Chapter 1: The Archaeology of the Genome p. 1
- Examples include Woese and Fox’s work on rRNA SSU16 from 1977 etc.
Chapter 2: Trees
2.1.1 Tree terminology p 11-13
- “A tree is mathematical structure which is used to model the actual evolutionary history of a group of sequences or organisms. the actual pattern of historical relationships is the phylogeny or evolutionary tree” [aka pedigree for humans/domesticated animals or family tree].
- A tree consists of nodes connected by branches aka edges.
- Terminal nodes represent sequences or organisms for which we have data; they may be either currently existing or extinct. Terminal nodes are also called leaves, leaf nodes, or OTUs (Operational Taxonomic Units).
- Internal nodes represent hypothetical ancestors; the ancestor of all sequences that comprise the tree is called the root of the tree.
- A weighted tree is a tree whose branches are drawn such that branch length (aka edge length) imply the amount of time that has passed.
- The number of branches connected to a node indicate the degree of the node. For the most part, this book seems to use tree (mostly) in the computer science sense of a rooted directional tree data structure.
- Polytomies
- If a node has a degree greater than three (i.e., the node is connected to one ancestor node and more than 2 immediate descendant nodes), then this node is referred to as a polytomy.
- If a tree has no polytomies, it is referred to as fully resolved.
- Polytomies can represent two rather different situations: (1) First they may represent simlutaneous divergence–all the descendants evolved at the same time, aka a hard polytomy. (2) Secondly, they may represent uncertainty about phylogenetic relationships; the lineages did not necessarily all diverge at once, but we are unsure as to the actual order of divergence; this is called a soft polytomy.
- Typically, polytomies are treated as soft.
2.1.2 A shorthand for trees
- Uses parentheses. See JH notes, Bio #3, 1/28/2021.
2.1.3 Cladograms, additive trees, and ultrametric trees
- Different kinds of tree can be used to depict different aspects of evolutonary history.
- The most basic tree is the cladogram aka n-tree which simply shows relative recency of common ancestry. For example, given three sequences A, B, and C, a cladogram shows when each sequence diverged from the other. (See Figure 2.5 on p. 14)
- Additive trees (aka metric trees aka phylograms)contain additional information, namely branch length or edge length. The number associated with each branch (aka edge) correspond to some attribute of the sequences, such as the amount of evolutionary change. In the example shown in Figure 2.5, sequence A has acquired four substitutions since it shared a common ancestro with sequence B.
- Ultrametric trees aka dendrograms are a special subset of additive tree. Here, all the tips of the trees are quidistant from the root of the tree. This kind of tree can be used to depict evolutionary time, expressed directly as years or indirectly as the amount of sequence divergence using the molecular clock.
2.1.4 Rooted and unrooted trees p. 16
- Cladograms and additive trees can be either rooted or unrooted.
- A rooted tree has one particular node identified as the root from which ultimately all the other nodes descend, hence a rooted tree has a direction. This direction corresponds to evolutionary time; the closer a node is to the root of the tree, the older it is in time.
- An unrooted tree does not have an explicitly named root node. However, this does not mean no root exists “in reality”; we simply don’t know where to place it on the diagram. As such, there is a set of possible rooted variants all represented by this single unrooted tree. See Figures 2.6 and 2.7 for more detail (p. 17).
- Many methods of reconstructing phylogenies generate unrooted trees as output. In other words, the output implies many different rooted trees are possible. In order to root an unrooted tree (i.e., to decide which of the seven trees from Fig 2.7 is the correct interpretation of the unrooted tree shown in Fig. 2.6), we need some other source of information.
- Note that ultrametric trees are rooted by definition.
- See Chapter 6 for more on how to root unrooted trees.
- See Table 2.1 (p. 18) to see how many unrooted and rooted trees are possible given x number of OTUs, sequences, species, or organisms are leaf nodes.
2.1.5 Tree Shape p. 18-19
- Figure 2.8 (p. 19) shows three possible shapes aka topologies for a rooted tree of five OTUs. These 5 topologies account for all 105 possible trees listed in Table 2.1.
2.1.6 Splits
- Trees can be represented in a variety of ways other than as graphs. One useful representation is as a set of sets, aka splits aka partitions. Each split takes a set of OTUs and partions them into two mutually exclusive (and collectively exhaustive) sets.
- One can think of a split as two sets of OTUs obtained by chopping (‘splitting’) the tree at a given branch.
- See Figure 2.9 (p. 19) for an example.
- Only the splits that result form chopping the original tree within internal branches (not terminal branches) provide useful partitions.
- Chapter 6 provides some methods for reconstructing phylogenies after a split where each partition was arbitrarily assigned letters representing nucleotides.
2.2 Reconstructing the history of character change
- The tree relating a set of sequences tells us only part of what we want to know. The tree alone does not tell us when a particular evolutionary change took place or whether the occurrence of the same amino acid in two sequences is: (a) the result of inheritance from a common ancestor–called an ancestral homology or (b) the result of independent evolution which is called independently evolved homoplasy.
- There are two kinds of homoplasy.
- First, convergence and parallel evolution both result in the independent evolution of the same feature in two unrelated OTUs; the difference is whether this homoplasy was caused by the same (parallel) or different (convergent) ancestral condition.
- Second, secondary loss may cause a homoplasy wherein a recently derived character has been lost, thereby reverting the final OTU to what appears to be an earlier, ancestral state. For example, consider the loss of legs in snakes which is a secondary loss back to earlier pre-reptilian legless bilateran ancestors.
- Given a tree, we can distinguish between ancestral (aka primitive aka plesiomorphic) character states versus derived (aka apomorphic) character states.
- If an OTU has the same base as the common ancestor of all the sequences under study, then we say that OTU is in the primitive or plesiomorphic state. Such an ancestral character seen in an OTU is called a plesiomorphy.
- Alternately, if a character state is derived aka it is not in the ancestral state, then we call that the OTU an apomorphy. The OTU is then said to be in a derived or apomorphic state.
- If an OTU has is apomorphic and it is a unique derived character state (aka a sequence that we do not see in any of ther other OTUs), then we call this unique apomorphy an autapomorphy.
- If a derived, apomorphic character state is seen in multiple OTUs, then this shared apomorphy is called a synapomorphy.
- To address the question of homology vs. homoplasy, we need to be able to reconstruct the history of character change. Chapter 5 delves more deeply into this topic; this section is just a taste.
2.2.1 Ancestors
- Phylogenies presuppose ancstors. Ancestors are represented by internal nodes and are often hypothetical; some methods of phylogenetic reconstruction allow us to infer what they (or their sequence) may have looked like.
- In the past, phylogenetics assumed that all internal nodes were simply hypothetical ancestors. However, the rise of: (1) the ability to extract DNA from extinct taxa; and (2) the increasing number of sequences obtained from human viruses like HIV which evolve quickly enough to be tracked within direct human observation.
- If all sequences are from extant organisms, then they can be safely placed at the terminal leaf nodes of tres. However, if some of the sequences are extinct, it is possible, if unlikely, that they were ancestral to one or more of the extant sequences.
- Given this, is a sequence extracted from an extinct taxa an ancestor to modern taxa or is it an evolutionary sidebranch?
- Cladists have adopted the convention that it is equally parsimonious to consider extinct taxa which lack autapomorphies: (a) as sister taxa – such that they are each other’s closest relative; or (b) as ancestors.
- Note that under this rule, a taxon with no atapomorphies need not be an ancester; rather ther is nothing to refute that possibility. See Figure 2.13 on p. 23.
- Let us consider a rapidly evolving modern virus and view Figure 2.14 which lists 8 HIV sequences labeled D1 - D8. All eight sequences were extracted from the same patient over the course of 3 years. (p. 23)
- We can draw both a cladogram version and an evolutionary tree version depicting their relationships.
Chapter 3: Genes: Organization, Functions, and Evolution p. 37
Chapter 4: Genes in Populations p. 89
Chapter 5: Measuring Genetic Change p. 135
Chapter 6: Inferring Molecular Phylogeny p. 172
Chapter 7: Models of Molecular Evolution p. 228
Chapter 8: Applications of Molecular Phylogenetics p. 280