phylogeny and the tree of life chapter 26 bcor 012 february 4,7, 2011
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Systematics: Connecting Classification to Phylogeny
Systematics, Taxonomy, and PhylogenyConstructing 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 Linnaeus1707-1778
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. 26-4Species
Canislupus
Pantherapardus
Taxideataxus
Lutra lutra
Canislatrans
Order Family Genus
Carn
ivora
Felidae
Mu
stelidaeC
anidae
Canis
Lu
traT
axideaP
anthera
“Our classificationswill come to be, asfar as they can beso 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, 1913 - 1976
Founder of PhylogeneticSystematics
(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.
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 - FruitflyTc - BeetleJc - ButterflyAk - Onycho- phoran
Amino acid sequences compared for the homeotic gene Ubx
insects
arthropods
Decides six legs or more
Under the principle of parsimony, tree A would bepreferred 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 characterstates in the study group. It should be the group most closely related (on the basis of other lines ofevidence) 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
A monophyletic group includes a common ancestor andall 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.
The nested relationship of cladesclades is reflected in the nested relationship of taxataxa in the resultant classification. All are monophyletic groups.
Fungi
EUKARYA
Trypanosomes
Green algaeLand plants
Red algae
ForamsCiliates
Dinoflagellates
Diatoms
Animals
AmoebasCellular slime molds
Leishmania
Euglena
Green nonsulfur bacteria
Thermophiles
Halophiles
Methanobacterium
Sulfolobus
ARCHAEA
COMMONANCESTOR
OF ALLLIFE
BACTERIA
(Plastids, includingchloroplasts)
Greensulfur bacteria
(Mitochondrion)
Cyanobacteria
ChlamydiaSpirochetes
both are prokaryotic
eukaryotes
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