Introduction to Biosystematics Lecture - Outline. Four steps in Phylogenetic Inference 2. Data - Selection 3. - What is it? - How does one recognize it? 4.. haracter (data) selection (not too fast, not too slow) 2. lignment of Data (hypotheses of primary homology) 3. nalysis selection (choose the best model / method(s)) 4. onduct analysis Four steps Four steps Remember the following: he data are the things Much that is taught on phylogenetic inference deals methods of analysis Do not neglect the quality of the data Garbage in, garbage out Selection of characters Morphologists typically choose:. haracters that are not constant 2. haracters that are not too variable Molecular systematists use the same criteria to select which gene(s) to sequence Genes that are virtually constant don t have enough information Genes that are hypervariable have too much misinformation Selection of characters haracters should be:. Independent of one another (not correlated) - because each is a single argument for or against a particular relationship - correlated characters artificially increase the strength of the argument in one direction haracter states should be: 2. Heritable (not just morphology & molecules, behaviors, pheromones, songs ) 3. (pparently) homologous
In regard to classification and all the endless disputes about the "Natural System," which no two authors define in the same way, I believe it ought, in accordance to my heterodox notions, to be simply genealogical. for it will clear away an immense amount of rubbish about the value of characters, and will make the difference between analogy and homology clear. Darwin in a letter to Huxley, 857 central concept of, (the key to) phylogenetic analysis But hard to define & identify ladistics ladistics - Hennig s original method:. Distinguish homologies from analogies - Hennig s original method:. Distinguish homologies from analogies 2. Distinguish derived homologies (apomorphies) from ancestral (plesiomorphies) homologies 2. Distinguish derived homologies (apomorphies) from ancestral (plesiomorphies) homologies 3. ree then built from apomorphies (evidence of common ancestry) 3. ree then built from apomorphies (evidence of common ancestry) - Morphology Hypothesis of primary homology the heads of sp and sp 2 are homologous Head Wings Legs ail - DN Site Site 2 Site 3 Site 4 species species G species2 red smooth no species2 species3 wide species3 G haracter variation is coded into a character by taxon matrix termed coding of characters 2
- first discussed by ristotle / nalogy - first contrasted by MacLeay (82) - later reinforced by Owen (843) MacLeay, W. S. (82) Horae Entomologicae: or Essays on the nnulose nimals, Vol. I, part II. ontinuing an attempt to scertain the Rank and Situation which the elebrated Insect, Scarabaeus sacer, Holds mong Organised Beings. S. Bagster, London. Owen, R. (843) Lectures on the comparative anatomy and physiology of the invertebrate animals, Delivered at the Royal ollege of Surgeons, in 843. Longman, Brown, Green, and Longmans, London. Homologue he same organ in different animals under every variety of form and function nalogue part or organ in one animal which has the same function as another part or organ in a different animal Richard Owen (843) [in glossary] Richard Owen (843) - interpreted under a creationist paradigm - Each homologue was related to a common archetype, or idealized source (cause) - Variation from the archetype was due to the creative whim of God. Special homology - definition above 2. General homology - similarity to an archetype (cause of similarity) 3. Serial homology - repetition of corresponding structures in an organism Owen called these repetitive parts homotypes and, therefore, serial homology is sometimes referred to as homonomy. Darwinian - similarity explained due to evolution, not a God-created archetype Homologous features (or states of features) in two or more organisms are those that can be traced back to the same feature (or state) in the common ancestor of those organisms. Darwinian Similarity due to inheritance from a common ancestor (Hillis 994) In general, homology means inferred common ancestry, although it is commonly misused to mean similarity. Moritz & Hillis (997) Molecular Systematics Ernst Mayr, 969 3
Darwinian - similarity explained due to evolution - nalogy: similarity due to something other than common ancestry (aka ) Question: are the wings of birds and bats homologous? nswer: s forelimbs they are homologous. s wings they are analagous. How to recognize? Distinguish nalogy from? two step process: Step one involves hypothesis of homology using 3 criteria of of Remane (956) Similarity that passes some or all of these are strong contenders for homology Some use the term Primary statement or Hypotheses of primary homology de Pinna (99), for similarities at this step. De Pinna, M... 99. oncepts and tests of homology in the cladistic paradigm. ladistics. 7: 367-394. How to recognize? Distinguish nalogy from? Remane s (956) criteria:. Similarity in position and details of structure (the criterion of position) 2. Similarity in developmental origin (ontogeny, genetics) (the criterion of quality of resemblance) 3. Similarity connected through intermediate forms (fossils) (the criterion of continuance) For DN data all we can use is similarity of position Remane,. 956. Die Grundlagen des natürlichen Systems, der vergleichenden natomie und Phylogenetik. Leipzig: Geest und Portig. How to recognize? Distinguish nalogy from? hese criteria are not to be thought of as a means to absolutely identify homologies hey are best thought of as criteria to help find characters that will be of value for phylogenetic inference Wiley (98) Example Forelimbs of tetrapods. Similar position 2. Similar development 3. Good fossil record Strong evidence for homology of skeletal elements 4
How to recognize? Distinguish nalogy from? Similarity alone (criteria -3) is not enough: - analogous features may appear quite similar - homologous features may have diverged so greatly they appear dissimilar (e.g. inner ear bone & jaw bone in fish) - requires a 4th criterion (step two) How to recognize? Distinguish nalogy from? Step 2 - he final and most powerful criterion for identification of homology: 4. ongruence other characters (Patterson, 982) Patterson,. 982. Morphological characters and homology. Pp. 2 74, In Problems of Phylogenetic Reconstruction. (K.. Joysey and.e. Friday, eds.). Systematics ssociation Special Volume. London, cademic Press he importance of congruence he value indeed of an aggregate of characters is very evident... a classification founded on any single character, however important that may be, has always failed. How to recognize? Distinguish nalogy from? Example State YELLOW was thought to be homologous among three species harles Darwin: Origin of Species, h. 3 nalysis demonstrates it is not homologous How to recognize? Distinguish nalogy from? Similarities that pass the final test of congruence other characters become - Putative homologies - Homologies - Synapomorphies, (apomorphies) Given this tree, metamerism had to have evolved twice - i.e. arthropod metamerism is not homologous annelid i.e. it is a case of convergence Note: remain tentative, new data can reject! 5
How to recognize? Distinguish nalogy from? Reciprocal illumination Survey of variation Remane s 3 criteria Synapomorphies are character states hypothesized to be present in the most recent common ancestor Primary homology statements hus their presence in descendent organisms is thought to be due to inheritance (i.e. they are homologous) New data can show homologies to be homoplasies (analogies) Incongruent ongruence test (phylogenetic nalysis) ongruent Rieppel, O.. (988) Fundamentals of omparative Biology, Basel: Birkhäuser Verlag Head Wings 2 Legs 3 ail 4 Reciprocal Illumination - elimination of homoplasy species B speciesb red smooth no species wide haracter (state ) is homoplasious on this tree 2 3 4 Head Wings 2 Legs 3 ail 4 Reciprocal Illumination - elimination of homoplasy species (/4w) B speciesb species (/2w) wide red smooth no Homoplastic states may, after restudy, show differences that were initially missed. If so, one can re-code the data haracter (state ) is no longer homoplasious on this tree because one state is now two a b 2 3 4 6
Site Site 2 Site 3 Site 4 What about DN? species species2 species3 Some homoplasy is due to a mistake of coding, erroneously considering two states homologous - other homoplasy is real - indistinguishable a priori G G. statement of hypotheses of primary homology (step ) = alignment of the data 2. test of hypotheses of primary homology (step 2) - phylogenetic analysis Problem of circularity:. We define homology on the basis of common ancestry 2. We define (via phylogenetic analysis) common ancestry on the basis of homologies 3. his is circular 4. -or is it? Solutions to circularity problem - Homologies aren t used to infer phylogenies - hypotheses of primary homology are (mixture of homologies & homoplasies) - Homologies are found after the analysis - o be certain of a homology: simply run the analysis out that character & later map the character Solutions to circularity problem - If the character is not in the dataset then it can t have influenced the phylogeny - Its mapping on the tree indicates what the other characters say about whether it is homologous or not erm introduced by Lankester (870) nalogous similarity = homoplasy : a character state found in two or more taxa that was not present in their most recent common ancestor Similarity not due to homology, misinformation Independent evolution, two or more evolutionary changes (events) 7
- 3 types. onvergence: true analogy, e.g. wings of birds and insects; usually distantly related taxa 2. Parallelism: similar nonhomologous state in closely related taxa, often same/similar development & genetic basis (most likely to pass all 3 of Remane s criteria for homology & thus hardest to identify as homoplasy before analysis) 3. Reversal: change to an earlier state, e.g. he aquatic lifestyle of whales is not homologous that of fish If homoplasy is mistaken for homology If there are more homoplastic characters than homologous characters Your analysis will be confounded (e.g. you will think bats & birds belong together) One of a few major sources of phylogenetic error Loss of tails evolved independently in humans and frogs - there are two steps on the true tree If misinterpreted as homology, the absence of tails would be evidence for a wrong tree: grouping humans frogs and lizards dogs Lizard Frog Human Dog IL (adult) absent present Human Frog Lizard Dog IL (adult) absent present Reversals are evolutionary changes back to an ancestral condition Reversals can provide misleading evidence of relationships rue tree 2 3 4 5 6 7 8 9 0 Wrong tree 2 7 8 3 4 5 6 9 0 in molecular data can be common in molecular sequence data here are a limited number of alternative character states ( e.g. Only, G, and in DN) Rates of evolution are sometimes high haracter states are chemically identical cannot be distinguished by detailed study of similarity and differences cannot weed out likely homoplastic characters before analysis 8
Review Hypotheses of Primary Phylogenetic nalysis : hey are due to common ancestry hese beetles are : hey are due to something other than common ancestry Summary. Data Selection: best characters are not constant nor too variable, are heritable, and potentially homologous. - his reduces homoplasy in the dataset & improves chance of getting correct tree 2. he amount of homology (that is properly coded) in a dataset is often referred to as the phylogenetic signal and the amount of homoplasy in a dataset (that is coded as potential homology) is often referred to as noise 3. Morphological phylogenetic analysis is not that different from molecular - both can be done poorly and both can suffer from weak data (absence of information and / or misleading information) erms - from lecture & readings character by taxon matrix oding homology / analogy serial homology Homonomy Darwinian homology onvergence Parallelism Reversal Primary homology statement Synapomorphies reciprocal illumination lignment You should be able to Describe 3 types of homoplasy & examples of each Explain differences between DN & morphological data respect to homology identification Know how to recognize homology - 2 steps (step has 3 criteria) What is the circularity problem for homology & its solution? 9