The Tree of Life Phylogeny

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

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

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

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

Parsimony The principle of parsimony implies that we should prefer the phylogeny that requires the fewest evolutionary changes.

Which tree is demonstrating maximum parsimony?

Phylogenetic Systematics - Introduction orangutan Gorilla Pan H. sapien Phylogeny for four different taxa

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

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

Phylogenetic Systematics - Introduction orangutan Gorilla Pan H. 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 rise to gorilla, lineage gives pan, H. sapien time root

Phylogenetic Systematics - Introduction orangutan Gorilla Pan H. 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 rise to gorilla, lineage gives pan, H. sapien time root

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

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 rise to gorilla, lineage gives pan, H. sapien time root

Phylogenetic Systematics - Introduction orangutan Gorilla Pan H. 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

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 Pan H. sapien most recent common ancestor to gorilla, Pan, H. sapien. time root

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

Phylogenetic Systematics - Characters and Taxa orangutan Gorilla Pan H. 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

1 2 3 MRP 3 2 1 (Matrix Representation Parsimony) Homo sapiens 1 1 1 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

Example A 1 B C D E zero-root m characters C1 C2 C3 C4 C5 A E D C B C2 Input: Possible output: zero-root m characters C1 C2 C3 C4 C5 A 1 B C D E (00000) (11000) (01000) (00100) A E D C B C2 n species C3 (11000) (00100) (01000) (00110) (11001)

monophyletic taxon includes a group of organisms descended from a single ancestor polyphyletic taxon is composed of unrelated organisms descended from more than one ancestor paraphyletic taxon, which includes an ancestor and a group of organisms descended from it

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

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

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

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

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

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

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

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