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**1. Four steps in Phylogenetic Inference
- Data - Selection
- Homology**
- What is it?
- How does one recognize it? 4. Homoplasy
Outline
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
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”
Four steps Selection of characters
Morphologists typically choose:
- Characters that are not constant
- 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 mis- information
Selection of characters Characters 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 Character states should be:
- Heritable (not just morphology & molecules, behaviors, pheromones, songs…)
- (Apparently) 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, 1857
Homology
A central concept of,
(the key to)
phylogenetic
analysis
But hard to define
& identify
2000 1994
Homology
Cladistics
- Hennig’s original method:
- Distinguish homologies from analogies
- Distinguish derived homologies ( apomorphies ) from ancestral ( plesiomorphies ) homologies
- Tree then built from apomorphies (evidence of common ancestry)
Homology
Cladistics
- Hennig’s original method:
- Distinguish homologies from analogies
- Distinguish derived homologies ( apomorphies ) from ancestral ( plesiomorphies ) homologies
- Tree then built from apomorphies (evidence of common ancestry)
Homology
Darwinian Homology
- 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.” Ernst Mayr, 1969
Homology
Darwinian Homology “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
Homology
Darwinian Homology
- similarity explained due to evolution
- Analogy : similarity due to something other than common ancestry (aka Homoplasy )
Homology
Question : are the wings of birds and bats homologous? Answer: As forelimbs they are homologous. As wings they are analagous. 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 Homology 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. How to recognize? Distinguish Analogy from Homology? Remane’s (1956) criteria:
- Similarity in position and details of structure (the criterion of position)
- Similarity in developmental origin (ontogeny, genetics) (the criterion of quality of resemblance)
- 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. How to recognize? Distinguish Analogy from Homology?
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) How to recognize? Distinguish Analogy from Homology? Example Forelimbs of tetrapods
- Similar position
- Similar development
- Good fossil record Strong evidence for homology of skeletal elements How to recognize? Distinguish Analogy from Homology? 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) How to recognize? Distinguish Analogy from Homology? Step 2 - The final and most powerful criterion for identification of homology:
- 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.” Charles Darwin: Origin of Species, Ch. 13 How to recognize? Distinguish Analogy from Homology? Example State YELLOW was thought to be homologous among three species Analysis demonstrates it is not homologous
Homology
Head 1 Wings 2 Legs 3 Tail 4 speciesA narrow (1/4w) black hairy with spines speciesB narrow (1/2w) red smooth no spines speciesC wide black hairy with spines Homoplastic states may, after restudy, show differences that were initially missed. If so, one can re-code the data
Homology
Reciprocal Illumination - elimination of homoplasy B A C 2 3 4 1a^ 1b Character 1 (state “narrow”) is no longer homoplasious on this tree because one state is now two
Homology
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
Homology
What about DNA?
- statement of hypotheses of primary homology (step 1) = alignment of the data
- test of hypotheses of primary homology (step 2) - phylogenetic analysis
Homology
Problem of circularity:
- We define homology on the basis of common ancestry
- We define (via phylogenetic analysis) common ancestry on the basis of homologies
- This is circular
- -or is it?
Homology
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
Homology
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
Homoplasy
1996
Homoplasy
Term introduced by Lankester (1870) Analogous similarity = homoplasy 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)
Homoplasy - 3 types
- Convergence : true analogy, e.g. wings of birds and insects; usually distantly related taxa
- 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)
- Reversal : change to an earlier state, e.g. The aquatic lifestyle of whales is not homologous with that of fish
Homoplasy
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 Lizard Human Frog Dog TAIL (adult) absent present Loss of tails evolved independently in humans and frogs - there are two steps on the true tree
Homoplasy
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?" You should be able to
