Phylogeny & Systematics: The Tree of Life

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1 Phylogeny & Systematics: The Tree of Life An unexpected family tree. What are the evolutionary relationships among a human, a mushroom, and a tulip? Molecular systematics has revealed that despite appearances animals, including humans, and fungi, such as mushrooms, are more closely related to each other than either are to plants.

2 What We Can and Cannot Learn from Phylogenetic Trees: Phylogenetic trees show patterns of descent, not phenotypic similarity Phylogenetic trees do not indicate when species evolved or how much change occurred in a clade Phylogenetic trees do not assumed that a taxon evolved from the taxon next to it, e.g. Dogs did not evolve from wolves and vice versa.

3 Applying Phylogenies: Phylogeny provides important information about similar characteristics in closely related species A phylogeny was used to identify the species of whale from which whale meat originated by analyzing the relatedness of mtdna sequences from different organisms. Specific whale sp. are protected by the inter. marine mammal act. It is illegal to harvest them.

4 What is the species identity of food being sold as whale meat? Scientists constructed a gene tree, a phylogenetic tree that shows patterns of relatedness among mtdna sequences rather than among taxa. Only Minke whales can be legally sold in Japan. Conclusion: This analysis indicated that mtdna sequences of 6 of the unknown Samples (in red), were most closely related to mtdna sequences of whales that are not legal to harvest. Minke (Southern Hemisphere) Unknowns #1a, 2, 3, 4, 5, 6, 7, 8 Minke (North Atlantic) Unknown #9 Humpback Unknown #1b Blue Unknowns #10, 11, 12, 13 Fin

5 Phylogenies are inferred from morphological and molecular data: To infer phylogenies, systematists gather information about morphologies, genes, behavior and biochemistry of living organisms Phenotypic and genetic similarities due to shared ancestry are called homologies Organisms with similar morphologies or DNA sequences are likely to be more closely related than organisms with different structures or sequences

6 Sorting Homology from Analogy: When constructing a phylogeny, systematists need to distinguish whether a similarity is the result of homology or analogy Homology is similarity due to shared ancestry eg, bat wing and whale fin Analogy is similarity due to convergent evolution eg, marsupial v. placental mammal Bat and bird wings are homologous as forelimbs, but analogous as functional wings. Analogous structures or molecular sequences that evolved independently are also called homoplasies eg. the eye

7 Convergent evolution in burrowers: Convergent evolution occurs when similar environmental pressures and natural selection produce similar Australian marsupial mole (analogous) adaptations in organisms from different evolutionary lineages - it is no indicator of phylogenetic relations! North American eutherian mole A long body, large front paws, small eyes, and a pad of thick skin that protects the nose all evolved independently in these species.

8 Phylogeny & Systematics: Phylogeny u evolutionary history of a species u based on common ancestries inferred from fossil record morphological & biochemical resemblances molecular evidence Systematics u connects classification system to phylogeny by categorizing & naming organisms

9 Fossil record: Sedimentary rock are richest source of fossils u fossil record is a substantial, but incomplete, chronicle of evolutionary history incomplete historical documents of biology u history of life on Earth is punctuated by mass extinctions u Homology can be distinguished from analogy by comparing fossil evidence and the degree of complexity Otzi ; 5,300 year old ice mummy found on an Alpine ridge dividing Austria from Italy at 10,500 feet above sea level. 2015; Discovered 19 living relatives in Austria.

10 Paleontology: Study of fossils u fossils provide the strongest evidence of change u links past & current organisms Woolly mammoth tusks

11 Fossils:

12 Building phylogenies: Morphological & molecular homologies u similarities based on shared ancestries bone structure DNA sequences u beware of analogous structures convergent evolution Analogous structures or molecular sequences that evolved independently are also called homoplasies marsupial mole placental mole

13 Evaluating molecular homologies: Aligning DNA sequences u more bases in common = more closely related u analyzed by software

14 Systematics: Connecting classification to phylogeny u hierarchical system u Carolus Linnaeas u latin binomial genus species

15 Building trees: Connection between classification & phylogeny Tracing possible evolutionary relationships between some of the taxa of the order Carnivora, a branch of the class Mammalia

16 Illustrating phylogeny: Cladistics Cladograms (CLAY-doe-grams) show: u Clade - patterns of shared characteristics u groups organisms by common descent u probable relationships Classify organisms according to the order in time at which branches arise along a phylogenetic tree

17 Shared Ancestral and Shared Derived Characters: In comparison with its ancestor, an organism has both shared and different characteristics A shared ancestral character is a character that originated in an ancestor of the taxon eg. vertebrates A shared derived character is an evolutionary novelty unique to a particular clade, eg. hair in mammals A derived trait is a trait that the current organism has, but the previous one did not have. An ancestral trait is a trait that you, and your ancestors had. A vestigial structure is a structure that had some sort of use in your ancestor, but none in your current body.

18 Inferring Phylogenies Using Derived Characters: When inferring evolutionary relationships, it is useful to know in which clade a shared derived character first appeared A shared derived character is shared by the ancestral species and a single group: it is the only reliable guide to inferring phylogeny. Phylogenies showing the terminology used to describe different patterns of ancestral and derived character or trait

19 Constructing a phylogenetic tree using shared derived characters: CHARACTERS Vertebral column (backbone) Hinged jaws Four walking legs Amnion Lancelet (outgroup) Lamprey Bass TAXA Frog Turtle Leopard Vertebral column Hinged jaws Four walking legs Lancelet (outgroup) Lamprey Bass Frog Turtle Hair Amnion Hair Leopard (a) Character table (b) Phylogenetic tree

20 Phylogenetic Trees with Proportional Branch Lengths In some trees, the length of a branch can reflect the number of genetic changes that have taken place in a particular DNA sequence involved in development. The lengths are proportional to the amount of genetic change in each lineage; the change has evolved at different rates. Question: Which lineage shows the greatest genetic change since they diverged? Chicken Human Mouse Lancelet Frog Zebrafish Drosophila

21 In other trees, branch length can represent chronological time, and branching points can be determined from the fossil record. (This tree is based on the same molecular data as the previous slide). The lengths are proportional to time. Each lineage has the same total length from the base of the tree to the branch tip, indicating that all the lineages have diverged from the common ancestor for equal amounts of time. PALEOZOIC MESOZOIC CENO- ZOIC Drosophila Lancelet Zebrafish Frog Chicken Human Mouse Present Millions of years ago

22 Molecular Systematics: Hypothesizing phylogenies using molecular data u apply principle of parsimony simplest explanation based on statistics fewest evolutionary events that explain data hypothetical bird species 3 possible phylogenies (there are more)

23 Maximum Parsimony and Maximum Likelihood: Systematists can never be sure of finding the best tree in a large data set They narrow possibilities by applying the principles of maximum parsimony and maximum likelihood the shortest possible tree that explains the data is considered best

24 Maximum parsimony assumes that the tree that requires the fewest evolutionary events (appearances of shared derived characters) is the most likely model The principle of maximum likelihood states that, given certain rules about how DNA changes over time, a tree can be found that reflects the most likely sequence of evolutionary events In modern cladistics, advances in computer programs and molecular genetics are used to search for trees that are parsimonious and likely

25 Technique Research method: Determine all the base change events and by applying parsimony to a problem in molecular systematics Figure /C 1/C I I III Species I Species II Species III II III 1/C III II 1/C 1/C II I 1 Three phylogenetic hypotheses: I I III 4 2/T 3/A I 3/A 2/T I 4/C 3/A III II III III II II I 4/C 3/A 4/C II III 2/T 4/C 4/C III II 2/T 2/T 3/A II I 2 Species I Species II Site C C T T A T T C Results I II I III III II Species III Ancestral sequence A A G G A T C T III II I 6 events 7 events 7 events

26 Parsimony: Choose the tree that explains the data invoking the fewest number of evolutionary events the shortest possible tree that explains the data is considered best

27 Parsimony: Phylogenetic trees are hypotheses Which is the most parsimonious tree?

28 Modern Systematics: Shaking up some trees! Crocodiles are now thought to be closer to birds than other reptiles

29 Of Mice and Men good book Evolving genomes u now that we can compare the entire genomes of different organisms, we find humans & mice have 99% of their genes in common 50% of human genes have a close match with those of yeast! w the simplest eukaryote

30 Molecular clocks: Trace variations in genomes to date evolutionary changes Rate of change is calculated and then extrapolate back What does this assume? Index of base changes between HIV gene sequences HIV-1M samples were collected from patients between early 1980s & late 1990s. The gene evolved at a relatively constant rate. Concluded that HIV-1M Cell division error strain first infected humans in 1930s. HIV Range Adjusted best-fit line (accounts for uncertain dates of HIV sequences) Year

31 Potential Problems with Molecular Clocks: The molecular clock does not run as smoothly as expected if mutations were neutral Irregularities result from natural selection in which some DNA changes are favored over others The use of multiple genes or genes that evolved in different taxa may improve estimates

32 Universal Tree of Life. Says who? 3 Domains u Bacteria u Eukarya u Archaea This branch point forms a polytomy: an unresolved pattern of More than two divergence

33 From Two Kingdoms to Three Domains: Early taxonomists classified all species as either plants or animals Later, five kingdoms were recognized: Monera (prokaryotes), Protista, Plantae, Fungi, and Animalia Most recent, the three-domain system has been adopted: Bacteria (the largest), Archaea, and Eukarya The three-domain system is supported by data from many sequenced genomes

34 The three domains of life: Cell division error Euglenozoans Forams Diatoms This branch point forms a polytomy COMMON ANCESTOR OF ALL LIFE Ciliates Red algae Green algae Land plants Amoebas Fungi Animals Nanoarchaeotes Methanogens Thermophiles Proteobacteria (Mitochondria)* Chlamydias Spirochetes Gram-positive bacteria Cyanobacteria (Chloroplasts)* Domain Eukarya Domain Archaea Domain Bacteria

35 Scientists Unveil New Tree of Life By CARL ZIMMER APRIL 11, 2016 The new tree of life that researchers published. It shows that much of Earth s biodiversity is bacteria, top, half of which includes candidate phyla radiation that are still waiting to be discovered. Humans are in the bottom branch of eukaryotes. CreditJill Banfield/UC Berkeley, Laura Hug/University of Waterloo we are here

36 Hominid Phylogeny

37 Summary of a phylogenetic tree: Branch point: where lineages diverge ANCESTRAL LINEAGE This branch point represents the common ancestor of taxa A G Common ancestor to A-C 5 4 Sister taxa-share an Immediate common ancestor to B-C Taxon A Taxon B Taxon C Taxon D Taxon E Taxon F Taxon G This branch point forms a polytomy: an unresolved pattern of divergence. Sister taxa Basal taxon Basal taxa- lineage that diverges early in the history of the group

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