Reconstructing the History of Lineages

Chapter 11

Tereza JezkovaSchool of Life Sciences,

University of Nevada, Las Vegas

March 2011

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

PHYLOGENETICS

Cladograms

ABCDEOtaxon

Common Ancestor

Sister taxa

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

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

ABCDEO

Fig. 11.4A

ABCDEO

Other kinds of groups are not natural:paraphyletic groups (some, but not all

descendant taxa and their common ancestor)

Fig. 11.4B

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

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

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

Characters (morphological, ecological, behavioral, molecular): traits that vary across taxa and clades

primitive character state

derived character state

character state change

homologous characters (homology): characters whose traits are shared between two

or more taxa or clades because of inheritance from a common ancestor

homologous characters (homology): characters whose traits are shared between two

or more taxa or clades because of inheritance from a common ancestor

pouch

pouchpouch

KOALA

POSSUM

homoplasious characters (homoplasy): characters whose traits are shared between two

or more taxa but evolved independently

homoplasious characters (homoplasy): characters whose traits are shared between two

or more taxa but evolved independently

FINS

FINS

FINSFINS

NOT USEFUL

character state evolution

primitive character state

derived character state

character state change

characters:

Primitive character state is not to have feathers

birds crocodiles

dinosaurs

feathersFeathers are derived character state for birds

characters:

snakes lizards dinosaurs crocodiles

leglessness

Primitive character state is to have legs

Leglessness is a derived character state for snakes

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

primitive vs. derived characters:shared primitive

shared-primitive for this clade

primitive vs. derived characters:

shared-primitive for this clade

shared-derived for this clade

primitive vs. derived characters:shared primitive characters are not useful in

diagnosing a monophyletic group

primitive vs. derived characters:Unique derived characters are not useful in

diagnosing a monophyletic group

primitive vs. derived characters:Only shared derived characters can be used to

diagnose a monophyletic group.

primitive vs. derived characters:Only shared derived characters can be used to

diagnose a monophyletic group.

Outgroupsused to polarize primitive derived

direction of character state changes in the ingroup

Fig. 11.5

ABCDEO

outgroup

Reconstructing trees1.Choose the taxa

ex: Vertebrates

Reconstructing trees2. Determine the characters

Reconstructing trees3. Determine polarity of characters

Reconstructing trees4. Group taxa by shared derived characters

Reconstructing trees5. Repeat with all characters

work out conflicts (none in this example)

Reconstructing trees6. Complete the tree

Reconstructing trees6. Use parsimony principle to choose the best tree

one change better (shorter tree) than two

Outgroup Species A Species B

Species C Species D Species E

EXCERCISE

Data MatrixCharacter OG Sp A Sp B Sp C Sp D Sp E

Claws 0 1 1 1 0 1

Chin Hair 0 1 1 1 0 1

Horn 0 0 0 1 0 1

Tail 0 1 1 1 1 1

Spikes 0 0 0 1 0 0

Digits 0 0 0 1 0 0

Spots 0 0 0 0 1 0

Tympanum 1 0 0 1 1 1

Lateral Fold 0 1 1 0 1 1

Nostril 1 1 0 1 1 1

Data MatrixCharacter OG Sp A Sp B Sp C Sp D Sp E

Claws 0 1 1 1 0 1

Chin Hair 0 1 1 1 0 1

Horn 0 0 0 1 0 1

Tail 0 1 1 1 1 1

Spikes 0 0 0 1 0 0

Digits 0 0 0 1 0 0

Spots 0 0 0 0 1 0

Tympanum 1 0 0 1 1 1

Lateral Fold 0 1 1 0 1 1

Nostril 1 1 0 1 1 1

ABCE

ABCE

CE

ABCDE

C

C

D

AB

ABDE

B

Molecular phylogenetics

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--T—CA-T-AT--C-CTT--C-AACA--AGC-AT-TTTGA---GAAA-GGC-A-GAGACAA-T-G-CAT--TAGATT--TTCTT-A-C---CAAA-TCCTATG-A-T

EXCERCISE