• Phylogenetic reconstruction

– What are the relationships between species?

• Ancestral, descendant, sister, cousin,"

– Modern methods

• DNA

– number of differences in the sequence

• Biological Species concept

• Habitat, geographic ranges

• Comparative morphology

Classification - Concerns the grouping of

species into sets of similar organisms at any

level in the Linnaean taxonomic hierarchy

Taxonomy – the theories and techniques of

describing, naming, and classifying organisms

(the practice of classification)

Systematics – scientific study of the kinds and

diversity of organisms as well as any and all

relationships among them (who is related to

whom, and how they are related)

• In classification

– Taxonomist asks whether a species being classified contains the defining feature of a particular taxonomic class.

• In systematics

– Taxonomist asks whether the characteristics of a species confirm or reject the hypothesis that it descends from the most recent common ancestor of a particular taxon.

• A major goal of systematics is to infer the evolutionary tree or:

– phylogeny – the evolutionary history of a species or group of related species.

Node: a branchpoint in a tree (an  ancestral OTU)

Branch: defines the relationship between the taxa in terms of descent and ancestry

Topology: the branching patterns of the tree

Branch length (scaled trees only): reps the # of changes that have occurred in the branch

Root: the common ancestor of all taxa

Clade: a group of 2 or more taxa or DNA sequences that includes both their common ancestor and all their descendents

Operational Taxonomic Unit (OTU): taxonomic level of sampling selected by the user to be used in a study, such as individuals, populations, species, genera, or bacterial strains

• Binomial Nomenclature is the science of naming organisms

– Combination of two names

• Genus and species
Homo sapiens

• Types–each species has a name bearing type – holotype – the standard

• Priority–a valid name of a taxon is the oldest name applied to it

– The senior name always stays with new discoveries

• Naming depends on what is used –

• Traditional view Hominid – Evolutionary Taxonomy

• Hominin

– Based on DNA evidence

• How can we recreate relationships with the fragmentary fossil record?

– Observable differences = Evolutionary relationship?

• Methods

– EXAMINE MORPHOLOGY

• Phenetics

• Cladistics

• Sokal and Sneath (1963) – Numerical Taxonomy

– Applied mathematics rather than observation differences to recreate phylogeny

– Measured as many characters as they could

• All equally weighted

• Calculated differences using similarities and differences

– Create a phenogram

• Phenetics

– Mixes ancestral traits and derived traits

– Gives all characters equal weight

• Regardless of evolutionary significance

• Not every character is useful in determining relationships

– Characters are chosen by the researcher

• Willi Hennig

– Believed relationships need to based on ancestor- descendant relationships

• Taxonomy must reflect phylogeny

– Begin by analyzing characters

• Discrete variable

– Apomorphy

– Pleisiomorphy

1. Characters shows more variability among the taxa you are interested in than within the taxon.

2. Variation must be heritable

3. The characters must be truly comparable

– Homologous NOT a homoplasy

• Homologous traits are those that are the same in two organisms due to a common ancestor (identical by descent)

• Homoplastic traits are those that only appear to be identical by descent, but are similar due to convergence or parallelism.

– Shark and dolphin dorsal fin and streamline body

• A potential misconception in constructing a phylogeny is similarity due to convergent evolution, called analogy, rather than shared ancestry.

• Convergent evolution occurs when similar environmental pressures and natural selection produce similar (analogous) adaptations in organisms from different evolutionary lineages.

4. Determining polarity of a character involves

determining what character states are ancestral and what are derived.

– Ancestral (plesiomorphic) characters are those that are present in the common ancestor of the entire group (ancient homologue)

– Derived (apomorphic) characters are those that are novel and have arisen after the split with a last common ancestor (recent homologue)

• Polarity is determined by using outgroup comparison.

– An outgroup is closely related, but not part of the group being examined (the ingroup).

– If a character is found in both the study group and the outgroup, it is considered ancestral for the study group.

– Characters found in the study groups but not the outgroups are derived.

• Once polarity is determined a cladogram

can be created based on:

– Synapomorphies - derived character shared by the members of the taxa.

• Determine branches in groups

– Synplesiomorphies – shared ancestral traits

• Determine monophyletic groups

• Monophyletic group.

– Consists of the ancestor species and all its descendants

• The simplest explanation is most often the correct one (Occam’s razor)

– Organisms reproduce

– Character states and changes are inherited, giving rise to transformational homologies

• Descent with modification

– Homoplasy is assumed to be rare

• Compatibility

– The number of conflicting characters

• Those that have fewer conflicting characters are considered stronger

• Structural Complexity

– Simple structures are likely to evolve via convergence and hence are weaker evidence than more complex characters

• Diagram of nested synapomorphies that define relationships

• Each node represents a speciation event

• Taxa appear at the end of the branches, not at the nodes

– Does not take time frame into account

• All nodes include a list of synapomorphies common to all taxa above the node

• Fossils

– What is the ancestral condition of the LCA if we don’t know what they looked like

• Diagnostic problems – with closely related species it is difficult to determine if a trait is homologous or slightly derived

– Researcher defines the characters and chooses which are to be used and how they are weighted

– Time is ignored

– Location is ignored