Phylogenetics Reconstructing the Tree of Life Carol E. Lee University of Wisconsin Copyright©2020; do not upload without permission • In the Speciation lecture, I talked about a “Phylogenetic Species Concept” –What is a “Phylogeny?” –How do you construct one? –Why on earth should I care? 2 Why you should care: • All biological relationships can be determined by constructing phylogenies: Even if phylogenies are not always the best way to define species boundaries, they do indeed tell you the genetic and evolutionary relationships among groups and individuals – Your ancestry – Diseases—figure out evolutionary origins and evolutionary pathways of disease, like HIV, Ebola, SARS, etc. – Crops and livestock (food security)—rescue from inbreeding, create new varieties – Endangered Species— figure out how endangered populations are related and how to perform genetic rescue 3 Tree of Life Web Project http://www.tolweb.org/tree/ Tree of Life 2016 Hug et al. 2016 Nature Microbiology Bacteria Eukarya Archaea Outline 1. What is a phylogeny? 2. How do you construct a phylogeny? The Molecular Clock Statistical Methods Think about relationships among the major lineages of life and when they appeared in the fossil record Are Genetic Distances and fossil record roughly congruent? Fossil Record vs Molecular Clock • Molecular clock and fossil record are not always congruent – Fossil record is incomplete, and soft bodied species are usually not preserved – Mutation rates can vary among species (depending on generation time, replication error, mismatch repair) • But they provide complementary information – Fossil record contains extinct species, while molecular data is based on extant taxa – Major events in fossil record could be used to calibrate the molecular clock Evolutionary History of HIV HIV evolved multiple times from SIV (Simian Immunodeficiency Syndrome) Evolutionary Analysis Time Freeman& Herron, 2004 Charles Darwin (1809 -1882) On the Origin of Species (1859) – Living species are related by common ancestry – Change through time occurs at the population not the organism level – The main cause of adaptive evolution is natural selection Darwin envisaged evolution as a tree The affinities of all the beings of the same class have sometimes been represented by a great tree. I believe this simile largely speaks the truth…… …The green and budding twigs may represent existing species; and those produced during former years may represent the long succession of extinct species….. ….the great Tree of Life….covers the earth with ever-branching and beautiful ramifications Charles Darwin, On the Origin of Species; pages 131-132 Reconstructing the Tree of Life The only figure in The Origin of Species What did people believe before Darwin? Lamarck proposed a ladder of life Past Future Jean-Baptiste Lamarck • French Naturalist (1744-1829) • “Professor of Worms and Insects” in Paris • The first scientific theory of evolution (inheritance of acquired traits) Lamarck’s View of Evolution Being God • Continuum between physical Angels Realm and biological world (followed of Being Aristotle) Demons Man Animals • Scala Naturae (“Ladder of Life” or “Great Chain of Realm of Plants Becoming Being”) Minerals Non-Being What is wrong with a ladder? • Evolution is not linear but branching • Living organisms are not ancestors of one another • The ladder implies progress What is right with the tree? • Evolution is a branching process • If a mutation occurs, one species is not turning into another, but there is a split, and both lineages continue to evolve • So, evolution is not progressive - all living taxa are equally “successful” • Phylogenies (Trees) reflect the hierarchical structuring of relationships The only figure in The Origin of Species The Tree of Life is a Fractal Genealogical structures • Phylogeny – A depiction of the ancestry relations between species (it includes speciation events) – Tree-like (divergent) • Pedigree – A depiction of the ancestry relations within populations – Net-like (reticulating) Four butterflies connected to their parents offspring parents Population Individuals past future Population Species Lineage/ Lineage/ What happened here? Lineage-branching Phylogeny Speciation What happened here? Extinction Representation of phylogenies? A B C A B C A simplified The True History representation Some terms used to describe a phylogenetic tree Taxon (taxa) Tip Internal branch Internode Node (Speciation event) Root Outline 1. What is a phylogeny? 2. How do you construct a phylogeny? The Molecular Clock Statistical Methods What is a Phylogeny? • A phylogenetic tree represents a hypothesis about evolutionary relationships • Each branch point represents the divergence of two taxa (e.g. species) • Sister taxa are groups that share an immediate common ancestor Branch point (node) Taxon A Taxon B Sister taxa Taxon C ANCESTRAL LINEAGE Taxon D Taxon E Taxon F Common ancestor of taxa A–F Polytomy (unresolved branching point) Molecular Clock • Phylogenies rely on the “Molecular Clock,” namely the fact that Mutations on average, occur at a given rate • So, on average, more mutational differences between taxa means that they branched from a common ancestor longer ago Example: • So longer branches on Mitochondria: 1 mutation every phylogeny often à greater ~2.2%/million years evolutionary distance 31 Phylogeny of 53 humans (Homo sapiens) just based on mtDNA A different locus might yield a different tree The horizontal branch lengths reflect genetic distance ≈ # of mutations Cladogram of mitochondrial cytochrome oxidase II alleles in humans and the African Great Apes (Ruvolo et al. 1994) This is not a phylogeny, but a cladogram. A cladogram shows the hierarchical relationships among the taxa, but the branch lengths do not reflect evolutionary time. Molecular Clock Problem: mutation rate can vary among species • Mutation rate is faster: – Shorter generation time (greater number of meiosis or mitosis events in a given time) – Replication Error (e.g. Sloppy DNA or RNA polymerase; poor mismatch repair mechanisms) 35 Order Family Genus Species Panthera Felidae Panthera pardus Taxidea Carnivora Mustelidae Taxidea taxus Lutra Lutra lutra Canis Canidae Canis latrans Canis lupus A monophyletic clade consists of an ancestral taxa and all its descendants A A A B Group I B B C C C D D D E E Group II E Group III F F F G G G (a) Monophyletic group (clade) (b) Paraphyletic group (c) Polyphyletic group A B Group I C D E F G (a) Monophyletic group (clade) (In the lecture on species concepts we discussed that the “smallest” monophyletic group is a “phylogenetic species”) Examples of Paraphyletic Groups (not recognized as legitimate groups in the Phylogenetic Species Concept, which only recognizes monophyletic groups) Synapomorphies • Synapomorphies are shared derived homologous traits • They can be DNA nucleotides or other heritable traits • They are used to group taxa that are more closely related to one another synapomorphies Sometimes similar looking traits are not homologous, and are not synapomorphies, but are the result of convergent evolution How do we construct Phylogenies? Phylogenetic Methods • Parsimony: Minimize # steps • Distance Matrix: minimize pairwise genetic distances • Maximum Likelihood: Probability of the data given the tree • Bayesian: Probability of the tree given the data Parsimony Uses Discrete Characters (like mutations, or some heritable trait) Select the tree with the minimum number of character-state transitions summed across all characters Fig. 26-15-1 Parsimony: Example 1 Species I Species II Species III Three phylogenetic hypotheses: I I III II III II III II I Fig. 26-15-2 Site 1 2 3 4 1/C Species I C T A T I 1/C I III Species II C T T C II III II 1/C Species III G C A A III II I Ancestral A G T T 1/C 1/C sequence Fig. 26-15-3 Site 1 2 3 4 1/C Species I C T A T I 1/C I III Species II C T T C II III II 1/C Species III G C A A III II I Ancestral A G T T 1/C 1/C sequence 3/A 2/T 3/A I 2/T I 3/A 4/C III II III II 4/C 4/C 2/T III II I 3/A 4/C 2/T 4/C 2/T 3/A Fig. 26-15-4 Site 1 2 3 4 1/C Species I C T A T I 1/C I III Species II C T T C II III II 1/C Species III G C A A III II I Ancestral A G T T 1/C 1/C sequence 3/A 2/T 3/A I 2/T I 3/A 4/C III II III II 4/C 4/C 2/T III II I 3/A 4/C 2/T 4/C 2/T 3/A I I III II III II III II I 6 events 7 events 7 events Parsimony: Example 2 Three possible trees O C B A O A OO A B C C C B A B Tree 1 Tree 2 O B A C O A B Tree 3 C Map the characters (mutations) onto tree 1 1 2 3 4 5 O C B A O T G G A A A G C G A A 1 B G C A A A 2 C G C A C T Map the characters (mutations) onto tree 1 1 2 3 4 5 O C B A O T G G A A 4 3 A G C G A A 5 1 B G C A A A 2 C G C A C T 3 Total # number of steps = 6 Actually, there is more than one way to map character 3 3 O C B A O C B A O G 3 3 A G 3 B A C A 3 Either way the character contributes 2 steps to the overall tree length Map the characters onto tree 2 1 2 3 4 5 O A B C O T G G A A A G C G A A 45 B G C A A A 1 3 C G C A C T 2 # steps = 5 Tree 3 1 2 3 4 5 O B A 3 C O T G G A A 3 A G C G A A 45 B G C A A A 1 C G C A C T 2 Length = 6 steps Which tree had the shortest branch lengths (most parsimonious)? Most parsimonious tree O C B A O A O A B C C B Tree 1: length = 6 Tree 2: length = 5 O O B A CA Tree 3: length = 6 B C Where do the Whales belong? Example from Freeman & Herron, Fig.