Reconstructing Evolutionary Trees. Chapter 14

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1 Reconstructing Evolutionary Trees Chapter 14

2 Phylogenetic trees The evolutionary history of a group of species = phylogeny The problem: Evolutionary histories can never truly be known. Once again, we are using current day patterns to reconstruct past processes. We have an advantage since in some cases: Because of fossils we also have insights into past patterns.

3 Common ancestry (homology) this is the interesting one it has phylogenetic information Primitive characters (predates the evolution of the group) carries no phylogenetic signal. Common environment (homoplasy, analogy) carries no phylogenetic signal Random events: reverse mutation can cause this The logic of phylogenetic inference The basic idea: Organisms that are similar in heritable traits are related. The more similar, the more closely related. There are lots of reasons we need to be careful Organisms may be similar because of:

4 Shared Derived traits The evolution of photosynthesis in algae

5 Synapomorphies Synapomorphy: A shared, derived character; in a phylogenetic analysis synapomorphies are used to define clades and distinguish them from outgroups.

6 Shared Ancestral Traits? QuickTime and a GIF decompressor are needed to see this picture. Who is a reptile? Shared Ancestral Traits Tetrapods Scales cold blooded Amniotic egg

7 Homoplasy Sometimes Homoplasy is easy to detect.

8 Sometimes homoplasy is not so easy Is photosynthesis homoplasious? Is warm bloodedness homoplasious?

9 Birds type 1 type 2 type 3a type 3a+b type 2 When did complex feathers (3a+b) arise?

10 Birds

11 Molecular data Particularly serious problems arise with molecular data Each trait (nucleotide) can take on only one of four states, ATCG ATTGCTATTC ATTGCTATTC Homoplas y mutation ATTGCTTTTC mutation

12 Molecular Data

13 Problem: there will always be conflicts. Good phylogenies are based on many traits, frequently hundreds of traits may be used. Some will have changes that are consistent, some won t. That is some traits will reflect homology, some will be homoplasius. How do we decide which are which? Inferring process from pattern: We need rules.

14 Parsimony We have run into parsimony before in group selection Parsimony: The simplest explanation is the most likely to be correct In phylogenetic inference the simplest explanation is the tree that requires the fewest evolutionary changes. Because of back mutations, homoplasies etc. there will be conflicts among traits in the optimal tree. Parsimony is the idea that we minimize the number of changes across all traits.

15 In this example the tree is the same as Fig. 14.3, as is yellow sequence. In this set of sequences there must be at least one reversion.

16 ATTGCGATTC GCCTGAATCC TATAGTCAAT ATTGCGATTC GC CGAATCC TATAATCAAT ATTGCGTTTC ATTGCGTTTC GCCTGAATCC GCCTGAATCC TATAATCAAT TATAATCAAT ATTGCGTTTC GC CGAATCC TATAATCAAT GCCTGAATCC GCCCGAATCC GCCTGAATCC GCCCGAATCC ATTGCGATTC ATTGCGTTTC TATAGTCAAT TATAATCAAT These two trees are equally parsimonious (4 changes). There is no way, using parsimony, to distinguish between these two trees. The answer as always: MORE DATA!

17 Outgroups Phylogenetics is based on similarity of shared derived characte Shared primitive characters do not contain information. How do we determine what is derived and what is primitive? The answer is to use an outgroup : A taxa that is closely related but outside of (diverged before) the set of taxa being analyzed. Selection of appropriate outgroups can be difficult, and the choice can change your answer. Often multiple outgroups are used.

18 Which is better? Morphology or Molecules Answer is as usual: It depends. Molecules: Lots of data (base pairs) Objective, but may be biased by available primers Traits are mostly neutral (no ecological convergence) Only 4 states (homoplasy common) Morphology: Usually less data Subjective choice of trait states Convergence due to ecological similarity an issue Potentially many states, homoplasy less common

19 Example: Whales The origin of whales was a major mystery as recently as 10 years ago. The problem was: modern whales are so modified that tracing their ancestry based on modern morphology is nearly hopeless. Two things broke this long standing mystery (1) The recent discovery of fossil whales (2) Modern molecular analysis.

20 Whale History The ancestor of whales has been reasoned to be many things, ranging from Carnivora to the more recently generally accepted Artiodactyles

21 Astragalus Morphology What should place Whales as Artiodactyles is the shape of the Astragalus, an ankle bone that allows Artiodactyles to run efficiently. This bone is lost in modern whales! Pulley shaped Astragalus lost Pulley shaped Astragalus Pulley shaped Astragalus Parsimony favors this!

22 Ambulocetus natans

23 Pulley shaped Astragalus

24 The Ambulocetus s astragallus tells us: 1. Whales are Artiodactyles 2. Whales had, but modern whales have lost, one of the shared derived traits that distinguishes the Artiodactyles. QuickTime and a TIFF (LZW) decompressor are needed to see this picture. Dorudon Basilosaurus

25 Molecular Data

26 The best analyses use both molecular and morphological For whales: data Morphology provides clear evidence in the form of morphology (ankle bones) that are unique to Artiodactyles Molecular data: has the mass of data to accurately place whales within the Artiodactyle tree.

27 Finding the most parsimonius tree can be problematical! With more than a few taxa the number of possible trees becomes enourmous. With more than a few traits, finding the best fit tree is VERY difficult. Methods for finding the best tree is an extremely active field of research, and there are a number of available packages. Approaches: Maximum Likelihood Bootstrapping MC Markov Chain MCMC -Markov Chain, Metropolis coupled methods

28 Why do we care? We would like to group organisms into evolutionarily related set Species: A set of interbreeding organisms Genus: A set of species derived from a single ancestral specie Family: A set of genera derived from a single ancestral specie (In practice: drived from a single ancestral genus) Etc. This is cladistic view. A raving cladist ONLY allows monophyletic groups NEVER allows polyphyletic groups NEVER allows paraphyletic groups

29 Types of groups Monophyletic Paraphyletic Polyphyletic Paraphyletic and polyphyletic are very nearly the same thing.

30 Many groups are paraphyletic reptiles

31 Should Paraphyletic groups be allowed? Some argue that they have no business being considered scientifically valid groups Others argue that such paraphyletic groups are inevitable, and are not bad. Question: Why are they inevitable?

32 Speciation by Remote Control A and A are two populations of the same species, A range includes a cave. A group of A moves into the cave and becomes species B. Are A and A different species?* *I got this conundrum from Alan Templeton

33 What to do with phylogenies Can we use phylogenetics and fossils to calibrate a molecular clock? Why are certain species found in some regions of the world and not others? Do hosts and predators cospeciate? Did unusual adaptations etc. evolve multiple times, or only once?

34

35 Cospeciation QuickTime and a TIFF (LZW) decompressor are needed to see this picture. Tanglegram showing host parasite associations between pocket gophers and their chewing lice (modified from Hafner, M.S. & Nadler, S.A. (1988) "Phylogenetic trees support the coevolution of parasites and their hosts." Nature 332: )

36 Phylogenetically independent comparisons QuickTime and a TIFF ( LZW) decompressor are needed to see this picture.

37 Is a trait homologous?

38 The Origins of AIDS cpz = chimpanzee smm = sooty mangabee agm = African green monkeys mnd = Mandrill syk = sykes monkeys

39 Phylogenetics & Disease Control The story revolves around Dr. David Acer, a Florida dentist who died in 1990 from complications of AIDS. Dr. Acer's death would have been far from remarkable at the time -- the AIDS epidemic was quite visible by the late 1980s, and one death earned no more attention than any other. Dr. Acer's story, however, extends beyond his private life and into his practice. You see, Dr. Acer had multiple patients that had been diagnosed as infected with HIV within a couple of years of his death. Many of the infected patients showed no risk factors associated with HIV infection. One elderly woman (hardly the at risk type that Tara described) had been married for more than 25 (her spouse was HIV negative), had never used intravenous drugs, never had sex with any at risk individuals, and never received a blood transfusion. Another patient was not an intravenous drug user, had no history of transfusion, and all recent sexual contacts were HIV negative. A phylogeny created using DNA sequences of the HIV virus taken from the dentist, patients, and other individuals within a 90 mile radius is shown below. Note the cluster containing sequences from the Dentist, Patient A, Patient B (the elderly woman), and Patient C (the second patient described above).

40 Flu Phylogenies Flu phylogenies show interference among sublines. This is the effect of host immunity

41 Bird Flu H5N1

42 Show Google Earth here if possible.

43

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