Phylogeny: Reconstructing Evolutionary Trees

1. Phylogeny:Reconstructing Evolutionary Trees Chapter 14

2. Phylogenetic trees • The phylogeny of a group of taxa (species, etc.) is its evolutionary history • A phylogenetic tree is a graphical summary of this history — indicating the sequence in which lineages appeared and how the lineages are related to one another • Because we do not have direct knowledge of evolutionary history, every phylogenetic tree is an hypothesis about relationships • Of course, some hypotheses are well supported by data, others are not

3. Questions • How do we make phylogenetic trees? • Cladistic methodology • Similarity (phenetics) • What kinds of data do we use? • Morphology • Physiology • Behavior • Molecules • How do we decide among competing alternative trees?

4. leopard lion wolf coyote Similarity • The basic idea of phylogenetic reconstruction is simple: • Taxa that are closely related (descended from a relatively recent common ancestor) should be more similar to each other than taxa that are more distantly related — so, all we need to do is build trees that put similar taxa on nearby branches — this is the phenetic approach to tree building • Consider, as a trivial example, leopards, lions, wolves and coyotes: all are mammals, all are carnivores, but no one would have any difficulty recognizing the basic similarity between leopards and lions, on the one hand, and between wolves and coyotes, on the other, and producing this tree; which, it would probably be universally agreed, reflects the true relationships of these 4 taxa

5. Causes of similarity • Things are seldom as simple as in the preceding example • We need to consider the concept of biological similarity, and the way in which similarity conveys phylogenetic information, in greater depth: • Homology • Homoplasy

6. cat hawk dove wings Homology • A character is similar (or present) in two taxa because their common ancestor had that character: • In this diagram, wings are homologous characters in hawks and doves because both inherited wings from their common winged ancestor

7. hawk bat cat wings Homoplasy • A character is similar (or present) in two taxa because of independent evolutionary origin (i.e., the similarity does not derive from common ancestry): • In this diagram, wings are a homoplasy in hawks and bats because their common ancestor was an un-winged tetrapod reptile. Bird wings and bat wings evolved independently.

8. Types of homoplasy • Convergence • Independent evolution of similar traits in distantly related taxa — streamlined shape, dorsal fins, etc. in sharks and dolphins • Parallelism • Independent evolution of similar traits in closely related taxa — evolution of blindness in different cave populations of the same fish species • Reversal • A character in one taxon reverts to an earlier state (not present in its immediate ancestor)

9. Reversal • A character is similar (or present) in two taxa because a reversal to an earlier state occurred in the lineage leading to one of the taxa: • In this diagram, hawks and cats share the ancestral nucleotide sequence ACCT, but this is due to a reversal on the lineage leading to cats hawk bat cat ACCT ACTT ACCT

10. Cladistics • By definition, homology indicates evolutionary relationship — when we see a shared homologous character in two species, we know that they share a common ancestor • Build phylogenetic trees by analyzing shared homologous characters • Of course, we still have the problem of deciding which shared similarities are homologies and which are homoplasies (to which we shall return)

11. Two kinds of homology – 1 • Shared ancestral homology — a trait found in all members of a group for which we are making a phylogenetic tree (and which was present in their common ancestor) — symplesiomorphy • For example: a backbone is a shared ancestral homology for dogs, humans, and lizards • Symplesiomorphies DO NOT provide phylogenetic information about relationships within the group being studied

12. Two kinds of homology – 2 • Shared derived homology — a trait found in some members of a group for which we are making a phylogenetic tree (and which was NOT present in the common ancestor of the entire group) — synapomorphy • For example: hair is (potentially) a shared derived homology in the group [dogs, humans, lizards] • Synapomorphies DO provide phylogenetic information about relationships within the group being studied • In this particular case, if hair is a synapomorphy in dogs and humans, then dogs and humans share a common ancestor that is not shared with lizards, and the common dog-human ancestor must have lived more recently than the common ancestor of all three taxa

13. lizard human dog hair backbone A tree for [dogs, humans, lizards] – 1 • The TWO major assumptions that we are making when we build this tree are: • hair is homologous in humans and dogs • hair is a derived trait within tetrapods

14. lizard human dog hair backbone A tree for [dogs, humans, lizards] – 2 • In the absence of other information, the assumption of homology of hair in humans and dogs is justified by parsimony (fewest number of evolutionary steps is most likely = simplest explanation) • Also we can check to see that hair is formed in the same way by the same kinds of cells, etc.

15. human lizard dog dog lizard human hair hair hair hair backbone backbone A tree for [dogs, humans, lizards] – 3 • These trees (in which hair is considered a homoplasy in dogs and humans) are less parsimonious than the one on the previous slide, because they require two independent evolutionary origins of hair

16. Character Polarity • What’s the basis for our second major assumption – that hair is a derived trait within this group (and that absence of hair is primitive)? • Fossil record • Outgroup analysis

17. Outgroups – 1 • An outgroup is a taxon that is related to, but not part of the set of taxa for which we are constructing the tree (the “in group”) • Selection of an outgroup requires that we already have a phylogenetic hypothesis • A character state that is present in both the outgroup and the in group is taken to be primitive by the principle of parsimony (present in the common ancestor of both the outgroup and the in group and, therefore, homologous)

18. Outgroups – 2 • In the present example, [dog, human, lizard] are all amniote tetrapods. The anamniote tetrapods (amphibia) make a reasonable outgroup for this problem • No amphibia have hair, therefore absence of hair [amphibia, lizards] is primitive (plesiomorphic) and presence of hair [dogs, humans] is derived (apomorphic) • So, presence of hair is a shared derived character (synapomorphy), and dogs and humans are more closely related to each other than either is to lizards

19. Amphibia lizard human dog hair amniotic egg backbone A tree for [dogs, humans, lizards] – 4 • The presence of hair is apomorphic (derived) because no amphibians have hair

20. Cladistic methodology • Determine character state polarity by reference to outgroup or fossil record • Construct all possible trees for the taxa in the in group • Map evolutionary transitions in character states onto each tree • Find the most parsimonious tree — the one with the fewest evolutionary changes • Only synapomorphies are informative

21. human lizard dog dog lizard human lizard human dog hair hair hair hair hair backbone backbone backbone A tree for [dogs, humans, lizards] – 5 (a) (c) (b) • Tree (a) is most parsimonious, so we’ll take that as our best estimate of the true phylogeny of [dog, human, lizard] • Of course, if we studied different characters, or used a different outgroup, our phylogenetic tree could change

22. The phylogeny of whales • Based on skeletal characteristics, several studies have placed whales (Cetaceans) as close relatives of ungulates (hoofed mammals) – Cetaceans are possibly the sister group of the even-toed ungulates (Artiodactyla) – “Artiodactyla hypothesis”

23. The Artiodactlya hypothesis for the evolutionary relationships of Cetacea (Fig. 14.4 a)Odd-toed ungulates (Perissodactyla [horses, rhinos]) are the outgroup

24. The whale + hippo hypothesis for the evolutionary relationships of Cetacea (Fig. 14.4 a)This tree was proposed based on nucleotide sequence of a milk protein gene

25. Sequence data for parsimony analysis (Fig. 14.6)Blue shaded bars represent invariant (uninformative sites, but note error for site 192), and red shaded bars represent synapomorphies (note, site 177 does not agree with tree as drawn). Tree is based on parsimony

26. Which phylogeny for whales, if either, is correct? • According to the whale + hippo hypothesis, whales are artiodactyls – not the sister group to artiodactyls • Artiodactyls are defined by a particular adaptation of the astragalus, an ankle bone • Since modern whales don’t have legs, they don’t have ankle bones, so without more data it’s hard to resolve the conflict between these two phylogenetic hypotheses

27. Whale phylogeny – more molecular data(Nikaido et al. 1999) • SINEs and LINEs — Short Interspersed Elements and Long Interspersed Elements • Transposable elements present in hundreds of thousands of copies in mammalian genomes – transposition is relatively infrequent • Independent transposition into the same location in two different genomes is unlikely (homoplasy) • Therefore, if SINEs and LINEs are present at the same location in two taxa, it is most likely homologous.

28. Presence/absence of SINEs and LINEs at 20 loci in a whale (Baird’s beaked whale) and six artiodactyls(Nikaido et al. 1999) (Fig. 14.8)

29. Presence/absence of SINEs and LINEs at 20 loci in a whale (Baird’s beaked whale) and six artiodactyls(Nikaido et al. 1999) (Fig. 14.8)

30. Presence/absence of SINEs and LINEs at 20 loci in a whale (Baird’s beaked whale) and six artiodactyls(Nikaido et al. 1999) (Fig. 14.8)

31. Presence/absence of SINEs and LINEs at 20 loci in a whale (Baird’s beaked whale) and six artiodactyls(Nikaido et al. 1999) (Fig. 14.8)

32. Presence/absence of SINEs and LINEs at 20 loci in a whale (Baird’s beaked whale) and six artiodactyls(Nikaido et al. 1999) (Fig. 14.8)

33. Whale phylogeny – more fossilsIchthyolestes, Pakicetus, Ambulocetus, Rhodocetus: whale-like ear bones; artiodactyl-like astragalusWhales are an evolutionary line of artiodactyls The whale + hippo tree is supported by additional data