Investigating the Evolutionary History of Life

How are phylogenetic trees useful?

Assumptions• Mutations that are not expressed are maintained. They

are neutral.• They should accumulate at a constant rate = the

mutation rate. • This serves as a molecular clock.• Kittler et al. (2003,2004) compare genetic differences in

lice between chimpanzees and humans. Also considered fossil record. • Common ancestor of chimps and humans – 5.5. mya. • Able to determine # of base changes during that time

between chimp lice and human lice – the molecular clock. • Then applied that rate of change to the difference

between human head lice (Pediculus humanus capitis) and body lice (Pediculus humanus corporis)

A. Head B. Body

How are phylogenetic trees useful?

Assumptions

The rate of mutation accumulations between Chimp lice - Human lice = Human head lice / Body lice.

Multiply the rate of change by the number of differences ~ 107, 000 years.

Origin of body lice was not more than 107,000 years ago.

Since Pediculus humanus corporis lives in clothing (though it feeds on the body), we can infer that humans began wearing clothing not more than 107,000 years ago.

Ethiopian lineage of head lice.

Augustin Augier’s detailed tree of life for plants in 1801

Jean-Baptiste Lamarck sketchy diagram for animals in 1809.

Vestiges of the Natural History of Creation, anonymously published by Robert Chambers in 1844, had an even sketchier one, where fish, reptiles, and birds are represented by branches from a path leading to mammals.

in 1858, just a year before the Origin of Species, Heinrich Georg Bronn published a hypothetical phylogenetic tree labeled with letters.

Phylogenetic trees existed before OOS, but they were more like organizational charts.

“Paleontological chart” from Edward Hitchcock’s Elementary Geology, first published in 1840.

Phylogenetic trees existed before OOS, or histories of life.

Indeed, once the tree of life image became associated with transmutations, Hitchcock dropped the image from later editions, since he strongly disagreed with the transmutation hypotheses of Lamarck, Haeckel, Darwin and others.

The first phylogenetic tree

The first real phylogenetic tree.

The root of the tree – the common ancestor

The only figure in Darwin’s Origin of Species

Sister

Cousin Vinny

Cousin Flossie

Time

Ancestors Me

Linking Classification and Phylogeny

Systematicists depict evolutionary relationships in branching phylogenetic trees

Much like a family tree

Reading a Phylogenetic Tree

• A phylogeny, or evolutionary tree, represents the evolutionary relationships among a set of organisms or groups of organisms, called taxa (singular: taxon).

• Because no one was present to observe the splitting of taxa from a common ancestor, many evolutionary biologists consider a phylogenetic tree to be a hypothesis of those relationships

Reading a Phylogenetic Tree

• The root is the common ancestor of the species in the tree.• The tips represent the descendant taxa (often species)• The nodes represent the common ancestor of those descendants.

Node

Tips – descendent species

Root

Reading a Phylogenetic Tree

• Two descendants that split from the same node are called sister groups.

• The outgroup is a taxa that is outside the group of interest.

It stems from the base of the tree and provides perspective to the group of organisms being examined.

Node

Outgroup

Sister groups

Character state – One of the variant conditions of a character (e.g. melanic or typical moth color. Or presence and absence of a trait. ).

Derived character state - same as apomorphy; a derived

character / trait is inferred to be a modified version of a more primitive condition of that character and therefore inferred to have arisen later in the evolution of the clade.

Clade - a group of organisms that share a common ancestor; lineage; a monophyletic group.

Monophyletic group - terms applied to a group of organisms that includes an ancestral species and all of its descendants; e.g. Aves, Mammalia. This group is a complete branch of the tree of life, the phylogeny of life. Such a branch is called a clade.

Character – beak length

State

Long

Short

Beak is the character, the state is its length.

Apomorphy – a derived, or evolutionary novel character. It is context specific.

When all four species are considered, the presence of the mask is considered novel relative to the presence of the ancestral form.

When just the three species are considered, the presence of the mask is considered a pre-existing trait, or ancestral. This is called a plesiomorphy.

Plesiomorphy - An original character state for the taxa under consideration

Apomorphy and plesiomorphy illustrated together

What about primitive and derived characters?You might hear people use the term "primitive" instead of plesiomorphic and "derived" instead of apomorphic. However, many biologists avoid using these words because they have inaccurate connotations. We often think of primitive things as being simpler and inferior — but in many cases the original (or plesiomorphic) state of a character is more complex than the changed (or apomorphic state). For example, as they have evolved, many animals have lost complex traits (like vision and limbs). In the case of snakes, the plesiomorphic characteristic is "has legs" and the apomorphic characteristic is "doesn't have legs."

Original state

Changed state

A synapomorphy is a trait that is shared by two or more taxa and inferred to have been present in their most recent common ancestor, whose own ancestor in turn is inferred to not possess the trait.

The mask is a synapomorphy because it is shared by the most recent common ancestor.

But not this ancestor.

A clade is a grouping that includes a common ancestor and all the descendants (living and extinct) of that ancestor. Using a phylogeny, it is easy to tell if a group of lineages forms a clade. Imagine clipping a single branch off the phylogeny — all of the organisms on that pruned branch make up a clade.

Evo. Edu. Outreach (2009) 2:303-309

Taxonomically, an organism accumulates all the names of all the clades to which it belongs.

A member of the most recent clade is also a member of all the ancestral (preceding clades).

Clade - a group of organisms that share a common ancestor; lineage; a monophyletic group.

Transition - a change in the character state along a branch.

Note that each one of these groups can be separated by “one snip”.

They are each a clade (monophyletic).

Practice to review – phylogenetic trees

Phylogenetically thinking – birds are dinosaurs.• Birds evolved from dinosaurs.• Cannot clip (make a clade) a branch that includes: a) dinosaurs and b) more dinosaurs without including c) birds.• Q: Using tree thinking, are all reptiles cold-blooded? Can reptiles be

defined as being cold-blooded?

Evo. Edu. Outreach (2009) 2:303-309

Using tree thinking and the concept of clades, we can see that Ostriches belong to every clade preceding them (their ancestors).

Conclusion – Birds are descendants of dinosaurs.

Evo. Edu. Outreach (2009) 2:303-309

Depending on how many branches of the tree you are including however, the descendants at the tips might be different populations of a species, different species, or different clades, each composed of many species.

These are all clades (monophyletic)

A paraphyletic grouping consists of an ancestral species and some, but not all, of the descendants.

Note that two scissor snips rules out that this is a clade.

A polyphyletic grouping consists of various taxa with different ancestors.

Note that the taxa (tips) do not have the same common ancestor.

Reading Phylogenetic Trees

Understanding a phylogeny is a lot like reading a family tree. The root of the tree represents the ancestral lineage, and the tips of the branches represent the descendants of that ancestor. As you move from the root to the tips, you are moving forward in time.

Evolution.berkeley.edu

Reading Phylogenetic Trees

Evolution.berkeley.edu

When a lineage splits (speciation), it is represented as branching on a phylogeny. When a speciation event occurs, a single ancestral lineage gives rise to two or more daughter lineages.

Reading Phylogenetic Trees

Evolution.berkeley.edu

Phylogenies trace patterns of shared ancestry between lineages. Each lineage has a part of its history that is unique to it alone and parts that are shared with other lineages.

Reading Phylogenetic Trees

Evolution.berkeley.edu

Similarly, each lineage has ancestors that are unique to that lineage and ancestors that are shared with other lineages — common ancestors.

Reading Phylogenetic Trees

Evolution.berkeley.edu

Evolution produces a pattern of relationships among lineages that is tree-like, not ladder-like.

Reading Phylogenetic Trees

Evolution.berkeley.edu

Just because we tend to read phylogenies from left to right, there is no correlation with level of "advancement."

One form of a trait may be ancestral to another more derived form, but to say that one is primitive and the other advanced implies that evolution entails progress — which is not the case.

An organism's position on a phylogeny only indicates its relationship to other organisms, not how adaptive or specialized or extreme its traits are.

Reading Phylogenetic Trees

Evolution.berkeley.edu

Just because we tend to read phylogenies from left to right, there is no correlation with level of "advancement."

Aristotle's vision of a Great Chain of Being, above. We now know that this idea is incorrect.

University of California Museum of Paleontology's Understanding Evolution (http://evolution.berkeley.edu).

Although mosses branch off early on the tree of life and share many features with the ancestor of all land plants, living moss species are not ancestral to other land plants. Nor are they more primitive. Mosses are the cousins of other land plants.

Reading Phylogenetic Trees

Reading Phylogenetic Trees

Evolution.berkeley.edu

For any speciation event on a phylogeny, the choice of which lineage goes to the right and which goes to the left is arbitrary. The following phylogenies are equivalent:

Practice Reading Phylogenetic Trees