Understanding phylogenetic trees 3 class exercises

Phylogeny)

Understanding phylogenetic trees 3 class exercises

Class exercise – interpreting phylogenetic trees

Which of the trees on the right is/are NOT the same as the tree on the left?

Phylogenetic trees which depict the same relationships are said to have the same topology, regardless of how they are drawn

Class exercise – interpreting phylogenetic trees

What is the most recent common ancestor of: 1) F and G 2) C and E 3) A and B

time past present

1

2

3

Phylogeny!is!o%en!presented!as!a!diagram!(a)phylogene,c)tree).!

What)is)phylogeny?)

1. Haeckel, 1866 2. Wikipedia 3. APweb 4. Gomez, 2010 5. Cameron, 2000

1

2

3

4

5

Node

H G F E D C B A Terminal branch

Internal branch (internode) = ancestral species

Root = common ancestor

Group 1 Group 2 Outgroup Ingroup

Ingroup = the lineage under consideration. Outgroup = a lineage that is not part of the ingroup. Sister group = the lineage that is most closely related to the lineage under consideration.

time

Interpre,ng)phylogene,c)trees)

Tip = extant species

Sister relationships are reciprocal; sister groups are each other’s closest relatives (share a more recent common ancestor with each other than with any other group).

Topology = the branching pattern of a phylogenetic tree

Interpre,ng)phylogene,c)trees)

H G F E D C B A

Monophyletic group (or clade) = a single lineage; a group composed of a common ancestor and all of its descendants.

mono = one, phylum = tribe

Interpre,ng)phylogene,c)trees)

H G F E D C B A

Interpre,ng)phylogene,c)trees)

Paraphyletic group = a group containing a common ancestor and some, but not all, of its descendants.

para = near, �not quite�, phylum = tribe

H G F E D C B A

Interpre,ng)phylogene,c)trees)

Polyphyletic group = multiple lineages; a group that does not contain the common ancestor of its members.

poly = many, phylum = tribe

Phylogenetic classification = a hierarchical ordering of taxa, according to phylogenetic relationships. Our goal is to recognize and name only monophyletic groups, to achieve nested sets that are hierarchically organized.

Phylogene,c)classifica,on)

The use of phylogeny to produce the classification. Often referred to as cladistics.

Chordates)Amniotes)

Mammals)

evolu5on.berkeley.edu!

Phylogene,c)classifica,on)

Homeothermia!(animals!that!are!“warm!blooded”):!mammals!and!birds!Homeothermia:!an!example!of!a!polyphyle,c)group!

biology.unm.edu!

Phylogene,c)classifica,on)

Rep5les:!flightless!animals!with!kera5n!scales! Birds:!flying!animals!with!kera5n!feathers!Rep5les,!dinosaurs:!examples!of!a!paraphyle,c!group!

xkcd.com!

Phylogene,c)classifica,on)

Why)no)polyphyle,c)groups?)–  Natural!classifica5on!should!reflect!evolu5onary!rela5onship!

Why)no)paraphyle,c)groups?)–  Taxa!at!same!rank!should!not!contain!one!another!

–  All!members!of!a!group!should!have!their!closest!rela5ve!also!belong!to!that!group!

Recognizing!only!monophyle5c!groups!allows!for!greater!predic5ve!power!

Before: Lycopersicon esculentum Now: Solanum lycopersicum

(Spooner et al., 1993)!

Taxonomic)revision)

tomato!

•  You have the last question from the midterm exam of spring quarter, 2009.

•  Take 15 minutes to work on it with your group.

•  Trade your paper with another group when you’re done.

Class)exercise)–)phylogene,c)classifica,on)

Phylogenetic inference = the process by which the branching pattern of evolutionary relationship (phylogeny) is estimated. A phylogenetic tree is a hypothesis; it is subject to re-evaluation upon the discovery of new evidence.

How do we infer phylogeny?

Reconstruc,ng)phylogeny)

�The characters which naturalists consider as showing true affinity between any two or more species, are those which have been inherited from a common parent, all true classification being genealogical.��Charles Darwin, On the Origin of Species (1859)

From comparable similarities (characters); shared traits between species.

Character/trait = a variable characteristic of an organism, or group of organisms.

Character states = the different forms a character can take.

Reconstruc,ng)phylogeny)

Charles!Darwin!photo!by!Leonard!Darwin,!1874.!From!Woodall,!1884:!Transac5ons!of!the!Shropshire!Archaeological!Society!

Eg.!Body)covering;!flower)color)

scales!

feathe

rs!

white!

yellow!

Homology = homologous characters are those inherited from a common ancestor.

Reconstruc,ng)phylogeny:)characters)

The states of homologous characters are comparable with one another, and may provide insight into evolutionary relationship.

Analogy = analogous characters have multiple, independent evolutionary origins.

Analogous characters do not provide useful indicators of evolutionary relationship.

Dial,!1992!

Synapomorphy = shared, derived character. (from Greek: syn—together (shared) + apo—away + morph—form) A derived state shared by two or more lineages, which was present in their common ancestor, and is not found in other organisms.

Synapomorphies diagnose monophyletic groups.

Reconstruc,ng)phylogeny:)characters)

Ovules!enclosed!in!carpels:!synapomorphy!defining!angiosperms!

Symplesiomorphy = shared, ancestral character. (from Greek: syn—together (shared) + plesio—near + morph—form) An ancestral state shared by two or more lineages, which was present in their common ancestor, but is not found in all of its descendants. Symplesiomorphies diagnose paraphyletic groups.

Reconstruc,ng)phylogeny:)characters)

Two!seed!leaves:!!Symplesiomorphy!defining!“dicots”!

One!seed!leaf:!!Synapomorphy!defining!monocots!

Homoplasy = convergent character, analogy. (from Greek: homo—same + plassein—to mold) A state shared by two or more lineages which is not due to common ancestry. Convergent evolution, or parallelism. Convergent characters diagnose polyphyletic groups.

Reconstruc,ng)phylogeny:)characters)

“Amen5ferae”:!defined!by!homoplas,c)characters)associated!with!wind!pollina5on!

Reconstruc,ng)phylogeny:)characters)

Polarity!=!direc5on!of!evolu5onary!change.!

Outgroup)comparison)Character!states!occurring!in!the!outgroup!represent!the!ancestral!condi5on!in!the!ingroup.!

The!preferred!outgroup!for!determining!polarity!is!the!closest!lineage!to!the!ingroup:!the!sister!group.!

Many!parts,!unfused!=!ancestral!

out 1 2 3

4 steps

acb

b

out 1 23

5 steps

aa cc

b

out 1 32

6 steps

aa ccb

b

Parsimony = the principle that the best explanation is the simplest one.

Trait)a) Trait)b) Trait)c)

Taxon!1! Absent!(0)! Present!(1)! Absent!(0)!

Taxon!2! Present!(1)! Absent!(0)! Present!(1)!

Taxon!3! Present!(1)! Present!(1)! Present!(1)!

Outgroup! Absent!(0)! Absent!(0)! Absent!(0)!

Most parsimonious tree a,!c!=!synapomorphies!for!2+3!b!=!homoplasy!(convergence)!

Reconstruc,ng)phylogeny:)in)prac,ce)

In practice: many taxa, many characters Computationally intensive

Felsenstein,!1978!

Reconstruc,ng)phylogeny:)in)prac,ce)

Real example with DNA sequence data (nucleotide characters).

Reconstruc,ng)phylogeny:)in)prac,ce)

•  You have DNA sequences from three taxa: A, B, and C, and an outgroup:

A: TATGTCCACACGGCGG! B: TTTGTTCATACAGCGG! C: TATGTTCATATAGTGG! OUT:!TATCTCCACATGGCTG!

•  Working with your group, infer the most

parsimonious phylogenetic tree for these taxa from these sequences.

Class)exercise)–)inferring)phylogeny)

Class)exercise)–)inferring)phylogeny)

A B C B C C B A A

A: TATGTCCACACGGCGG! B: TTTGTTCATACAGCGG! C: TATGTTCATATAGTGG!

OUT:!TATCTCCACATGGCTG!

7!steps! 10!steps! 9!steps!

Most)parsimonious)tree)

Next)week:)plant)morphology)