Phylogeny

The Tree of Life

Phylogenetics

• Phylogenetic trees illustrate theevolutionary 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.

PhylogenyEvolutionary treePhylogenetic treeCladogram

Are synonymous

Tree terminology

a b c d

{a,b}

{a,b,c}

{a,b,c,d} root

Taxa

nodecluster

d is the outgroup of abc

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?

Phylogeny forfour different taxa

orangutan Gorilla Pan H. sapien

Phylogenetic Systematics - Introduction

Start at the ROOT.

The root is the earliest point of time shown in this particular phylogeny…

orangutan Gorilla Pan H. sapien

roottime

Phylogenetic Systematics - Introduction

The root representsthe common ancestorto orangutans, gorilla,Pan and H. sapien.

orangutan Gorilla Pan H. sapien

roottime

Phylogenetic Systematics - Introduction

At some point this commonancestor 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 Gorilla Pan H. sapien

roottimeora

nguta

nlin

eage

lineag

e

giv

es

rise

to g

ori

lla,

pan,

H. sa

pie

n

Phylogenetic Systematics - Introduction

The common ancestral lineage to Gorilla, Panand H. sapien eventuallysplits to form the lineagethat leads to modern gorillas and a lineage that will give rise to Pan and H. sapien.

orangutan Gorilla Pan H. sapien

roottimeora

nguta

nlin

eage

lineag

e

giv

es

rise

to g

ori

lla,

pan,

H. sa

pie

n

Phylogenetic Systematics - Introduction

The common ancestral lineage to Pan and H. sapien eventually splits to form the ancestors to chimpanzees and H. sapien.

orangutan Gorilla Pan H. sapien

roottimeora

nguta

nlin

eage

lineag

e

giv

es

rise

to g

ori

lla,

pan,

H. sa

pie

n

Phylogenetic Systematics - Introduction

orangutan Gorilla Pan H. sapien

roottimeora

nguta

nlin

eage

lineag

e

giv

es

rise

to g

ori

lla,

pan,

H. sa

pie

n

In summary, therehas been three splittingevents (circles) that leadto four taxa at the tips of the tree.

What is most closely related toGorillas?

Phylogenetic Systematics - Introduction

orangutan Gorilla Pan H. sapien

roottime

Gorillas share a morerecent commonancestor with Pan and H. sapien than with organutan.

most recentcommon ancestor togorilla, Pan,H. sapien.

Phylogenetic Systematics - Introduction

orangutan Gorilla Pan H. sapien

roottime

Pan and H. Sapien arecalled sister taxa becausethey are most closely relatedto each other than to any otherspecies.

Is there a sister taxon to theGorilla? most recent

common ancestor togorilla, Pan,H. sapien.

sister taxa

Phylogenetic Systematics - Introduction

Phylogenetic Systematics - Characters and Taxa

orangutan Gorilla Pan H. sapien

time

A phylogeny is a summary of both characters and taxa.

Characters diagnose branchesof a phylogeny.

upright posture

use of tools

reducedhairiness

bipedalcomplex language

orangutan Gorilla Pan H. sapien

time

Characters that allgroups in a phylogenyshare are plesiomorhies

Characters shared but derivedare called synapomorphies

Characters shared only in one tip taxon are autapomorphies upright posture

use of tools

reducedhairiness

bipedalcomplex language

Phylogenetic Systematics - Characters and Taxa

Homo sapiens 1 1 1

Pan paniscus 1 1 1

Gorilla gorilla 1 1 0

Pongo pygmaeus 1 0 0

Hylobates 0 0 0

1 2 3

1

2

3

MRP(Matrix Representation Parsimony)

23

A

ED

C

B

(11000)

(00100)

(01000)

(00110)

(11001)

m characters

n s

peci

es

Example

C1 C2 C3 C4 C5

A 1 1 0 0 0

B 0 0 1 0 0

C 1 1 0 0 1

D 0 0 1 1 0

E 0 1 0 0 0

Input: Possible output:

(00000)

(11000)

(01000)(00100)

C2

C3

zero-root

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

Rules for writing species names

1.Latin is the language of scientific names (Latin is no longer spoken, so it does not change)

2.Italicize in print and underline when hand written

3.1st letter of the genus is CAPITALIZED & 1st letter of specific epithet is lowercase

Canis lupus = Grey wolf

Canis latrans = Coyote

Cougar?

Puma?

Panther?

Catamount?

Mountain lion? Or…

Felis concolor?

• 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

Eubacteria· Prokaryotic · True bacteria · RNA is simple · Have true cell walls· Unicellular

Archaebacteria· Prokaryotic · RNA more complex· Unicellular

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

Six KingdomsPlantae

· Eukaryotic

· Autotrophs

· Multicellular

· Photosynthetic

Animalia

· Eukaryotic

· Heterotrophs

· Multicellular