Classification and Phylogeny: What’s In a Name?

Alice in Wonderland “What’s the use of their having names,” the Gnat said, “if they don’t answer to them?” “No use to them,” said Alice, “but it’s useful to the people that name them, I suppose.”

What’s in a name?

Carolus Linnaeus: the father of modern taxonomy In the 1700s a Swedish physician and biologist, Carolus Linnaeus, refined classification into a hierarchy where groups of similar organisms can be subdivided into smaller more distinctive groups.

Linnaeus classified organisms into a hierarchy of groups: Eventually, as one works through such a system, each unique form of organism is left to occupy its own small, but distinct category.Eventually, as one works through such a system, each unique form of organism is left to occupy its own small, but distinct category. Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species

Here are the classification hierarchies for several different species of organisms:

A bee by any other name… Genus species Scientific name: Genus species Taxonomy= the science of naming and classifying living things

The science of taxonomy underwent a fundamental revolution when Darwin published On the Origin of Species Darwin suggested organisms cluster together due to common ancestry: Species that are in the same genus have a more recent common ancestor than those in different genera Likewise, genera within the same family have a more Recent common ancestor than those in different families

Systematics Darwin showed that the classification of living organisms has a natural basis: their evolutionary history Taxonomy expanded into systematics: the study of the diversity of living organisms and their evolutionary relationships

Homology: the same component and structures of organisms are repeated in many forms Darwin viewed homology as evidence that development of one structure is a modification or variant of the development of another (implies a common origin as a feature present in a common ancestor) How do we determine evolutionary relationships?

Evolutionary Homologies features that share common origin in a common ancestor Recognizing homologies: position relative to other parts and of its parts to each other humerus ulna radius

Evolutionary Homologies features that share common origin in a common ancestor Recognizing homologies: Transitional forms Ex: horses run on their toes (actually on the tip of a single toe on each foot) Which toe? the fossil record for horses is exceptional, and we can trace the transitional stages through time to discover that it is the third toe IN FACT, we can trace to a common ancestor with rhinos and tapirs (Hyracotherium) and discover that the habit of walking on the 3rd toe is homologous in this group

Why do we care about homologies? Homologies imply that the most recent common ancestor had the trait Nesting homologies allows us to heirarchically classify organisms in an evolutionarily meaningful way

Homoplasy Homoplasy (also analogy or analogous traits) same or similar character in two or more taxa was not present in the most recent common ancestor Can be difficult to distinguish from homology

Homoplasy results from convergent evolution similar structure/trait has arisen in 2 or more species, but is not possessed by a common ancestor (and all intervening ancestors) cooperative hunting in canids and felids growth form of aloe (related to lillies) and agave (cactus)

Homoplasy results from evolutionary reversals similar structure/trait has arisen in 2 or more species, but is not possessed by a common ancestor (and all intervening ancestors) secondary wing loss in birds and insects eye loss in cave fish and cave salamanders Texas blind salamander Typhlomolge rathbuni Eyed (surface dwelling) and eyeless (cave dwelling) Astyanax mexicanus

Evolutionary modifications Evolutionary change (modification) is a change in a character state Do not confuse character with character state eg., Characters include: number of digits, eye color,height Characters states are: 3, 4, 5 blue, green 2m, 2.5m, 3m Character state changes can be any character, behavioral, physiological, morphological, biochemical, molecular, etc. 1) presence/absence (0,1) for any character 2) qualitative, multistate - arbitrarily 1, 2, 3 for any character 3) quantitative, multistate - difficult to handle. How do you separate variation from difference?

Systematics systematists infer the historical pattern of evolutionary descent for an organism to build a PHYLOGENY - the genealogy of a group of taxa (the practice of developing phylogenies is called phylogenetics) Interpretation: B&C evolved from a common ancestor 1; 1 is no longer present, only B&C. outgroupABC D ‘tips’- represent terminal taxa (extant species) Nodes’ - represent common ancestors that no longer exist

Cladistics is a modern approach Goal is to group organisms according to evolutionary history (phylogeny) Note: in practice, collect data on character states and then reconstruct topology Use data to construct cladograms Cladistics

cladograms can be derived by observing shared character states –3 types: 1. shared derived character states -- synapomorphy 2. shared ancestral states -- sympleisiomorphy 3. shared but independently evolved state -- homoplasy Only #1 are useful in constructing cladograms SYNAPOMORPHIES DEFINE CLADES, and are evidence of a most recent common ancestor individual taxa are recognized by unique, unshared character states (autapomorphies) Cladistics

If a character state was present before a clade split off, it is ancestral If a character state is new to a group, it is derived Ancestral vs. derived can be answered with outgroups (which define the ancestral state for a clade) Ancestral vs. Derived autopomorphy sympleisiomorphy synapomorphy

Constructing a cladogram How many synapomorphies do each pair of organisms share?

How many trees? With 3 taxa, there are the following possible trees: The problem that arises is that even with complete knowledge of shared derived characters, there are many possible phylogenies that can be generated: # of taxa bifurcating trees How do we chose between them? ABCABC ABC

Choosing the correct tree There are many possible methods for selecting trees, most are built on the principle of parsimony - the most likely alternative is the simplest and least complex in the phylogenetic context, the favored phylogeny includes the fewest number of changes in character state There are other ways to choose between trees (e.g., Maximum likelihood) that weight some kinds of character state changes differently than others e.g., for molecular data, we know that transversions (A, G C, T) are less common than transitions (A T, C G) - we can calculate the probabilities for any taxon and weight each change differently

Defining Groups: Cladistics Monophyletic: includes all taxa from a single common ancestor Paraphyletic: does not include all taxa from a single common ancestor Polyphyletic: includes all taxa not from a common ancestor

Cladistics argues that many traditional groups are paraphyletic Example: Reptiles are not a valid group Impact of cladistics

Reptiles are a paraphyletic group

Cladistics would group birds with the reptiles

Traditional and cladistic classification of vertebrates