Fixations along phylogenetic lineages. Phylogenetic reconstruction: a simplification of the...
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Fixations along phylogenetic lineages
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Transcript of Fixations along phylogenetic lineages. Phylogenetic reconstruction: a simplification of the...
Fixations along phylogenetic lineages
Phylogenetic reconstruction: a simplification of the evolutionary
process
Cladists and pheneticists
Anatomy of a phylogenetic tree
Edges and nodes
Depictions of phylogenetic trees
1 A MitDloop
24 A MitDloop
18 A MitDloop
19 A MitDloop
15 A MitDloop
16 A MitDloop
17 A MitDloop21 A MitDloop
23 A MitDloop
22 A MitDloop
40 A MitDloop
48 A MitDloop
10 A MitDloop
4 A MitDloop
6 A MitDloop
5 A MitDloop
20 A MitDloop
2 A MitDloop
3 A MitDloop
42 A MitDloop
9 A MitDloop
45 A MitDloop
8 A MitDloop11 A MitDloop
12 A MitDloop
33 A MitDloop
47 A MitDloop
13 A MitDloop
7 A MitDloop
34 A MitDloop
30 A MitDloop
25 A MitDloop
28 A MitDloop
29 A MitDloop
27 A MitDloop
31 A MitDloop
32 A MitDloop
41 A MitDloop
1 A MitDloop
24 A MitDloop
18 A MitDloop
19 A MitDloop
15 A MitDloop
16 A MitDloop
17 A MitDloop
21 A MitDloop
23 A MitDloop
22 A MitDloop
40 A MitDloop
48 A MitDloop
10 A MitDloop
4 A MitDloop
6 A MitDloop
5 A MitDloop
20 A MitDloop
2 A MitDloop
3 A MitDloop
42 A MitDloop
9 A MitDloop
45 A MitDloop
8 A MitDloop
11 A MitDloop
12 A MitDloop
33 A MitDloop
47 A MitDloop
13 A MitDloop
7 A MitDloop
34 A MitDloop
30 A MitDloop
25 A MitDloop
28 A MitDloop
29 A MitDloop
27 A MitDloop
31 A MitDloop
32 A MitDloop
41 A MitDloop
1 A MitDloop
24 A MitDloop
18 A MitDloop
19 A MitDloop
15 A MitDloop
16 A MitDloop
17 A MitDloop
21 A MitDloop
23 A MitDloop
22 A MitDloop
40 A MitDloop
48 A MitDloop
10 A MitDloop
4 A MitDloop
6 A MitDloop
5 A MitDloop
20 A MitDloop
2 A MitDloop
3 A MitDloop
42 A MitDloop
9 A MitDloop
45 A MitDloop
8 A MitDloop
11 A MitDloop
12 A MitDloop
33 A MitDloop
47 A MitDloop
13 A MitDloop
7 A MitDloop
34 A MitDloop
30 A MitDloop
25 A MitDloop
28 A MitDloop
29 A MitDloop
27 A MitDloop
31 A MitDloop
32 A MitDloop
41 A MitDloop
Slanted Cladogram Rectangular Cladogram Phylogram
1 A MitDloop
24 A MitDloop
18 A MitDloop
19 A MitDloop
15 A MitDloop
16 A MitDloop
17 A MitDloop21 A MitDloop
23 A MitDloop22 A MitDloop40 A MitDloop48 A MitDloop10 A MitDloop
4 A MitDloop
6 A MitDloop
5 A MitDloop
20 A MitDloop
2 A MitDloop
3 A MitDloop
42 A MitDloop
9 A MitDloop
45 A MitDloop
8 A MitDloop
11 A MitDloop
12 A MitDloop
33 A MitDloop47 A MitDloop
13 A MitDloop7 A MitDloop 34 A MitDloop30 A MitDloop25 A MitDloop
28 A MitDloop
29 A MitDloop
27 A MitDloop
31 A MitDloop
32 A MitDloop
41 A MitDloop
10 A MitDloop
4 A MitDloop
6 A MitDloop
5 A MitDloop
24 A MitDloop1 A MitDloop
19 A MitDloop18 A MitDloop17 A MitDloop
21 A MitDloop
15 A MitDloop
16 A MitDloop
23 A MitDloop
22 A MitDloop
40 A MitDloop 48 A MitDloop
30 A MitDloop13 A MitDloop
47 A MitDloop34 A MitDloop
7 A MitDloop
12 A MitDloop
33 A MitDloop
8 A MitDloop 11 A MitDloop
45 A MitDloop
42 A MitDloop9 A MitDloop
3 A MitDloop
20 A MitDloop2 A MitDloop
32 A MitDloop
31 A MitDloop
41 A MitDloop25 A MitDloop
28 A MitDloop
29 A MitDloop27 A MitDloop
10 A MitDloop4 A MitDloop6 A MitDloop5 A MitDloop24 A MitDloop
1 A MitDloop19 A MitDloop18 A MitDloop17 A MitDloop21 A MitDloop15 A MitDloop16 A MitDloop
23 A MitDloop22 A MitDloop40 A MitDloop48 A MitDloop30 A MitDloop13 A MitDloop47 A MitDloop34 A MitDloop7 A MitDloop12 A MitDloop33 A MitDloop8 A MitDloop11 A MitDloop45 A MitDloop42 A MitDloop9 A MitDloop
3 A MitDloop20 A MitDloop2 A MitDloop
32 A MitDloop
31 A MitDloop
41 A MitDloop
25 A MitDloop28 A MitDloop
29 A MitDloop27 A MitDloop
Circle tree Unrooted cladogram
Unrooted phylogram
1 A MitDloop
24 A MitDloop
18 A MitDloop
19 A MitDloop
15 A MitDloop
16 A MitDloop
17 A MitDloop
21 A MitDloop
23 A MitDloop
22 A MitDloop
40 A MitDloop
48 A MitDloop
10 A MitDloop
4 A MitDloop
6 A MitDloop
5 A MitDloop
20 A MitDloop
2 A MitDloop
3 A MitDloop
42 A MitDloop
9 A MitDloop
45 A MitDloop
8 A MitDloop
11 A MitDloop
12 A MitDloop
33 A MitDloop
47 A MitDloop
13 A MitDloop
7 A MitDloop
34 A MitDloop
30 A MitDloop
25 A MitDloop
28 A MitDloop
29 A MitDloop
27 A MitDloop
31 A MitDloop
32 A MitDloop
41 A MitDloop
1 A MitDloop
24 A MitDloop
18 A MitDloop
19 A MitDloop
10 A MitDloop
6 A MitDloop
5 A MitDloop
4 A MitDloop
30 A MitDloop
15 A MitDloop
16 A MitDloop
17 A MitDloop
21 A MitDloop
22 A MitDloop
40 A MitDloop
48 A MitDloop
23 A MitDloop
20 A MitDloop
42 A MitDloop
45 A MitDloop
9 A MitDloop
47 A MitDloop
13 A MitDloop
7 A MitDloop
34 A MitDloop
2 A MitDloop
3 A MitDloop
8 A MitDloop
11 A MitDloop
12 A MitDloop
33 A MitDloop
25 A MitDloop
27 A MitDloop
28 A MitDloop
29 A MitDloop
31 A MitDloop
32 A MitDloop
41 A MitDloop
Ultrametric treeUnconstrained tree
Depicting trees with branch lengths
Time
Present
Time
Branch lengths and phylogenetic trees
Ultrametric trees
Unequalbranch lengths
Trees with and without branch lengths
A character matrix
Character or site1 2 3 4 5 6
Human C A T G T ARat C A T A T AWhale C G A G T AElephant T G C A T TAardvark T G G G A A
Counting the number of steps on a phylogenetic tree
Sites 4 and 6 on the same tree
Rooted and unrooted trees
Convergence and homoplasy in mantids
Parsimony, Hennig and Occam’s razor
“One should not increase, beyond what is necessary, the number of entities required to explain anything.”
William of Ockham (ca. 1285-1349)
Synapomorphies designate clades…But what if synapomorphies are reversed?
Willi Hennig
The number of rooted, labelled, bifurcating trees
€
(2n − 3)!
2n−2(n − 2)!
Informative and uninformative site patterns
Long-branch attraction
p, q probability of observing a change between nodes orFrom node to tip
Parsimony is consistent when p2 < q(1-q)
The “Felsenstein zone”
Parsimony: pros and cons
Pros:Simple and fast (sometimes)
Cons:Depends on a very simple ‘model’ of substitutionDoes not estimate branch lengths wellSusceptible to long-branch attraction
