Recall speciation by hybridization and polyploidy

This is an important mechanism of speciation in many plant groups

Example: Tragopogon ("Goatsbeard")
Three diploid European species were introduced into the Northwestern US.
Over the years, a number of new tetraploid species have appeared in the region in which the three original diploids are found.
These have been shown genetically to be derived from the diploid species.

Since the tetraploids have the entire genomes of two of the parent species, they have some new combinations for enzymes that are formed from dimers.

Such cases, in which polyploidy appears in a hybrid, are known as Allopolyploidy.

It is also possible for polyploidy to occur in a non-hybrid genome. This process, known as Autopolyploidy can also lead to speciation, since the new organism is tetraploid and thus not able to interbreed with its diploid relatives.

Within many plant genera there are different species with different chromosome numbers that are all multiples of the lowest number.
Example: In the genus Chrysanthenum we find species with 2n = 18, 36, 54, 72, & 90.
If n = 9 for the ancestor, then these correspond to 2n, 4n, 6n, 8n, &10n.

Speciation involving polyploidy is much less common among animals, apparently because animals rarely self fertilize, but is occasionally seen.

Phylogeny

Note: When considering phylogenetic trees, what matters is the pattern of common ancestry (referred to as the "Topology"). This means that we can rotate the branches around any node without changing the tree (this just changes the way that we draw the tree).
Thus, the following two trees are identical:
 
 

Structure of a phylogeny described in terms of monophyletic groups.

Monophyletic group - All and only the descendants of a common ancestor (including that ancestor).

Each member of a monophyletic group is more closely related to all other members of that group than to members of any other group.

For comparison:
    Paraphyletic group - Does not include all of the descendants of the common ancestor.

    Polyphyletic group - Does not include the common ancestor.
 
 
 

Note: Many groups in classical taxonomy were not monophyletic.
For example, "Reptiles" is not a monophyletic group if it excludes Birds, since Crocodiles are more closely related to Birds than they are to Lizards.
In recent years, many biologists have simply started to include Birds as a subclade within Reptiles, making the latter monophyletic.

Monophyly diagnosed by noting homologies.

Homology: Two traits in two different organisms are said to be homologous if they are derived through a continuous sequence from the same trait in a common ancestor.

Derived Character States = Those not present in the common ancestor of all of the organisms under study.

Example:
 

	Gills?	Lungs?	Tetrapod?	Jaws?	Tailfin?
Lamprey	Yes	No	No	No	Yes
Trout	Yes	No	No	Yes*	Yes
Lungfish	Yes	Yes*	No	Yes*	Yes
Human	No*	Yes*	Yes*	Yes*	No*
Bird	No*	Yes*	Yes*	Yes*	No*

* indicated derived character state.

If we use overall similarity to construct the tree, we come up with something like the tree on the left below.
 
 
 

In the tree on the left, lampreys, trout, and lungfish are grouped together because they share traits like having a tailfin and having gills.

Note, though, that the ancestor of all of these organisms had a tailfin and gills, so these traits give us no real information about relationships within the vertebrates.
Similarly, the ancestors of all vertebrates had no lungs, no jaws, and were not tetrapods.

The fact that Humans, Birds, and lungfish all have lungs, though, does count as evidence of more recent common ancestry, since that trait arose sometime after the common ancestor of all vertebrates.

Similarly, the presence of Jaws is evidence that Humans, Birds, Lungfish, and Trout share a common ancestor more recent than that shared by all vertebrates.

Using only the derived character states (indicated by asterisks), we get the tree on the right -- which is the correct tree (confirmed by a huge number of morphological and molecular traits).

The overall tree of vertebrates looks like this:
 
 
 

Such a tree is a "cladogram". The monophyletic groups contained in it are clades.

Some vocabulary:

Apomorphy - Derived character state (e.g. jaws in the example).
    Synapomorphy - Shared derived state.
    Autapomorphy - Possessed by only one group.

Plesiomorphy - Ancestral character state, such as having gills and being jawless in the example.
    Symplesiomorphy - Plesiomorphy shared by two or more groups.

Note that what category a character falls into depends on which organisms we are studying. Being a tetrapod would be a symplesiomorphy if we were only studying terrestrial vertebrates.

We thus seek Synapomorphies to diagnose monophyletic groups. Identifying these requires knowledge of the ancestral states of characters.

Choosing the best tree:
Of course, it's possible that Humans and Lampreys are closest relatives and that jaws, lungs, etc. arose more than once. We thus need to evaluate the probabilities of different outcomes.

Maximum Likelihood: Choose the tree that, if correct, would maximize the probability of seeing the data that we see.
    If Humans and Birds really are closest among these groups, then we should expect to see some derived character(s) that Humans and Birds share but that the others lack (such as being tetrapods and lacking gills).

The tree that we chose thus maximizes the probability of seeing the kind of data that we have.

Put another way, the maximum likelihood tree is the tree that makes the most sense out of the date (has the greatest explanatory power).

Bayesian Tree Construction:

Similar to Maximum Likelihood, except that here we choose the tree that has the highest probability given the data.

Maximum Parsimony: Choose the tree that has the smallest number of character state changes on it.
    This is a much simpler rule to implement in practice and it usually gives the same answer as the likelihood criterion. It is thus still used. Jul 8, 2021