ECOL335 Evolutionary Biology Lecture 3 Building Phylogenies PDF

ECOL335 Evolutionary Biology Spring 2025 January 23 Lecture 3 Building and using phylogenies Our learning objectives today Understand and apply the basic principles of phylogenetic reconstruction. Get introduced to current computational methods. Use phylogenies to infer evolutionary events...

ECOL335 Evolutionary Biology Spring 2025 January 23 Lecture 3 Building and using phylogenies Our learning objectives today Understand and apply the basic principles of phylogenetic reconstruction. Get introduced to current computational methods. Use phylogenies to infer evolutionary events such as changes in character state, transitional forms. How to reconstruct evolutionary trees… The basics Looking for similarities in characters 1. Populations or species are sampled for characters recorded from individuals. Character: morphological, behavioral, genetic (DNA sequence)… Character state = ‘trait’ 2. We look for similarities among populations/species in terms of ‘shared characters’ 3. Hypothesize that shared characters are due to common ancestry, i.e. these similarities are homologies. Shared characters and common ancestry The character arises on a branch and remains present in all descendants: synapomorphy = shared derived character FIGURES 5.2  Shared characters and common ancestry (or not) The character arises on a branch The character evolves The character was present in and remain present in all independently on two branches: the common ancestor but got descendants: synapomorphy homoplasy lost along some branches: (shared derived character) symplesiomorphy FIGURES 5.2-5.4 Let’s look at a simple example... Characters Fish Frog Kangaroo Human Vertebrae 1 1 1 1 Character shared by all, it must be ancestral to the clade. Two pairs of 0 1 1 1 limbs These two characters are derived and shared. Mammary 0 0 1 1 glands Placenta 0 0 0 1 Character uniquely derived, it must have evolved in that one species’ branch.  Building evolutionary trees… The principle of evolutionary tree (phylogeny) reconstruction for a given set of populations or species is to identify similarities among them and hypothesize that these similarities are due to common ancestry. Similarities (synapomorphies) that are shared among fewer species can be hypothesized to have evolved more recently. To reconstruct the tree, start by grouping species with the similarity that is shared the least, then build larger groups that branch further back in time, as defined by similarities that are shared by an increasingly larger number of species. Let’s reconstruct that tree! What is the most recent synapomorphy and what are the species it characterizes? Start drawing the tree by grouping them out of a common ancestor. Repeat for the next to most recent synapomorphy. Work backward in time to complete the tree. Rooted trees from unrooted trees FIGURE 4.3 FIGURE 4.14 Unrooted Tree of Life. Unrooted tree of proteobacteria. Rooted trees from an unrooted tree Rooted trees from an unrooted tree Redraw the tree If the root is in A If the root is in B If the root is in C Rooted trees from an unrooted tree FIGURE 4.15 How to root an evolutionary tree A species that does not belong in a clade is equally related to all species in that clade. In particular, an outgroup is a species (or group of species) that is related to the clade of interest but which branched off earlier in evolutionary history. To identify the root of a clade’s tree, construct the evolutionary tree including the outgroup; where the outgroup branches out indicates the root. How to reconstruct evolutionary trees… Using DNA sequences Characters can be molecular To build phylogenies we need shared derived characters. Characters can be sites and character states can be nucleotides (A, G, C, T) along a DNA sequence. Aligning sequences to maximize homology First, we need to reduce the risk of inferring spurious derived characters from our sequences. We do this by aligning the sequences to maximize their homology. For example, what needs to be done to the COW sequence to align it to the WHALE sequences? For example, what needs to be done to the COW sequence to align it to the WHALE sequences? Parsimony method Step 1: Take a large sample of possible trees, with a given outgroup. Step 2: For each tree, find the fewest susbstitutions that may have occurred along each branch. Step 3: Find the tree with lowest total number of substitutions. Maximum Likelihood methods These methods take evolutionary time into account. Branch length = how many substitutions have occurred. long branch = « a lot of molecular evolution has happened »  Molecular evolution is driven by substitutions in the DNA. Models of molecular evolution Different models make different assumptions about substitution rates between nucleotides (A, T, G, C).  Circle sizes ~ nucleotide frequencies when  Arrow thickness ~ rate of substitution. substitution process is in equilibrium. Maximum Likelihood methods Given a tree and its branch lengths, given a model of molecular evolution, we can compute the probability (likelihood) of the tree & branch lengths. Given a model of molecular evolution, we look for the tree & branch lengths that have highest likelihood. Example: Maximum Likelihood phylogeny of artiodactyls How much confidence can we have in a phylogenetic tree? Bootstrapping methods To evaluate a phylogeny, we could use more data (more characters, that is, more sites) and see whether the phylogeny changes. But what if we don’t have more data?? We take the alternate approach: use less, randomly selected data, and see how the phylogeny is affected. Example: Bootstrap probabilities for the Maximum Likelihood phylogeny of artiodactyls Using phylogenetic trees… Using trees reconstructed from known homologies to infer some other, unknown homologies.  For example: Sequence alignment allows to hypothesize sequence homologies, from which we infer a phylogeny. The phylogenies can then be used to infer homologies of other characters. Figure 4.5. Characters and trees. Another example: is the similarity of flight structures (wings) between bats and birds a homology? That is, did bats and birds inherit their wings from their common ancestor? Using known homologies and synapomorphies, we can Amphibians reconstruct a phylogeny of Mouse tetrapods. Bats The blue mark indicates the origin Snakes of the tetrapods’ synapomorphy Turtles (two pairs of limbs). Crocodiles In this phylogeny, bats and birds Birds have been placed.  Based on the tetrapod phylogeny, using the parsimony principle, we conclude that the wings of birds and bats are NOT homologous. We say that they are analogous. Similarity that is not homology is called homoplasy. Homoplasy can be due to convergent evolution = natural selection drives the independent evolution of different lineages towards similar traits, as in the case of wings in birds and bats. Using phylogenetic trees… Using trees to infer transitional forms. Let’s use the evolutionary tree of vertebrates as an example again. Lobe-finned fishes are the closest relatives of tetrapods. Among them is the coelacanth, a ‘living fossil’, and lungfish. The fins of lobe-finned fishes are homologous to tetrapod forelimb. If Darwin’s hypothesis of gradual evolution (‘modification’) is correct, there should be species with intermediate ‘fin- limb’ structures between CV coelacanth and lungfish ? CV on the one hand, and the CV extant tetrapod that diverged the earliest: CV salamanders. = transitional forms Clade of tetrapods In other words, Darwin’s theory of evolution as descent with modification predicts that we should find fossils of transitional forms that CV ? share some homologies ? CV with species that diverged ? earlier (here, coelacanth and ? lungfish) and other homologies with species that diverged later (here, living tetrapods). Here is what paleontologists found! First, they discovered Eusthenopteron, which is still very fish-like, and Acanthostega and Ichtyostega, which are already quite tetrapod-like. There was still a large gap in the fossil record, in terms of structure and time, between 380 and 360 Mya. Can you see all this on the figure? Scientists predicted where fossils of transitional form between Eusthenopteron and Acanthostega would be found… Mid-Devonian rocks in Northern Canada have appropriate age and habitat. In 2004, the ‘fishapod’ Tiktaalik was discovered by Harvard professor Neil Shubin’s team. Has arm-like structures: shoulder, elbow, wrist Neck moves independently of body  Evolution as descent with modification predicts the existence of transitional forms (nicknamed ‘missing links’). They fit not as ‘missing steps’ in a ladder, but as ‘missing branches’ in the evolutionary tree. Today’s keywords Homology, analogy Synapomorphy, homoplasy, symplesiomorphy Parsimony, maximum likelihood Bootstrapping Convergent evolution Transitional forms