Population Genetics Undergrad Class

We’re teaching Population and Quantitative Genetics (undergrad EVE102) this quarter. We’re posting our materials here, in case they are of interest.

A pdf of the popgen notes is here

The slide pdfs are linked to below

Lecture One [Introduction and HWE]. Reading  notes up to end of Section 1.2.

lecture_2_rellys_inbreeding  [HWE, Relatedness (IBD), Inbreeding loops] Read Sections 1.3-1.5

lecture_3_population structure [Inbreeding, FST and population structure]

1/2 class Reading Discussion Simons Genome Diversity Project and Kreitman 1983 + 1/2 class on  lecture_4 [Other common approaches to population structure, Section 1.7 of Notes optional reading]

lecture_5_ld_drift [Linkage Disequilibrium + Discussion of Neutral Polymorphism] Reading Section 1.8 of notes.

lecture_6_drift_loss_of_heterozygosity[Genetic Drift & mutation, effective population size. Read Chapter 2, up to end of Section 2.3]

Lecture 7. Finishing up lecture 6 & Discussion of Canid paper.

lecture_8_coalescent. [Pairwise Coalescent & n sample Coalescent. Read Notes Section 24-2.5].

lecture_9_coalescent_demography [Non-constant population size, and demography inference].

Lecture 10: Midterm 1.practice_problems_1_2016

lecture_10_pop_struct_divergence [demography, pop-structure, divergence. Read sections 2.6-2.7 of notes].

lecture_11_divergence [Molecular Clock, Neutral theory, MK test]

lecture_12_ILS [incomplete lineage sorting, reading & discussion of Li & Durbin]

lecture_13_abba_baba_quantgen [ABBA-BABA & quantitative genetics]

lecture_14_quantgen [heritability and response to selection]

lecture_15_sel_mult_traits [Long term response, interpretations of breeder’s eqn. & Correlated traits]

lecture_16_tradeoffs_indirect_benefits[Correlated traits, Sexual selection]

lecture_17_1_locus_models [1 locus popgen selection model]

lecture_18_directional_sel_balancing_sel [directional & heterozygote advantage]

lecture_19_balsel_mutsel_balance[-ve frequency dependence, mutation selection balance, inbreeding depression]

lecture_20_migsel_seldrift [Migration-selection balance, Drift-Selection interaction]

lecture_21_seldrift [Nearly Neutral Theory]

lecture_22_hitchhiking [Hitchhiking]

lecture_23_selection_rec [interaction between selection & recombination]

lecture_24_supergenes_sex [inversions & supergenes, short-term benefits and long term costs of asexual reproduction]

lecture_25_sex_chromosomes_selfish_elements [sex chromosomes, sex ratio, sex ratio distortors]

lecture_26_selfish_elements [Selfish elements, selection below level of gene]

lecture_27_speciation [The population genetics of Speciation & Hybrid zones]

 

 

 

 

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Congrats to Vince on passing his quals

VInce.jpg

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Coopons in Austin

Two generations of Coopons (Brandvain & Ralph lab folks) out for BBQ in Austin

Cooplab_Austin_BBQ.jpgLeft to Right: Yaniv, Emily, Erin, Josh [Ralph lab]. Kristin, Vince, Jeremy, Nancy, Graham, Peter,  Alex [Branvain Lab].

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A Genealogical Look at Shared Ancestry on the X Chromosome

Congratulations to Vince on the publication of his paper “A Genealogical Look at Shared Ancestry on the X Chromosome”, which has been published in Genetics . In this paper, in collaboration with Steve Mount and myself, he explores how the transmission properties of the X chromosome make it useful for learning about relationships between close relatives. It is available on the bioRxiv. You can read Vince’s  blog post on this here, and watch his talk at Evolution on this topic.

A: Simulated X genealogy of a present-day female, back nine generations. Each arc is an ancestor, with female ancestors colored red, and male ancestors colored blue. The transparency of each arc reflects the genetic contribution of this ancestor to the present-day female. White arcs correspond to an X genealogical ancestor that shares no genetic material with the present-day female, and gray arcs are genealogical ancestors that are not X ancestors.

Screen Shot 2016-06-30 at 8.53.45 AM.png

Simulated X genealogy of a present-day female, back nine generations. Each arc is an ancestor, with female ancestors colored red, and male ancestors colored blue. The transparency of each arc reflects the genetic contribution of this ancestor to the present-day female. White arcs correspond to an X genealogical ancestor that shares no genetic material with the present-day female, and gray arcs are genealogical ancestors that are not X ancestors.

 

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Coopons at Evolution 2016 Austin

Kristin Lee
Mutation, migration, standing variation: the where and how of convergent adaptation
Sat. 2:45, Ballroom B, SSE Hamilton Award Symposium 3

Jeremy Berg
Understanding the impact of directional selection on the evolution of human quantitative traits
Sat 3:30, Ballroom B, SSE Hamilton Award Symposium 3

Graham Coop
Using pedigrees and genomics to understand the consequences of limited and sex-biased dispersal
Sat. 2.45 MR6B Population genetics theory/methods 2

Nancy Chen
Genomic patterns of selection through time in a wild pedigreed population
Sunday 10:15 AM MR6B Population genetics: inference of selection 2

Vince Buffalo
A genealogical look at recent X chromosome ancestry
Monday 11.15 MR6B Sex/recombination 1.

Emily Josephs
“The evolutionary forces maintaining within-population variation for gene expression” Monday, 9AM room 6B, Population genetics: inference of selection

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Jeremy’s exit seminar & outstanding dissertation prize

Congratulations to Jeremy Berg on his exit seminar & on winning the UCDavis Merton Love Evolution and Ecology outstanding dissertation prize. Jeremy gave a great seminar on his dissertation work on soft sweeps and polygenic adaptation on human height.

Jeremy_sweep_softly.jpg

The lab made cookies showing human height variation

Cookie_2_lab_2016-06-01.jpg

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Nancy’s biology of genomes talk

Nancy presented her work on the genomics of short-term selection in the Florida Scrub Jays  at the CSHL Biology of genomes meeting. You can read a writeup of the work here.

Nancy’s talk was wonderfully illustrated by Alex Cagan:

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