1. Gene trees and species trees (cont.)

2. If we pick the adjacent nucleotide, what gene tree do we expect?

3. If we pick a nucleotide from a distant part of the genome, what gene tree do we expect?

4. 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 CD E T(A-B) T(AB-C) T(ABC-DE)

5. 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).

6. A B CD E A B CD E A D B C E Dominant tree Minor tree Population “trees” may not be trees

7. A B CD E A B CD E A B CD E Dominant tree Minor tree Introgression

8. ABHD ABCD Codominant tree 1 C H ABCDH Codominant tree 2 Population “trees” may not be trees

9. ABCD Gene tree H1H2 ABHDC Population “trees” may not be trees

10. 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)

11. 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?

12. 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?

13. 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 % %

14. What is a taxon? An exclusive group of organisms Taxa will be nested hierarchically

15. 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