Systematics - BIO 615

Outline - History and introduction to

phylogenetic inference

1.  Pre Lamarck, Pre Darwin

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

Outline - History and introduction to History

phylogenetic inference
Lamarck - 1800 - Major impact on Biology:

1.  Pre Lamarck, Pre Darwin - First public account of evolution - proposed that modern
species had descended from common ancestors over
“Classification without phylogeny”
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” taxon

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 history of
Biology - 1809
-  Classifications were taken as proxies - representations
of the “natural order,” 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 nature 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

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

But as we have no written pedigrees you will, perhaps, say

Lamarck’s ideas, which lacked an accurate
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 homology
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 kingdom of Nature.”
who knew the fossil 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) On the Origin of Species

History History
Ernst Haeckel (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
- “Ontogeny recapitulates as
phylogeny” - not a law,
as he thought
- Coined terms:
Evolutionary Taxonomy
Ecology - spanned from the 1800s to the 1960s
Phylum
Phylogeny (1866)
monophyletic
- formed the “roots” of the discipline of
polyphyletic phylogenetics

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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
(morphology, development, fossils, 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
about their organisms!)
= “Guessograms”

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

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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. Phenetics - similarity / distances only, not
“Classification without phylogeny” evolution, not phylogeny, no weighting

2. Lamarck & Darwin to Hennig (et al.)

2. Cladistics - phylogeny inferred using
“Classification with phylogeny but
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

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

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History
And sometimes doesn’t… Phenetics - the good

1. Demanded explicit character analysis & laid

Lizard Crocodile Bird
groundwork for numerical phylogenetics
True tree: 2. Still used for lower-level problems
e.g. morphometrics, species demarcations…
3. And some higher-level problems
Lizard Lizard

Crocodile
Crocodile Survives in various forms - an issue of debate…
Bird
(see lecture on Distance methods)
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 - Willi Hennig “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 phylogenetic tree 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 Class Reptilia
Order Anapsida (turtles)
Order Lepidosauria (lizards & snakes)
1. Not based on similarity but on phylogeny Order Crocodilia
(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 clade
Order Anapsida (turtles)
Order Lepidosauria (lizards & snakes) Turtles
Order Crocodilia Fish 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, computer, evolutionary, Statistical Phylogenetics
numerical studies, not as much from systematics - Cavalli-Sforza & Edwards had been students of
- Concurrent with first protein sequence data the population geneticist R. A. Fisher
(Zuckerkandl & Pauling, 1962) - Worked on trees of human populations from
- 1960s numerical techniques that used characters gene 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
“Caminalcules”
& 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 / homoplasy)
search for the most parsimonious tree - prefer trees with the greatest number of
apomorphies (and thus the fewest
homoplasies)

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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 & computers 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

Phenetics
today
Statistical Aristotle's Scala naturae apomorphy
Phylogenetics
Lamarck plesiomorphy
1980s Cladistics
Darwin monophyly
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?