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 PresentationTRANSCRIPT
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 tree2. Gene divergence often precedes population divergence
Gene tree
Species tree
T/4Ne
2Ne
Two rules of gene trees near the species boundary
‘Deep coalescence’ = discordance between gene and species tree
Deep coalescence vs. branch length heterogeneity
Edwards 2009. Evolution 63:1-19
Discordance is a function of t/Ne in the internode
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 /
Likely phylogeny of Poephila finches
hecki acuticauda c. atropygialis
Long-tailed FinchBlack-throated Finch
30 gene trees from Australian finches
Jennings & Edwards (2005) Evolution 59, 2033-2047.
P. acuticauda P. hecki P. cincta
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
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
Div
erg
en
ce T
ime (
MY
A)
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
Hierarchical nature of phylogeny
Liu, Yu, Kubatko, Pearl and Edwards 2009. Mol. Phyl. Evol. 53:320-328
Likelihood of gene trees given a species tree
Liu, Yu, Kubatko, Pearl and Edwards 2009. Mol. Phyl. Evol. 53: 320-328
The multispecies coalescent
Degnan & Rosenberg (2009) TREE 24: 332-340
Gene flow erodes population monophyly
Gene flow erodes population monophyly
Migration eventreconstructed byparsimony