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Home , Cladistics, Phenetics, Phylogenetics, Systematics

Systematics - BIO 615

Outline - History and introduction to phylogenetic inference

1. Pre Lamarck, Pre “Classification without phylogeny”

2. Lamarck & Darwin to Hennig (et al.) “Classification with phylogeny but without a reproducible method”

3. Hennig (et al.) to today “Classification with phylogeny & a reproducible method”

Biosystematics History

alpha - Scala Naturae - ladder of perfection with humans at top - DIFFICULT mental concept to dislodge! (use of terms like “higher” and “lower” for persist) character identification Linnaeus - perpetuated the ladder-like view of linear, pre evolution descriptions phylogeny 1758 - Linnaeus grouped all animals into 6 higher taxa: 1. ( top ) 2. collections classification 3. 4. 5. Describing taxa = assigning names to groups () 6. Worms ( bottom ) = classification

Outline - History and introduction to History phylogenetic inference Lamarck - 1800 - Major impact on :

1. Pre Lamarck, Pre Darwin - First public account of evolution - proposed that modern “Classification without phylogeny” had descended from common ancestors over immense periods of time - Radical! evolution = descent with modification 2. Lamarck & Darwin to Hennig (et al.) “Classification with phylogeny but - Began with a ladder-like description… but considered Linnaeus’s “worms” to be a chaotic “wastebucket” without a reproducible method”

3. Hennig (et al.) to today - He raided the worm group to liberate disparate taxa “Classification with phylogeny & a - Early and MAJOR example of using data interpreted reproducible method” within an evolutionary framework to classify

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History

Lamarck, J. B. 1809. Philosophie Zoologique

History Perhaps the first branching diagram, “phylogentic tree” - Phylogenetics began before “evolutionary trees” published in the - 1809 - Classifications were taken as proxies - representations of the “natural ,” these were the “trees” Lamarck’s ideas:

- By putting taxa together in a group, one was saying Two origins of life (since both “these taxa are closer to one another than to were “equally primitive”) anything else - they belong together” Insects et al - side branch - “Closer” meant different things to different workers: e.g. Greater body form similarity / complexity Removed birds to side branch e.g. Greater evolutionary relationship rather than “below” mammals e.g. more shared homologies… (natural vs artificial) Lamarck, J. B. 1809. Philosophie Zoologique

Biosystematics History

alpha phylogenetics “Dans sa production des differents animaux, la taxonomy n'a pas execute une serie unique et character simple.” identification evolution (In its production of the different animals, descriptions phylogeny nature has not fashioned a single and simple series.) 1809 collections classification biogeography - Lamarck 1815

Phylogenetics began with the emergence of the idea of = the beginning of the end of the Scala evolution applied to classification Naturae

2 Systematics - BIO 615

History History

Charles Darwin (& Alfred Russel Wallace) - “In regard to classification and all the endless disputes about the "Natural System," which no two authors define provided the mechanism () to in the same way, I believe it ought, in accordance to my explain evolution - 1858 & 1859 heterodox notions, to be simply genealogical.

Lamarck’s ideas, which lacked an accurate But as we have no written pedigrees you will, perhaps, say this will not help much; but I think it ultimately will, whenever mechanism, hadn’t spread heterodoxy becomes orthodoxy, for it will clear away an immense amount of rubbish about the value of characters, Darwin’s ideas did… and will make the difference between analogy and clear. The time will come, I believe, though I shall not live to see it, when we shall have very fairly true genealogical (That evolution occurred was apparent to many trees of each great of Nature.” who knew the record, the problem, was “How?”) Darwin in a letter to Huxley, 1857

History History

Classifications (starting in the mid to late 1800s)

- Based on inferred evolutionary history

- End of artificial classifications for convenience or for understanding the creator

- But, “How does one infer evolutionary history?” no reproducible method, yet, to do so…

Darwin (1859)

History History (late 1800s) The “method” of phylogenetic inference - Heavy supporter of (from which one may or may not derive a evolution, but not Darwin classification) that developed is referred to - “ recapitulates as phylogeny” - not a law, as he thought - Coined terms: Evolutionary Taxonomy - spanned from the 1800s to the 1960s Phylogeny (1866) monophyletic - formed the “roots” of the discipline of polyphyletic phylogenetics

3 Systematics - BIO 615

History History Evolutionary Taxonomy (<1960s) Evolutionary Taxonomy (<1960s) - “Method” involved a reliance on - During the modern synthesis authority, not reproducible: systematics was marginalized “not a science” - Leading figures: Mayr & Simpson 1940s 1. Spend a lifetime learning as much as - Without a reproducible method, possible about the biology of a group hypotheses couldn’t be tested (, development, , etc.) 2. Publish a drawing of a phylogeny - No longer used, but exists in some forms based on one’s (informed) opinion today (in contrast to systematists who know nothing = “Guessograms” about their organisms!)

Haeckel, 1872 - tree depicts 1) relationships, 2) timing of Haeckel, 1872 - tree lacks: 1) data? Characters supporting branching events, 3) diversity of groups through time branches? 2) quantification of support - strength of argument

History Summary of contributions Evolutionary Taxonomy (<1960s)

Good: “Know your organisms”

Bad: not reproducible; no objective method; arbitrary, intuitive, no way to

ET - many hypotheses generated, but no method to test. resolve conflicts Modern methods to test show many of the relationships to be “good”, or at least close… but many also rejected

4 Systematics - BIO 615

Outline - History and introduction to Lack of a reproducible method resulted in three phylogenetic inference major approaches: (Explosion in 1960s)

1. Pre Lamarck, Pre Darwin 1. - similarity / distances only, not “Classification without phylogeny” evolution, not phylogeny, no weighting

2. Lamarck & Darwin to Hennig (et al.) “Classification with phylogeny but 2. - phylogeny inferred using characters & parsimony without a reproducible method”

3. Hennig (et al.) to today 3. Statistical Phylogenetics - phylogeny “Classification with phylogeny & a inferred using corrected data & “best fitting reproducible method” model”

History Phenetics - similarity only, not evolution, not phylogeny (1950-1960) - computerized, reproducible, “objective,” modern, sexy… - goal to remove all subjectivity, measure everything, use matrix of distances - sometimes called “Numerical Taxonomy” after book by Sokal & Sneath (1963) - cluster based on overall similarity - not evolutionary trees, but phenograms 1957 - first numerical phylogeny published (Michener & Sokal)

History Phenetics - Problems Similarity sometimes reflects evolution… 1. Reproducible but no agreement on which clustering algorithm or statistic to use… Rhino Beetle Butterfly - different algorithms = different trees e.g. UPGMA, PCA… etc. True tree: - although there is only one true evolutionary tree, there are many alternative ‘similarity’ trees depending on the Butterfly Butterfly data & algorithm used Beetle Beetle

2. Similarity doesn’t always = evolutionary Rhino Rhino relationship! Phenogram

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History And sometimes doesn’t… Phenetics - the good

1. Demanded explicit character analysis & laid Crocodile groundwork for numerical phylogenetics True tree: 2. Still used for lower-level problems e.g. , species demarcations… 3. And some higher-level problems Lizard Lizard

Crocodile Crocodile Survives in various forms - an issue of debate… (see lecture on Distance methods) Bird Bird Phenogram Cladogram

Definition - Phenetics Lack of a reproducible method resulted in three major approaches: Phenetics as originally applied, by Cain and Harrison (1960), refers to the "arrangement by overall 1. Phenetics - similarity / distances only, not similarity, based on all available characters without evolution, not phylogeny any weighting ...since it employs all observable characters (including of course genetic data when available)". 2. Cladistics - phylogeny inferred using characters & parsimony Cain, A. J., Harrison, G.A. (1960) Phyletic weighting. Proceedings of the Zoological Society of London 3. Statistical Phylogenetics - phylogeny 131: 1-31 inferred using corrected data & “best fitting model”

History History Cladistics Cladistics 1950 - “Grundzüge einer Theorie der - method explicit, reproducible phylogenetischen Systematik” - hypotheses of phylogeny could now be “tested” - German entomologist of Diptera - Hennig’s original method: - 1966 English translation of Phylogenetic 1. Distinguish homologies from analogies Systematics 2. Distinguish derived homologies - key: distinguish derived from (apomorphies) from ancestral ancestral homology (plesiomorphies) homologies - yields 3. Tree then built from apomorphies (evidence - Vitriolic attacks on phenetics of common ancestry) during the 1970s - more on how this is done later Willi Hennig (1913-1976)

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History Classifications and Phylogenies Cladistics - monophyletic classification Given this classification: - a new method for phylogenetic inference AND - a new method to derive classifications Reptilia Order Anapsida () Order ( & ) 1. Not based on similarity but on phylogeny Order (attacked phenetic clusterers) Class Aves Class Mammalia 2. Taxa must be natural (monophyletic) = common ancestor and ALL What evolutionary tree would you envision? descendents included (attacked ET classifications that accepted non-monophyletic groups)

Classifications and Phylogenies Reptilia is not monophyletic

Class Reptilia It is a grade, not a Order Anapsida (turtles)

Order Lepidosauria (lizards & snakes) Turtles Order Crocodilia Amphibia Mammals Lizards Snakes Crocodiles Birds Class Aves Class Mammalia

Anapsida Crocodilia Lepidosauria Aves Mammalia

Does not include at least 1 descendent group: birds

History Lack of a reproducible method resulted in three Cladistics major approaches: - Originally lacked an explicit method to deal with character conflict: “Hennig’s dilemma” 1. Phenetics - similarity / distances only, not evolution, not phylogeny - Hennig’s approach was to remove the conflict by restudy of the characters 2. Cladistics - phylogeny inferred using characters & parsimony - The principle of Parsimony was later employed to deal with character conflict 3. Statistical Phylogenetics - phylogeny (to be continued…) inferred using corrected data & “best fitting model”

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Statistical Phylogenetics History - Grew from mathematical, , evolutionary, Statistical Phylogenetics numerical studies, not as much from systematics - Cavalli-Sforza & Edwards had been students of - Concurrent with first sequence data the geneticist R. A. Fisher (Zuckerkandl & Pauling, 1962) - Worked on trees of human populations from - 1960s numerical techniques that used characters frequencies & blood group alleles rather than distances/similarities: - Arrived at 2 methods initially: 1. Parsimony (Cavalli-Sforza & Edwards, 1963) 1. Parsimony tree with minimum changes preferred 2. Least-squares (a distance method) 2. Maximum Likelihood (Cavalli-Sforza & - 3rd method to reconcile the two: Edwards, 1964) 3. Maximum Likelihood (Fisher’s method) tree that maximizes probability of the data is (published 1964 & 1967) preferred

Luca Cavalli-Sforva History Statistical Phylogenetics - Parsimony was made a workable method for morphological analysis by Camin & Sokal, 1965

- evolved cartoon “” & tested methods to infer the “known” phylogeny - parsimony was best Anthony Edwards First published tree using parsimony (1965)

History History Statistical Phylogenetics Statistical Phylogenetics & Cladistics - Camin & Sokal’s parsimony required irreversible - Cladists state that Hennig’s methods “implied” change & ordered states (problem) parsimony: 0 => 1 => 2 => 3 - Parsimony becomes adopted by the cladists: Hennig’s Auxiliary Principle: assume homology if there is no evidence to the contrary - Kluge (1969) and Farris (1970) published - one change (homology) is the default algorithms for unordered parsimony assumption over termed “Wagner Parsimony” & how to - two or more changes (analogy / ) search for the most parsimonious tree - prefer trees with the greatest number of apomorphies (and thus the fewest )

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History History Statistical Phylogenetics & Cladistics Statistical Phylogenetics - Cladists (most) reject statistical approaches to - Initially overshadowed by cladistics phylogenetics difficulties with complexity of approach

- In so doing they consider parsimony to not be - Rapidly expanding field statistical but philosophical initially for molecular data as of 2001 for morphological data too - Claim justification for a “parsimony-only” method faster algorithms & making using arguments on hypothesis testing of approach fully practical philosopher Karl Popper (more on this later…) - Cladists continue the battle for their method

Terms - from lecture & readings today Phenetics

Statistical Aristotle's Scala naturae apomorphy Phylogenetics Lamarck plesiomorphy Cladistics 1980s Darwin Wallace monophyletic classification 1960s Haeckel parsimony Cladism overshadowed Evolutionary Taxonomy maximum likelihood ET & Phenetics Mayr & Simpson 1940s Cavalli-Sforza Evolutionary Taxonomy phenetics Edwards Now head to head with Sokal & Sneath Camin rapidly growing cladistics Kluge Statistical Phylogenetics statistical phylogenetics Farris Hennig Hennig's Auxiliary Principle Grade 1800s clade

You should be able to

Describe the 3 phases in the history of phylogenetic inference

When did Phylogenetic Inference begin (approximately) & by whom?

Describe the “method” of Evolutionary Taxonomy

Describe explosion of methods in 1960s

Describe the pros & cons to each method

Who was key to each method?

Why isn’t a phenogram a phylogeny?

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