2. The Tree of life (second half)

Drawing/ interpreting trees

A phylogenetic tree can be drawn in any of several ways. The branches could be angled or they could be aligned vertically and horizontally. What is important is the pattern of relationships. All these trees show exactly the same relationships. 

All the trees in Figure 2.6A are the same because branches can be rotated at nodes. The two trees (below) on the left are the same. The two trees on the right are both different to each other and to the trees on the left (B and C are sister species in the two left trees whereas sister species differ on the right)  

The relative lengths of the branches usually have no significance. If, however, the tree is presented with a time scale (Fig. 2.7B), the positions of the nodes indicate when speciation events are estimated to have occurred.  

Could have different scales.... time (relative), Time (absolute, Ma), base pair substitutions (branch length) 

A tree constructed using molecular data may be calibrated against the number of evolutionary changes. In Figure 2.7C the branch lengths reflect the number of base pair substitutions that have been reconstructed for the branches.

Phylogenetic methodology reconstructs…

Phylogenetic methodology reconstructs interrelationships of taxa using homologous characters. It does not use similarity. Closeness of relationship is not the same as similarity. 

Does not use similarity. Disregards convergent evolution. 

Inferring Phylogenies: An Introduction  

-The main principle of phylogenetic systematics is that taxa should be grouped together on the basis of homologous characters.  

-This principle is based on the idea that traits found in some taxa and are shared by those taxa (and not with others) were inherited from a common ancestor in which those traits first evolved. The shared homologous traits are evolutionary novelties that are modification of older (∴ primitive) traits 

Homologous characters are similar because they are inherited by a common ancestor 

Analogous characters: look similar but are inherited by different ancestors. 

A classic example of homology

-A classic example of homology is the organization of the forelimb skeleton of tetrapods (limbed vertebrates). From should joint to the tips of the digits, a common pattern emerges for the forelimb bones because of inheritance from a common ancestor (Fig. 2.9) that evolved those traits in the Devonian Period 

-In mammals, the primate arm is least modified (modified for brachiating through the trees) among the three examples. The forelimb of the horse has been modified by loss of distal bones and the relative lengthening of the foot (lost phalanges, essentially running on its middle finger lol). The forelimb of the seal has been modified by the addition of toe bones (hyperphalangy) as the foot evolved to be a flipper  (addition of phlanyx on 4th and 5th digit) 

three groups of tetrapods evolved….

-Three groups of tetrapods evolved wings for active flight. Bats use and pterosaurs (extinct) used integumentary membranes to create wings. In bats the membranes mainly stretch between elongated bones of all digits in the forelimb and the body. In pterosaurs the membrane extended from the elongated bones of the fourth digit and the body. 

-In birds some of the bones were lost and others fused together, and the integument anchors feathers that create the airfoil of the wing 

Only 3 digits in the manus of the birds (loss of digits).  Bats elongate (added more phlanx?) to the digits 

Phylogenetic systematics was devised in the

-Phylogenetic systematics was devised in the 1950s and the first cladograms used morphological data. A researcher would identify characters or traits, such as number of toes per foot, and divide the trait into character states, such as five toes, four toes, three toes, two toes, or a single toe.  

-Phylogenetic analysis using molecular data uses amino-acid sequences (from proteins) or nitrogenous-base sequences (from DNA or RNA) as characters. For the latter, the character states are adenine, thymine, cytosine, and guanine (or A, T, C, and G) 

4 toes- rhino front feet    3 toes- rhino back feet    2 toes-cloven hooves   1 toe- horses 

Phylogenetic systematics was devised in the

 

Phylogenetic systematics was devised in the 1950s and the first cladograms used morphological data. A researcher would identify characters or traits, such as number of toes per foot, and divide the trait into character states, such as five toes, four toes, three toes, two toes, or a single toe. Phylogenetic analysis using molecular data uses amino-acid sequences (from proteins) or nitrogenous-base sequences (from DNA or RNA) as characters. For the latter, the character states are adenine, thymine, cytosine, and guanine (or A, T, C, and G) 

 

A short DNA sequence has been worked out for each, with ATTAATGAT for the fox squirrel, ATAAATGAA for the eastern gray squirrel, and ATAAATGAA for the western gray.  

Each DNA sequence has 9 characters

Each DNA sequence has 9 characters (or “site” for DNA). For example, character 1 is scored as A (adenine) in all three species, and character 2 is scored as T (thymine) in all three species; the three species are scored the same for remaining characters 4 to 8. However, characters 3 and 9 are scored as T for the fox squirrel and as A for the eastern gray and western gray squirrels. 

Fox:                   ATT AAT GAT 

Eastern Grey:   ATA AAT GAA 

Western gray:  ATA AAT GAA 

We add another squirrel from a different but (closely?) related genus and we use this to compare. This is called outgroup comparison, it is premised on the basis that we can use a relative of the group we are studying that is not in the group, whatever this relative has is the primative trait? 

ANOTHER SLIDE THAT MAY BE HELPFUL ABOUT INGROUP AND OUTGROUP hopefully on moodle soon  and another … maybe a few extra slides 

Assuming nature works parsimoniously ( the simplest solution is your answer) that’s why we choose tree 1 for the principle of parsimony. It also satisfies the criteria of having an evolutionary novelty to appear in one of the ancestors of the in group clade 

For example, among species of the genus Sciurus…

For example, among species of the genus Sciurus, the fox squirrel, eastern gray squirrel, and western gray squirrel, which two are most closely related? There are three possibilities: (1) the eastern gray and western gray squirrels are sister species; (2) the fox and western gray squirrels are sister species; or (3) the fox and eastern gray squirrels are sister species

A short DNA sequence has been worked out for each, with ATTAATGAT for the fox squirrel, ATAAATGAA for the eastern gray squirrel, and ATAAATGAA for the western gray (Fig. 2.11). Each DNA sequence has 9 characters (or “site” for DNA). For example, character 1 is scored as A (adenine) in all three species, and character 2 is scored as T (thymine) in all three species; the three species are scored the same for characters 4 to 8. However, characters 3 and 9 are scored as T for the fox squirrel and as A for the eastern gray and western gray squirrels

We add another squirrel from a different but (closely?) related genus and we use this to compare. This is called outgroup comparison, it is premised on the basis that we can use a relative of the group we are studying that is not in the group, whatever this relative has is the primative trait? 

What do we do with this molecular data?

What do we do with this molecular data? How can it inform us as to the sister group relationships among these three squirrels? Recall that phylogenetic systematics groups taxa together on the basis of homologies or evolutionary novelties. How do we determine which character states are evolutionary novelties? We need another taxon for comparative purposes. One that is related closely enough to our species of Sciurus but clearly not a member of the same genus. The solution is to choose a squirrel from a different genus. Here, a ground squirrel of the genus Spermophilus (nucl. sequence ATTAATGAA) is chosen.

Method of using a closely related but not part of the same group…

This method is called outgroup comparison. Here, the ground squirrel is the outgroup. The taxa of interest (here, fox, eastern gray, and western gray squirrels) form the ingroup. Characters with traits that vary in the ingroup are used to form trees. Those that do not vary (sites 1, 2, and 4-8) are uninformative.

Examination of the characters with the outgroup sequence

Examination of the characters with the outgroup sequence inferred to be ancestral to the Sciurus ancestor, it is clear that only characters 3 and 9 have the potential to work out the interrelationships with the ingroup; the other characters can be ignored because they are uninformative. By “mapping” the informative characters onto the three possible trees (hypotheses), we can now begin the process of determining which tree would be chosen as our preferred hypothesis.

Parsimonious

Assuming nature works parsimoniously ( the simplest solution is your answer) that’s why we choose tree 1 for the principle of parsimony. It also satisfies the criteria of having an evolutionary novelty to appear in one of the ancestors of the in group clade 

Things to be aware of:

Things to be aware of: the ingroup is assumed to be monophyletic; this means we do not need an evolutionary novelty (homologous character) to appear on the MRCA for the ingroup. We do need a homologous character to appear on the internode within the ingroup.

Finally, a tenet of phylogenetic systematics is that homology should be maximized: this can be translated to mean our preferred tree should show the fewer or fewest number of evolutionary novelties. This procedure is known as the principle of parsimony

Accordingly, Tree 1 is our preferred tree;

Accordingly, Tree 1 is our preferred tree; we can disregard trees 2 and 3. Looking at the evolutionary novelties mapped onto the tree, we infer that the eastern and western gray squirrels are sister taxa and that they are grouped together because they have the derived state for character 3: both exhibit A (adenine) at site 3, whereas both the outgroup and the fox squirrel exhibit T (thymine) at the same site. (the evolutionary history for site 9 in the fox squirrel is T → A). The derived state A (versus the primitive state T) at site 3 is a shared evolutionary novelty of the eastern and western gray squirrels that is termed a synapomorphy.

The T at site 9 for the fox squirrel is also a derived trait…

The T at site 9 for the fox squirrel is also a derived trait (the evol. history for site 9 in the fox squirrel is A → T). However, this particular derived evolutionary novelty is not shared with other taxa and is unique to the fox squirrel; it does not help to reconstruct clades. Such a derived evolutionary step is an autapomorphy.