Phylogenies & Classifying species (AKA Cladistics & Taxonomy)

Phylogenies & Classifying species (AKA Cladistics &

Taxonomy)What are phylogenies?How do we read them?

How do we estimate them?

Carolus Linneaus:Systema Naturae (1735)

• Swedish botanist & natural theologist

• Hierarchical classification based on “ideal of unchanging types”.

• Binomial nomenclature - replaced polynomials

• Categories:• K, P,C, O, F, G, S• Assumes a static,

unchanging Universe

Charles Darwin and Fig. 1

• Origin of Species (1859)

• Species diverge; they do so gradually

• Articulated idea of shared ancestry, branching of lineages (cladogenesis) and change along branches (anagenesis)

• Only figure in OS: a dendrogram

Problems with Linnean system

• It does NOT represent evolutionary history.• Hierarchical categories do not imply

degree of evolutionary change or divergence.– Are Rabbits as different from Rodents as they

are from Elephants?

• When and how should we split groups into separate categories? - splitting vs. lumping– How different is different enough to warrant

separate groupings?– Ex: Dogs & wolves

Dendrogram ~ Phylogenies

• Phylogeny: Interpretation of the evolutionary history and relationships between a group of organisms

• Phylogenetic tree: Hypothesis of ancestor-descendent relationships among populations, species, or larger groups*

Why construct phylogenies?

1. Understand evolutionary history2. System of classifying organisms &

organizing diversity– Most biologists agree: most efficient

way to classify organisms is based on phylogenetic relatedness

All species coalesce to a common ancestor:

• Recall our lab:• Just as all genes coalesce

to a single ancestral gene, all individuals coalesce to a single ancestor.

• Like tracing a family tree

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•Tips•Branches•Nodes•Root•Most Recent Common Ancestor (MRCA)

Phylogeny of Vertebrates

Name another tipName another node

Monophyletic groupings

Who is the MRCA of Mammals and Crocodiles?

Monophyletic groupings

Nodes name monophyletic groups:An ancestor and ALL of its descendents

Reading phylogenies• 5 of these are identical• Which one is not the same?*

Paraphyletic groupings

Tree of Life

What data should we use to generate trees?

• What data do you use?• Often do it without understanding why

What data should we use to determine evolutionary relationships?

• Characters: distinguishable variations of an organism

1.Morphologic2.Developmental3.Genetic• Quantifiable• Independent of each other• Homologous: due to common ancestry

ACGTTGAAACCTTGTA

Phenetic approach• Sokal (1950) Made classification rigorous.

Based groupings on many characters rather than few “important” ones.– Calculated overall SIMILARITY. Generated

phenograms (Basically, phylogenetic trees)

• Characters: Vary independently of other features. Homologous among ingroups.

• Character states: alternative versions of character.– Presence/absence– 1/2/3/4…etc.

Characters• Are the bones of the upper

limb homologous structures?• Are wings of bats, birds and

pterosaurs homologous structures?

PitfallsWhen Similarity ≠ Close

Relationship!• 2 taxa may share a derived character state• OR may share an ancestral character state• OR may share a character state due to

convergence to same phenotype (MRCA did not have the character) These are analogous traits– Bird and bat wings– Dermopterans, Flying squirrels, Sugar gliders

• Only if first case is true will you ALWAYS infer correct phylogenetic relationship.

Anura Caudata Caecilians Mammals Turtles Crocs Birds Tuatara Lizards Snakes

Diapsida

Where is the MRCA of Tuatara and Crocs?

Anura Caudata Caecilians Mammals Turtles Crocs Birds Tuatara Lizards Snakes

B

C

A

D

The Monophyletic group that includes Birds, Crocs & Turtles begins at node:

Willi Hennig and Cladistics

• Grouping scheme based ONLY on phylogenetic relationships– Not on degree of similarity

and adaptive divergence

• Used presence of shared derived characters (synapomorphies) to infer evolutionary relationships

• Based trees upon total weight of ALL synapomorphies

Phylogenetic terms*• Plesiomorphy: Ancestral character state• Symplesiomorphy: Ancestral character

state shared by many taxa - phylogenetically uninformative

• Apomorphy: Derived (novel) character - phylogenetically uninformative

• Synapomorphy: Shared derived character - GOLD

• ”Hennig has indeed emphasized and defined some procedures of phylogenetic analysis that have long been used by systematists. He might even have clarified them if he had not unnecessarily replaced the usual plain-language terms by a bizarre and idiosyncratic new terminology." (1978) G. G. Simpson

Similarity ≠ Relationship

• 2 taxa may share a derived character state• OR may share an ancestral character state• OR may share a state due to convergence

– Bird and bat wings– Dermopterans, Flying squirrels, Sugar gliders

• Only if first case is true will you infer the phylogenetic relationship correctly.

synapomorphysymplesiomor

phyanalogy

Synapomorphies identify monophyletic groups

• Unite groups with shared, (only among each other) derived (from some ancestral group) characters

Problems• What characters (traits) are “best” for

assessing evolutionary relationships?– Skull length, body size, pelage color, limb

modification and specialization, chromosome #?• When and how should we split groups into

separate categories? - splitting vs. lumping– How different is different enough to warrant

separate groupings?• Can/should hierarchical categories imply

degree of evolutionary change or divergence?– Are Hyraxes as different from Manatees as they

are from Bats?– Are dogs as different from cats as they are from

humans?

Problems with characters

• Which characters are phylogenetically informative?

• How do we quantify # of possible states & frequency of change among them?

• How do we establish polarity?• How do we deal with continuous

traits: Quantify or discard them?

Ideal character• States are discrete• # of states are knowable (across taxa)• Transition frequencies (rates of change)

are estimable

DNAONLY 4 states; A C G TNo polarityCan measure transition

frequencies

Method of inferring a tree• Choose the most parsimonious one• Parsimony: Methodological reductionism;

Explanation which requires the fewest undocumented assumptions is probably correct.– Occam’s Razor: The easiest explanation is

probably the correct one.– William of Occam: 14th century Franciscan monk

• In cladistics/phylogeny: The tree which requires us to postulate the least evolutionary change & fewest homoplasies is probably correct

Parsimony• Find all possible tree topologies; calculate

total number of changes required to produce each topology.

• Topology with fewest changes = the most parsimonious tree*

A B C D C A B D

Taxa: A, B, C, DCharacters: › › ›

Placement of Cetaceans• Morphology of astragalus unites Artiodactyls• Most parsimonious placement = one gain of

pulley-shaped astragalus

Placement of Cetaceans• Mounting genetic evidence suggests Hippos

have shared genes with Cetaceans more recently than they have with other Artiodactyls (e.g. deer)

Placement of Cetaceans• Appearance of SINE’s (mutations)

throughout the genome suggests that Cetaceans & Hippos are close relatives– Rare; Selectively neutral; Once established, lost

only via drift