Slide 1

Reconstructing the History of Lineages Chapter 11 Tereza Jezkova School of Life Sciences, University of Nevada, Las Vegas March 2011

Slide 2

study of evolutionary relatedness among organisms (through molecular data and morphological data) PHYLOGENETICS

Slide 3

Cladograms ABCDEO taxon Common Ancestor Sister taxa

Slide 4

THE basic logic of phylogenetics: a natural taxon is a monophyletic group (all descendant taxa and their common ancestor) ABCDEO Common Ancestor monophyletic Common Ancestor monophyletic Fig. 11.4A

Slide 5

THE basic logic of phylogenetic systematics: a natural taxon is a monophyletic group (all descendant taxa and their common ancestor) ABCDEO Fig. 11.4A

Slide 6

ABCDEO Other kinds of groups are not natural: paraphyletic groups (some, but not all descendant taxa and their common ancestor) Fig. 11.4B

Slide 7

Example of a paraphyletic group: Reptiles are paraphyletic if birds are removed

Slide 8

Other kinds of groups are not natural: polyphyletic groups (descendant taxa trace back through two or more ancestors before reaching a common ancestor) Fig. 11.4C ABCDEO

Slide 9

Example of a polyphyletic group: warm- blooded animals (Mammals+Birds)

Slide 10

Characters (morphological, ecological, behavioral, molecular): traits that vary across taxa and clades primitive character state derived character state character state change

Slide 11

homologous characters (homology): characters whose traits are shared between two or more taxa or clades because of inheritance from a common ancestor

Slide 12

homologous characters (homology): characters whose traits are shared between two or more taxa or clades because of inheritance from a common ancestor pouch KOALA POSSUM

Slide 13

homoplasious characters (homoplasy): characters whose traits are shared between two or more taxa but evolved independently

Slide 14

homoplasious characters (homoplasy): characters whose traits are shared between two or more taxa but evolved independently FINS NOT USEFUL

Slide 15

character state evolution primitive character state derived character state character state change

Slide 16

characters: Primitive character state is not to have feathers birds crocodiles dinosaurs feathers Feathers are derived character state for birds

Slide 17

characters: snakes lizards dinosaurs crocodiles leglessness Primitive character state is to have legs Leglessness is a derived character state for snakes

Slide 18

primitive vs. derived characters: unique derived (one clade) shared derived (two or more clades)

Slide 19

primitive vs. derived characters: shared primitive shared-primitive for this clade

Slide 20

primitive vs. derived characters: shared-primitive for this clade shared-derived for this clade

Slide 21

primitive vs. derived characters: shared primitive characters are not useful in diagnosing a monophyletic group

Slide 22

primitive vs. derived characters: Unique derived characters are not useful in diagnosing a monophyletic group

Slide 23

primitive vs. derived characters: Only shared derived characters can be used to diagnose a monophyletic group.

Slide 24

primitive vs. derived characters: Only shared derived characters can be used to diagnose a monophyletic group.

Slide 25

Outgroups used to polarize primitive derived direction of character state changes in the ingroup Fig. 11.5 ABCDEO outgroup

Slide 26

Reconstructing trees 1.Choose the taxa ex: Vertebrates

Slide 27

Reconstructing trees 2. Determine the characters

Slide 28

Reconstructing trees 3. Determine polarity of characters

Slide 29

Reconstructing trees 4. Group taxa by shared derived characters

Slide 30

Reconstructing trees 5. Repeat with all characters work out conflicts (none in this example)

Slide 31

Reconstructing trees 6. Complete the tree

Slide 32

Reconstructing trees 6. Use parsimony principle to choose the best tree one change better (shorter tree) than two

Slide 33

OutgroupSpecies ASpecies B Species CSpecies DSpecies E EXCERCISE

Slide 34

Data Matrix CharacterOGSp ASp BSp CSp DSp E Claws011101 Chin Hair011101 Horn000101 Tail011111 Spikes000100 Digits000100 Spots000010 Tympanum100111 Lateral Fold011011 Nostril110111

Slide 35

Data Matrix CharacterOGSp ASp BSp CSp DSp E Claws011101 Chin Hair011101 Horn000101 Tail011111 Spikes000100 Digits000100 Spots000010 Tympanum100111 Lateral Fold011011 Nostril110111 ABCE CE ABCDE C D AB ABDE B

Slide 36

Molecular phylogenetics

Slide 37

EXCERCISE #Elephas_maximus_(Asian_elephant) AG-G--CT--TGA-AG--GA-AT-TC--T-TGAG-A- A-CAACAAAGCA--A-TCATTTGA-T-TTA---A- GT--AT-AGATGC-T-CAGTATA-AGA-AA-A-A- CA-AA-G-AGAGAC-ATTC-CATCC-C-A--A--- TTCCT-T-TGA-ATGT--GTTTTATG-AG-TT- TAT-CAGTCAG-A-ACA--TCA-T-AT--C-CTT- -C-AACA--AGC-AT-TTTGA---GAAA-GGC-A- GAGACAA-T-G-CAT--TAGATT--TTCTT-A-C-- -CAAA-TCCTATG-A-T

Slide 38

EXCERCISE