Demographic Inference with Admixture CoalHMM PhD Student: Jade Y. - - PowerPoint PPT Presentation

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Demographic Inference with Admixture CoalHMM PhD Student: Jade Y. Cheng Supervisor: Thomas Mailund Institution: Bioinformatics Research Centre Department of Computer Science Aarhus University Jade Cheng BiRC Aarhus University

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Jade Cheng · BiRC · Aarhus University · September 09, 2015

Demographic Inference with Admixture CoalHMM

Jade Y. Cheng PhD Student: Thomas Mailund Supervisor: Bioinformatics Research Centre Department of Computer Science · Aarhus University Institution:

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Jade Cheng · BiRC · Aarhus University · September 09, 2015

General Admixture Demographic Scenario

A C B BC AC ABC 1-α α BC' AC'

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Jade Cheng · BiRC · Aarhus University · September 09, 2015

Admixture CoalHMM Models

A B C Samples per population Model Population #1 #2 #3-1 #3-2 #3-3

One pair per configuration All pairwise

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Jade Cheng · BiRC · Aarhus University · September 09, 2015

Admixture CoalHMM Model HMMs

Model #1 Model #2 Model #3-1 Model #3-2 Model #3-3

A B C

AB split

A B C

AC split Isolation AB split

A B C

BC split Isolation AB split

A B C

AB split

A B C

AB split

A B C

Isolation AB split

A B C

AC split Isolation AB split

A B C

AB split

A B C

BC split Isolation AB split

A B C

AB split

A B C

AC split Isolation AB split

A B C

BC split Isolation AB split

A B C

AB split

A B C

AC split Isolation AB split

A B C

BC split Isolation AB split

A B C

AB split

A B C

AC split Isolation AB split

A B C

BC split Isolation AB split

A B C

AB split

A B C

AB split

A B C

Isolation AB split

A B C

AB split

A B C

AC split Isolation AB split

A B C

BC split Isolation AB split

A B C

AB split

A B C

AC split Isolation AB split

A B C

Isolation AB split

A B C

Isolation AB split

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Jade Cheng · BiRC · Aarhus University · September 09, 2015

CTMCs for HMM

1 2 3

1 2 3 4 5 6 7 8 9 10 11 12 13 14

A B C

AB split

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Jade Cheng · BiRC · Aarhus University · September 09, 2015

CTMCs for HMM

1 2 3 4 5 6 7 8 9 10 11 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28

A B C

AC split Isolation AB split

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Jade Cheng · BiRC · Aarhus University · September 09, 2015

Admixture CoalHMM Estimates - Distant Events

A B C

Isolation AC Split BC Split AB Split α 1-α

Model #1: admixed population · 1 HMM Model #2: admixed population and one source population · 3 HMM

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Jade Cheng · BiRC · Aarhus University · September 09, 2015

Admixture CoalHMM Estimates - Distant Events

Model #3-1: all three populations 3 HMM Model #3-2: all three populations 6 HMM Model #3-3: all three populations 15 HMM

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Jade Cheng · BiRC · Aarhus University · September 09, 2015

Admixture CoalHMM Estimates - Recent Events

A B C

Isolation AC Split BC Split AB Split α 1-α

Model #1: admixed population · 1 HMM Model #2: admixed population and one source population · 3 HMM

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Jade Cheng · BiRC · Aarhus University · September 09, 2015

Admixture CoalHMM Estimates - Recent Events

Model #3-1: all three populations 3 HMM Model #3-2: all three populations 6 HMM Model #3-3: all three populations 15 HMM

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Jade Cheng · BiRC · Aarhus University · September 09, 2015

Admixture CoalHMM Estimates - Admixture

Model #1: admixed population · 1 HMM Model #2: admixed population and one source population · 3 HMM

A B C

Isolation AC Split BC Split AB Split α 1-α

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Jade Cheng · BiRC · Aarhus University · September 09, 2015

Admixture CoalHMM Estimates - Admixture

Model #3-1: all three populations · 3 HMM Model #3-2: all three populations · 6 HMM Model #3-3: all three populations · 15 HMM

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Jade Cheng · BiRC · Aarhus University · September 09, 2015

Admixture CoalHMM Estimates - Bears

One-time admixture scenario

ABC2Lucy BB049 PB8 ~290,000 ~0.9 ~0.1 ~34,000 ~15,000 ~280,000 ~41,000 ~28,000 ~0.9 ~0.1 ABC2Lucy BB049 PB8

General admixture scenario