Systematics

Systematics and species

John Wilkins

Lecture 1: ClassificationThe mind is finite in its powers of

comprehension; the objects, on the contrary, which are presented to it are, in proportion to its

limited capacities, infinite in number. … How can the infinity of nature be brought down to the finitude of man? This is done by means of

Classification. [Sir William Hamilton, Lectures on Metaphysics,

lect. XXXIV]

Classification

• The basic statement of classification:– A is more closely related to B than

either is to C

A

B

C

Characters

• Symbols for the traits of organisms

• Homologous - similar by descent or ancestry (homo- = same + logy)

– Molecular homology: orthology– Serial homology

• Homoplasious - similar in form (homo- + plasty = form)

– Convergent evolution– Not informative of evolutionary past

Hierarchy

• Ever since Aristotle, all proper classification is hierarchical

• That is: nested sets

Never this

Linnaean hierarchy:

KingdomPhylum[Bot.: Division]

ClassOrder

Family[Tribe]

Genus Species

• Artificial, absolute ranks, limited branching

Representing hierarchies

• Tree diagrams• Indented lists

Systematics approaches (sect 6.3)

We can relate organisms:• By similarity

– Morphological (form)– Phenetic (clusters)– Essentialist (essences)

• By genealogy– Cladistic– Evolutionary

Similarity relations taxa

• Morphological– using a key characters of form, or several– Problems: arbitrary choice of characters

• Phenetic– Using any characters, plotting in a graph to find

clusters– Problems: sensitive to characters used

• Essentialist– Necessary and sufficient criteria– Problems: species are usually

polymodal/polytypic– Can be species with no N&S criteria (sibling

species)

Cladism

• Cladism draws branching trees• A “natural” group is

monophyletic

Shared derived states

Shared derived A+(B+C+D)Shared derived A+(B+C+D)

Ancestral stateAncestral state

Shared derived D+(B+C)Shared derived D+(B+C)

Shared derived B+CShared derived B+C

Unique derivedUnique derived

Evolutionary systematics

• Genealogy plus grade• Can be paraphyletic or polyphyletic

Mole Wolf Thylacine

Converginggroup

Lizard Crocodile Bird

“Primitive”group

Clouds, clades and grades• Which is the “right” way to proceed?• Monist: My way or the highway• Pluralist: Whatever gets you through

the night• Clouds - phenetic clusters of similar

things, or essentialist classes of identical things

• Clades: branches in pattern or process• Grades: what the observer thinks is

theoretically important

Theory, observation and taxa• Theory-free classification

– Operationalism– Instrumentalism or conventionalism

• Theory-relative classification– Is evolution the foundation for

hierarchy?

• Theory-testing classification– Should a classification test other

aspects of the theory of a field?

Lecture 2: Species

John Wilkins

The One-Eyed Species Problem

Summary slide

• Two sides to it: what scientists do and say (mostly one-eyed), and the philosophical issues (multiple PoVs)

• Some [false] history - the Received View of Species

• Five kinds of species concepts used by scientists

Review

• Definitions - necessary and sufficient (N&S) criteria

• Gradual thinking versus black and white thinking

• Lineages - series of parent-child entities (populations)

The [False] Received History of Species

Plato defined Form (eidos, trans. species) as something that had an essence, and Aristotle set up a way of dividing genera (genē) into species (eidē) so that each species shared the essence of the genus, and each individual in the species shared the essence of the species. Linnaeus took this idea and made species into constant and essentialistic types. Darwin overcame this essentialism. Later naturalists, under the influence of genetics, discovered the biological species concept, in which species are found to be populations without essences, but with common ancestry. Population thinking replaces typological essentialism.

The Received History of Species, briefly• In older view a species has an

essence shared by all its members• Shares in the essence of the genus• Linnaeus took the logical species and

applied it to biology• Morphological conception (based on

form)• Darwin discovered population thinking• Others later invented the “biological”

species concept

• Morphological (Linnaean)• Reproductive isolation

(Biological)• Evolutionary• Phylogenetic (3? kinds)• Ecological

Species concepts in play

A reference diagram

• Biospecies or BSC• Speciation by evolution of RIMs• Hybrid infertility• Gene pool concepts• Shared mating mechanisms

Biological species concepts

• AKA evospecies or ESC.

• Independent lineages - unique evolutionary fate (B, C, and D)

• Chronospecies - species across time and form (A to B) not 2 but 1 evolutionary species!

Evolutionary species concepts

HennigianHennigianMonophyleticMonophyletic

• Phylospecies or PSC• Between two nodes

(Hennigian concept)• Descended from a

single population (Monophyletic concept)

• Defined by a unique set of characters (Autapomorphic concept – a morphological concept?)

Phylogenetic species concepts

AutapomorphicAutapomorphic

• Ecological species concepts (Ecospecies)

• Paleontological species concept (Paleospecies)

• Asexual species concepts (Agamospecies)

• Taxonomic species concept (Cynical species)

Other concepts

Summary of concepts

• Older morphological view based on essences

• Modern “biological” concepts based on reproduction and genetic exchange

• Evolutionary and phylogenetic concepts based on history

• Ecological and other conceptions

Categories and Taxa

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Species Categories

Species Taxa



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On the traditional view, the species category is a class of classes defined in terms of the properties which particular species possess … and particular organisms are individuals … The relation between organisms, species and the species category is membership. An organism is a member of its species and each species is a member of the species category. On the view being urged [by Ghiselin and Hull], both particular species and the species category must be moved down one category level. Organisms remain individuals, but they are no longer members of their species. Instead an organism is part of a more inclusive individual, its species, and the names of both particular organisms (like Gargantua) and particular species (like Gorilla gorilla) become proper names. The species concept is no longer a class of classes but merely a class. [David Hull 1976: 174f]

Philosophical issues

Four major issues

1. Realism versus idealism2. Class versus group3. Functionally coherent or not?4. Identifiable or not?

First issue: Realism

• Species are either real things, or they are not

• If not, then they are conceptions in the mind only (i.e.,the concepts do not refer to anything)

• Conventionalism (Locke, T. H. Morgan, Maynard Smith)

• Real things are objects, mere concepts are ideas. Hence, “species realism” vs “species idealism [nominalism]”

Second issue: Class or group?• Issue whether or not species are

abstract entities that are timeless, or whether they are groups of organisms that begin and end and have a location (but not nec. one single location).

• Philosophically, the problem of “universals” (both in the definitions, and in the essences) versus “particulars”

Third issue: functional or not?• Issue of whether a species must

have some kind of functional identity - whether genes flow between all populations, or whether there are “developmental constraints”, or whether they occupy a particular niche that means they are maintained by selection.

Fourth issue: identifiable or not?• Issue of whether or not a species

must be salient to human observers or their tests

• Often confused with whether or not a species has “key characters” and can be diagnosed

Species as classes - 3 claims1. That species have universal

characters2. That species are natural kinds3. That species are abstractions• Each of these suggests that a

species can be “reborn” after extinction (The Jurassic Park Scenario)

Species as individuals - 3 claims1. A species has a historical

duration (birth and death) and a physical location (the historical individual thesis)

2. A species has parts rather than members (organisms are components)

3. A species has a causal cohesion (the functional individual thesis)

Historical species

Do:• Species act like an individual

organism?• Species reproduce?• Species have sharp beginning and

endings?Species, once extinct, cannot be revived (otherwise a new historical species) - the Respeciation Problem

Functional species

• Some argue that species are functional entities, the same way a gun is a functional entity (not just parts, but parts organised in a functioning way). The gene pool would be seen as a functional individual.

• Ship of Theseus problem of identity• If species are not functionally

organised, are they still individuals?

Summary of species ontology

Individual type Logical Functional Phenomenal

Ideal

A. Pure abstraction [Idea]

B. Phenomenal individual [Appearance]

C. Integrative individual [Effect]

D. Phenomenal, Integrative individual [Apparent Effect]

Real

E. Historical individual [Particular]

F. Historical, Phenomenal individual [Apparent Particular]

G. Historical, Integrative individual [System]

H. Full individual

Punctuated Equilibrium Theory and the Individuality Thesis• The idea that species have a

beginning and end fit well with PE

• The Individuality Thesis doesn’t need “sharp” edges in time or space

Species nominalism

We may say, for example, that some dogs are white and not … commit ourselves to recognizing either doghood or whiteness. … On the other hand, when we say that some zöological species are cross-fertile we are committing ourselves to recognizing the several species themselves, abstract though they are … at least until we devise some way of paraphrasing the statement as to show that the seeming reference to species … was an avoidable manner of speaking.”

- Quine “On what there is” (1948)

Nominalism? Conventionalism• Nominalism denies the reality of

abstract general terms, that cover many objects

• So-called species nominalists do not deny that the species exist, but only that they are not classes (do not have N&S properties)

• Species are named for convenience

Conclusion

• Species can be one of four kinds of individuals

• They can be real individuals, or ideal individuals, or real classes or ideal classes, and so on

Education

Systematics