A Knyght ther was, and that a worthy man, A Knyght ther was, and he was a worthy man, A Knyght ther was, and that a worthy man, A Knyght ther was, and he was a worthy man, A Knyght ther was, and he wasn t a worthy man, 1. Four steps in Phylogenetic Inference 2. Data - Selection Outline 3. - What is it? - How does one recognize it? 4. 1. Character (data) selection (not too fast, not too slow) 2. Alignment of Data (hypotheses of primary homology) 3. Analysis selection (choose the best model / method(s)) 4. Conduct analysis Four steps Four steps Remember the following: The data are the things Much that is taught on phylogenetic inference deals with methods of analysis Do not neglect the quality of the data Garbage in, garbage out Selection of characters Morphologists typically choose: 1. Characters that are not constant 2. Characters 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 1
Selection of characters Characters should be: 1. 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 Character states should be: 2. Heritable (not just morphology & molecules, behaviors, pheromones, songs ) 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, 1857 3. (Apparently) homologous 2000 1994 A central concept of, (the key to) phylogenetic analysis But hard to define & identify Cladistics Cladistics - Hennig s original method: 1. Distinguish homologies from analogies 2. Distinguish derived homologies (apomorphies) from ancestral (plesiomorphies) homologies 3. Tree then built from apomorphies (evidence of common ancestry) - Hennig s original method: 1. Distinguish homologies from analogies 2. Distinguish derived homologies (apomorphies) from ancestral (plesiomorphies) homologies 3. Tree then built from apomorphies (evidence of common ancestry) 2
- Morphology Hypothesis of primary homology the narrow heads of sp 1 and sp 2 are homologous Head Wings Legs Tail - DNA Site 1 Site 2 Site 3 Site 4 species1 narrow black hairy with species2 narrow red smooth no species1 A C G A species2 A T C T species3 wide black hairy with species3 T C G A Character variation is coded into a character by taxon matrix termed coding of characters - first discussed by Aristotle / Analogy - first contrasted by MacLeay (1821) - later reinforced by Owen (1843) Homologue The same organ in different animals under every variety of form and function Analogue A part or organ in one animal which has the same function as another part or organ in a different animal MacLeay, W. S. (1821) Horae Entomologicae: or Essays on the Annulose Animals, Vol. I, part II. Continuing an attempt to Ascertain the Rank and Situation which the Celebrated Insect, Scarabaeus sacer, Holds Among Organised Beings. S. Bagster, London. Owen, R. (1843) Lectures on the comparative anatomy and physiology of the invertebrate animals, Delivered at the Royal College of Surgeons, in 1843. Longman, Brown, Green, and Longmans, London. Richard Owen (1843) [in glossary] Richard Owen (1843) - interpreted under a creationist paradigm - Each homologue was related to a common archetype, or idealized source (cause) 1. Special homology - definition above 2. General homology - similarity to an archetype (cause of similarity) 3. Serial homology - repetition of corresponding structures in an organism - Variation from the archetype was due to the creative whim of God Owen called these repetitive parts homotypes and, therefore, serial homology is sometimes referred to as homonomy. 3
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 1994) In general, homology means inferred common ancestry, although it is commonly misused to mean similarity. Moritz & Hillis (1997) Molecular Systematics Ernst Mayr, 1969 Darwinian - similarity explained due to evolution - Analogy: similarity due to something other than common ancestry (aka ) Question: are the wings of birds and bats homologous? Answer: As forelimbs they are homologous. As wings they are analagous. from? A two step process: Step one involves hypothesis of homology using 3 criteria of of Remane (1956) 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 (1991), for similarities at this step. De Pinna, M.C.C. 1991. Concepts and tests of homology in the cladistic paradigm. Cladistics. 7: 367-394. from? Remane s (1956) criteria: 1. 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 DNA data all we can use is similarity of position Remane, A. 1956. Die Grundlagen des natürlichen Systems, der vergleichenden Anatomie und Phylogenetik. Leipzig: Geest und Portig. 4
from? These criteria are not to be thought of as a means to absolutely identify homologies They are best thought of as criteria to help find characters that will be of value for phylogenetic inference Wiley (1981) Example Forelimbs of tetrapods 1. Similar position 2. Similar development 3. Good fossil record Strong evidence for homology of skeletal elements from? Similarity alone (criteria 1-3) 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) from? Step 2 - The final and most powerful criterion for identification of homology: 4. Congruence with other characters (Patterson, 1982) Patterson, C. 1982. Morphological characters and homology. Pp. 21 74, In Problems of Phylogenetic Reconstruction. (K.A. Joysey and A.E. Friday, eds.). Systematics Association Special Volume. London, Academic Press The importance of congruence The 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. from? Example State YELLOW was thought to be homologous among three species Charles Darwin: Origin of Species, Ch. 13 Analysis demonstrates it is not homologous 5
from? Similarities that pass the final test of congruence with other characters become - Putative homologies - Homologies - Synapomorphies, (apomorphies) Given this tree, metamerism had to have evolved twice - i.e. arthropod metamerism is not homologous with annelid i.e. it is a case of convergence Note: remain tentative, new data can reject! 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 Thus 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 Congruence test (phylogenetic Analysis) Congruent Rieppel, O. C. (1988) Fundamentals of Comparative Biology, Basel: Birkhäuser Verlag Head 1 Wings 2 Legs 3 Tail 4 speciesa narrow black hairy with Reciprocal Illumination - elimination of homoplasy B A C speciesb narrow red smooth no 1 1 speciesc wide black hairy with Character 1 (state narrow ) is homoplasious on this tree 2 3 4 6
Head 1 speciesa narrow (1/4w) Wings 2 Legs 3 Tail 4 black hairy with Reciprocal Illumination - elimination of homoplasy B A C speciesb narrow (1/2w) red smooth no speciesc wide black hairy with Homoplastic states may, after restudy, show differences that were initially missed. If so, one can re-code the data Character 1 (state narrow ) is no longer homoplasious on this tree because one state is now two 1a 1b 2 3 4 Site 1 Site 2 Site 3 Site 4 species1 A C G A species2 A T C T species3 T C G A Some homoplasy is due to a mistake of coding, erroneously considering two states homologous - other homoplasy is real - indistinguishable a priori What about DNA? 1. statement of hypotheses of primary homology (step 1) = alignment of the data 2. test of hypotheses of primary homology (step 2) - phylogenetic analysis Problem of circularity: 1. We define homology on the basis of common ancestry 2. We define (via phylogenetic analysis) common ancestry on the basis of homologies 3. This 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 - To be certain of a homology: simply run the analysis without that character & later map the character 7
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 1996 Term introduced by Lankester (1870) Analogous similarity = homoplasy : a character state found in two or more taxa that was not present in their most recent common ancestor - 3 types 1. Convergence: true analogy, e.g. wings of birds and insects; usually distantly related taxa 2. Parallelism: similar nonhomologous state in closely related taxa, often with 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) Similarity not due to homology, misinformation Independent evolution, two or more evolutionary changes (events) 3. Reversal: change to an earlier state, e.g. The aquatic lifestyle of whales is not homologous with that of fish If homoplasy is mistaken for homology If there are more homoplastic characters than homologous characters Loss of tails evolved independently in humans and frogs - there are two steps on the true tree Your analysis will be confounded (e.g. you will think bats & birds belong together) One of a few major sources of phylogenetic error Lizard Frog Human Dog TAIL (adult) absent present 8
If misinterpreted as homology, the absence of tails would be evidence for a wrong tree: grouping humans with frogs and lizards with dogs Reversals are evolutionary changes back to an ancestral condition Reversals can provide misleading evidence of relationships Human Frog Lizard Dog TAIL (adult) absent present True tree 1 2 3 4 5 6 7 8 9 10 Wrong tree 1 2 7 8 3 4 5 6 9 10 in molecular data can be common in molecular sequence data There are a limited number of alternative character states ( e.g. Only A, G, C and T in DNA) Rates of evolution are sometimes high Character states are chemically identical cannot be distinguished by detailed study of similarity and differences cannot weed out likely homoplastic characters before analysis Review Hypotheses of Primary Phylogenetic Analysis : They are black due to common ancestry These beetles are black : They are black due to something other than common ancestry Summary 1. Data Selection: best characters are not constant nor too variable, are heritable, and potentially homologous. - This reduces homoplasy in the dataset & improves chance of getting correct tree 2. The 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) Terms - from lecture & readings character by taxon matrix" Coding" homology / analogy" serial homology" Homonomy" Darwinian homology" " Convergence" Parallelism" Reversal" Primary homology statement" Synapomorphies" reciprocal illumination" Alignment" 9
You should be able to Describe 3 types of homoplasy & examples of each" Explain differences between DNA & morphological data with respect to homology identification" Know how to recognize homology - 2 steps (step 1 has 3 criteria)" What is the circularity problem for homology & its solution?" 10