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Discordance due to gene flow or horizontal gene transfer

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. Two rules of gene trees near the species boundary.

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Discordance due to gene flow or horizontal gene transfer

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  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. Two rules of gene trees near the species boundary 1. Gene trees don’t always match the species tree2. Gene divergence often precedes population divergence Species tree Gene tree 2Ne T/4Ne

  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/Ne in the internode

  9.  Pincongruence = 2/3e-2  / Probability of incongruence 1 2 3 1 3 2 2 3 1 congruent gene tree incongruent gene tree incongruent gene tree

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

  11. 30 gene trees from Australian finches P. acuticauda P. hecki P. cincta Jennings & Edwards (2005) Evolution59, 2033-2047.

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

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

  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. Gene flow erodes population monophyly Migration event reconstructed by parsimony

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