UW-Madison BOTANY 940 - Agreement Among Gene Trees Could Be Used as Evidence of Common Ancestry (33 pages)

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Agreement Among Gene Trees Could Be Used as Evidence of Common Ancestry



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Agreement Among Gene Trees Could Be Used as Evidence of Common Ancestry

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Pages:
33
School:
University of Wisconsin, Madison
Course:
Botany 940 - Seminar in Plant Systematics and Evolution
Seminar in Plant Systematics and Evolution Documents
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Agreement among gene trees could be used as evidence of common ancestry Jessica Clarke and Flor Rodriguez March 21st 2006 Arguments for common ancestry the genetic code is a frozen accident when life first arises it alters the environment so as to make subsequent start ups much less probable species with common ancestor are more likely to exhibit congruence in character state patterns than species that originated separately Hypothesis of common ancestry by Penny et al 1982 Prediction Orthologous genes should lead to similar trees because they are expected to share the same evolutionary history developed an algorithm that guaranteed to find all minimal length trees implemented a tree comparison metric to measure closeness calculated the expected distribution of this metric Conclusion Theory of evolution leads to quantitative predictions that are testable and falsifiable Measuring the difference T1 T11 complete data set T12 T17 T18 T19 T26 cytochrome c fibrinopeptide A fibrinopeptide B T27 T32 T33 T39 haemoglobin haemoglobin Measuring the difference The symmetric difference metric on two trees counts the number of edges that occur in one but not both trees Critic by Sober and Steel 2002 Common ancestry might be untestable Long ages of time might have erased the pertinent evidence I X Y ne 4rt n 1000 t 20 million years r 1 in 2million years No method can infer X from Y with a probability that is any better than simply ignoring Y and blindly guessing X I X Z 4k maxi nie 4rti n 100 t 20 million years r 1 in 100 million years K 10 000 No method can reliably determine from this data how these four groups are related historically Response from Penny et al 2003 Methods of tree construction based on parsimony assume common ancestry Methods other than parsimony can be used and should be favored if they give more consistent results when analyzing and comparing different data sets Response from Penny et al 2003 The hypothesis of common ancestry CA might be untestable Some alternatives of the theory of common ancestry can be formulated tested and rejected The theory of influenza viruses from outer space The theory that every species was created separately ID Influenza viruses continue to arrive from outer space via comets Hoyle and Wickramasinghe 1984 1986 under the theory of descent linear tree is expected if each epidemic was carried on different comets a correlation between their order of arrival and their phylogeny is not expected Test 1 Probability of sequences occurring on a linear tree in the same order as the year of appearance P 10 6 that the linear tree observed order occurs by chance The theory of descent was not rejected Influenza viruses from space Test 2 t1 t2 t3 t4 Binary tree t1 t2 t3 t4 Star tree 1 in 1064 Steiner tree Binary tree was not rejected It is not necessary that all possible alternatives to a model MUST be rejected simultaneously Intelligent design Theory of descent vs theory of individual creation Example Photosynthetic enzymes from plants living in hot dry environments and those living in a moist temperate lawn correct prediction Theory of descent leads to testable predictions Agreement Between Gene Trees Evidence for common descent or NOT History of Life 3 5byo oldest prokayotic fossils 1 7byo oldest eukaryotic fossils 545 525myo cambrian explosion 475myo first land plants 400myo origin of vascular tissue 300myo origin of seed plants 130myo origin of flowering plants Campbell 1999 Main Sources www talkorigins org www trueorigins org Main Arguments Trees do not match Design not ruled out Evolution is not falsifiable Molecules do not evolve according to predictions Predictions Violated Common ancestry predicts agreement among trees Trees do not agree perfectly Therefore the common ancestry claim is rejected Response Number of Taxa Rooted Unrooted 2 3 3 4 4 5 5 6 6 7 7 8 8 9 9 10 10 11 20 21 Number of Possible Trees 1 3 15 105 945 10 395 135 135 2 027 025 654 729 075 8 200 794 532 637 890 000 000 NR 2n 3 2n 3 2n 2 n 2 Theobald 2006 Design Not Rejected Anatomy and biochemistry are not independent Organisms similar anatomically are similar biochemically and vise versa Thus gene agreement could reflect design Brand 1997 Response There is no biological reason besides common descent that similar morphologies should have similar biochemestry Besides we can use neutral genes and genes with vastly different functions to construct trees Theobald 2006 Not Falsifiable Not Science Evolutionary predictions are shown false Evolution is not falsified Thus evolution is not falsifiable and is not science Possible examples horizontal transfer hybridization Predictions Violated Evolution predicts that divergence between lineages is proportional to evolutionary distance constant rate of evolution bp changes between lineages does not match predictions Therefore claim is false molecular data are bunk Camp 2001 Cytochrome C Turtle Rattlesnake Human 22 bp 14 bp Cytochrome C Kangaroo Horse 12 bp 10 bp Human Response Common ancestry does not predict uniform rates Even given uniform rates events are stochastic and thus should not match predictions exactly Distribution of genetic distances between human and mouse genes The histogram is the actual data from 2 019 human and mouse genes The solid curve shows the expected distribution of genetic distances assuming only a constant rate of background mutation 10 9 substitutions per site per year reproduced from Figure 3a in Kumar and Subramanian 2002 Theobald 2006 References Brand Leonard 1997 Faith Reason and Earth History Andrews University Press Berrien Springs MI Camp Ashby 2001 A critique of Douglas Theobald s 29 Evidences for Evolution 09 March 2006 www trueorigin org theobald1a asp Campbell N Reece J Mitchell L 1999 Biology fifth edition Benjamin Cummings Menol Park CA Kumar S and Subramanian S 2002 Mutation rates in mammalian genomes Proc Natl Acad Sci 99 803 808 Penny D Hendy M Zimmer E and R Hamby 1990 Trees from sequences Panacea or Pandora s box Aus Syst Bot 3 21 38 Penny D Hendy M and M Steel 1991 Testing the theory of descent In Phylogenetic analysis of DNA sequences 155 183 Penny D Foulds L and M Hendy 1982 Testing the theory of evolution by comparing phylogenetic trees constructed from five different protein sequences Nature 297 197200 Penny D Hendy M and A Poole 2003 Testing fundamental evolutionary hypotheses J Theor Biol 223 377 385 Robinson D and L Foulds 1981 Comparison of phylogenetic trees Math Biosc 53 131147 References


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