read chapter 4 of zimmer and emlen text all living organisms are related to each other having...

Read Chapter 4 of Zimmer and Emlen text

All living organisms are related to each other having descended from common ancestors. Understanding the evolutionary relationships between groups enables us to reconstruct the tree of life and gain insight into history of evolutionary change.

Phylogeny is the study of the branching relationships between populations over evolutionary time. A phylogenetic tree is built up by analyzing the distribution of traits across populations.

A trait (or character) is any observable characteristic of an organism. Could be anatomical features, behaviors, gene sequences, etc.

Traits are used to infer patterns of ancestry and descent among populations. These patterns are then depicted in phylogenetic trees. By mapping other traits onto trees it is possible to study the sequence and timing (history) of evolutionary events.

Its important to bear in mind that phylogenetic trees are hypotheses about the evolutionary relationships between groups. When additional evidence is acquired it can be used to test a tree.

Each branch tip represents a taxon (a group of related organisms). Interior nodes (where branches meet) represent ancestral populations that are the common ancestors of the taxa at the ends of the branches.

Phylogenetic trees are generally drawn in either a Tree format or a Ladder format. They convey the same information about the relatedness of taxa

It is important to remember that a particular set of evolutionary relationships can be depicted in multiple different ways in a phylogenetic tree. Any node in a phylogenetic tree can be rotated without altering the relationships between taxa.

The purpose of building phylogenetic trees is to use them to figure out the evolutionary relationships between taxa and to identify natural groupings among taxa, those that reflect their true evolutionary relationships. A key idea is that natural groupings called clades are monophyletic groups.

Clade : a group of taxa that share a common ancestor. Monophyletic group: consists of an ancestor and all of the taxa that are descendants of that ancestor.

Clades are monophyletic groups

In the next slides elephants, manatees and hyraxes plus their common ancestor form a monophyletic group. Similarly tapirs, rhinoceroses and horses plus their common ancestor form another monophyletic group.

A taxon is polyphyletic if it does not contain the most recent common ancestor of all members of the group.

A polyphyletic group requires the group members to have each had an independent evolutionary origin of some diagnostic feature. E.g. Referring to Elephants, rhinoceroses and hippopotamuses as pachyderms. Pachyderms are a polyphyletic group because each group evolved thick skin separately.

A taxon is paraphyletic if it includes the most recent common ancestor of a group and some but not all of its descendents.

An example of a paraphyletic group among vertebrates would be fish. All of the tetrapods (four-legged animals) are descended from lobe- finned fish ancestors, but are not considered fish hence fish is a paraphyletic group because the tetrapods are excluded.

Trees weve seen so far have been rooted and these trees give a clear indication of the direction of time. However, computer programs that produce phylogenetic trees often produce unrooted trees.

In an unrooted tree, branch tips are more recent than interior nodes, but you cannot tell which of multiple interior nodes is more recent than others.

An unrooted tree can be rooted at any point and depending where it is rooted very different rooted trees will be produced.

E.g. Using root A (the red dot) in previous slide. (1) Draw vertical line leading to A and horizontal line leading to A (making a T shape). Mark A at intersection of the T. (2) Remember you also want the tree to bifurcate (split into two branches (3) Looking at the unrooted tree because A is the root and splits the tree into two halves: one branch of the rooted tree leads to species 4&5 and the other branch to species 1,2&3. (4) Draw vertical branch that splits into two and indicate species 4&5. (that completes that side of tree).

(5) looking at the left side of the unrooted tree we can see it splits into two branches. One branch leads to species 3 and the other branch leads to species 1&2. (6) Draw a bifurcation (or split) where one branch tip is labelled 3 and the other branch leads to a second split which are labeled 1&2

Obviously, there is only one true tree of evolutionary relationships and we would like to identify that tree. To do that we need to root the tree correctly. One of the easiest ways to root a tree is to use an outgroup to root it.

An outgroup is a close relative of the members of the ingroup (the various species being studied) that provides a basis for comparison with the others.

The outgroup lets us know if a character state within the ingroup is ancestral or not. If the outgroup and some of the ingroup possess a character state then that character state is considered ancestral.

Consider an unrooted tree of four magpie species.

To root the tree we need a group that split off earlier from the lineage that led to these four species of magpies. Azure-winged magpie is a suitable outgroup. One this is added to the unrooted tree we can root the tree.

In some phylogenetic trees branches are drawn with different lengths. In these trees the branch lengths represent the amount of evolutionary change that has occurred in that lineage.

Homologous traits are those derived from a common ancestor. E.g. all mammals possess hair. This is a homologous trait all mammals share because they inherited it from a common ancestor. Analagous traits are shared by different species not because they were inherited from a common ancestor but because they evolved independently.

Divergent evolution occurs when closely related populations diverge from each other because selection operates differently on them. Such new species will possess many homologous traits in common.

Analagous traits are the result of a process of convergent evolution whereby the same or similar solution to an evolutionary problem is converged upon by different organisms independently of each other.

When building a phylogenetic tree we want to use characters inherited from ancestors. Such a character found in two or more taxa is referred to as a shared derived character or synapomorphy. Example B on the next slide is a synapomorphy.

If all shared traits were shared derived traits tree-building would be straightforward. However, many traits are not e.g. analagous traits

We want to avoid including analagous traits when constructing phylogenetic trees because they can mislead us. An analagous trait in a tree is referred to as a homoplasy.

Homoplasy: character state similarity not due to common descent Convergent evolution: independent evolution of similar trait Evolutionary reversals: reversion back to an ancestral character state

In the next slide (A) we do not know the ancestral color state so we have to represent it as unresolved (a polytomy). If we know that our phylogenetic tree (B) correctly indicates the relationships between taxa then we know that dark coloration is a homoplasy having evolved independently twice.

Another way in which we could be mistaken is if a new trait arises in a lineage and is not shared with other taxa. This is called a symplesiomorphy. In the next slide, light coloration has recently arisen in taxon 3. If we thought dark coloration was a shared derived character we would group species 1+2, (as in A) but it isnt. Instead dark coloration is an ancestral trait and the correct phylogeny is shown in B.

Several strategies exist to limit homoplasies and synapomorphies. 1. use traits that change relatively slowly in evolutionary time 2. use many traits to build the tree 3. use multiple outgroups to help identify ancestral values of traits.

The mammalian order Carnivora includes cats, dogs and other familiar predatory mammals. Certain synapomorphies such as carnassial teeth (enlarged side teeth used to shear meat) unite the group, but there has been debate about relationships within the group.

To analyze relationships among 10 species of carnivores we construct a data matrix of the distribution of a dozen traits across these taxa.

Using synapomorphies to identify clades we can construct a phylogentic tree. The numbers on the tree correspond to the character states in the matrix. Some clades in tree are clearly defined but others not so well.

One point where relationships are unresolved. Such uncertain branching is called a polytomy.

If we add a 13 th trait to the data matrix we may be able to resolve the polytomy. However, sometimes additional data doesnt help or introduce more uncertainty.

Absence of a lower premolar is a character shared by cats, hyenas and otters, but that doesnt fit with our previous tree. Most likely this is a homoplasy (and the tooth was lost independently in different lineages).

In reality phylogentic analyses inevitably involved dealing with conflicting evidence. The most commonly applied rule to resolve conflict is the principle of parsimony choosing the simplest explanation i.e., the phylogeny that requires the fewest trait changes to construct it.

Applying the principle of phylogeny to a larger (20 character) matrix of data reveals three equally parsimonious phylogenetic trees that differ somewhat from each other. Notice, however, that certain portions of the tree are consistent across all three trees. Using some mathematical analysis a consensus tree can be constructed that represents a best estimate of the true tree.

Three equally parsimonious trees (above) Consensus tree (below).

Archaeopteryx, discovered in 1860, dates to 145 mya

Traits often change function over time. Phylogenies allow us to track such changes over evolutionary time. The oldest known fossil bird is Archaeopteryx (145mya), which possesses a suite of both avian and reptilian characteristics.

Birds today are defined by the possession of feathers and obviously they are used to fly, but phylogenetic analysis shows that this was not the original function of feathers as feathers are present in non- flying ancestral groups. Phylogenetic analysis also reveals that birds evolved from dinosaurs.

Velociraptor ulna with bumps resembling quill nodes in living birds (A+B) Turkey Vulture ulna with feathers attached to quill nodes (C-F)

Feathers must have played a different role in dinosaurs than flight. Most likely they served as insulation and for display (functions they are still used for today in birds).

Exaptation: natural selection co-opts a trait for a new function

(i) 1, 3, 2, 4, 5, 6 (ii) 1, 6, 5, 4, 3, 2 (iii) 1, 6, 5, 4, 2, 3

(i) 5&7 (ii) 2&7 (iii) 3&5

Shark : jaws Turtle: jaws, dentary bone, lungs.

2 3 1 4 5 6 A Rooting the tree at A draw the rooted tree for the above unrooted tree.

A 231456 Answer

Do the other problems in your text!

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