gene trees and species trees (cont.). if we pick the adjacent nucleotide, what gene tree do we...
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Gene trees and species trees (cont.)
If we pick the adjacent nucleotide, what gene
tree do we expect?
A CB
A-B coalescen
ceAB-C coalescence
Split 2
Split 1
If we pick a nucleotide from a distant part of
the genome, what gene tree do we expect?
A CB
A-B coalescen
ceAB-C coalescence
Split 2
Split 1
Time of coalescence
• When will a gene from A & B coalesce?
• Must it be before T(A-B)?
• If it is before T(AB-C) what topologies are possible?
• If it is before T(ABC-DE) what topologies are possible?
A B C D E
T(A-B)
T(AB-C)
T(ABC-DE)
We expect a preponderance of gene trees that match the population tree
The distribution depends on the length (time) of internal branches of the population tree relative to their “width” (effective population size).
A B C D E
A B C D E
A DB C E
Dominant tree
Minor tree
Population “trees” may not be trees
Population “trees” may not be trees
A B C D EA B C D E
A B C D E
Dominant tree
Minor tree
Introgression
A B H DA B C D
Codominant tree 1
CH
A B C DH
Codominant tree 2
Population “trees” may not be trees
A B C D
Gene tree
H1 H2
A B H DC
Population “trees” may not be trees
Can we still use tree diagrams to summarize relationship?
• Yes – if we use a concordance tree• Shows those clades that are true of a plurality
of the genome (“exclusive” groups)
Gene tree 1
Gene tree 2
Gene tree 3
Gene tree 4
Gene tree 5
Gene tree 6
Gene tree 7
Concordance tree
43%%
100%%
57%%
86%%
100%%
What is the concordance factor of the F+G clade?
Gene tree 1
Gene tree 2
Gene tree 3
Gene tree 4
Gene tree 5
Gene tree 6
Gene tree 7
Concordance tree
43%%
100%%
57%%
86%%
100%%
What is the concordance factor of the D+E clade?
Gene tree 1
Gene tree 2
Gene tree 3
Gene tree 4
Gene tree 5
Gene tree 6
Gene tree 7
Concordance tree
43%%
100%%
57%%
86%%
100%%
What is a taxon?
• An exclusive group of organisms• Taxa will be nested hierarchically
What is a species?
• Option 1: A taxon– Which taxon?– That which has been (somewhat arbitrarily)
assigned the rank of species• Option 2: Not a taxon – something else– Many options for what else– Because they are not taxa they need not be
hierarchically nested with other taxa