Interpreting and Estimating Phylogenies

Exercise answers

Aidan Budd


Data Formats

Tree (NEWICK/PHYLIP Format) Data

Exercise 3
The following image is one possible representation of the (rooted unscaled) tree described by the NEWICK format string given below

((A,(B,(F,C))),(D,E));

unscaled tree

The following image is one possible representation of the (unrooted scaled) tree described by the NEWICK format string given below

(A:1,D:6,(((E:1,F:1):1,B:2):1,(C:4,G:2):2):1);

scaled unrooted tree image

(A:1,D:6,((E:1.01,F:1.2):1,B:2):0.21,(C:4,G:2.2):2):1);"

Exercise 5a (Identify Errors in a NEWICK String)

The following "broken" strings can be fixed by adding the parentheses shown in red in the following string

1.
Broken: "((A,(E,D)),(C,(B,F));"
Fixed: "((A,(E,D)),(C,(B,F)));"

2.
Broken: "(A:1,D:6,((E:1.01,F:1.2):1,B:2):0.21,(C:4,G:2.2):2):1);"
Fixed: "(A:1,D:6,(((E:1.01,F:1.2):1,B:2):0.21,(C:4,G:2.2):2):1);"

Splits

Exercise 7
(iii) The only bifurcating tree consistent with this set of splits is shown below

EC | HNGA

ECH | GAN

GA | NHEC
small tree from splits image

(iv) The only bifurcating tree consistent with this set of splits is shown below

CB | ADEFGHKMNP

EH | ABCDGHKMNP

BCEH | ADFGKMNP

FN | ABCDEGHKMP

FNM | ABCDEGHKP

FNMK | ABCDEGHP

FNMKA | BCDEGHP

GP | ABCDEFHKMN

GPD | ABCEFHKMN
large tree built from splits

Building Consensus Trees by Hand

Exercise 8
(i) unrooted strict consensus tree
strict consensus tree

(ii) unrooted 50% majority tree
majority tree

Using SplitsTree and CONSENSE to build Consensus Trees and Networks

Exercise 9A - Using SplitsTree
Strict consensus tree
strict consensus tree

Majority consensus tree
majority consensus tree

Consensus network
consensus network
Exercise 9B
The trees have the following numbers of polytomies
However, none of the trees are identical
Exercise 10
If you included several invertebrate lineages in your tree, you will have noticed that the substitution rate of these sequences is generally relatively low - suggesting that the embryonic lineage experienced an increase in the substitution rate (rather than the non-embryonic lineage experiencing a reduced rate).

To decide in which lineage the amino-acid substitution rate changed in the Polyadenylate-binding proteins, you might assume that such large changes in substitution rate occur relatively rarely, so that you would prefer a scenario in which the smallest number of such rate changes occurred. In this case, you would infer that the change occurred in the embryonic lineage before diversification of vertebrates into sarcopterygians (includes humans, birds, amphibians, and a few "fish"), and actinopterygians (including most "fish" e.g. zebrafish, fugu), and after the duplication event.
Exercise 15
I'd choose from using the following tools:
One way of linking these together would be to:

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