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

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40 A MitDloop

48 A MitDloop

10 A MitDloop

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20 A MitDloop

2 A MitDloop

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42 A MitDloop

9 A MitDloop

45 A MitDloop

8 A MitDloop11 A MitDloop

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33 A MitDloop

47 A MitDloop

13 A MitDloop

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31 A MitDloop

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41 A MitDloop

1 A MitDloop

24 A MitDloop

18 A MitDloop

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40 A MitDloop

48 A MitDloop

10 A MitDloop

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20 A MitDloop

2 A MitDloop

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42 A MitDloop

9 A MitDloop

45 A MitDloop

8 A MitDloop

11 A MitDloop

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33 A MitDloop

47 A MitDloop

13 A MitDloop

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34 A MitDloop

30 A MitDloop

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31 A MitDloop

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41 A MitDloop

1 A MitDloop

24 A MitDloop

18 A MitDloop

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40 A MitDloop

48 A MitDloop

10 A MitDloop

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2 A MitDloop

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42 A MitDloop

9 A MitDloop

45 A MitDloop

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33 A MitDloop

47 A MitDloop

13 A MitDloop

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34 A MitDloop

30 A MitDloop

25 A MitDloop

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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

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31 A MitDloop

32 A MitDloop

41 A MitDloop

10 A MitDloop

4 A MitDloop

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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

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17 A MitDloop

21 A MitDloop

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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

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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