Phylogenetics - Revision history

Christoph at 18:58, 30 September 2006

2006-09-30T18:58:59Z

Christoph at 04:45, 13 September 2006

2006-09-13T04:45:54Z

Christoph at 04:40, 1 September 2006

2006-09-01T04:40:14Z

Christoph: /* Phylogenetic trees */ "more information rich..."

2005-12-31T00:51:24Z

‎Phylogenetic trees: "more information rich..."

Christoph: /* References */ +"Sneath" ref.

2005-12-31T00:49:10Z

‎References: +"Sneath" ref.

Christoph: /* Phylogenetic trees */ "much faster..."

2005-12-31T00:41:53Z

‎Phylogenetic trees: "much faster..."

Christoph: /* Distance-matrix methods */ +"Cavalli-Sforza-Edwards Method"

2005-12-31T00:40:30Z

‎Distance-matrix methods: +"Cavalli-Sforza-Edwards Method"

Christoph: /* References */ Added more refs

2005-12-31T00:31:00Z

‎References: Added more refs

Christoph: /* Trees */ Added "Methods"

2005-12-31T00:30:11Z

‎Trees: Added "Methods"

Christoph: /* Roots */ "Kantor" -> "Cantor"

2005-12-30T23:48:08Z

‎Roots: "Kantor" -> "Cantor"

← Older revision		Revision as of 18:58, 30 September 2006
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	{{Phylogenetics}}		{{Phylogenetics}}
−	~~[[Category:Academic Research]]~~
	[[Category:Phylogenetics\| Phylogenetics]]		[[Category:Phylogenetics\| Phylogenetics]]

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 * [http://www.ohiou.edu/phylocode/ PhyloCode]
 [[Category:Academic Research]]
 [[Category:Phylogenetics| Phylogenetics]]

← Older revision		Revision as of 04:40, 1 September 2006
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	[[Category:Academic Research]]		[[Category:Academic Research]]
−	[[Category:Phylogenetics]]	+	[[Category:Phylogenetics\| Phylogenetics]]

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 The methods for calculating phylogenetic trees fall into two general categories (Hall, 2000):
 # Distance-matrix methods (also known as clustering or algorithmic methods; much faster than the discrete data methods); and
-# Discrete data methods (also known as tree searching methods)
+# Discrete data methods (also known as tree searching methods; more information rich than distance-matrix methods)
 ==== Distance-matrix methods ====

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 * Hall BG (2000). ''Phylogenetic Trees Made Easy: A How-To Manual for Molecular Biologists''. Sinauer Associates.
 * Nei M and Kumar S (2000). ''Molecular Evolution and Phylogenetics''. Oxford University Press, New York; pp73-113.
 == External links ==

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 ; [[UPGMA]] : involves clustering of closely distant species. At each stage of clustering, tree branches are being built, and the branch lengths are calculated. UPGMA assumes a constant evolutionary rate, and so the two species in a cluster are given the same branch length from the node. It is a simple and fast method; however, because of the assumption, it often produces incorrect topologies when the assumption is not met.
-; [[Least squares (phylogenetics)|Least Squares]] (LS) Method : calculates the differences between the observed and estimated branch lengths between species. After it evaluates all possible topologies, it chooses the topology with the smallest difference. The estimation of branch lengths has two methods, [[Fitch-Margoliash]] and Least Squares.
+; [[Least squares (phylogenetics)|Least Squares]] (LS) Method (or the ''Cavalli-Sforza-Edwards Method''): calculates the differences between the observed and estimated branch lengths between species. After it evaluates all possible topologies, it chooses the topology with the smallest difference. The estimation of branch lengths has two methods, [[Fitch-Margoliash]] and Least Squares.
 ; [[Minimum evolution|Minimum Evolution]] (ME) Method : estimates the total branch length of each topology. After it evaluates all possible topologies, it chooses the topology with the least total branch length. This method is computationally intensive and therefore slow, and with a small number of species to compare, the NJ method usually gives the same result as the ME method in less time.
 ; [[Neighbour joining|Neighbour-Joining]] (NJ) Method : involves clustering of neighbour species that are joined by one node. It does not evaluate all the possible tree topologies, but at each stage of clustering the ME method is used. Thus, the NJ method is considered a simplified version of the ME method.

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 == References ==
 * Baldauf S (2003). Phylogeny for the faint of heart: a tutorial. ''TRENDS in Genetics'' '''19(6)''':345-351.
 == External links ==

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 [[Image:Mono-para-polyphyletic.gif|center]]
-=== Trees ===
+=== Phylogenetic trees ===
 === Roots ===
 [[Image:Cladogram example.gif|center|Figure 2]]

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 ; autapomorphy : uninformative differences unique to particular ingroup taxa. Characters <small><font color=blue>9, 10, and 11</font></small> are all autapomorphies for their respective taxa. Even though these characters are different between the taxa, they provide no cladistically useful information. Bear in mind though that they do provide information on branch length. A cladogram that shows branch length proportional to the amount of character change (including autapomorphic changes) is called a ''phylogram''.
 ; holapomorphy : present in the ingroup and their ancestor.
-; homoplasy : uninformative similarity (i.e., due to convergence or parallelism) or independent evolution of the same character(see [[Jukes-Kantor correction]]). Character <small><font color=blue>12</font></small> is an example where it is present in only some of the ingroup taxa. Clade A, B supported by character <small><font color=blue>12</font></small>. Clade B,C supported by characters <small><font color=blue>6, 7, and 8</font></small>. So, by the principle of parsimony, clade A, B is favored. Character <small><font color=blue>12</font></small> can also be interpreted as convergent in A and B or as ''holapomorphic'' (i.e. present in the ingroup and their ancestor) but was lost in taxon C. [[Parsimony]] simply means "economy in reasoning", or, if all things are equal, the simplest explanation is the preferred one ([[Occam's Razor]]).
+; homoplasy : uninformative similarity (i.e., due to convergence or parallelism) or independent evolution of the same character(see [[Jukes-Cantor correction]]). Character <small><font color=blue>12</font></small> is an example where it is present in only some of the ingroup taxa. Clade A, B supported by character <small><font color=blue>12</font></small>. Clade B,C supported by characters <small><font color=blue>6, 7, and 8</font></small>. So, by the principle of parsimony, clade A, B is favored. Character <small><font color=blue>12</font></small> can also be interpreted as convergent in A and B or as ''holapomorphic'' (i.e. present in the ingroup and their ancestor) but was lost in taxon C. [[Parsimony]] simply means "economy in reasoning", or, if all things are equal, the simplest explanation is the preferred one ([[Occam's Razor]]).
 === Homology ===