Some Linnean classifications are not monophyletic

31 Figure 4.12 Phylogenetic tree of the vertebrates
The tetrapod vertebrates (bracketed in green) form one monophyletic group including birds, crocodilians, turtles, reptiles, mammals, and amphibians. Their unique common ancestor is circled in green. “Fish”—lampreys, cartilaginous fishes, ray-finned fishes, and lobe-finned fishes  are not a monophyletic group. Adapted from the Center for North American Herpetology (2010).Evolution, 1st EditionCopyright © W.W. Norton & CompanyFigure 4.12 Phylogenetic tree of the vertebrates

32 Rooted vs. unrooted trees
Trees we’ve seen so far have been rooted and these trees give a clear indication of the direction of time.However, computer programs that produce phylogenetic trees often produce unrooted trees.

33 

Rooted vs. unrooted trees
In an unrooted tree, branch tips are more recent than interior nodes, but you cannot tell which of multiple interior nodes is more recent than others.

34 Figure 4.13 Unrooted tree of proteobacteria
An unrooted tree illustrates the evolutionary relationships among the proteobacteria, a large group of bacteria including human- associated species such as E. coli and nitrogen- fixing species such as A. tumefaciens. Here we do not have enough information to say whether, for example, interior node A represents a more recent or less recent population than does interior node B. Adapted from Shin et al. (1993).Evolution, 1st EditionCopyright © W.W. Norton & CompanyFigure 4.13 Unrooted tree of proteobacteria

35 Rooted vs. unrooted trees
An unrooted tree can be rooted at any point and depending where it is rooted very different rooted trees will be produced.

36 Figure 4.14 Rooted trees from unrooted trees
An unrooted tree and three corresponding rooted trees. Each rooted tree is rooted around the labeled point on the unrooted tree.Evolution, 1st EditionCopyright © W.W. Norton & CompanyFigure 4.14 Rooted trees from unrooted trees

37 Rooted vs. unrooted trees
There is only one true tree of evolutionary relationships.To identify that tree we must root the tree correctly.Using an outgroup is the easiest way to root a tree.

38 Rooted vs. unrooted trees
An outgroup is a close relative of the members of the ingroup (the various species being studied) that provides a basis for comparison with the others.

39 Rooted vs. unrooted trees
The outgroup lets us know if a character state within the ingroup is ancestral or not.If the outgroup and some of the ingroup possess a character state then that character state is considered ancestral.

40 Rooted vs. unrooted trees
Consider an unrooted tree of four magpie species.

41 Figure 5.15 Phylogeny of magpie populations.
(A) The black-billed magpie (Pica hudsonia). (B) An unrooted phylogenetic tree showing relationships among four magpie populations: the Korean magpie (Pica pica sericea), the Eurasian magpie (Pica pica pica), the black-billed magpie (Pica hudsonia), and the yellow-billed magpie (Pica nuttalli). This phylogeny is based on a maximum parsimony phylogeny derived using mitochondrial DNA sequences. Part B adapted from Lee et al. (2003).

42 Rooted vs. unrooted trees
To root the tree we need a group that split off earlier from the lineage that led to these four species of magpies.Azure-winged magpie is a suitable outgroup. One this is added to the unrooted tree we can root the tree.

43 Figure 5.16a Rooting the magpie phylogeny using an outgroup.
The azure-winged magpie (Cyanopica cyana) serves as an outgroup for the genus Pica. On the unrooted tree (A), the red dot indicates the point around which we will root the tree. The rooted tree (B) has the azure-winged magpie as an outgroup. Adapted from Lee et al. (2003).

44 Figure 5.16b Rooting the magpie phylogeny using an outgroup.
The azure-winged magpie (Cyanopica cyana) serves as an outgroup for the genus Pica. On the unrooted tree (A), the red dot indicates the point around which we will root the tree. The rooted tree (B) has the azure-winged magpie as an outgroup. Adapted from Lee et al. (2003).

45 Branch lengths of trees
In some phylogenetic trees branches are drawn with different lengths.In these trees branch lengths represent the amount of evolutionary change that has occurred in that lineage.

46 Figure 4.15 Cladograms and phylograms
Phylogenies can indicate evolutionary relationships only, or they can convey information regarding the amount of character change that has occurred along each branch. (A) A cladogram, such as this phylogeny of the primates, has the branch tips aligned and indicates only the evolutionary relationships among the species shown. (B) A phylogram indicates evolutionary relationships and also represents the amount of sequence change along each branch by means of differing branch lengths. Here we see a phylogram of primate lentiviruses, including human immunodeficiency viruses HIV-1 and HIV-2, and various forms of simian immunodeficiency virus (SIV). Adapted from Beer et al. (1999).Evolution, 1st EditionCopyright © W.W. Norton & CompanyFigure 4.15 Cladograms and phylograms

47 Building a phylogenetic tree--Homologous and analagous traits
Homologous traits are derived from a common ancestor.E.g. all mammals possess hair. This is a homologous trait all mammals share because they inherited it from a common ancestor.Analagous traits are shared by different species not because they were inherited from a common ancestor but because they evolved independently.