Coop lab talks at Evolution 2017

Emily Josephs “Detecting polygenic adaptation in maize” 9am, Sunday, b117_119.

Gideon Bradburd. “Isolation by distance as a null hypothesis of population structure” Sunday, 9:00AM-9:15AM Oregon Ballroom 204. “ASN Spotlight Symposium- Processes underlying pattern: considering the evolutionary mechanisms underlying population-level differentiation”

Nancy Chen: Detecting short-term selection in a pedigreed natural population.  Sunday. 4:00 PM – 4:14 PM In session: Contemporary evolution 2. room C123.
Kristin Lee. “Distinguishing among modes of convergent evolution using population genomic data” Sunday, 3:45 PM – 4:14 PM. Oregon ballroom 202. SSB Symposium – Phylogenetic approaches to connecting genotypes to phenotypes 2
Vince Buffalo: “The Temporal Signature of Linked Selection.”  Monday 9.15 AM-9.30AM Population genetics: inference of selection 2.  B114-115
Erin Calfee “Detecting selection for ancestry in admixed populations with arbitrary population structure.”  2:15 Monday. Pop gen: Theory and methods. Room B114-115
Sivan Yair: “Characterizing adaptive Neanderthal introgression in modern humans” 6:30pm. Poster session: population genetics: theory and methods
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Guest lecture on archaic genomics

Had fun giving a guest lecture in TIm Weaver’s Anthro. course on Neanderthals, pdf of slides here:

Neanderthal_genomics_lecture_Weaver_class

Graham

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In defense of Science

In Defense of Science

 

We are deeply concerned by the Trump administration’s move to gag scientists working at various governmental agencies. The US government employs scientists working on medicine, public health, agriculture, energy, space, clean water and air, weather, the climate and many other important areas. Their job is to produce data to inform decisions by policymakers, businesses and individuals. We are all best served by allowing these scientists to discuss their findings openly and without the intrusion of politics. Any attack on their ability to do so is an attack on our ability to make informed decisions as individuals, as communities and as a nation.

 

If you are a government scientist who is blocked from discussing their work, we will share it on your behalf, publicly or with the appropriate recipients. You can email us at USScienceFacts@gmail.com.

 

If you use this address please use PGP encryption using this PGP public key: http://pgp.mit.edu/pks/lookup?op=get&search=0x52C7139DE0A3D350

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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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