Stanford, 12/02/2023

Welcome to the site for the 22nd Bay Area Population Genomics (#BAPGXXII) Conference at Stanford hosted by the Petrov Lab! The conference will be held on December 2, 2023 at the Huang Engineering Center on Stanford Campus. Parking is free on campus on weekends. The closest parking structure is the Via Ortega Garage. Registration is free (but required) and will include coffee/breakfast and lunch. Talk/poster submissions are now closed, but you can still register here

Schedule

8:30-8:55: Check-in and breakfast

9:00-9:05: Welcome Remarks - Dmitri Petrov, Stanford University

9:05-10:25: Talk Session 1 - Moderator: Dmitri Petrov, Stanford University

• 9:05-9:25: Challenges in ARG inference and applications: how to interpret and can we fix them? - Yun Deng, UC Berkeley Graduate Student, Nielsen Lab and Song Lab
• 9:25-9:45: The Genetic Architecture of Bronchopulmonary Dysplasia in Extremely Preterm Infants. - Miguel Guardado, UCSF, Graduate Student, Hernandez Lab and Torgerson Lab
• 9:45-10:05: Contextual Embedding-Based Weighted Relevance Scoring for Improved Clinical Trial Matching - Mozhgan Saeidi,Stanford University
• 10:05-10:25: Population genetics models of complex trait variation - Roshni Patel, Stanford University, Graduate Student, Pritchard Lab

10:25-11:00: Coffee Break

11:00-12:30: Talk Session 2 - Moderator: Jean Vila, Stanford University

• 11:00-11:20: Covarying Levels of Water Pollution and Admixture in a Swordtail Fish Hybrid Zone - Ben Moran, Stanford University, Graduate Student, Schumer Lab
• 11:20-11:40: Archaic introgression into present-day humans: Insights into human history and biology - Laurits Skov, UC Berkeley, Postdoc, Moorjani lab
• 11:40-12:00: High-resolution lineage tracking of within-host evolution and transmission of a prominent gut symbiont across ecological scales - Daniel Wong, Stanford University, Graduate Student, Good Lab
• 12:00-12:20: Prolonged delays in human microbiota transmission after a controlled antibiotic perturbation - Katherine Xue, Stanford University, Postdoc, Relman Lab and Petrov Lab

12:20-1:30: Lunch

1:30-2:30: Talk Session 3 - Moderator: Sophie Jean Walton, Stanford University

• 1:30-1:50: Leveraging ARGs for the estimation of selection coefficients and allele histories from ancient DNA - Andrew Vaughn, UC Berkeley Graduate Student,Nielsen Lab
• 1:50-2:10: The effectiveness of selection drives the direction of protein evolution - Hanon McShea, Stanford University, Graduate Student, Welander Lab
• 2:10-2:30: Fluctuating selection reveals extreme granularity and parallelism of adaptive tracking - Mark Bitter, Stanford University, Postdoc, Petrov lab

2:30-3:00: Keynote Talk - Moderator: Dmitri Petrov, Stanford University

• Building cell atlases - Barbara Engelhardt, Stanford University/Gladstone Institutes

3:00-5:00: Poster session and happy hour

• Mitochondrial haplotype and mito-nuclear matching drive somatic mutation and selection throughout aging - Isabel Serrano, UC Berkeley, Sudmant Lab
• Recovering signatures of ghost admixture using ancestral recombination graphs - Yulin Zhang, UC Berkeley, Moorjani Lab
• Elucidating the population genetics of structural variants with 68 chromosome-level long-read genomes of Drosophila melanogaster - James Hemker, Stanford University, Petrov Lab
• Enhancing Sediment DNA Analysis: An Automated Pipeline for Genomic Analysis - Jierui Xu, UC Berkeley, Moorjani Lab
• Revisiting the Evolution of Lactase Persistence: Insights from South Asian Genomes - Meaghan Marohn, UC Berkeley, Moorjani Lab
• Large genotype frequency fluctuations are linked to decorrelated offspring number stochasticity - Joao Ascensao, UC Berkeley, Hallatschek Lab
• Bacterial Recombination Overwhelms the Signal of Purifying Selection in dN/dS Dynamics - Zhiru Liu, Stanford University, Good Lab
• Genetic diversity loss continues long after habitat destruction ends - Kristy Mualim, Stanford University, Exposito-Alonso Lab
• Reconstructing the locations of genetic ancestors for a recombining sequence - James Kitchens, UC Davis, Coop Lab
• Tracking barcoded transposon mutants of a plant pathogen - Milo Johnson, UC Berkeley / Lawrence Berkeley National Lab, Deutschbauer Lab, Arkin Lab, and Koskella Lab
• Mating system variation influences gene expression across the male reproductive tract in Peromyscus mice - Erin Voss, UC Berkeley, Nachman Lab
• Simulation-Based Evaluation of f-statistics to Detect Admixture in Ancient Human Genomes - Sarah Johnson, UC Berkeley, Moorjani Lab
• snpArcher: A fast, reproducible, high-throughput variant calling workflow for population genomics - Cade Mirchandani, UCSC, Corbett-Detig Lab
• Detecting Admixture Tracts From the Origin Population of the TCC>TTC Mutation “Europulse” - Philippa Steinberg, University of Washington, Harris Lab
• Gene regulatory network structure affects the distribution of expression heritability - Matthew Aguirre, Stanford University, Pritchard Lab
• Simple model with resistance acquisition and negative selection explains coexistence of resistant and susceptible strains - Pleuni Pennings, SFSU
• The evolutionary history of 17q21.31 structural haplotypes in ancient and modern humans - Samvardhini Sridharan, UC Berkeley, Sudmant Lab
• Newly Sequenced Genomes Reveal Patterns of Gene Family Expansion in select Dragonflies (Odonata: Anisoptera) - Christopher Beatty, Stanford University
• How Old Is It: Molecular Dating for Ancient eDNA Samples - Maya Lemmon-Kishi, UC Berkeley, Nielsen Lab
• The dynamics of Pareto fronts underlying natural resource specialization in S. cerevisae - Elisa Visher, Stanford University, Petrov Lab
• Navigating Climate Resilience: Genomic Strategies for Kelp Ecosystem Management and Restoration - Roy Roberts, UCSC, Pinsky Lab
• The dynamics of accumulation of gametic segregation distorters in Arabidopsis - Christopher Condon, UCSC
• Early warning signs of kidney disease in PKD1 and PKD2 loss of function carriers - Natalie Telis, Helix
• Phylogenomics reveals microgeographic population structuring in a genus of California trapdoor spiders and an enigmatic new species (Euctenizidae: Promyrmekiaphila korematsui sp. nov.) - James Starrett, UC Davis, Bond Lab
• Adaptive immune response as a platform for experimental evolution - William DeWitt, UC Berkeley,Song Lab
• Testing the Levene Model using experimental evolution of herbivorous Drosophilidae - Diler Haji, University of Connecticut
• Differences in CNV calling methods drive variation in CNVs more than population structure or assembly choice - Lucia Bazan-Williamson, UC Merced, McTavish Lab
• Creating a Global Reference Phylogeny of the Mycobacterium Tuberculosis Complex - Lily Karim, UCSC, Corbett-Detig Lab
• Tracing genealogical ancestors in Mexican populations - Juan Esteban Rodriguez Rodriguez, Stanford University, Rosenberg Lab
• The evolution of structural variants in sulfide adapted fishes - Kara Ryan, UCSC, Kelley Lab
• TBA - Elena Zavala, UC Berkeley, Moorjani Lab and Rohlfs Lab
• TBA - Alexander Starr, Stanford University, Fraser Lab
• TBA - Meaghan Marohn, UC Berkeley, Moorjani Lab
• TBA - Chandler Sutherland, UC Berkeley, Krasileva Lab
• TBA - Zehua Zhou, UC Berkeley,
• TBA - Kaleda Denton, Stanford University, Feldman Lab
• TBA - Megan Ruffley, Stanford University, Exposito-Alonso Lab