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

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 · September 09, 2015

α General Admixture Demographic Scenario ABC BC AC BC' AC' 1- α A C B Jade Cheng · BiRC · Aarhus University · September 09, 2015

Admixture CoalHMM Models Population Samples per population A B C Model #1 #2 #3-1 #3-2 One pair per con fi guration #3-3 All pairwise Jade Cheng · BiRC · Aarhus University · September 09, 2015

Admixture CoalHMM Model HMMs Model #1 Model #2 AB split AB split AB split AB split AC split Isolation Isolation Isolation A C B A C B A C B A C B Model #3-1 AB split AB split AB split AB split AB split AB split AC split BC split Isolation Isolation AC split A C B A C B A C B BC split Isolation Isolation A C B A C B A C B AB split AB split AB split AC split BC split Isolation Isolation Model #3-3 A C B A C B A C B AB split AB split AB split AC split AB split AB split AB split BC split Isolation Isolation Model #3-2 A C B A C B A C B AC split BC split Isolation Isolation A C B A C B A C B AB split AB split AB split AC split BC split Isolation Isolation A C B A C B A C B AB split AB split AB split AB split AB split AB split Isolation Isolation A C B A C B A C B A C B A C B A C B Jade Cheng · BiRC · Aarhus University · September 09, 2015

CTMCs for HMM 0 1 2 3 AB split 0 1 2 3 4 A C B 5 6 7 8 9 10 11 12 13 14 Jade Cheng · BiRC · Aarhus University · September 09, 2015

CTMCs for HMM 0 1 2 3 AB split AC split 4 5 6 7 Isolation A C B 8 9 10 11 12 13 14 15 0 1 2 16 17 18 19 3 4 5 20 21 22 23 6 7 8 24 25 26 27 9 10 11 28 Jade Cheng · BiRC · Aarhus University · September 09, 2015

Admixture CoalHMM Estimates - Distant Events AB Split α 1- α AC Split BC Split Isolation A C B Model #1: admixed population · 1 HMM Model #2: admixed population and one source population · 3 HMM 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 Jade Cheng · BiRC · Aarhus University · September 09, 2015

Admixture CoalHMM Estimates - Recent Events AB Split α 1- α AC Split BC Split Isolation A C B Model #1: admixed population · 1 HMM Model #2: admixed population and one source population · 3 HMM 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 Jade Cheng · BiRC · Aarhus University · September 09, 2015

Admixture CoalHMM Estimates - Admixture AB Split α 1- α AC Split BC Split Isolation A C B Model #1: admixed population · 1 HMM Model #2: admixed population and one source population · 3 HMM 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 Jade Cheng · BiRC · Aarhus University · September 09, 2015

Admixture CoalHMM Estimates - Bears ~290,000 ~280,000 ~0.9 ~0.1 ~0.9 ~0.1 ~41,000 ~28,000 ~34,000 ~15,000 BB049 ABC2Lucy PB8 BB049 ABC2Lucy PB8 One-time admixture scenario General admixture scenario Jade Cheng · BiRC · Aarhus University · September 09, 2015