19-10-31 Phylogenetics 2: Phylogenetic and genealogical homology - PDF document

19-10-31 Phylogenetics 2: Phylogenetic and genealogical homology Alignment of mammalian beta-globin gene sequences human cow rabbit rat opossum GTG CTG TCT CCT GCC GAC AAG ACC AAC GTC AAG GCC GCC TGG GGC AAG GTT GGC GCG CAC ... ... ... G.C ... ... ... T.. ..T ... ... ... ... ... ... ... ... ... .GC A.. ... ... ... ..C ..T ... ... ... ... A.. ... A.T ... ... .AA ... A.C ... AGC ... ... ..C ... G.A .AT ... ..A ... ... A.. ... AA. TG. ... ..G ... A.. ..T .GC ..T ... ..C ..G GA. ..T ... ... ..T C.. ..G ..A ... AT. ... ..T ... ..G ..A .GC ... GCT GGC GAG TAT GGT GCG GAG GCC CTG GAG AGG ATG TTC CTG TCC TTC CCC ACC ACC AAG ... ..A .CT ... ..C ..A ... ..T ... ... ... ... ... ... AG. ... ... ... ... ... .G. ... ... ... ..C ..C ... ... G.. ... ... ... ... T.. GG. ... ... ... ... ... .G. ..T ..A ... ..C .A. ... ... ..A C.. ... ... ... GCT G.. ... ... ... ... ... ..C ..T .CC ..C .CA ..T ..A ..T ..T .CC ..A .CC ... ..C ... ... ... ..T ... ..A ACC TAC TTC CCG CAC TTC GAC CTG AGC CAC GGC TCT GCC CAG GTT AAG GGC CAC GGC AAG ... ... ... ..C ... ... ... ... ... ... ... ..G ... ... ..C ... ... ... ... G.. ... ... ... ..C ... ... ... T.C .C. ... ... ... .AG ... A.C ..A .C. ... ... ... ... ... ... T.T ... A.T ..T G.A ... .C. ... ... ... ... ..C ... .CT ... ... ... ..T ... ... ..C ... ... ... ... TC. .C. ... ..C ... ... A.C C.. ..T ..T ..T ... 1

19-10-31 human cow Rabbit GTG CTG TCT CCT GCC GAC ACG TAC TAA GTC AAG GCC GCC TGG GGC AAG GTT GGC GCG CAC ... ... ... G.C ... ... ... ..T ... ... ... ... ... ... ... ... ... ... .GC A.. ... ... ... ..C ..T ... ... ..T ... A.. ... A.T ... ... .AA ... A.C ... AGC ... Homology: similarity among two or more individuals or lineages in a feature/character, or character-state, that is the result of inheritance from a common ancestor Homologous character verses Homologous character state ACG TAC TAA ACG TAC TAA C C ACG TAT TAA ACG TAT TAA DNA alignment T T ACG TAT TAA ACG TAT TAA 2

19-10-31 Analogy: non-phylogenetic similarity (filled squares) Homology: inherited from a common ancestor (filled circles) Homology: similarity among two or more individuals or lineages in a feature/character, or character-state, that is the result of inheritance from a common ancestor Homologous character verses Homologous character state ACG TAC TAA ACG TAC TAA C C ACG TAT TAA ACG TAT TAA DNA alignment T T ACG TAT TAA ACG TAT TAA change somewhere along this branch Molecular evolution: positional homology of a character 3

19-10-31 1 2 3 4 5 6 7 8 9 ACG TAC TAA ACG TAC TAA C C ACG TAT TAA ACG TAT TAA T T ACG TAT TAA ACG TAT TAA 1. position 6 is homologous ( posit positional ional homolgy homolgy ) 2. state “ T ” is homologous homologous (shared ancestry) Phylogenies distinguish homology from similarity It is possible for character-states to be identical but non- homologous (Homoplasy) 1. Convergence 2. Reversal 3. Parallelism Homoplsy arises in molecular datasets when multiple substitutions occur at a single site. - “ multiple substitutions ” - “ multiple hits ” - “ superimposed substitutions ” 4

19-10-31 Phylogenies distinguish homology from similarity: convergence Convergent (non-phylogenetic) similarity of nucleotide character states; i.e., homoplasy T ⇒ C ⇒ A ACG GAA TAA ACG GAT TAA T T ACG GAG TAA G G ⇒ A ACG GAA TAA 1. position 6 is homologous (positional homolgy) 2. state “A” is not homologous not homologous (non-phylogenetic similarity) Phylogenies distinguish homology from similarity: reversal Reversal leads to non-homologous similarities in character state. A ⇒ C ⇒ A ACG GAA TAA ACG GAA TAA A A ACG GAT TAA T ACG GAT TAA 1. position 6 is homologous (positional homolgy) 2. state “A” is not homologous not homologous (non-phylogenetic similarity) 5

19-10-31 Phylogenies distinguish homology from similarity: parallelism Parallel evolution leads to non-homologous similarities in character states. A ⇒ T ACG GAT TAA ACG GAA TAA A A ⇒ T A ACG GAT TAA A ACG GAA TAA 1. position 6 is homologous (positional homolgy) 2. state “A” is not homologous not homologous (non-phylogenetic similarity) VERY IMPORTANT consequences of phylogenetic homology 1. Homologous characters can have NON-homologous states in different species! 2. Homologous characters can gave IDENTCIAL states in different species and those states are NOT homologous! (Don’t confuse similarities in state with homology!) 6

19-10-31 Alternatives to phylogenetic concept of homology percent homology For DNA (or amino acid) sequences use percent similarity Trees within trees 7

19-10-31 Trees within trees: reticulation Conventional representation Conventional representation Path 1 Path 1 Path 2 Path 2 A A B B A A A B B B C C D D C C C C C C D D D D D D E E F F E E E F F F E E E F F F I I I I I I I I Trees within trees Species 1 Species 3 Species 2 Species 4 8

Species 1 Species 1 Trees within trees Trees within trees Species 2 Species 2 Species 3 Species 3 Species 4 Species 4 19-10-31 9

19-10-31 Trees within trees Species 1 Species 3 Species 2 Species 4 Trees within trees Drift Selection time Population history 10

19-10-31 Trees within trees Polymorphism and substitution (highly simplified) along a branch of a phylogeny Residence time: the time that Mean residence time is a particular neutral determined by effective polymorphism is present in a population size (N e ) Coalescent population. Time Population substitution 1 Population substitution 2 Population substitution 3 A ⇒ C C ⇒ A A ⇒ G A ⇒ C ⇒ A ⇒ G GAG GAC A A GAT T GAT Forms of homology (for genes) 1 . O RTHOLOGY . Orthologous genes are derived from the divergence of an organismal lineage; i.e., a speciation event. Thus if we look at orthologs on a phylogeny we see that their most recent common ancestor represents the coalescence of two organismal lineages. 2. P ARALOGY . Paralogous genes are derived from the divergence event within a genomes; i.e., a gene duplication event. In this case if we look at paralogs on a phylogeny we see that they coalesce at a gene duplication event. 3. P RO - ORTHOLOGY . A gene is pro-orthologous to another gene if they coalesce at a speciation event that predates a gene duplication event. Thus a single-copy gene in organism A is pro- orthologous to a gene that is present in multiple copies in organism B due to gene duplication events that followed the divergence of organisms A and B. 4. S EMI - ORTHOLGY . This is a term that simply takes the reverse perspective of pro-orthology. Any one of the multi-copy genes in the genome of organism B is said to be semi-orthologous to a single copy gene in the genome of organism A, if the most recent common ancestors of those genes coalesce at a point in time that predates the gene duplication event. 5. P ARTIAL HOMOLOGY . This refers to the situation that arises when the evolutionary histories of different segments within the same gene coalesce at different ancestors. This can arise from evolutionary processes such as homologous recombination or exon shuffling. 6. G AMETOLOGY . Gametologs coalesce at an event that isolated those genes on opposite sex chromosomes; i.e., they coalesce at the point when they became isolated from the process of recombination. 7. X ENOLOGY Genes that coalesce at either a speciation or duplication event, but whose evolutionary histories do not fit with that of the organismal lineages which carry such genes due to one or more lateral gene transfer events. 8. S INOLOGY . Homologous genes found within the same organism’s genome have different evolutionary histories due to the fusion of formerly evolutionarily independent genomes, such as in endosymbiosis. 11

19-10-31 Mus Gene duplication Rattus event Cricetinae Ldh-C Sus Homo Sus Homo Rabbit Ldh-A Mus Rattus Gallus Pro-orthologs pre-date the Sceloporus involved duplication event Examples of different types of homology in gene families: Homo and Rattus (rat) Ldh-C are orthologous. Homo Ldh-C and Homo Ldh-A are paralogous. Homo Ldh-C and Rattus Ldh-A also are paralogous. Gallus (chicken) Ldh-A is pro-orthologous to both Homo Ldh-C and Homo Ldh-A . Homo Ldh-C is semi-orthologous to the Gallus Ldh-A. All mammalian Ldh-A genes are semi-orthologous to the non-mammalian Ldh-A. Note that the gene duplication that gave rise to the Ldh-C gene is specific to an ancestor of all present-day mammals. Mammalian Ldh-C and Ldh-A genes are paralogous. human Ldh-C and human Ldh-A are paralogs paralogs Mus Rattus Gene duplication event Cricetinae Ldh-C Sus Homo Sus Homo Rabbit Ldh-A Mus Rattus Gallus Pro-orthologs pre-date the Sceloporus involved duplication event (all these genes ar (all these genes are homologs) e homologs) 12

19-10-31 mouse Ldh-C and human Ldh-C are ort orthologs hologs speciation event Mus Gene duplication Rattus event Cricetinae Ldh-C Sus Homo Sus Homo Rabbit Ldh-A Mus Rattus Gallus Pro-orthologs pre-date the Sceloporus involved duplication event (all these genes ar (all these genes are homologs) e homologs) Organism history can be different from gene history Selected examples (in notes): • Non-phylogenetic lineage sorting due to DRIFT • Birth-death evolution in gene families • Trans-species evolution • Recombination • Lateral gene transfer (LGT) Other sources: • Statistical error • Human error 13