Spring 2023

When What Who Details
Jan. 13 Lab meeting Minyoung Wyman Transcription-coupled repair in the germline.
Journal club Hannah Munby Schield et al. 2022, The roles of balancing selection and recombination in the evolution of rattlesnake venom (Nat Ecol Evol).
Feb. 10 Lab meeting Vanesa Getseva An approach to identify mutator alleles in humans.
Journal club Akanksha Bhat Muralidhar et al. 2022, Assortative mating enhances postzygotic barriers to gene flow via ancestry bundling (PNAS).
Mar. 3 Lab meeting Natanael Spisak Modeling helps to identify key parameters of human mutagenesis.
Carla Hoge A tug of war between PRDM9 and promoter-like features revealed by the study of a non-mammalian vertebrate.
Journal club Andrés Bendesky
and Magnus Nordborg
Dutrow et al. 2022, Domestic dog lineages reveal genetic drivers of behavioral diversification (Cell).
Mar. 13 Lab meeting Simon Myers
Apr. 7 Journal club Natanael Spisak Jumper et al. 2021, Highly accurate protein structure prediction with AlphaFold (Nature).
Apr. 14 Lab meeting Robin Burns Cycles of satellite and transposon evolution in arabidopsis centromeres.
Apr. 21 Lab meeting Marc de Manuel
and Natanael Spisak
Mechanisms behind mutational signatures.
Apr. 28 Lab meeting Djivan Prentout Recombination in zebra finch.
May 5 Lab meeting Aleksandra Kornienko Extensive natural variation and silencing of lncRNAs in Arabidopsis thaliana.
May 8 Lab meeting Joyce Wang The poor portability of polygenic scores is only partially attributable to genetic ancestry.
May 12 Thesis defense Will Milligan
May 19 Lab meeting Vladimir Seplyarskiy Evolution of mutational processes in mammals.
July 6 Lab meeting Hannah Munby Investigating long-lived balancing selection using shared variation between human and chimpanzee.

Fall 2022


When What Who Details
Sept. 30 Journal club Young Mi Kwon Tilk et al. 2022, Most cancers carry a substantial deleterious load due to Hill-Robertson interference (eLife).
Oct. 7 Lab meeting Magnus Nordborg Methylation madness.
Oct. 21 Lab meeting Yige Zhao Predicting functional and fitness effect of missense variants.
Nov. 4 Lab meeting Magnus Nordborg Methylation madness continued.
Journal club Minyoung Wyman Cosby et al. 2021, Recurrent evolution of vertebrate transcription factors by transposase capture (Science).
Nov. 11 Journal club Carla Hoge Wang et al. 2022, Comparative genome anatomy reveals evolutionary insights into a unique amphitriploid fish (Nat Ecol Evol).
Nov. 14 Lab meeting Jeremy Berg
Nov. 18 Journal club Marc de Manuel Kaplanis et al. 2022, Genetic and chemotherapeutic influences on germline hypermutation (Nature).
Dec. 2 Lab meeting Meret Arter
Journal club Vanesa Getseva Mbatchou et al. 2021, Computationally efficient whole-genome regression for quantitative and binary traits (Nature Genetics).
Dec. 9 Lab meeting Manyuan Long The Origination of Genes from Scratch under Sexual Conflict.
Journal club Magnus Nordborg Brovkina et al. 2022, A common genomic architecture for interacting with the external world (bioRxiv).
Dec. 16 Lab meeting David Stern
Lab meeting Joy Bergelson
and Magnus Nordborg
Field GWAS and experimental evolution experiments reveal genetic tradeoffs in response to temporally and spatially variable selection

Spring 2022

When What Who Details
January 28th Lab Meeting Pei-Yin Shih Population genetics of fighting fish
February 18th Lab Meeting Margaret Antonio Using ancient DNA to explore recent human population structure.
Journal Club Hannah Munby Ebel et al. 2022,
Revisiting the malaria hypothesis: accounting for polygenicity and pleiotropy
Trends in Parasitology.
March 4th Lab Meeting Alison Barton Investigating the contribution of rare coding variants to phenotypes in UK Biobank.
Journal Club Carla Hoge Marcovitz et al. 2019,
A functional enrichment test for molecular convergent evolution finds a clear protein-coding signal in echolocating bats and whales
March 11th Lab Meeting Jeff Spence Simulation-based machine learning in population genetics as approximate Bayesian inference
Journal Club Marc de Manuel Rockweiler et al. 2022,
The origins and functional effects of postzygotic mutations throughout the human lifespan
March 18th Lab Meeting Carla Hoge Recombination patterns in cornsnakes suggest a tug of war between PRDM9 and promoter-like features
Journal Club Djivan Prentout Lenormand and Roze 2022,
Y recombination arrest and degeneration in the absence of sexual dimorphism
Science and Jay et al. 2022
Modeling the stepwise extension of recombination suppression on sex chromosomes and other supergenes through deleterious mutation sheltering
March 25th Lab Meeting Minyoung Wyman T-asymmetry in the human germline
April 29th Journal Club Will Milligan Genetics of participation
May 6th Lab Meeting Carrie Zhu Amplification is the primary mode of gene-by-sex interaction in complex human traits
May 11th Lab Meeting Will Milligan Conditions for large effect fixations under polygenic adaptation
May 13th Lab Meeting Djivan Prentour TBD
June 3rd Lab Meeting Carla Hoge TBD
Lab Meeting Will Milligan Practice PEQG talk
June 13th Lab Meeting Jiarun Chen Polygenic Adaptation under Recurrent Changes in Environment
June 17th Journal Club Molly Przeworski Okbay et al. 2022,
Polygenic prediction of educational attainment within and between families from genome-wide association analyses in 3 million individuals
Nature genetics.
July 13th Lab Meeting Marc de Manuel TBD
July 20th Lab Meeting Ana Pinharanda TBD
July 27th Lab Meeting Flora Borne TBD

Fall 2021

Schedule for Fall 2021:

When What Who Details
September 17th Lab Meeting (1:30 PM – 2:45 PM) Will Milligan Polygenic adaptation with low polygenicity
Journal Club Felix Wu LeCun et al. 2015, Deep Learning Nature.
September 24th Lab Meeting Felix Wu and Marc de Manuel The evolution of sex bias in mutation across amniotes
Journal Club TBD Deep Learning part 2
October 1st Lab Meeting Michael Goldberg Variation in germline de novo mutagenesis in human families
Journal Club Will Milligan Cagan et al. 2021,
Somatic mutation rates scale with lifespan across mammals
October 8th Journal Club Hannah Munby Ferris et al. 2021,
The genomics of rapid climatic adaptation and parallel evolution in North American house mice
PLOS Genetics.
October 22st Journal Club Ziqing Pan Dukler et al. 2021,
Extreme purifying selection against point mutations in the human genome
October 29th Journal Club Group Deep learning part 2
Journal Club Minyoung Wyman Svensson et al. 2021,
Correlational selection in the age of genomics
Nature Ecology & Evolution.
November 5th @ 12pm Lab Meeting Ipsita Agarwal Fitness effects of new mutations
Journal Club Group Deep learning part 3
November 19th Lab Meeting Natanael Spisak Insights into affinity maturation from B cell repertoire sequencing
Journal Club Hannah Munby Ferris et al. 2021,
The genomics of rapid climatic adaptation and parallel evolution in North American house mice
PLOS Genetics.
December 3rd Journal Club Marc de Manuel Montero Murat et al. 2021, The molecular evolution of spermatogenesis across mammal BioRxiv.
December 10th Lab Meeting Nicholas Lillis TBD
Journal Club Jiarun Chen Cortes et al. 2020,
Identifying cross-disease components of genetic
risk across hospital data in the UK Biobank
Nature Genetics.

Spring 2021

When What Who Details
January 8th Lab Meeting Ipsita Agarwal Mutation saturation in current samples
Journal club Marc de Manuel Baur & Berger 2020, Experimental evidence for effects of sexual selection on condition-dependent mutation rates Nature Ecology & Evolution
January 15th Lab Meeting Eric Turkheimer Are SNPs related to complex human behavior causal? Does it matter?
Journal club Eric Turkheimer Fisher 1919, The causes of human variability Eugenics Review
January 29th Lab Meeting Felix Wu and Marc de Manuel Estimating male mutation bias across mammals
February 5th Journal club Felix Wu Bhutani et al. 2021, Widespread haploid-biased gene expression enables sperm-level natural selection/a> Science
February 12th Journal club Ana Pinharanda Kennedy and Reade 2017, Why does drug resistance readily evolve but vaccine resistance does not? Proceedings of the Royal Society B
March 5th Lab Meeting Hakhamanesh Mostafavi
March 12th Lab Meeting Vince Buffalo Why do species get a thin slice of π? Revisiting Lewontin’s Paradox of Variation.
March 19th Lab Meeting Arslan Zaidi
March 26th Lab Meeting Molly Schumer The genetic architecture and evolutionary origin of a lethal hybrid incompatibility.
Journal Club Zach Fuller Jones et al. 2020, Convergent evolution of seasonal camouflage in response to reduced snow cover across the snowshoe hare range Evolution
April 2nd Lab Meeting Ben Strober Diverse transcriptomic signatures identify functional rare genetic variation.
Journal Club Will Milligan Strogatz, Exploring complex networks Nature
April 9th Lab Meeting Thomas Sasani A wild-derived antimutator drives germline mutation spectrum differences in a genetically diverse murine family.
April 15th @ 9:30 AM Lab Meeting Flora Borne Evolution of the glue produced by Drosophila larvae.
April 16th Journal Club Anna Yoney Bizzotto et al. 2021, Landmarks of human embryonic development
April 23rd Lab Meeting Chris Large
Journal Club Ana Pinharanda Gokhman et al. 2021, Human–chimpanzee fused cells reveal cis-regulatory divergence underlying skeletal evolution Nature Genetics
May 13th @ 10:30 AM (EDT) Lab Meeting Djivan Prentout Plant genera Cannabis and Humulus share the same pair of well-differentiated sex chromosomes.
May 14th Journal Club Marc de Manuel Montero Abascal et al. 2021, Somatic mutation landscapes at single-molecule resolution nature.
May 21st Lab Meeting Ellen Leffler Host-parasite genetic interactions in malaria
May 28th 10:30 AM -12 PM Lab Meeting Ziyue Gao
June 11th Journal Club Carla Hoge Pratt et al. 2021, Germline DNA replication shapes the recombination landscape in mammals BioRxiv.
Journal Club Daniel Hooper Wang et al. 2021, Transcriptional regulatory divergence underpinning species-specific learned vocalization in songbirds PLOS Biology.
July 16th Lab Meeting Florian Labourel A mechanistic view of the Evolution of diversity.

Fall 2020

When What Who Details
August 14th Journal Club Ipsita Agarwal Sinnott-Armstrong et al. 2020, GWAS of three molecular traits highlights core genes and pathways alongside a highly polygenic background bioRxiv.
August 21th Journal Club Carla Hoge Murakami et al. 2020, Multilayered mechanisms ensure that short chromosomes recombine in meiosis Nature.
August 28th Journal Club Felix Wu Pearce and Vandenbroucke 2020, Educational note: types of causes International Journal of Epidemiology.
October 23rd Lab Meeting Vagheesh Narasimhan Natural selection through different time epochs in ancient Europeans.
October 30th Journal club Zach Fuller and Carla Hoge Kuntz et al. 2020, Juvenile corals inherit mutations acquired during the parent’s lifespan bioRxiv and Barfield et al. 2016, Evolutionary origins of germline segregation in Metazoa: evidence for a germ stem cell lineage in the coral Orbicella faveolata (Cnidaria, Anthozoa) Proceedings of the Royal Society B
November 13th Lab Meeting Ipsita Agarwal Fitness consequences of DNMs
Journal club Daniel Hooper
November 20th Lab Meeting Arbel Harpak Interpreting signals of polygenic adaptation – Part 1
Journal club Anna Yoney Guo et al. 2020 The Dynamic Transcriptional Cell Atlas of Testis Development during Human Puberty, Cell Stem Cell
December 4th Lab Meeting Carla Hoge
December 11th Lab Meeting Laura Hayward & Guy Sella Interpreting signals of polygenic adaptation – Part 2
December 18th Lab Meeting Peter Andolfatto Diet unmasks cryptic genetic variants that regulate lifespan in outbred Drosophila

Spring 2020

When What Who Details
January 24th Lab Meeting Zach Fuller Towards a genetic prediction of bleaching in Corals.
January 31st Journal club Carla Hoge Jung et al. 2019, Unified single-cell analysis of testis gene regulation and pathology in five mouse strains eLife
Journal club Luke Sarre Lopez and Palumbi 2019, Somatic mutations and genome stability maintenance in clonal coral colonies bioRxiv
March 6th Lab Meeting Ana Pinharanda Gene regulatory network evolution in morphological divergence between Drosophila species.
Journal Club Felix Wu Seplyarskiy et al. 2020, Population sequencing data reveal a compendium of mutational processes in human germline. BioRxiv
March 13th Journal Club Will Milligan Watson et al. 2016, Germline replications and somatic mutation accumulation are independent of vegetative life span in Arabidopsis PNAS and Schmid-Siegert et al. 2017 Low number of fixed somatic mutations in a long-lived oak tree Nature Plants.
March 20th Journal Club Zach Fuller Cirulli et al. 2020, Genome-wide rare variant analysis for thousands of phenotypes in over 70,000 exomes from two cohorts Nature.
March 26th Journal Club Collective COVID19 Part 1
April 3rd Lab Meeting Carla Hoge Towards identifying determinants of meiotic recombination landscapes in non-mammalian animals
Journal Club Collective COVID19 Part 2
April 10th Journal Club Arbel Harpak Howe et al. 2020, Assortative mating and within-spouse pair comparisons BioRxiv.
April 29th Lab Meeting Ipsita Agarwal Estimating fitness consequences of de novo mutations
May 15th Lab Meeting Daniel Hooper Evaluating the Faster-Z Effect in a recent radiation of Australian grassfinches
Journal Club Carla Hoge Malinsky et al. 2018, Whole-genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow Nature Ecology and Evolution and Svardal et al. 2019 Ancestral Hybridization Facilitated Species Diversification in the Lake Malawi Cichlid Fish Adaptive Radiation Molecular Biology and Evolution.
May 22th Journal Club Arbel Harpak Wang et al. 2020, Theoretical and empirical quantification of the accuracy of polygenic scores in ancestry divergent populations BioRxiv.
May 29th Lab Meeting Aaron Stern Quantifying & disentangling selection on genetically-correlated complex traits
Journal Club Laura Hayward Buffalo and Coop 2009 Genetics The Linked Selection Signature of Rapid Adaptation in Temporal Genomic Data.
June 5th Journal Club Ana Pinharanda Meier et al. 2020, Haplotype tagging reveals parallel formation of hybrid races in two butterfly species BioRxiv.
June 12th Lab Meeting Izabel Alves The evolution and coevolution of PRDM9.
June 26th Lab Meeting Will Milligan Evolution of Genetic Variance in Mutation Rates
Journal Club Ipsita Agarwal and Zach Fuller Karczewski et al. 2020, The mutational constraint spectrum quantified from variation in 141,456 humans Nature and Collins et al. 2020, A structural variation reference for medical and population genetics Nature.
July 3rd Journal Club Arbel Harpak Wang et al. 2020, Theoretical and empirical quantification of the accuracy of polygenic scores in ancestry divergent populations BioRxiv.
July 10th Journal Club Felix Wu Volkova et al. 2020, Mutational signatures are jointly shaped by DNA damage and repair BioRxiv.
July 17th Journal Club Luke Sarre Cantina et al. 2020, Evolutionary Persistence of DNA Methylation for Millions of Years after Ancient Loss of a De Novo Methyltransferase BioRxiv.
July 24th Journal Club Marc de Manuel Montero Bell et al. 2020, Insights into variation in meiosis from 31,228 human sperm genomes Nature.

Fall 2019

Our weekly lab meetings and journal clubs were held together with the Andolfatto and Sella labs.

Meeting times: Fridays 2:15-3:30 pm (lab meeting) & 3:45-5:00 pm (journal club)

Full Schedule:

When What Who Details
August 2nd Lab Meeting Xiaoheng Cheng Statistical approaches for detecting ancient positive selection and balancing selection
Journal Club Carla Hoge Mihola et al. 2019, Histone methyltransferase PRDM9 is not essential for meiosis in male mice Genome Research and Genomic structure of Hstx2 modifier of Prdm9-dependent hybrid male sterility in mice BioRxiv.
August 9th Lab Meeting Tom Sasani Rates and patterns of de novo mutation in large human pedigrees.
Journal club Will Milligan Ruan et al. 2019, Mutations beget more mutations – The baseline mutation rate and runaway accumulation. bioRxiv
August 28th Lab Meeting (10:30AM -12:00PM) Nasa Sinnott-Armstrong GWAS of biomarkers reveals core genes and recapitulates omnigenic inheritance
September 6th Lab Meeting Nicole Rockweiler Whole-body maps of postzygotic mutations in 946 normal individuals.
Journal club Arbel Harpak Morrison et al. 2019, Mendelian randomization accounting for horizontal and correlated pleiotropic effects using genome-wide summary statistics bioRxiv
September 13th Lab Meeting Ipsita Agarwal, Zach Fuller Practice Talks for Biological Sciences Retreat
Sept. 16th Lab Meeting: 12:00PM – 1:30PM Kira Delmore Studying speciation using hybrid zones and focusing on seasonal migration.
September 18th Lab Meeting (1:00PM – 2:00PM) Zach Baker Practice Talk for Biology Retreat
September 20th Lab Meeting Marc de Manuel Chimpanzees, lions and sled dogs; case studies of genetic introgression and adaptation
Journal club Felix Wu Mackintosh et al. 2019, The determinants of genetic diversity in butterflies Nature Communications
September 24th Lab Meeting (10:30AM – 12:00PM) Simon Myers Tree reconstruction method and applications (the Siedel et al. preprint)
September 27th Lab Meeting 10:00AM – 11:00AM Felix Wu Practice talk for Systems Biology Retreat
Lab Meeting Brielin Brown Cross-population complex trait genetics
Journal club Daniel Hooper Toews et al. 2019, Selection on VPS13A linked to migration in a songbird PNAS and Toews et al. 2016, Plumage Genes and Little Else Distinguish the Genomes of Hybridizing Warblers Current Biology
September 30th Lab Meeting (1:00PM – 2:00PM) Laura Hayward & Will Milligan Practice Probgen Talks
November 1st Lab Meeting Dalton Conley Social Science Genomics
Journal club Ipsita Agarwal Speidel et al. 2019, A method for genome-wide genealogy estimation for thousands of samples Nature Genetics
November 8th Lab Meeting Stephen Gaughran Mutation accumulation in endangered and abundant mammal species.
Journal club Laura Hayward Kelleher et al. 2019, Inferring whole-genome histories in large population datasets Nature Genetics
November 15th Journal club Will Milligan Goldberg and Harris 2019, Great ape mutation spectra vary across the phylogeny and the genome due to distinct mutational processes that evolve at different rates BioRxiv

For examples of topics previously discussed by our lab, please view schedules from previous semesters.

Spring 2019

Full Schedule:

When What Who Details
January 25th Lab Meeting Bárbara Bitarello Ancestry effects on the accuracy of polygenic scores for height in African-Americans
(second talk) Iain Mathieson Polygenic scores for height in Ancient Europeans, and the evolution of skeletal morphology
February 11th Journal club Carla Hoge Halldorsson et al. 2019, Characterizing mutagenic effects of recombination through a sequence level genetic map
February 18thJournal club Ipsita Agarwal Warrington et al. 2019, Maternal and fetal genetic effects on birth weight and their relevance to cardio-metabolic risk factors. bioRxiv.
February 22nd, time TBD Lab Meeting Nancy Chen Tracking short-term evolution in a pedigreed wild population
March 4th Journal club Laura Hayward Hou et al. 2019, Accurate estimation of SNP-heritability from biobank-scale data irrespective of genetic architecture. bioRxiv.
March 13th, 9AM Lab Meeting Dan Belsky Phenotypic Annotation: Polygenic Score Analysis of Human Development to Advance Translation of GWAS Discovery
March 18th Lab Meeting Jeremy Berg Polygenic mutation selection drift balance under the liability threshold model
March 19th @10:30 Lab Meeting Elora López Molecular processes associated with long life span and resilience to stress in reef-building corals
March 25th Lab Meeting Tyler Joseph Time-series models for population structure.
April 29th Journal club Arbel Harpak Selzam et al. 2019, Comparing within- and between-family polygenic score prediction. bioRxiv.
May 6th Lab Meeting Mikkel Schierup Neanderthal fragments lengths and mutational signatures suggests different historical generation times in non-African population over the past 50,000 years
May 13th Lab Meeting Lucas Moreira Genomics of parallel divergence and local adaptation in two North American woodpeckers
May 20th Lab Meeting Kristin Lee Evolution of Color Vision in New World Monkeys
May 28th Lab Meeting Felix Wu Directly estimating the sex-specific mutation rate in olive baboons
June 3rd Lab Meeting Carla Hoge Towards Understanding the Evolution of Recombination Localization in Vertebrates
June 10th Lab Meeting Shyamalika Gopalan Characterizing the natural genetic and epigenetic diversity of human populations
Journal Club Zach Fuller Weghorn et al 2019 Applicability of the Mutation–Selection Balance Model to Population Genetics of Heterozygous Protein-Truncating Variants in Humans. Molecular Biology and Evolution.
June 13th @ 10am Thesis Defense Hakhamamesh Mostafavi Quantitative trait variation and adaptation in contemporary humans.
June 14th @ 9am Lab Meeting Will Milligan Selection against mutator alleles limits their impact on mutation rates
June 17th Journal club Isabel Alves Shanfelter et al. 2019, Divergent fine-scale recombination landscapes between a freshwater and marine population of threespine stickleback fish. Genome Biology and Evolution.
June 24th Lab Meeting Zach Baker An evolutionary perspective on the localization of meiotic recombination events.

Winter 2018

Full Schedule:

When What Who Details
July 26th Lab Meeting Lluis Q-M Unraveling the genetic and evolutionary sources of variation in immune response phenotypes
July 27th Journal Club Jeremy Berg Cvijovic et al 2018 The effect of strong purifying selection on genetic diversity. Genetics.
August 16th (@2:00pm) Lab Meeting Will Milligan TBD
August 17th Lab Meeting Hakhamanesh Mostafavi Decomposing pitfalls of polygenic score portability across populations
September 12th (Wednesday) @9:30am Lab Meeting Wynn Meyer From blue eyes to the deep blue sea: exploring the genetic basis of convergent traits in mammals
October 16th, 9am Lab Meeting Zach Fuller Using genomics to understand adaptation in the coral Acropora millepora
Nov 14th Journal Club Arbel Harpak O’Connor et al. 2018, Distinguishing genetic correlation from causation across 52 diseases and complex traits. Nature Genetics.
Nov 27th @9AM Journal Club @9AM Jeremy Berg O’Connor et al. 2018 Polygenicity of complex traits is explained by negative selection. bioRxiv.
Dec 12th Journal Club @9AM Will Milligan Young and Donelly 2018 Identifying loci affecting trait variability and detecting interactions in genome-wide association studies. Nature Genetics.
Dec 19th Journal Club @9AM Laura Hayward Hoellinger et al. 2018 Polygenic Adaptation: From sweeps to subtle frequency shifts. bioRxiv.