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Phylogenetic InferenceBiologists have used many approaches to estimating the evolutionary history of organisms and using that history to y y g g yconstruct classifications.

Willi 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 phylogenetic systematics.

The process of developing an estimate of the evolutionary history of 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 group of organisms. They can be anatomical (morphological),group 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 differ in their nucleotide sequence, etc.

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

Using 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.

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

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

Derived states of a character provide information about the degree f l t d f t i A d i d t t th t i h dof relatedness of two or more species. A derived state that is shared

by two or more species is called a synapomorphy.

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

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A character state matrix

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

CharacterSpecies

a b c d e f g h i j

1 0 0 1 1 1 0 0 0 0 0

The task is determine the relatedness of a group of

1 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(outgroup)

1 1 0 0 0 0 0 0 0 0

ancestor 0 0 0 0 0 0 0 0 0 0

species in the “ingroup.”

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

Th t f thThe common ancestor of the whole group is hypothesized to have had the ancestral state of all characteristics.

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 03 0 0 1 0 0 1 1 0 0 14 1 1 0 0 0 0 0 0 0 0

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

4(outgroup)

1 1 0 0 0 0 0 0 0 0

ancestor 0 0 0 0 0 0 0 0 0 0

A derived state that has evolved only once is

0 = ancestral 1= derived

only once is called homologous in all the species that share it.

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CharacterSpecies

a 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 04 (outgroup) 1 1 0 0 0 0 0 0 0 0

An example with variable rates of evolution among branches.Overall sp. 1 & sp. 3 are most similar

ancestor 0 0 0 0 0 0 0 0 0 0

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

Character a b c d e f g h i j Species 1 0 1 1 0 0 0 1 1 0 1 2 0 1 1 1 1 1 0 1 0 0 3 0 1 1 1 1 1 1 0 1 1

An example with evolutionary reversals and multiple origins of the derived state of some characters.

3 0 1 1 1 1 1 1 0 1 14 (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

more than once are called homoplasious.

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

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

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

Outgroup comparison is the most commonly used method. The state of a character found in species outside the group being analyzed is the ancestral state.analyzed 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 themselves provide no information about the direction of evolution because the amnion could have been gained or lost during evolution Thethe amnion could have been gained or lost during evolution. The outgroup, 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 misleading information about the relationships of species.

How can one decide among competing hypothesis of evolutionary history?

Derived character states:1: the presence of dorsal fin2: the presence of a pectoral girdle3: the presence of limbs4: the presence of lungs5: the presence of cervical vertebrae6: the presence of a single aortic arch6: the presence of a single aortic arch7: the presence of a dentary jawbone8: the presence of mammary glands9: the presence of a 4-chambered heart

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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 fin2: the presence of a pectoral girdle3: the presence of limbs4: the presence of lungs5: the presence of cervical vertebrae6: the presence of a single aortic arch6: the presence of a single aortic arch7: the presence of a dentary jawbone8: the presence of mammary glands9: the presence of a 4-chambered heart

The method of maximum parsimony -the estimate of evolutionary relationship that requires the fewest character state changes is the simplest hypothesis.

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

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1 2 3 4 51 x 5 4 2 12 x 3 3 2

1 2 3 4 51 x 4 3 0 02 x 2 0 0

Shared statesShared derived states

2 x 3 3 23 x 3 24 x 65 x

2 x 2 0 03 x 0 04 x 05 x

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

High 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 p y y q y ppphylogenetic 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 base pair changes at a single site (A C T G)

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When very large data sets are analyzed, with many species and many characters, there are often many trees that are nearly equally parsimonious.

One way of distinguishing among different phylogenetic estimates is by bootstrap resampling. Bootstrapping procedures take random boo s p es p g. oo s pp g p ocedu es e dosubsamples of a data set and develop the best tree or trees from each subsample. 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 clade.

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Killian et al.’s bootstrapped estimate of the phylogeny of mammals.

Hypotheses of evolutionary relationship can be modified or further

lid d b h ivalidated by gathering additional data.

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

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The fossil record can also be used to estimate evoluationary relationships.Horse evolution – many horse fossils exhibit a mixture of characteristics of intermediate forms (“missing link”) but also have features that the intermediate ancestor shouldn’t have had. Thus h b bl id b h h i d h i i fthey 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 horses• Feet : walking on three toes → walking on single central toe• Teeth : evolution of complex ridges of enamel (lophs) with change• Teeth : evolution of complex ridges of enamel (lophs) with change

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

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Rhipidistian fishes appeared in the early Devonian (408 mya), had a complex jointed skull with many bones, teeth on several bones in

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

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 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 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 for appendages stronger pectoral and pelvic girdle and increased sizeappendages, stronger pectoral and pelvic girdle and increased size of bones in limbs

Ichthyostega

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