Classification and Phylogeny: What’s In a Name?

Alice in Wonderland

“What’s the use of their having names,” the Gnat said, “if they don’t answer to them?”

“No use to them,” said Alice, “but it’s useful to the people that name them, I suppose.”

What’s in a name?

Carolus Linnaeus: the father of modern taxonomy

In the 1700s a Swedish In the 1700s a Swedish physician and biologist, physician and biologist, Carolus Linnaeus, refined Carolus Linnaeus, refined classification into a hierarchy classification into a hierarchy where groups of similar where groups of similar organisms can be subdivided organisms can be subdivided into smaller more distinctive into smaller more distinctive groups. groups.

Linnaeus classified organisms into a hierarchy of groups:

• Eventually, as one Eventually, as one works through such a works through such a system, each unique system, each unique form of organism is left form of organism is left to occupy its own small, to occupy its own small, but distinct category.but distinct category.

• Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species

Here are the classification hierarchies for Here are the classification hierarchies for several different species of organisms:several different species of organisms:

A bee by any other name…

Scientific name: Genus speciesGenus species Taxonomy= the science of naming and classifying living things

The science of taxonomy underwent a fundamental revolution when Darwin published On the Origin of Species

Darwin suggested organisms cluster together due to common ancestry:

Species that are in the same genus have a more recentcommon ancestor than those in different genera

Likewise, genera within the same family have a more Recent common ancestor than those in different families

SystematicsDarwin showed that the classification of living organisms has a natural basis: their evolutionary history

Taxonomy expanded into systematics: the studyof the diversity of living organisms and their evolutionary relationships

• Homology: the same component and structures of organisms are repeated in many forms

• Darwin viewed homology as evidence that development of one structure is a modification or variant of the development of another (implies a common origin as a feature present in a common ancestor)

How do we determine evolutionary relationships?

Evolutionary Homologiesfeatures that share common origin in a common ancestor

Recognizing homologies: position relative to other parts and of its parts to each other

humerus

ulna

radius

Evolutionary Homologiesfeatures that share common origin in a common ancestor

Recognizing homologies: Transitional forms

Ex: horses run on their toes (actually on the tip of a single toe on each foot) Which toe?

the fossil record for horses is exceptional, and we can trace the transitional stages through time to discover that it is the third toe

IN FACT, we can trace to a common ancestor with rhinos and tapirs (Hyracotherium) and discover that the habit of walking on the 3rd toe is homologous in this group

Why do we care about homologies?

Homologies imply that the most recent common ancestor had the trait

Nesting homologies allows us to heirarchically classify organisms in an evolutionarily meaningful way

Homoplasy

Homoplasy (also analogy or analogous traits)same or similar character in two or more taxa was not present in the most recent common ancestorCan be difficult to distinguish from homology

Homoplasy results from convergent evolution

similar structure/trait has arisen in 2 or more species, but is not possessed by a common ancestor (and all intervening ancestors)

• cooperative hunting in canids and felids

• growth form of aloe (related to lillies) and agave (cactus)

Homoplasy results from evolutionary reversalssimilar structure/trait has arisen in 2 or more species, but is not possessed by a common ancestor (and all intervening ancestors)

• secondary wing loss in birds and insects

• eye loss in cave fish and cave salamanders

Texas blind salamanderTyphlomolge rathbuni Eyed (surface dwelling) and eyeless

(cave dwelling) Astyanax mexicanus

Evolutionary modifications

Evolutionary change (modification) is a change in a character state

• Do not confuse character with character state

• eg., Characters include: number of digits, eye color, heightCharacters states are: 3, 4, 5 blue, green 2m, 2.5m, 3m

Character state changes can be any character, behavioral, physiological, morphological, biochemical, molecular, etc.

1) presence/absence (0,1) for any character

2) qualitative, multistate - arbitrarily 1, 2, 3 for any character

3) quantitative, multistate - difficult to handle. How do you separate variation from difference?

Systematics

systematists infer the historical pattern of evolutionary descent for an organism to build a

PHYLOGENY - the genealogy of a group of taxa (the practice of developing phylogenies is called phylogenetics)

Interpretation: B&C evolved from a common ancestor 1; 1 is no longer present, only B&C.

outgroup A B C D

1

2

3

‘tips’- represent terminal taxa (extant species)

Nodes’ - represent common ancestors that no longer exist

• Cladistics is a modern approach

• Goal is to group organisms according to evolutionary history (phylogeny)

• Note: in practice, collect data on character states and then reconstruct topology

• Use data to construct cladograms

Cladistics

• cladograms can be derived by observing shared character states– 3 types:

1. shared derived character states -- synapomorphy

2. shared ancestral states -- sympleisiomorphy

3. shared but independently evolved state -- homoplasy

• Only #1 are useful in constructing cladograms• SYNAPOMORPHIES DEFINE CLADES, and are evidence of

a most recent common ancestor• individual taxa are recognized by unique, unshared character

states (autapomorphies)

Cladistics

• If a character state was present before a clade split off, it is ancestral

• If a character state is new to a group, it is derived

• Ancestral vs. derived can be answered with outgroups (which define the ancestral state for a clade)

Ancestral vs. Derived

autopomorphy

sympleisiomorphy

synapomorphy

Constructing a cladogram

How many synapomorphies do each pair of organisms share?

How many trees?

With 3 taxa, there are the following possible trees:

The problem that arises is that even with complete knowledge of shared derived characters, there are many possible phylogenies that can be generated:  # of taxa bifurcating trees

3 34 15 5 105 6 945

How do we chose between them?

A B C AB C ABC

Choosing the correct tree

There are many possible methods for selecting trees, most are built on the principle of parsimony - the most likely alternative is the simplest and least complex in the phylogenetic context, the favored phylogeny includes the fewest number of changes in character state

There are other ways to choose between trees (e.g., Maximum likelihood) that weight some kinds of character state changes differently than others

e.g., for molecular data, we know that transversions (A, G <--> C, T) are less common than transitions (A<-->T, C<-->G) - we can calculate the probabilities for any taxon and weight each change differently

Defining Groups: Cladistics

Monophyletic: includes all taxa from a single common ancestor

Paraphyletic: does not include all taxa from a single common ancestor

Polyphyletic: includes all taxa not from a common ancestor

• Cladistics argues that many traditional groups are paraphyletic

• Example: Reptiles are not a valid group

Impact of cladistics

Reptiles are a paraphyletic group

Cladistics would group birds with the reptiles

Traditional and cladistic classification of vertebrates