Phylogenetic InferencePhylogenetic InferenceBiologists have used many approaches to estimating the evolutionary history of organisms and using that history to construct classifications.

illi i d l d h h i h f h b i f hWilli Hennig developed the techniques that form the basis for the modern methods of estimating evolutionary history and then using that history for classification. He called his method g yphylogenetic systematics.

The process of developing an estimate of the evolutionary history of a group of organisms is called phylogenetic inferenceof a group of organisms is called phylogenetic inference.

The unit of data used in phylogenetic inference is the characteror trait. Characters are any measurable or identifiable aspect of a y pgroup of organisms. They can be anatomical (morphological), behavioral, physiological, biochemical, molecular.

Characters may be useful for phylogenetic inference if they come in alternate character states - different shapes of the same bone, enzymes that differ in their amino acid sequence, genes that differenzymes that differ in their amino acid sequence, genes that differ in their nucleotide sequence, etc.

A set of characters with multiple states can be used to construct a phylogenyphylogeny

Using character state data to develop a hypothesis of evolutionaryUsing character state data to develop a hypothesis of evolutionary relationships is called phylogenetic inference.

Alternate states of a character may represent evolutionary changes. For any two states of a character one may have originated earlier in the evolutionary history of the group and one may have originated later.later.

Character states that originated earlier in the evolutionary history of a group can be called primitive or ancestral or plesiomorphic.g p p p p

Character states that originated later are called advanced or derived or apomorphic.

Derived states of a character provide information about the degree of relatedness of two or more species. A derived state that is shared b i i ll d hby two or more species is called a synapomorphy.

Synapomorphies allow species to be grouped and organized into a phylogenyphylogeny.

Phylogenetic inference - using character states to develop an estimate of evolutionary relationship

A character state matrix

estimate of evolutionary relationship

Character a b c d e f g h i jThe task is determine the

l d f fSpecies1 0 0 1 1 1 0 0 0 0 02 0 0 1 0 0 1 1 1 1 03 0 0 1 0 0 1 1 0 0 14( )

1 1 0 0 0 0 0 0 0 0

relatedness of a group of species in the “ingroup.”

An outgroup a group that is(outgroup)ancestor 0 0 0 0 0 0 0 0 0 0

An outgroup - a group that is related to the ingroup, but clearly not a member of the ingroup, provides orientation.

The common ancestor of the h l i h h i dwhole group is hypothesized

to have had the ancestral state of all characteristics.

A simple example - a constant rate of evolution with no evolutionary reversals or multiple origins of the derived state

CharacterSpecies

a b c d e f g h i j

1 0 0 1 1 1 0 0 0 0 02 0 0 1 0 0 1 1 1 1 0

evolutionary reversals or multiple origins of the derived state

2 0 0 1 0 0 1 1 1 1 03 0 0 1 0 0 1 1 0 0 14(outgroup)

1 1 0 0 0 0 0 0 0 0

ancestor 0 0 0 0 0 0 0 0 0 0

l d i d

A derived state

0 = ancestral 1= derived

A derived state that has evolved only once is calledcalled homologous in all the species that share it.

An example with variable rates of evolution among branches.Character

Speciesa b c d e f g h i j

1 0 0 1 1 0 0 0 0 0 02 0 0 1 0 1 1 1 1 1 13 0 0 1 0 1 1 0 0 0 0

Overall sp. 1 & sp. 3 are most similar3 0 0 1 0 1 1 0 0 0 0

4 (outgroup) 1 1 0 0 0 0 0 0 0 0ancestor 0 0 0 0 0 0 0 0 0 0

most similar

This example shows phow synapomorphies and not overall similarity reflect evolutionary history

An example with evolutionary reversals and multiple origins of

Character a b c d e f g h i j Species 1 0 1 1 0 0 0 1 1 0 1

the derived state of some characters.

2 0 1 1 1 1 1 0 1 0 03 0 1 1 1 1 1 1 0 1 1 4 (outgroup)

1 0 0 0 0 0 0 0 0 0

ancestor 0 0 0 0 0 0 0 0 0 0 Character states that arise Character states that arise more than once are called homoplasious.

The derived state of characters g and h evolved twice they are examples oftwice - they are examples of convergent evolution.

The ancestral state of character j is present in species 2 This is anThe ancestral state of character j is present in species 2. This is an evolutionary reversal.

How can the ancestral and derived states of a character be identified?identified?

Outgroup comparison is the most commonly used method. The state of a character found in species outside the group being p g p ganalyzed is the ancestral state.

For example - among tetrapods (vertebrates with four limbs –amphibians, reptiles, birds, and mammals) there are those with amniotic development (the embryo forms and develops within an amniotic sac) and those without. The tetrapods themselvesamniotic sac) and those without. The tetrapods themselves provide no information about the direction of evolution because the amnion could have been gained or lost during evolution. The o tgro p all other ertebrates (the fishes) does not ha eoutgroup, all other vertebrates (the fishes), does not have amniotic development. Therefore, it is most likely that amniotic development is the derived state in tetrapods. The derived state (having amniotic development) can then be used as a potential synapomorphy and used in constructing a phylogeny.

Convergent evolution and evolutionary reversals provide i l di i f i b h l i hi f imisleading information about the relationships of species.

How can one decide among competing hypothesis of evolutionary history?evolutionary history?

Derived character states:1: the presence of dorsal fin1: the presence of dorsal fin2: the presence of a pectoral girdle3: the presence of limbs4: the presence of lungs4: the presence of lungs5: the presence of cervical vertebrae6: the presence of a single aortic arch7: the presence of a dentary jawbone7: the presence of a dentary jawbone8: the presence of mammary glands9: the presence of a 4-chambered heart

Simpler hypotheses are preferred - the principle of parsimony.

Here dorsal fins evolved twice but all other derived character states evolved once.

Derived character states:1: the presence of dorsal fin1: the presence of dorsal fin2: the presence of a pectoral girdle3: the presence of limbs4: the presence of lungs4: the presence of lungs5: the presence of cervical vertebrae6: the presence of a single aortic arch7: the presence of a dentary jawbone7: the presence of a dentary jawbone8: the presence of mammary glands9: the presence of a 4-chambered heart

The method of maximum parsimony -h i f l i l i hithe estimate of evolutionary relationship

that requires the fewest character state changes is the simplest hypothesis. g p yp

Among species 1, 2, and 3 - three different hypotheses are possible. Each can be evaluated for the number of character state changesEach can be evaluated for the number of character state changes.

Shared statesShared derived states

1 2 3 4 51 x 5 4 2 1

1 2 3 4 51 x 4 3 0 0

2 x 3 3 23 x 3 2

2 x 2 0 03 x 0 0

4 x 65 x

4 x 05 x5 x 5 x

High numbers of shared states can be due to shared derived shared ancestraldue to shared derived, shared ancestral, or both.

High numbers of shared derived statesHigh numbers of shared derived states indicate evolution within monophyletic groups.

Difficulties in phylogenetic analysis

1. Deciding what is a character and what are its states is difficult (example: teeth in mammals)

2. Homoplasy is common. This results in many equally supported phylogenetic estimates

3. The process of evolution can erase evidence of prior evolution. If a character goes through several state changes, it can be difficult to associate it with the original ancestral state. (example: multiple g ( p pbase pair changes at a single site (A C T G)

When very large data sets are analyzed, with many species and many h te the e e fte t ee th t e e l e llcharacters, there are often many trees that are nearly equally

parsimonious.

One way of distinguishing among different phylogenetic estimates is by y g g g p y g ybootstrap resampling. Bootstrapping procedures take random subsamples of a data set and develop the best tree or trees from each subsample. If a clade appears in many or most estimates, then thatsubsample. If a clade appears in many or most estimates, then that clade is supported by the data more than other potential groups. A number at the node indicates the percentage of bootstrap estimates that support that cladesupport that clade.

Killian et al.’s bootstrappedbootstrapped estimate of the phylogeny of

lmammals.

Hypotheses ofHypotheses of evolutionary relationship can be

difi d f thmodified or further validated by gathering additional data.

The robustness of a phylogenetic hypothesis can be evaluated by comparing hypotheses p g ypcreated with independent data sets.

The fossil record can also be used to estimate evoluationary relationshipsrelationships.Horse evolution – many horse fossils exhibit a mixture of characteristics of intermediate forms (“missing link”) but also have f t th t th i t di t t h ld ’t h h d Thfeatures that the intermediate ancestor shouldn’t have had. Thus they probably represent side branches that retained characteristics of an ancestor that was a link to other forms but had also evolved new characteristics since diverging from the common ancestor - overall several trends are still clear.Evolutionary trends in horsesEvolutionary trends in horses• Feet : walking on three toes → walking on single central toe• Teeth : evolution of complex ridges of enamel (lophs) with change

in diet from lea es (bro sers) to grasses (gra ers)in diet from leaves (browsers) to grasses (grazers) • Jaws: elongation - with increased space between incisors and

molars and shift in position of molars toward the front • Leg length and body size: increased – associated with change in

habitat from forests to plains

Tetrapod evolution - the phylogeny and evolutionary changes that resulted in four legged land dwelling vertebrates is well

Rhipidistian fishes appeared in the early Devonian (408 mya), had

that resulted in four-legged land-dwelling vertebrates is well documented by fossils

p pp y ( y ),a complex jointed skull with many bones, teeth on several bones in the jaws, lateral line canals on the head, internal and external nostrils lobed fins with bony supports and respired with both gillsnostrils, lobed fins with bony supports, and respired with both gills and lungs

Eusthenopteron

The first amphibians appeared in the late Devonian (380 mya). They had a complex skull similar to rhipidistians, with teeth on y p p ,the same bones. They had internal and external nostrils and lateral line canals on the head. They respired with both lungs and gills but were clearly not fish They had strong supports forgills, but were clearly not fish. They had strong supports for appendages, stronger pectoral and pelvic girdle and increased size of bones in limbs

Ichthyostega

Tiktallik is one of several intermediate forms known between Rhipidistians and Amphibians. It had gills, lungs, lobed fins, and a neck.and a neck.