1. Discordance due to gene flow or horizontal gene transfer

2. Gene trees in two species

3. Changing probabilities of reciprocal mono-, para- and polyphyly and

4. Gene trees in three populations

5. 1. Gene trees don’t always match the species tree 2. Gene divergence often precedes population divergence Gene tree Species tree T/4N e 2N e Two rules of gene trees near the species boundary

6. ‘Deep coalescence’ = discordance between gene and species tree

7. Deep coalescence vs. branch length heterogeneity Edwards 2009. Evolution 63:1-19

8. Discordance is a function of t/N e in the internode

9. 123132231 congruent gene treeincongruent gene tree   Probability of incongruence P incongruence = 2/3e -2  / 

10. Likely phylogeny of Poephila finches hecki acuticaudac. atropygialis Long-tailed Finch Black-throated Finch

11. 30 gene trees from Australian finches Jennings & Edwards (2005) Evolution 59, 2033-2047. P. acuticaudaP. heckiP. cincta

12. Speciation history of Poephila grassfinches hecki acuticauda cincta Long-tailed Finch Black-throated Finch  ah  ahc N e = ~373,000 N e = ~99,000 0.61 MYA 0.10 MYA

13. 0.00 0.20 0.40 0.60 0.80 1.00 1.20 1.40 1.60 1.80 2.00 2.20 2.40 2.60 2.80 3.00 1 Divergence Time (MYA) Pleistocene Pliocene gene divergence (D/ 2) population divergence (  ) - MLE population divergence (  ) - Bayesian cincta vs.(acuticauda, hecki)acuticaudavs. hecki Gene divergence (D/2) Population divergence (  ) - MLE Population divergence (  ) - Bayesian Gene divergence substantially predates population divergence

14. Hierarchical nature of phylogeny Liu, Yu, Kubatko, Pearl and Edwards 2009. Mol. Phyl. Evol. 53:320-328

15. Likelihood of gene trees given a species tree Liu, Yu, Kubatko, Pearl and Edwards 2009. Mol. Phyl. Evol. 53: 320-328

16. The multispecies coalescent Degnan & Rosenberg (2009) TREE 24: 332-340

17. Gene flow erodes population monophyly

18. Migration event reconstructed by parsimony