7The terminology of phylogenetics is discombobulated.
8Graduate Student Assignments Instead of a stream of s that will yield unsatisfactory results, kindly set up appointments and let’s talk.
9In mathematics, a graph is an abstract representation of a set of objects called nodes (or vertices), some of which are connected to one another by links called branches (or edges). A path in a graph is a sequence of branches that connect any two nodes.
10Graphs = Trees + Non-Tree Graphs (or Networks) In a tree (b), any two nodes are connected by a single path.In a network (a), there may be multiple pathways connecting two nodes.
11The evolutionary relationships among a group of organisms are illustrated by means of phylogenetic trees (or dendrograms).
12External or Peripheral InternalExternal or PeripheralBranch
13The branching pattern of a tree is called its topology. Three different styles of trees, one topology.
17Terminal node = Operational taxonomic unit (OTU) Internal node = Hypothetical taxonomic unit (HTU)Peripheral ( or terminal) branch = relationship between OTU and HTUInternal branch = relationship between two HTUs
18Bifurcating and multifurcating trees A node is bifurcating (or binary or dichotomous) if it has only two immediate descendant lineages, but multifurcating (or polytomous) if it has three or more than two immediate descendant lineages. In a strictly bifurcating tree, each internal node is incident to exactly three branches, two derived and one ancestral.
19A bifurcation is always interpreted as a speciation event Two possible interpretations for a multifurcation (polytomy) in a tree:1. The polytomy represents the true sequence of events (hard polytomy), whereby an ancestral taxon gave rise to three or more descendant taxa simultaneously.2. The polytomy represents a lack of resolution. The exact order of two or more bifurcations cannot be determined unambiguously with the available data (soft polytomy).
20Rooted and unrooted trees In a rooted tree there exists a particular node, called the root, from which a unique path leads to any other node. The direction of each path corresponds to evolutionary time, and the root is the common ancestor of all the taxonomic units under study.
21In an unrooted tree with four external nodes, the internal branch is referred to as the central branch.
22How many unrooted topologies are here? bdd12baeecccaee34abddbc
23In an unrooted phylogenetic tree you cannot immediately assess evolutionary relationships. In a rooted phylogenetic tree, evolutionary relationships are evident.
24Phoronida (horseshoe worms) Brachiopoda (lampshells)Arthropoda (arthropods)Vertebrata (vertebrates)Which of the following taxa are evolutionarily the closest to Rick Perry? (a) Phoronida, (b) Brachiopoda, (c) Arthropoda, (d) all three taxa are equidistant from Perry, or (e) two taxa are closer to Perry than the third taxon.
25Cladograms & Phylograms (collectively Dendograms) Bacterium 1Bacterium 3Bacterium 2Eukaryote 1Eukaryote 4Eukaryote 3Eukaryote 2Phylograms show branch order and branch lengthsCladograms show branching order - branch lengths are meaningless
26Unscaled phylogramScaled phylogramThe branch length is number of changes (e.g., nucleotide substitutions) that have occurred along a branch. The total number of changes in a particular tree is called the tree length.
28Tree balanceTree balance is a measure of the degree of symmetry of a rooted phylogenetic tree. It serves as an indication of the pattern of speciation events in the group of taxa under study.Balanced tree Unbalanced or Pectinate (comb-like) tree
29Tree balanceIn an unbalanced tree, only one descendant of a node continues to speciate after a splitting event. In a balanced tree, all descendants of a node participate equally in cladogenesis.Balanced tree Unbalanced or Pectinate (comb-like) tree
30Tree balanceTree balance is an important indicator of the ease of phylogenetic reconstruction. Because, by definition, unbalanced trees contain long branches, they are more difficult to reconstruct phylogenetically than balanced trees. In fact, unbalanced and balanced tree are sometimes referred to as “good” and “bad” trees, respectively (Sackin 1972).Balanced tree Unbalanced or Pectinate (comb-like) tree
31How to describe a phylogenetic tree in computerese?
32The Newick formatIn computer programs, trees are represented in a linear form by a string of nested parentheses, enclosing taxon names (and possibly also branch lengths and bootstrap values), and separated by commas. This type of representation is called the Newick format. The originator of this format in mathematics was Arthur Cayley (1821–1895).
33The Newick formatThe Newick format for phylogenetic trees was adopted on June 26, 1986 at an informal meeting at Newick's Lobster House in Dover, New Hampshire. The Newick format currently serves as the de facto standard for representing phylogenetic tree and is employed by almost all phylogenetic software tools. Unfortunately, it has never been described in a formal publication; the first time it is mentioned in a publication is in 1992.
34The Newick formatIn the Newick format, the pattern of the parentheses indicates the topology of the tree by having each pair of parentheses enclose all members of a monophyletic group. A phylogenetic tree in the Newick format always ends in a semicolon (;).;
35The Newick formatOne can use the Newick format to write down rooted trees, unrooted trees, multifurcations, branch lengths, and bootstrap values.
39The number of possible bifurcating rooted trees (NR) for n 2 OTUs The number of possible bifurcating unrooted trees (NU) for n 3 OTUs
40¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾¾ Number of OTUs Number of possible rooted tree2 13 34 157 10,395,1359 2,027,025,459,425,458,046,676,87520 8,200,794,532,637,891,559,375
41Truth is one, falsehoods are many. Evolution is an historical process.Only one historical narrative is true.From 8,200,794,532,637,891,559,375 possibilities, 1 possibility is true and 8,200,794,532,637,891,559,374 are false.Truth is one, falsehoods are many.
42How do we know which of the 8,200,794,532,637,891,559,375 trees is true?
44True and inferred trees The sequence of speciation events that has led to the formation of a group of OTUs is historically unique. A tree representing the true evolutionary history is called the true tree.A tree that is obtained by using a certain set of data and a certain method of tree reconstruction is called an inferred tree.An inferred tree may or may not be the true tree.
45ancestorCladogenesis = the splitting of an evolutionary lineage into two genetically independent lineages.descendant 1descendant 2
46Anagenesis = changes occurring along an evolutionary lineage. descendant
47In molecular phylogenetics, we assume that species are only created by cladogenesis.
49At every locus, if we trace back the history of any two alleles from any two populations, we will eventually reach a common ancestral allele from which both contemporary alleles have been derived.
50The routes of inheritance represent the passage of genes from parents to offspring, and the branching pattern depicts a gene tree.
51Different genes, however, may have different evolutionary histories, i Different genes, however, may have different evolutionary histories, i.e., different routes of inheritance, different gene trees.
52The routes of inheritance are mostly confined by reproductive barriers—that is, gene flow occurs only within the species. A species is therefore like a bundle of genetic connections, in which many entangled parent-offspring lines form the ties that bundle individuals together into a species lineage.
53A gene tree may differ from a species tree S = Divergencetime for species 1 and 2
54A gene tree may differ from a species tree G1 = Inferred divergencetime by using alleles a and fS = Divergencetime for species 1 and 2
55A gene tree may differ from a species tree Alleles d and b are closer to each other than alleles d and f.
56Incomplete lineage sorting due to polymorphism at speciation time
57Gene trees and species trees bBcDIt is often assumed that gene trees always equal species trees. This may be not be true.
58Taxon (singular); Taxa (plural) A taxon is a species or a group of species that has been given a name, e.g., Homo sapiens (modern humans) or Lepidoptera (butterflies).There are codes of biological nomenclature which seek to ensure that every taxon has a single and stable name, and that every name is used for only one taxon.
59Clades*Strictly: A clade is a group of all the taxa that have been derived from a common ancestor plus the common ancestor itself.In molecular phylogenetics: A clade is a group of taxa under study that share a common ancestor, which is not shared by any other species outside the group.*also: monophyletic groups, natural clades
60Paraphyletic TaxaA taxon whose common ancestor is shared by any other taxon is called a paraphyletic taxon or an invalid taxon.Reptiles are paraphyletic.60
61A named taxon that lacks phylogenetic validity, but is nonetheless used, is called a convenience taxon.“a convenience fish”
62Sister TaxaIf a clade is composed of two taxa, these are referred to as sister taxa.Birds and crocodiles are sister taxa.
63Which of the following groups are not monophyletic? E. coliratmousebaboonchimphumana. human, chimpanzee, baboonb. mouse, chimpanzee, baboonc. rat, moused. human, chimpanzee, baboon, rat, mousee. E. coli, human, chimpanzee, baboon, rat, mouse
64Which of the following groups are not monophyletic? E. coliratmousebaboonchimphumana. human, chimpanzee, baboonb. mouse, chimpanzee, baboonc. rat, moused. human, chimpanzee, baboon, rat, mousee. E. coli, human, chimpanzee, baboon, rat, mouse
65Two or more sequences are said to be homologous if they are related by descent. Homology is often ascertained on the basis of sequence similarity. Thus, if two or more sequences exhibit high degrees of similarity, it is likely (but not always the case) that they are homologous. Sequence similarity may also arise without common ancestry: by chance, or due to convergence driven by similar selective pressures. Such sequences, which are similar but not homologous, are said to be analogous.
66Homology is a hypothesis. Homology is a qualitative statement.Similarity is a quantitative and, hence, quantifiable statement (e.g., percent similarity, percent identity).Similarity is a fact.Homology is a hypothesis.Of course, as with any other scientific hypothesis, homology between two sequences may be tested and every so often rejected.
67Types of homologyOrthology: Similarity due to speciation.Paralogy: Similarity due to gene duplication.Ohnology: A special case of paralogy in which similarity is due to genome duplication.Xenology: Similarity due to horizontal gene transfer.
68Orthologs and Paralogs paralogousorthologousorthologousabcCBADuplication yields 2 copies (paralogs) on the same genomeAncestral gene
69Orthologs and Paralogs Only b, C, and A are sampledbCAab*cCBAA mixture of orthologs and paralogs is sampled
77A character is unordered if a change from one character state to any other character state can occur in one step.
78A character is ordered if there exists a symmetrical path of change from one character state to another.
79A character is polar if there exists an asymmetrical (irreversible) path of change from one character state to another.Polar
80The number of steps between two character states is specified by a step matrix.
81Assumptions about character evolution Methods of phylogenetic reconstruction require that we make explicit assumptions about:(1) the number of discrete steps required for one character state to change into another.(2) the probability with which such a change may occur.
82Temporal Polarity of Character States Character states may be ranked by relative antiquity into:(1) primitive or ancestral (plesiomorphy)(2) derived or novel (apomorphy)
83Taxonomic Distribution of Character States A primitive state that is shared by several taxa is a symplesiomorphy.A derived state that is shared by several taxa is a synapomorphy.A derived character state unique to a particular taxon is an autapomorphy.A character state that is shared by several taxa due to convergence, parallelism and reversals, rather than due to common descent, is a homoplasy.symbioisissympathysynapsesynteny
84D C C B A A B C A A A A A homoplasy apomorphy (autapomorphy) synapomorphysymplesiomorphyDCCBAABCAAAAplesiomorphyA
85What is swimming in shark and carp? guppychickenbatrata. symplesiomorphicb. synapomorphicc. autapomorphicd. homoplasic
86What are scales in guppy and carp? sharkcarpguppychickenbatrata. symplesiomorphicb. synapomorphicc. autapomorphicd. homoplasic
87What are feathers in chicken? sharkcarpguppychickenbatrata. symplesiomorphicb. synapomorphicc. autapomorphicd. homoplasic
88What are wings in chicken and bat? sharkcarpguppychickenbatrata. symplesiomorphicb. synapomorphicc. autapomorphicd. homoplasic