Phylogeny and the Tree of Life Chapter 26 BCOR 012 February 4,7, 2011

Systematics: Connecting Classification to Phylogeny Systematics, Taxonomy, and Phylogeny Constructing cladograms Phylogenetic Classification Molecular Systematics Parsimony Outline for February 4,7 2011

Systematics is the study of biological diversity in an evolutionary context. It includes speciation taxonomy phylogeny.

Taxonomy is the branch of systematics concerned with naming and classification. Scientific names are binomials Example: Acer saccharum - Acer is the genus name - it is a Latin noun - saccharum is the specific epithet - it is a Latin adjective Carolus Linnaeus

Biological classifications are hierarchical: each taxonomic group is nested within a more inclusive higher order group. (Note that only the genus name and specific epithet are italicized.)

Fig Species Canis lupus Pantherap ardus Taxidea taxus Lutra lutra Canis latrans OrderFamilyGenus Carnivora Felidae Mustelidae Canidae Canis Lutra Taxidea Panthera

“Our classifications will come to be, as far as they can be so made, genealogies.” - Charles Darwin, 1859 Phylogeny and Classification

Phylogeny is the study of the pattern of divergence history. (as opposed to speciation, which addresses process.) Assembling a phylogeny using cladistics, taxa are associated on the basis of shared evolutionary innovations. Willi Hennig, Founder of Phylogenetic Systematics (also called cladistics)

One of the evolutionary innovations shared by birds is the feather … Homology, the sharing of an innovation (derived character) because of its invention in a common ancestor.

Serial Homology of the Lobster

Figure 34.4b-c Chordate segmentation

CRUSTACEANS COMPARED - EVOLUTIONARY HOMOLOGY

CRUSTACEANS COMPARED: EVOLUTIONARY TRANSFORMATION LOBSTER ROCK CRAB

Fig Deletion Insertion

Fig. 26-8a Deletion Insertion 1 2

Fig. 26-8b 3 4

DNA Evolution: stable and labile characters relate to function. Example: Homeobox genes, which govern variation in serial homologs.

The homeobox (in the gene) codes for a homeodomain (in the protein synthesized from the gene). The homeodomain has a precise three-dimensional structure related to its function. In evolution, the homeodomain is relatively stable because it has a precise job.

Dm - Fruitfly Tc - Beetle Jc - Butterfly Ak - Onycho- phoran Amino acid sequences compared for the homeotic gene Ubx insects arthropods Decides six legs or more

Parsimony

Under the principle of parsimony, tree A would be preferred over B and C as it is one step shorter. Ockham's razor.: when trying to choose between multiple competing theories the simplest theory is probably the best.

How to construct a cladogram: Choose a study group Choose an appropriate outgroup Compile data matrix Polarize characters Use shared derived characters to associate study group taxa and construct the cladogram

The outgroup is the group used to polarize character states in the study group. It should be the group most closely related (on the basis of other lines of evidence) to the study group that is not actually part of the study group. lancelet

How to construct a cladogram: Choose a study group Choose an appropriate outgroup Compile data matrix Polarize characters Use shared derived characters to associate study group taxa and construct the cladogram

The primitive character is the one shared by the outgroup and some, but not all, of the study group.

How to construct a cladogram: Choose a study group Choose an appropriate outgroup Compile data matrix Polarize characters Use shared derived characters to associate study group taxa and construct the cladogram

Kinds of Characters Apomorphy - a derived character state Synapomorphy - a shared derived character state Autapomorphy - a derived character state unique to one study group member Symplesiomorphy – a shared primitive character state

Cladistic Analysis and Classification: Kinds of Groups

A monophyletic group includes a common ancestor and all of its descendents Example: Reptilia (defined to include birds)

A paraphyletic group includes a common ancestor and some but not all of its descendents Example: Reptilia (defined to exclude birds)

A polyphyletic group is a group whose members do not share a recent common ancestor Example: homeotherms (warm-blooded animals)

In a phylogenetic classification, only monophyletic groups are named. If a paraphyletic group bears a name, it will be an informal one (e.g., ‘gymnosperms’) For Phylogenetic Classification, taxa (taxonomic groups) should be natural groups, that is groups reflecting phylogeny.

clades taxa The nested relationship of clades is reflected in the nested relationship of taxa in the resultant classification. All are monophyletic groups.

Fungi EUKARYA Trypanosomes Green algae Land plants Red algae Forams Ciliates Dinoflagellates Diatoms Animals Amoebas Cellular slime molds Leishmania Euglena Green nonsulfur bacteria Thermophiles Halophiles Methanobacterium Sulfolobus ARCHAEA COMMON ANCESTOR OF ALL LIFE BACTERIA (Plastids, including chloroplasts) Green sulfur bacteria (Mitochondrion) Cyanobacteria Chlamydia Spirochetes both are prokaryotic eukaryotes