Taxonomy : group or categorize organisms Before 1700, there were multiple long names for new species with no rules in naming process Carl Linnaeus (Swedish) 1735 grouped organisms by shared physical characteristics wrote Systems Naturae 3 Kingdoms: 1. Mineral 2. Vegetable 3. Animal 7

8. 8 Binomial nomenclature Linneaus ’ 2-name system Scientific name = species name Genus species First part – genus - capitalized Second part - species identifier Both italicized or underlined

9. Today naming is regulated by Nomenclature Codes allowing names to be divided into ranks: Binomial nomenclature (genus & species) 1740’s R A N K I N G S Y S T E M 9 CC Video: #19 Taxonomy (12 min)

10. 1859 Darwin insisted classification should reflect genetic relatedness 1900 Emil Willi Henning : grouped organisms by inferred evolutionary relatedness Homologous structures; inherited from common ancestors, so were related Phylogenetic taxonomy 10

11. Cladistic system : 1960’s scientists started using DNA sequences to determine common ancestry IGNORING RANKS This new field is making changes & revisions in classification everyday. International Code of Phylogenetic Nomenclature ( PhyloCode ) is currently under development Molecular Phylogenetics C L A D E S Y S T E M 11

12. 12 Cladistics Uses derived character A feature that evolved only within a group Used to establish evolutionary relationships

13. 13 MODERN SYSTEM Three-Domain System Compare ribosomal RNA All cells have ribosomes Bacteria, Archaea, Eukarya With Six-Kingdoms as subgroups

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15. 1990’s: New Grouping based on new discoveries in bacteria metabolism Archaea Bacteria Eukaryota D O M A I N S Separated these 2 Includes Protists 15 CC Video: #35 Archaea , Bacteria, Protists (12 min)

16. Prokayotes have evolved longer & are more flexible in their biochemistry, therefore they can live in more extreme environments than eukaryotes --Many, but not all are autotrophic (make their own sugars) p hototropic organisms chemotrophic organisms Eukaryotes perform metabolism in the organelles of the cells -- All but plants are heterotrophic Chloroplasts : photosynthesis Mitochondria : cellular respiration PROKARYOTES EUKARYOTES 16 REVIEW

17. 17 REPRODUCTION: binary fission TRANSPORT: through the membrane Archaea & Bacteria

18. 18 Archaea - ancient group of prokaryotic organisms that are still present today -- Extremphiles - types of archaea that live in very extreme places Some examples: Halophile : live in extreme salty conditions Thermophile : live in extremely hot conditions Methanogen : metabolize such that they use acidic conditions (sulfur) and release methane PROKARYOTE: No nucleus or organelles DNA in cytoplasm Binary fission Kingdom Archaebacteria

19. 19 Hiller Lake, Australia Halophilic archaea & bacteria live in this salty lake BACK

20. Under-ocean hot vent 20 Yellowstone hot vent, Wyoming thermophilic archaea & bacteria live in this hot vent BACK

21. 21 Methanogenic archaea BACK

22. 22 PROKARYOTE: No nucleus or organelles DNA in cytoplasm Binary fission Bacteria - ancient group of prokaryotes that are still present today Kingdom Eubacteria

23. 23 Bacteria in our world: Diseases Nitrogen-fixing Digestion Make vitamins Food production Diseases Caused by Bacteria Disease Transmission Symptoms Treatment Strep throat (Streptococcus) Inhale or ingest through mouth Fever, sore throat, swollen neck glands Antibiotic Tuberculosis Inhale Fatigue, fever, night sweats, cough, weight loss, chest pain Antibiotic Tetanus Puncture wound Stiff jaw, muscle spasms, paralysis Open and clean wound, antibiotic; give antitoxin Lyme disease Bite of infected tick Rash at site of bite, chills, body aches, joint swelling Antibiotic Dental cavities (caries) Bacteria in mouth Destruction of tooth enamel, toothache Remove and fill the destroyed area of tooth Diptheria Inhale or close contact Sore throat, fever, heart or breathing failure Vaccination to prevent, antibiotics

24. 24 Eukaryota - group of organisms whose cells contain a nucleus and membrane-bound organelles ALL THE REST 4 Kingdoms

25. P hylogenetic tree 25

26. PROKARYOTES EUKARYOTES Archaebacteria (Archaea) Eubacteria (Bacteria) Kingdom Protista- (microscopic organisms) Kingdom Plantae- Kingdom Fungi Kingdom Animalia 26 DOMAIN BACTERIA DOMAIN ARCHAEA DOMAIN BACTERIA REVIEW 6 Kingdoms

27. PLANT KINGDOM specific organelles ( autotrophs ) Large central vacuole No lysosome, but the recycling can happen in the vacuoles Plastids Chloroplasts Chromoplasts Leukoplasts ANIMAL KINGDOM specific organelles ( heterotrophs ) Smaller vacuoles lysosomes FUNGI KINGDOM closer related to animal than plant ( heterotrophic ) No lysosome, but the recycling can happen in the vacuoles PROTIST - microscopic organisms of a huge variety; some more related to plant metabolism ( autotrophic ), others more related to heterotrophs (fungi/animal ) MICRO MACRO COMPARISONS of EUKARYOTES 27 REVIEW ( have nucleus & organelles)

28. Protists - eukaryotic microscopic organisms; Kingdom Protista Most are single-celled, though some are multi-celled; some are colonial Some are more related to plant metabolism (autotrophic), others more related to heterotrophs (fungi/animal) Asexual reproduction: mitosis Transport: through membrane KINGDOM PROTISTA

29. H I S T O R Y O F C L A S S I F I C A T I O N 1735 Linnaeus 1866 Haeckel 1925 Chatton 1938 Copeland 1969 Whittaker 1990 Woesse 1998 Cavalier-Smith 2 Kingdoms 3 Kingdoms 2 Empires 4 Kingdoms 5 Kingdoms 3 Domains 6 Kingdoms Mineral Prokaryote Monera Monera Bacteria Bacteria Protist Protist Protist Archaea Protist Eukaryote Eukaryote Chromista Vegetable Plant Plant Plant Plant Fungi Fungi Animal Animal Animal Animal Animal To apply Darwin to Microscopic organisms To show having nucleus or not To show evolutionary history of life 29

30. 1969 Whittaker: 5 Kingdoms Protists Monera Plants Animals Fungi Prokaryotes: Eubacteria & Archeobacteria Eukaryotes Absorb & photosynthesize Asexual Reproduction Absorb & photosynthesize Asexual & Sexual Reproduction P hotosynthesize Asexual & Sexual Reproduction Non-mobile Ingest Asexual & Sexual Reproduction mobile Absorb Spores: asexual Reproduction Non-mobile 30

31. 1990 Woese : 3 Domains Eukaryotes Plants Animals Fungi Protists P hotosynthesize Asexual & Sexual Reproduction Non-mobile Absorb Spores: asexual Reproduction Non-mobile Archaea C Bacteria Monera Monera Absorb & photosynethsize A erobic respiration Asexual & Sexual Reproduction Various metabolism: photosynthesis, fermentation, Methanogenesis respiration Asexual Reproduction Various metabolism: photosynthesis, fermentation, Anaerobic & aerobic respiration Asexual Reproduction Ingest Asexual & Sexual Reproduction mobile NO NUCLEUS NO NUCLEUS NUCLEUS DOMAIN DOMAIN DOMAIN 31 NOTES LAB

32. 1990 Woese : 3 Domains Eukaryotes Plants Animals Fungi Protists P hotosynthesize Asexual & Sexual Reproduction Non-mobile Absorb Spores: Asexual Reproduction Non-mobile Archaea C Bacteria Monera Monera Absorb & photosynethsize A erobic respiration Asexual & Sexual Reproduction Various metabolism: photosynthesis, fermentation, Methanogenesis respiration Asexual Reproduction Various metabolism: photosynthesis, fermentation, Anaerobic & aerobic respiration Asexual Reproduction Ingest Asexual & Sexual Reproduction mobile NO NUCLEUS NO NUCLEUS NUCLEUS DOMAIN DOMAIN DOMAIN 32

33. Bacteria Archaea Plants Protist Animal Fungi Tree of life Web Project Tolweb.org 33

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