Discordance due to gene flow or horizontal gene transfer

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Discordance due to gene flow or horizontal gene transfer

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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. - PowerPoint PPT Presentation

Transcript of Discordance due to gene flow or horizontal gene transfer

Page 1: Discordance due to gene flow or horizontal gene transfer

Discordance due to gene flow or horizontal gene transfer

Page 2: Discordance due to gene flow or horizontal gene transfer

Gene trees in two species

Page 3: Discordance due to gene flow or horizontal gene transfer

Changing probabilities of reciprocal mono-, para- and

polyphyly and

Page 4: Discordance due to gene flow or horizontal gene transfer

Gene trees in three populations

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1. Gene trees don’t always match the species tree2. Gene divergence often precedes population divergence

Gene tree

Species tree

T/4Ne

2Ne

Two rules of gene trees near the species boundary

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‘Deep coalescence’ = discordance between gene and species tree

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Deep coalescence vs. branch length heterogeneity

Edwards 2009. Evolution 63:1-19

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Discordance is a function of t/Ne in the internode

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1 2 3 1 3 2 2 3 1

congruent gene tree incongruent gene tree incongruent gene tree

Probability of incongruence

Pincongruence = 2/3e-2 /

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Likely phylogeny of Poephila finches

hecki acuticauda c. atropygialis

Long-tailed FinchBlack-throated Finch

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30 gene trees from Australian finches

Jennings & Edwards (2005) Evolution 59, 2033-2047.

P. acuticauda P. hecki P. cincta

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Speciation history of Poephila grassfinches

hecki acuticauda cincta

Long-tailed FinchBlack-throated Finch

ah

ahc

Ne = ~373,000

Ne = ~99,0000.61 MYA

0.10 MYA

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Pleistocene

Pliocene

gene divergence (D / 2)

population divergence ( ) - MLE

population divergence ( ) - Bayesian

cincta vs. (acuticauda, hecki) acuticauda vs. hecki

Gene divergence (D/2)

Population divergence () - MLE

Population divergence () - Bayesian

Gene divergence substantially predates population divergence

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Hierarchical nature of phylogeny

Liu, Yu, Kubatko, Pearl and Edwards 2009. Mol. Phyl. Evol. 53:320-328

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Likelihood of gene trees given a species tree

Liu, Yu, Kubatko, Pearl and Edwards 2009. Mol. Phyl. Evol. 53: 320-328

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The multispecies coalescent

Degnan & Rosenberg (2009) TREE 24: 332-340

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Gene flow erodes population monophyly

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Gene flow erodes population monophyly

Migration eventreconstructed byparsimony