Phylogeny and the Tree of Life (Principles of classification)

All life is interconnected by descent

Bacterium Amoeba Pine tree Rattlesnake Humans

How to determine the pattern of descent?

Systematics - field of biology dealing with

diversity and evolutionary history of life
Includes Taxonomy: DINC
Description Identification Nomenclature Classification

Goal:
Determine Evolutionary History (Phylogeny) of Life

Description
= assign features Character = a feature (e.g., petal color) Character states = two or more forms of a character (e.g., red, white).

Identification
= associate an unknown with a known How? One way: Taxonomic Key, e.g.,
Tree . Species A Leaves simple . Species B Leaves pinnate ....... Species C Herb Flowers red . Species D Flowers white ... Species E

Nomenclature
Naming, according to a formal system. Binomial: Species are two names (Linnaeus): E.g., Homo sapiens Homo = genus name sapiens = specific epithet Homo sapiens = species name

Nomenclature
Hierarchical Ranks: Domain Kingdom Phylum Class Order Family Genus Species

Classification
Placing objects, e.g., life, into some type of order. Taxon = a taxonomic group (plural = taxa).

How to classify life

Phenetic classification
Based on overall similarity

Those organisms most similar are classified more closely together.

Problem with phenetic classification:

Can be arbitrary, e.g., classify these:

Phylogenetic classification
Based on known (inferred) evolutionary history. Advantage:
Classification reflects pattern of evolution Classification not ambiguous

lineage or clade TIME

Cladogram or Phylogenetic Tree

= representation of the history of life

TAXA

lineage or clade TIME

Cladogram or Phylogenetic Tree

TAXA

TIME speciation

Cladogram or Phylogenetic Tree

Ingroup group studied

Outgroup group not part of ingroup, used to root tree

Fig. 26-5

Branch point (node)

Taxon A
Taxon B Sister taxa

Taxon C
ANCESTRAL LINEAGE Taxon D

Taxon E
Taxon F Common ancestor of taxa AF Polytomy

Apomorphy (derived trait)

= a new, derived feature E.g., for this evolutionary transformation scales --------> feathers (ancestral feature) (derived feature)

Presence of feathers is an apomorphy for birds.

Taxa are grouped by apomorphies

Apomorphies are the result of evolution. Taxa sharing apomorphies underwent same evolutionary history should be grouped together.

Principle of Parsimony
That cladogram (tree) having the fewest number of steps (evolutionary changes) is the one accepted. Okhams razor: the simplest explanation, with fewest number of ad hoc hypotheses, is accepted.

Other methods of phylogeny reconstruction:

Maximum Likelihood or Bayesian analysis
Uses probabilities Advantage: can use evolutionary models.

TAXA

E
apomorphy (for Taxon D)

apomorphies (for Taxa B & C) TIME

apomorphy (for Taxa B,C,D,E,F)

Cladogram or Phylogenetic Tree

Sequentially group taxa by shared derived character states (apomorphies)

TAXA Leopard

Lancelet (outgroup)
Lamprey

Tuna

Vertebral column (backbone) Hinged jaws Four walking legs Amniotic (shelled) egg Hair (a) Character table

0 0 0 0 0

1 0 0 0 0

1 1 0 0 0

1 1 1 0 0

1 1 1 1 0

1 1 1

Tuna Vertebral column Salamander Hinged jaws Four walking legs Turtle

1 Amniotic egg 1 (b) Phylogenetic tree Hair Leopard

Fig. 26-11

DNA sequence data most important type of data 1

Deletion

Insertion
Fig. 26-8a

DNA sequence data - alignment 3

Fig. 26-8b

Each nucleotide position = Character Character states = specific nucleotide

Homology
Similarity resulting from common ancestry.
E.g., the forelimb bones of a bird, bat, and cat.

Homoplasy (analogy)
Similarity not due to common ancestry
Reversal loss of new (apomorphic) feature, resembles ancestral (old) feature. Convergence (parallelism) gain of new, similar features independently.

Convergent evolution: spines of cacti & euphorbs

Cactus

Euphorb

Convergent evolution: spines of cacti & euphorbs

euphorb spines

cactus spines

Leg-less lizards
Both examples of reversal within Tetrapods: loss of a derived feature forelimbs. Example of convergence relative to one another! Independently evolved.

Snake
snakes legged lizards leg-less lizards

*
*= loss of legs

gain of legs (Tetrapods)

Convergent evolution: wings of some animals evolved independently

Fig. 26-7

Convergent evolution: Australian mole and N. Am. mole

Gene Duplication can occur!

Ancestral gene

Ancestral species Speciation with divergence of gene

Species A

Orthologous genes

Species B

(a) Orthologous genes

Orthology genes homologous

Species A Gene duplication and divergence

Paralogous genes Species A after many generations (b) Paralogous genes

Fig. 26-18

Paralogy genes not homologous

Common ancestry
TAXA

TIME common ancestor (of taxon D, E, & F) common ancestor (of taxon A & taxa B-F)

Cladogram or Phylogenetic Tree

Monophyletic Group
a group consisting of:
a common ancestor + all descendents of that common ancestor

TAXA

D
monophyletic group

TIME common ancestor (of taxon D, E, & F) common ancestor (of taxon A & taxa B-F)

Cladogram or Phylogenetic Tree

TAXA

D
monophyletic group

TIME common ancestor (of taxon D, E, & F) common ancestor (of taxon A & taxa B-F)

Cladogram or Phylogenetic Tree

TAXA

D
monophyletic group

TIME common ancestor (of taxon D, E, & F) common ancestor (of taxon A & taxa B-F)

Cladogram or Phylogenetic Tree

TAXA

D
monophyletic group

TIME common ancestor (of taxon D, E, & F) common ancestor (of taxon A & taxa B-F)

Cladogram or Phylogenetic Tree

TAXA

D
monophyletic group

TIME common ancestor (of taxon D, E, & F) common ancestor (of taxon A & taxa B-F)

Cladogram or Phylogenetic Tree

TAXA

TIME speciation

Cladogram or Phylogenetic Tree

TAXA

C A

B B

F C

E D

D E

A F

TIME speciation

Cladogram or Phylogenetic Tree Cladograms can be flipped at nodes, show same relationships

Fig. 26-13

One can date divergence times with molecular clock and fossils
Drosophila

Lancelet

Zebrafish

Frog

Chicken

Human

Mouse
PALEOZOIC 542 251 MESOZOIC CENOZOIC 65.5 Present

Millions of years ago

Relationship
= recency of common ancestry i.e., taxa sharing a common ancestor more recent in time are more closely related than those sharing common ancestors more distant in time.

Example:
Are fish more closely related to sharks or to humans?

Shark

Fish

Humans

TIME

Shark

Fish

Humans

TIME common ancestor of Fish and Humans

common ancestor of Sharks, Fish, and Humans

Vertebrata Osteichthyes Shark Fish Humans

TIME

monophyletic group common ancestor of Fish and Humans

common ancestor of Sharks, Fish, and Humans

Example:
Are crocodyles more closely related to lizards or to birds?

Turtles

Lizards & Snakes

Crocodyles

Birds

"Reptilia"
Turtles Lizards & Snakes Crocodyles Birds

Paraphyletic group
Consist of common ancestor but not all descendents Paraphyletic groups are unnatural, distort evolutionary history, and should not be recognized.

"Reptilia"
Turtles Lizards & Snakes Crocodyles Birds

Reptilia here paraphyletic

"Reptilia"
Turtles Lizards & Snakes Crocodyles Birds

Re-defined Reptilia monophyletic

Reptilia
Turtles Lizards & Snakes Crocodyles Birds

Reptilia
Turtles Lizards & Snakes Dinosaurs Crocodyles Birds

Importance of a name: Did humans evolve from apes?

Orangatan Gorilla

Chimpanzees Humans

Pongidae Hominidae Great Apes Orangatan Gorilla Chimpanzees Humans

Pongidae Pongidaeor Hominidae Great Apes

Orangatan Gorilla Chimpanzees Humans

Pongidae or Hominidae
Orangatan Gorilla Chimpanzees Humans

Pongidae or Hominidae
Orangatan Gorilla Chimpanzees Humans

We are human, but we are also apes.

We share unique human features. We also share features with other apes (and with other animals, plants, fungi, bacteria, etc.). Humans didnt evolve from apes, humans are apes.

Importance of systematics & evolution:

1) Foundation of biology - study of biodiversity 2) Basis for classification of life 3) Gives insight into biological processes: speciation processes adaptation to environment 4) Can be aesthetically/intellectually pleasing!

E.g., schistosomiasis

Schistosomiasis:
knowledge of species diversity and evolutionary history of primary host can aid in controlling parasite (Schistosoma, a fluke)

Phylogeny of Oncomelania snails

All of life is interconnected by descent.

TAXA

lineage or clade TIME

Cladogram or Phylogenetic Tree

There are no higher or lower species.

TAXA

lineage or clade TIME

Cladogram or Phylogenetic Tree