1. CLASSIFICATION: The process and practice of describing, defining and ranking taxa within a hierarchical series of groups; permits organizing and ordering knowledge about organisms, and creates a simplified language for conveying information about order in the diversity of life. In biology, we use the Linnean classification hierarchy (Kingdom, Phylum, Class, Order, Family, Genus, Species).

2. Kingdom Metazoa Phylum Chordata Class Mammalia Order Primates
Family Hominidae
Genus Homo
species sapiens
Binomen
(scientific name) in
“binomial” or
“binominal”
nomenclature
Rules: Always capitalized (UNLESS it’s a derivative, e.g. “Hominidae” but “hominid”.) species epithet is exception.
Genus & species ALWAYS italicized or underlined EXCEPT if rest of the text is italicized or underlined. Context-dependent.
Genus capitalized, species not. Rarely

3. G.G. Simpson, 1945 Class Mammalia Subclass Infraclass Cohort
Superorder
Order Primates
Suborder Anthropoidea
Infraorder
Superfamily Hominoidea
Family Hominidae
Subfamily
Tribe
Subtribe
Genus Homo
Subgenus
species sapiens
subspecies
BUT, not all levels recognized in all groups. NONE of these ‘extra’ ranks used in his classification of humans.

4. Systematics: The field of biology that deals with the diversity of living organisms, usually divided into the two subdisciplines of taxonomy and phylogenetics.
Taxonomy: The science of describing, naming, and classifying (grouping) organisms.
Taxon (plural: taxa): Any named group of organisms (not necessarily a clade). A subspecies respresents a "taxon," as does every hierarchical level up to Kingdom.
Phylogenetics: The field of biology that deals with the relationships between organisms, including the discovery of these relationships and the study of the causes behind these patterns.

5. Phylogeny: The evolutionary relationships among organisms; the patterns of lineage branching produced by the evolutionary history of organisms.

6. time

7. Left: from his notes, Right: only figure published in 1859’s “On the origin of species” (this is partial)

8. Left: from his notes, Right: only figure published in 1859’s “On the origin of species” (this is partial)

9. Outgroups Terminal node (terminal) (=interior branch)
ingroup: The set of taxa which are hypothesized to be more closely related to each other than any are to the outgroup(s).
outgroup: Any taxon (or taxa) hypothesized to be less closely related to each of the taxa under consideration (the ingroup) than any members of the ingroup are to each other. Outgroups are typically used to "root" trees and to infer the direction (polarity) of character change.
sister group: The closest outgroup (living or extinct) to a given ingroup. "Sister taxa" refers to the two lineages or clades resulting from the splitting of a single lineage.
operational taxonomic units (OTUs): The taxa included in a phylogenetic analysis representing the terminal nodes.
node: A branch point representing lineage splitting (=cladogenesis), ultimately the result of speciation.
branch: A line, representing a lineage, connecting two internal nodes or an internal node with a terminal node (OTU).
internode: An internal branch connecting two internal nodes.
root: The internode at the bottom of a tree.

10. Most Recent Common Ancestor of B+C MRCA of A+B+C MRCA of N+A+B+C
“basal” to the ingroup
Most Recent Common
Ancestor of B+C
MRCA of A+B+C
MRCA of N+A+B+C
basal group: The earliest diverging group within a clade
e.g., we didn't evolve FROM chimpanzees; we share a MRCA with them.

11. A B C D A B C D D C
Orientation of tree doesn’t change patterns of shared ancestry B D C B A A

12. A B C D A B C D

13. A B C D A C D B
Homework will help with this.

14. Types of “trees”
DENDROGRAM: A branching diagram with nodes and branches.
PHYLOGENETIC TREE or CLADOGRAM: A dendrogram representing
the genealogic relationships between taxa with ancestry and relative time implied. A B C D

15. Types of “trees”
DENDROGRAM: A branching diagram with nodes and branches.
PHYLOGENETIC TREE or CLADOGRAM: A dendrogram representing
the genealogic relationships between taxa with ancestry and relative time implied.
EVOLUTIONARY TREE: A phylogenetic tree that includes a time axis
and (generally) all members, living and extinct.

17. Types of “trees”
PHYLOGRAM: A tree with branch lengths drawn to represent the degree of genetic (or other) divergence. A B C D
scale=10%

19. Monophyly
(monophyletic)
monophyletic group (monophyly): A group of organisms/taxa that includes ALL known descendants of that group's common ancestor (including the common ancestor). Monophyletic groups (clades) are grouped by shared derived characters (synapomorphies) not present in earlier ancestors or other groups. Monophyletic groups are also called "natural" groups. Mammalia is an example of a monophyletic group.

20. clade
clade
clade
subclade
Monophyly
(monophyletic)
clade: A monophyletic or “natural” group.
subclade: A clade nested within a larger, more inclusive clade.

21. Monophyly
(monophyletic)
Paraphyly
(paraphyletic)
paraphyletic group (paraphyly): An artificial group of organisms/taxa that includes some, but NOT ALL, of the descendants of a common ancestor. Paraphyletic groups are typically recognized by the sharing of primitive (plesiomorphic) characters. Reptiles are an example of a paraphyletic group. A "grade" is also, by definition, paraphyletic.

22. Monophyly
(monophyletic)
grade
Paraphyly
(paraphyletic)
grade: An artifical (non-monophyletic) taxon, frequently paraphyletic and sometimes polyphyletic. Grades are supposed to represent some level of evolutionary progress.

23. Monophyly
(monophyletic)
polyphyletic group (polyphyly): An artificial group of organisms/taxa derived from two or more independent, distinct ancestral taxa. The common ancestor, and many closely related taxa, are excluded from the group. Polyphyletic groups are generally recognized by superficial similarities resulting from convergence that do not reflect close evolutionary relationships.
Paraphyly
(paraphyletic)
Polyphyly is a type of PARAPHYLY!!!
Polyphyly
(polyphyletic)

24. Monophyly
(monophyletic)
Paraphyly
(paraphyletic)
Polyphyly
(polyphyletic)

26. Anapsida Diapsida Saurapsida Synapsida Amniota -ca. 320 mya
Lizards & snakes
Crocodiles
Dinosaurs & birds
Mammals &
reptile-like mammals
Turtles
Anapsida
Diapsida
Amphibians
“Homeothermia,” taxon once proposed to include birds and mammals. Monophyletic or paraphyletic?
Saurapsida
Synapsida
-ca. 320 mya
Amniota
-evolution of cleidoic (shelled) egg;
ca. 350 mya

28. Why do we care? Meaningful classifications.
Need pattern (=phylogeny) to study process (evolution, biogeography, etc.).
The “comparative method”
Predict properties of organisms

29. BUT, no cheetah or extinct cats here.

30. “cheetahlike cat” Miracinonyx
“cheetahlike cat” Miracinonyx. At one time thougth be be closely related to Cheeta (Acinonyx), but cheetalike morphology likely evolved twice.