Phylogeny

1. Phylogeny The Tree of Life

3. Phylogenetics • Phylogenetic trees illustrate the evolutionary relationships among groups of organisms, or among a family of related nucleic acid or protein sequences

4. Each branch represents a new species which inherits many (primitive) traits from the ancestor but also has a new (derived) trait which appear for the 1st time

5. Evolutionary trees depict clades. A clade is a group of organisms that includes an ancestor and all descendents of that ancestor. Phylogeny Evolutionary tree Phylogenetic tree Cladogram Are synonymous

6. Tree terminology d is the outgroup of abc d a b c Taxa { a,b } node cluster { a,b,c } root { a,b,c,d } Nodes represent the common ancestor

10. Which tree is demonstrating maximum parsimony?

11. Phylogenetic Systematics - Introduction orangutan GorillaPanH. sapien Phylogeny for four different taxa

12. Phylogenetic Systematics - Introduction orangutan GorillaPanH. sapien Start at the ROOT. The root is the earliest point of time shown in this particular phylogeny… time root

13. Phylogenetic Systematics - Introduction orangutan Gorilla PanH. sapien The root represents the common ancestor to orangutans, gorilla, Pan and H. sapien. time root

14. Phylogenetic Systematics - Introduction orangutan GorillaPanH. sapien At some point this common ancestor split into two new species, one of which gave rise to orangutans and one which is the common ancestor to gorilla, Pan, and H. sapien. orangutan lineage lineage gives rise to gorilla, pan, H. sapien time root

15. Phylogenetic Systematics - Introduction orangutan Gorilla PanH. sapien The common ancestral lineage to Gorilla, Pan and H. sapien eventually splits to form the lineage that leads to modern gorillas and a lineage that will give rise to Pan and H. sapien. orangutan lineage lineage gives rise to gorilla, pan, H. sapien time root

16. Phylogenetic Systematics - Introduction orangutan GorillaPanH. sapien The common ancestral lineage to Pan and H. sapien eventually splits to form the ancestors to chimpanzees and H. sapien. orangutan lineage lineage gives rise to gorilla, pan, H. sapien time root

17. Phylogenetic Systematics - Introduction In summary, there has been three splitting events (circles) that lead to four taxa at the tips of the tree. What is most closely related to Gorillas? orangutan Gorilla Pan H. sapien orangutan lineage lineage gives rise to gorilla, pan, H. sapien time root

18. Phylogenetic Systematics - Introduction orangutan Gorilla PanH. sapien Gorillas share a more recent common ancestor with Pan and H. sapien than with organutan. most recent common ancestor to gorilla, Pan, H. sapien. time root

19. Phylogenetic Systematics - Introduction sister taxa Pan and H. Sapien are called sister taxa because they are most closely related to each other than to any other species. Is there a sister taxon to the Gorilla? orangutan Gorilla PanH. sapien most recent common ancestor to gorilla, Pan, H. sapien. time root

20. Phylogenetic Systematics - Characters and Taxa orangutan Gorilla Pan H. sapien bipedal A phylogeny is a summary of both characters and taxa. Characters diagnose branches of a phylogeny. complex language use of tools reduced hairiness upright posture time

21. Phylogenetic Systematics - Characters and Taxa orangutan Gorilla PanH. sapien Characters that all groups in a phylogeny share are plesiomorhies Characters shared but derived are called synapomorphies Characters shared only in one tip taxon are autapomorphies bipedal complex language use of tools reduced hairiness upright posture time

22. 1 2 3 MRP (Matrix Representation Parsimony) Homo sapiens 1 1 1 Pan paniscus 1 1 1 Gorilla gorilla 1 1 0 Pongo pygmaeus 1 0 0 Hylobates 0 0 0 3 2 1

23. zero-root (00000) (01000) (00100) E (11000) B (01000) D (00110) (00100) A C (11000) (11001) Example Input: Possible output: m characters C2 n species C3

24. monophyletictaxon includes a group of organisms descended from a single ancestor polyphyletictaxon is composed of unrelated organisms descended from more than one ancestor paraphyletictaxon, which includes an ancestor and a group of organisms descended from it

25. Classification based on physical and structural similarities • Carolus Linnaeus (1707-1778) • Created binomial nomenclature (2 word naming system) • 1st word = Genus (genera if plural) = a group of similar species • 2nd word = specific epithet = Species • Scientific name = Genus + specific epithet e.g. Homo sapiens

26. Writing Species Names • Rules for writing species names • Latin is the language of scientific names (Latin is no longer spoken, so it does not change) • Italicize in print and underline when hand written • 1st letter of the genus is CAPITALIZED & 1st letter of specific epithet is lowercase

27. Writing Species Names Canis latrans = Coyote Canis lupus = Grey wolf

28. Cougar? Puma? Panther? Catamount? Mountain lion? Or… Felis concolor?

29. Taxonomic Rankings • Domain Did • Kingdom Kinky • Phylum Phil • Class Come • Order Over • Family For • Genus Good • Species Sex

31. All Living Organisms are grouped into... 3 DOMAINS • EUBACTERIA-   true bacteria • ARCHAEA-   ancient prokaryotes        • EUCARYA-  modern eukaryotes

33. Six Kingdoms Protista ·Eukoryotic ·Autotrophs and heterotrophs ·Lacks organs systems ·Lives in moist environments ·Unicellular or multicellular Fungi ·Eukaryotic ·Heterotrophs ·Unicellular or multicellular ·Absorbs nutrients from organic material in its environment ·Unicellular or multicellular Eubacteria ·Prokaryotic ·True bacteria ·RNA is simple ·Have true cell walls ·Unicellular Archaebacteria ·Prokaryotic ·RNA more complex ·Unicellular

34. Six Kingdoms Plantae ·Eukaryotic ·Autotrophs ·Multicellular ·Photosynthetic Animalia ·Eukaryotic ·Heterotrophs ·Multicellular