discordance due to gene flow or horizontal gene transfer
DESCRIPTION
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
![Page 1: Discordance due to gene flow or horizontal gene transfer](https://reader035.vdocuments.net/reader035/viewer/2022062802/56814607550346895db315fc/html5/thumbnails/1.jpg)
Discordance due to gene flow or horizontal gene transfer
![Page 2: Discordance due to gene flow or horizontal gene transfer](https://reader035.vdocuments.net/reader035/viewer/2022062802/56814607550346895db315fc/html5/thumbnails/2.jpg)
Gene trees in two species
![Page 3: Discordance due to gene flow or horizontal gene transfer](https://reader035.vdocuments.net/reader035/viewer/2022062802/56814607550346895db315fc/html5/thumbnails/3.jpg)
Changing probabilities of reciprocal mono-, para- and
polyphyly and
![Page 4: Discordance due to gene flow or horizontal gene transfer](https://reader035.vdocuments.net/reader035/viewer/2022062802/56814607550346895db315fc/html5/thumbnails/4.jpg)
Gene trees in three populations
![Page 5: Discordance due to gene flow or horizontal gene transfer](https://reader035.vdocuments.net/reader035/viewer/2022062802/56814607550346895db315fc/html5/thumbnails/5.jpg)
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
![Page 6: Discordance due to gene flow or horizontal gene transfer](https://reader035.vdocuments.net/reader035/viewer/2022062802/56814607550346895db315fc/html5/thumbnails/6.jpg)
‘Deep coalescence’ = discordance between gene and species tree
![Page 7: Discordance due to gene flow or horizontal gene transfer](https://reader035.vdocuments.net/reader035/viewer/2022062802/56814607550346895db315fc/html5/thumbnails/7.jpg)
Deep coalescence vs. branch length heterogeneity
Edwards 2009. Evolution 63:1-19
![Page 8: Discordance due to gene flow or horizontal gene transfer](https://reader035.vdocuments.net/reader035/viewer/2022062802/56814607550346895db315fc/html5/thumbnails/8.jpg)
Discordance is a function of t/Ne in the internode
![Page 9: Discordance due to gene flow or horizontal gene transfer](https://reader035.vdocuments.net/reader035/viewer/2022062802/56814607550346895db315fc/html5/thumbnails/9.jpg)
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 /
![Page 10: Discordance due to gene flow or horizontal gene transfer](https://reader035.vdocuments.net/reader035/viewer/2022062802/56814607550346895db315fc/html5/thumbnails/10.jpg)
Likely phylogeny of Poephila finches
hecki acuticauda c. atropygialis
Long-tailed FinchBlack-throated Finch
![Page 11: Discordance due to gene flow or horizontal gene transfer](https://reader035.vdocuments.net/reader035/viewer/2022062802/56814607550346895db315fc/html5/thumbnails/11.jpg)
30 gene trees from Australian finches
Jennings & Edwards (2005) Evolution 59, 2033-2047.
P. acuticauda P. hecki P. cincta
![Page 12: Discordance due to gene flow or horizontal gene transfer](https://reader035.vdocuments.net/reader035/viewer/2022062802/56814607550346895db315fc/html5/thumbnails/12.jpg)
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
![Page 13: Discordance due to gene flow or horizontal gene transfer](https://reader035.vdocuments.net/reader035/viewer/2022062802/56814607550346895db315fc/html5/thumbnails/13.jpg)
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
![Page 14: Discordance due to gene flow or horizontal gene transfer](https://reader035.vdocuments.net/reader035/viewer/2022062802/56814607550346895db315fc/html5/thumbnails/14.jpg)
Hierarchical nature of phylogeny
Liu, Yu, Kubatko, Pearl and Edwards 2009. Mol. Phyl. Evol. 53:320-328
![Page 15: Discordance due to gene flow or horizontal gene transfer](https://reader035.vdocuments.net/reader035/viewer/2022062802/56814607550346895db315fc/html5/thumbnails/15.jpg)
Likelihood of gene trees given a species tree
Liu, Yu, Kubatko, Pearl and Edwards 2009. Mol. Phyl. Evol. 53: 320-328
![Page 16: Discordance due to gene flow or horizontal gene transfer](https://reader035.vdocuments.net/reader035/viewer/2022062802/56814607550346895db315fc/html5/thumbnails/16.jpg)
The multispecies coalescent
Degnan & Rosenberg (2009) TREE 24: 332-340
![Page 17: Discordance due to gene flow or horizontal gene transfer](https://reader035.vdocuments.net/reader035/viewer/2022062802/56814607550346895db315fc/html5/thumbnails/17.jpg)
Gene flow erodes population monophyly
![Page 18: Discordance due to gene flow or horizontal gene transfer](https://reader035.vdocuments.net/reader035/viewer/2022062802/56814607550346895db315fc/html5/thumbnails/18.jpg)
Gene flow erodes population monophyly
Migration eventreconstructed byparsimony