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