Q1.1. What does the following phylogenetic tree tell us about (a) the evolutionary relationships between the organisms represented, and (b) the rates of evolution in this group? [3 marks]

Although the root isn't indicated, this actually is a rooted tree. You can tell from the structure of the tree: the tree is structured to show the clades leading back to a common ancestor at the far left of the tree; if it were an unrooted tree you wouldn't be able to figure out the position of the common ancestor from the tree shape. The ancestor (root) must be in the left hand-most vertical line (indicated in red below); if it wasn't, then some of the lineages shown would be more distantly related to each other than to the root (which cannot be).  However, even if you thought the tree was unrooted your conclusions should have been the same.

The tree is a phylogram - i.e. the branch lengths are scaled. The tree tells us which species are most closely related in evolutionary terms by how recently they shared a common ancestor e.g. humans are more closely related to chimps than they are to orangutans. The nodes indicate speciation events and the branch lengths indicate the degree of divergence (number of substitutions per site) of each species from the ancestor, e.g. the branch representing the human lineage is longer than the branch leading to the chimp, indicating that the human has diverged further from the common ancestor of the human and the chimp than the chimp has in the same amount of time.

(a) A simple description of the relationships shown is all that was required here. All species shown are descended from a common ancestor (unnamed). An early speciation event split the lineage into two major monophyletic clades: the ‘true monkeys and apes’ and the ‘pro-simians’. Within the ‘true monkeys and apes’ a second speciation event split the group into a lineage leading to the modern day Silvery marmoset and a lineage leading to the clade of Orangutans, Chimpanzees and Humans. Within this clade, Humans and Chimps are more closely related to each other than either is to the Orangutan.Within the ‘Pro-simian’ group an early speciation event split the group into a lineage leading to the Zanzibar bushbaby and a lineage leading to sister species Mongoose lemur and Golden bamboo lemur.

(b) The lengths of the branches give some indication of the rate of evolution. Branch length is proportional to the amount of character change. The particular character change upon which this tree is based is most likely DNA or protein sequence of a chosen gene. However, how the tree was constructed doesn’t matter for answering the question.

Let’s consider the true monkeys and apes first: both the human and chimp are extant species but since diverging from their common ancestor the human has diverged further in the same amount of time. This indicates that humans have evolved (accumulated DNA sequence differences at the loci analyzed) at a faster rate than the chimps have. Similarly, in the Pro-simian group the Mongoose lemur has undergone the most change and the Zanzibar bushbaby the least amount of change in the time since the three shared a common ancestor. If we compare the ‘true monkeys and apes’ clade with the ‘pro-simian’ clade we can conclude that the rate of evolution has been faster within the true monkeys and apes group as a greater degree of divergence (longer branch lengths) since all 7 species shared a common ancestor is apparent. The Pro-siminan species have co-existed for the same length of time as the monkeys and apes (all are extant species) but in this time have accumulated fewer character changes.

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the root is here

Part 2a

Q2.1Q2.2Most people get these right. Ask me if you’re still stuck.

Part 3

Q3.1. Estimate the phylogeny of these taxa by plotting the changes on each of the three possible phylogenies for species 1, 2, and 3 and determining which tree requires the fewest evolutionary changes.

I gave some feedback on this question on your answer sheets. Most people got it pretty close to correct, and there was more than one correct answer for each tree. The fewest number of changes to construct the middle tree was 10, whereas the outer trees required a minimum of 12 changes each. Some of you forgot that not every edge required a mutational change. ALSO, don’t forget that ‘back mutation’ (reversion of a change back to the ancestral sequence) can also happen.

The best way to approach it is to look at each node and figure out what sequence the ancestral species at each node must have had in order to derive each species in the clade. Please ask me to go over it in class if you’re still not sure.

Q.3.2. Which tree is the most parsimonious? Explain your reasoning

Tree 2 as it requires a minimum of ten mutational changes whereas the other possible trees require a minimum of twelve changes each.