Discordance due to gene flow or horizontal gene transfer

Gene trees in two species

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

Gene trees in three populations

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

‘Deep coalescence’ = discordance between gene and species tree

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

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

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

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

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

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

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

Hierarchical nature of phylogeny Liu, Yu, Kubatko, Pearl and Edwards Mol. Phyl. Evol. 53:

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

The multispecies coalescent Degnan & Rosenberg (2009) TREE 24:

Gene flow erodes population monophyly

Migration event reconstructed by parsimony