Phylogenetics. Phylogenetic Trees. 1. Represent presumed patterns. 2. Analogous to family trees.

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1 Phylogenetics. Phylogenetic Trees. 1. Represent presumed patterns of descent. 2. Analogous to family trees. 3. Resolve taxa, e.g., species, into clades each of which includes an ancestral taxon and all its descendants. 4. In the figure at the right, we can define three non-trivial clades. 1 a. A (A+C+K), P (P+Y+S) and G (G+A+P). b. A and P are nested within G. 1 I define trivial clades are those consisting of a single taxon, in the present case, C and K (nested within A) and Y and S (nested within P). 1 Family trees and phylogenies. In a. your aunt, parent and grandparent may still be alive. In b. and c., species A, P and G are extinct.

2 Terminology. 1. Nodes are branching or terminating points. a. Internal nodes are points of lineage splitting. b. Terminal nodes are coeval taxa. 2. Taxa can be species or higher taxonomic groups. In the figure, they are labeled A, B, etc. 3. A pair of taxa that have a common ancestor not shared by any other taxon are called sister taxa, e.g., A and B. 4. F is called the outgroup. a. Outgroup inclusion completes the tree by identifying character states presumed ancestral and hence the characteristics of a presumptive common ancestor. 2

3 b. This is called rooting the tree. c. Typically, one chooses a taxon that, on other grounds, is believed to be Closely related to taxa of interest, but Less closely related to any of them than they are to each other. d. Example. If one were constructing a cladogram for birds, the outgroup could be Dromaeosauridae (includes Velocraptor and Deinonychus) if fossils included. Crocodilians if only living species considered. 3

4 Questions. 1. The node marked with a single asterisk in the figure on page 2 represents the most recent common ancestor of ; the node marked with two asterisks represents the most recent common ancestor of. 2. Identify the non-trivial clades by circling the appropriate nodes. 3. Among the tip taxa, identify sister taxa in addition to A and B. 4

5 4. Consider the mammalian cladogram below. Indicated are the following divisions: Class Mammalia, which is divided into Prototheria (monotremes) and Theria (mammals that bear their young alive), and Theria, which is divided into Metatheria (marsupials) and Eutheria (placental mammals). Indicate on the diagram, appropriate outgroup(s) for Eutheria and Theria. 5

6 Determining Relatedness. 1. Two approaches. a. Phenetic infers relatedness from overall similarity. b. Cladistic Distinguishes ancestral from derived characters. Infers relatedness from the presence of shared derived characters called synapomorphies. 2. In the table below, a. Two groups of species can be defined by presence or absence of character 2. b. The presence of characters 1, 3, 4 in all four species is uninformative. Trait Species A B C D

7 Questions. (# 5-7 relate to the preceding example.) 5. Assuming that characters 1, 3 and 4 are ancestral, and bearing in mind that characters can be lost as well as gained, draw two phylogenetic trees. Indicate on each where traits are acquired and lost. 6. Draw an additional tree assuming that characters 1, 3 and 4 are not ancestral. 7. Suppose now that you have an outgroup, O, for which characters 1-4 are present and distinguished by a fifth character not found in species A-D. Assume that trait 5 is derived. Draw two phylogenies corresponding to your answers to Question 5 above. Which is more likely? Why? 7

8 8. Assume that none of the trait absent characters in the table below reflect evolutionary reversals. Draw a phylogenetic tree. Which characters is (are) ancestral? Trait Species Four Live Limbs Birth Milk Pouch Platypus Echidna Kangaroo Dog Lemur

9 Principle of Parsimony. 1. In Question 7, you encountered the Principle of Parsimony: The most the plausible phylogeny is that which necessitates a. The fewest evolutionary reversals. b. Fewest independent character acquisitions. 2. An evolutionary reversal is the re-acquisition of an ancestral trait or the loss of a derived trait. 3. Fundamental point: a. Evolutionary history, H, uniquely determines character distribution, D. But b. D does not uniquely determine H. An infinite number of evolutionary histories are compatible with a given distribution of characters. c. Statistics used to determine the relative likelihood of alternative phylogenies especially when characters are easily reversed, e.g., nucleotide sequences. 9

10 Homology. 1. Similarity by virtue of common descent. a. The synapomorphies that define clades are homologies. b. Often used in the context of organs that have been modified to different ends in different species. 2. Serial homology (duplication and modification of parts in different ways) was first discussed by the poet, J. W. von Goethe, with reference to flower parts which he The modified forelimbs of humans, cats, whales and correctly believed were bats are homologous. modified leaves foliar theory of the flower. 10

11 Spirally-arranged floral organs illustrating serial homology in basal angiosperms. A: Magnolia watsoniana. B: Nymphaea caerulea; C: Nymphaea gigatea var. Perry s Baby; D: Nymphaea odorata. Note the gradual transition between petals and stamens. Bars indicate scale: A-C: 1.5cm; D: 600μm. From Dornelas and Dorneias (2005). 11

12 The nondescript flowers of wild poinsettias (Euphorbia pulcherrima) are surrounded by leaves that are partially red resembling petals and partially green resembling sepals. 12

13 Homology of head appendages in Onychophora and Arthropoda.. Abbreviations as follows: at, antenna; at1, first antenna; at2, second antenna; ch, chelicera; jw, jaw; le, leg; md, mandible; mx, maxilla; pp, pedipalp; sp, slime papilla. From Mayer et al (2013). 13

14 Homoplasy Similarity by independent acquisition. 1. Convergent evolution: acquisition of similar traits by distant lineages. 2. Parallel evolution: acquisition of similar traits by closely related lineages. 3. Distinguishing between homology and convergence requires appeal to other traits. Famous example of convergent evolution. Despite their superficial similarity (and the fact that ichthyosaurs gave birth to live young!), the two taxa are separable on the basis of other characters such as skull morphology. Which of the two sets of pointing hands is spouting nonsense? 14

15 4. Convergent or parallel? Distinction hinges on a. What one means by closely vs. distantly related. If ancestral species A 1 and A 2 closely related, the presence of an independently acquired character in descendant species D 1 and D 2 is said to be an example of parallel evolution; if A 1 and A 2 distant, convergent. b. Level one is looking at: i. At the morphological level, vertebrate and cephalopod eyes are convergent. ii. At genetic level, parallel the same regulatory genes determine their development. 15

16 5. Homologous or homoplastic? Depends on one s point of view. Pterodactyl, bat, bird wings are a. Homologous viewed as forelimbs the usual view; b. Homoplastic viewed as wings no winged common ancestor an alternative, but equally valid (IMO) view. c. See also Hall J. Hu. Evol. 52: ; Pearce Brit. J. Phil. Sci. 63: Right. The wings of flying vertebrates are traditionally cited as an example of convergent evolution. 16

17 Homology vs. Homoplasy in Mammal Dentition. 1. Four mammalian tooth types: a. incisors, b. canines, c. premolars, d. molars. 2. In living carnivores, P 4, and M1, specialized for slicing. a. Called carnassials b. A synapomorphy defining order Carnivora. c. Creodonts (now extinct) a. Independently evolved carnassials, but, b. Carnassial pair was M 1 /M2 or M 2 /M3. c. Convergent evolution if ref. is to which cheek teeth modified; parallel, if to cheek teeth. Carnassial pair, P 4 (blue) / M 1 (red) in a saber tooth tiger. Note the extreme reduction (observed in all felids) of the remaining postcanine dentition that consists primitively of four pre-molars and three molars. 17

18 When Data Conflict a Whale of a Tale. 1. Old theory: Whales descended from extinct carnivores. 2. New theory: Whales descended from artiodactyls even-toed ungulates Molecular evidence suggests that whales descended from artiodactyls. 4. Conflicts with morphological evidence: whales lack double pulley astragalus (DPA). a. DPA (ankle bone) is the synapomorphy that distinguishes artiodactyls from other ungulates. Foot bones of an Eocene artiodactyl. Its two articular surfaces (shaded red and blue) allow the astragalus to articulate with the tibia (above) and the os navicular (below). In most mammals, there is only one such surface. b. The term double pulley refers to the presence of two articular surfaces one with the tibia (leg bone), the other with the os navicular (another foot bone). 2 Hoofed mammals. 18

19 5. Deriving whales from artiodactyls necessitates an evolutionary reversal: DPA gained, then lost. 6. Whales from carnivores more parsimonious. 19

20 So which is it? 1. Fossil evidence: primitive whales had a double pulley astragalus. 2. In this case, paleontology confirms molecular biology; in other cases, e.g., putative derivation of amphibians from lungfish, not. 3. Fossils always trump anatomy, genetics, etc., of living organisms. Ankle bones of fossil whales (left, right) and a living pronghorn (center). Note the double pulley astragalus in all three. Restoration of a paddling proto-whale, Rodhocetus kasrani. Forelimbs were probably folded against the body during rapid swimming by pelvic paddling and caudal undulation when submerged. On land, Rodhocetus supported itself on hoofed digits II, III, and IV of the hands and the undersides of the feet. From Gingerich et al. (2001). 20

21 Astragalus anatomy in a typical mammal (left) and cetaceans / artiodactyls (right) 21

22 6. Types of Taxa. 1. Monophyletic. a. Includes the most recent common (MRCA) ancestor and all its descendants. b. Monophyletic taxa called clades. c. E.g., Mammals, birds. 2. Paraphyletic. a. Includes the MRCA, but not all descendants. b. E.g., Reptiles. 3. Polyphyletic. a. Does not include MRCA. b. E.g., Flying vertebrates the MRCA walked. 22

23 Question. 9. Historically, terrestrial vertebrates were divided into four classes: Amphibia, Reptilia, Mammalia and Aves (birds). Below is a cladistic analysis that reflects the fact that birds evolved from small, carnivorous dinosaurs. The four terrestrial vertebrate clades are shown in blue and their division into more familiar groups in black at the right. a. What are Tuataras and squamates? b. Which of the familiar groups are reptiles? c. If we lump these groups together, resulting class, Reptilia, is paraphyletic. Explain why. Be specific. 23

24 Reading Evolutionary Trees. 1. Unless otherwise indicated, branch length is arbitrary. 2. Order of tip taxa also arbitrary. a. The only information contained in a cladogram is the order of branching that defines the clades b. In particular, internal nodes can be rotated with no consequence to the clades defined. c. It follows that evolutionary relations These two cladograms look different, but contain exactly the same information. You can verify this by circling the clades in each. cannot be inferred by reading across the tips. See Figure caption, p

25 Question. 10. Three of the evolutionary trees below are equivalent. Which is different? 25