Discordance due to gene flow or horizontal gene transfer
Dec 18, 2015
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