An introduction to phylogenetics: building phylogenetic trees

Question 1

Phylogeny definition

Answer 1

*A hypothesis of the branching pattern of relatedness among organisms

*Visualised as a phylogenetic tree

*Trees can be referred to as “phylogenies”, “topologies”, “cladograms”, “phylograms”

Question 2

Phylogenetics definition

Answer 2

*A subfield of evolutionary biology concerned with reconstructing the relationships among organisms (e.g., species, populations), and using these reconstructions to test evolutionary hypotheses.

Question 3

Reading phylogenies - terminology

Answer 3

Relationships are determined by shared ancestry
- Taxon or OTU
- Tip – end
- Branch – line in a phylogeny connecting to nodes or tip
- Node – denotes speciation event. Nodes can rotate think in terms of a childrens mobile – nothing is changed in the relationship by turning the node.
- sister taxa – share most recent common ancestor and are the only descendents

(see diagram in notes)

Question 4

More tree terminology

Answer 4

*Polytomy - A node in a phylogeny that leads to more than 2 descendents. An unresolved node in a tree (i.e., has more than two descendants.) Hence represents uncertainty

*Clade - A group of taxa interchangeable with monophyletic group

*Monophyletic - A monophyletic group consists of all of the descendants of a common ancestor and no other taxa
“Monophyletic group” is interchangeable with “clade”

*Paraphyletic - A paraphyletic group contains the most common ancestor and some, but not all, of its descendants

*Polyphyletic - A polyphyletic group neither contains the group’s common ancestor nor all of its descendants.

Question 5

Rooted vs. Unrooted trees

Answer 5

*Trees, in fact, are just networks of relationships among species.
*Tree reconstruction methods only reconstruct the networks
*Unrooted trees do not indicate the direction of time (and as a result, do not represent ancestral states)

Deciding the root is difficult and will create completely diff phylogenetic trees – so location of root is critical

Question 6

Outgroups

Answer 6

*In order to infer patterns of ancestry, need to have an already existing hypothesis for how evolution happened

*Outgroups provide this ability for rooting a tree.

*e.g., New world warblers used as an outgroup for a recent tree of New world blackbirds (determined to be sister clade in previous study)

Question 7

Branch lengths

Answer 7

Branch lengths
*The lengths of branches on phylogenies can either be non-informative, tell us about the rate of sequence change, or be calibrated to represent times of divergence between groups.

^Non-informative branch lengths
E.g., arbitrary branch lengths to depict relationships among taxa

Informative branch lengths
*Sequence divergence is represented in phylograms
*Not “ultrametric” (different path lengths from root to tip for each OTU)

Question 8

Time calibrated phylogenies

Answer 8

*Can use known dates from fossils to “date” particular nodes

*Rely on molecular clock to estimate timing of other splits

*Molecular clock: method that uses the rate of sequence evolution to estimate the timing of evolutionary events (e.g., branching points)

Question 9

Molecular clock

Answer 9

*Time-calibrated branch length = Sequence divergence / mutation rate

-uses rate of sequence evolution

*This is an over-simplification, but actual applications are variations on this formula

Question 10

Mapping traits onto trees

Answer 10

*Once we have resolved the relationships among taxa in a tree, we can look to see how trait evolution unfolded

Ancestral states
*Traits inferred to be present in common ancestors

Derived states
*Traits that have evolve different states from those present in ancestors

Question 11

Cladistic terminology

Answer 11

Genomes can only be used for current or recent species and not possible for fossils so this method uses ancestral vs. derived states to understand relationships

Pleisomorphy - share character with ancestral state

Apomorphy - derived state

Autapomorphy - unique derived state

Synapomorphy – shared derived characters

Homology - shared character because both inherited it from their ancestor

Homoplasy – same character (at tips) but independent derivation

Question 12

Possible ways that homoplasy can occur
(same character but independent derivation)

Answer 12

Parallel evolution: If the change evolves independently from the same ancestor

Convergent evolution: independent but from different ancestors

Secondary loss: a reversal to an ancestral condition

Question 13

What are phylogenies used for?

Answer 13

*Reconstructing the sequence of evolutionary events

*Reconstructing the timing of evolutionary events

*Testing hypotheses about adaptation

*Many more…

Question 14

example: Body size and development in birds

Answer 14

Relationship between body mass and developmental period
Evolutionary changes in body mass correlate with evolutionary changes in developmental period

Question 15

Unanswered questions relating to phylogeny

Answer 15

Did mammals evolve larger body sizes after the (non-avian) dinosaurs went extinct?

How did giant ground sloths make their way into North America?

Do the tropics have more species of mammals because speciation rates are higher there?

Or is it because extinction is lower in the tropics?

Question 16

Phylogenetics summary

Answer 16

1.Features of trees (nodes, tips, branches, etc.)

2.Trees can be rooted or unrooted – rooted tree allows inference about the sequence of divergence

3.Phylogenies provide the backbone for testing many sorts of evolutionary hypotheses.