Previous Meetings

Dec 6, 2024 - Lead by Peter Morrell Caution, overload: The troubled past of genetic load
Teicher A (2018). Genetics 210: 747-755.
Nov 22, 2024 - Lead by Roland Akakpo The evaluation of Bcftools mpileup and GATK HaplotypeCaller for variant calling in non-human species
Lefouili M, Nam K (2022). Sci Rep. 2022; 12: 11331.
Nov 15, 2024 - Lead by Luis Arge fastp: an ultra-fast all-in-one FASTQ preprocessor
Chen S, Zhou Y, Chen Y, Gu J (2018). Bioinformatics. 2018; 34: i884-i890.
Nov 1, 2024 - Lead by Peter Morrell A partnership framework for scaling a workforce of research cyberprofessionals
Baller J, Henzler C, Wilgenbusch J (2022). ACM; 2022. pp. 1–6..
Oct 24, 2024 - Lead by Peter Morrell Unusual haplotype structure at the proximal breakpoint of In(2L)t in a natural population of Drosophila melanogaster
Andolfatto, P, Wall, JD, & Kreitman, M (1999). Genetics, 153(3) 1297–1311.
Oct 18, 2024 - Lead by Jacob Pacheco Twelve quick tips for software design
Wilson G (2022). PLoS Computational Biology.
Oct 11, 2024 - Lead by Peter Morrell Divergent population structure and climate associations of a chromosomal inversion polymorphism across the Mimulus guttatus species complex
Oneal E, Lowry DB, Wright KM, Zhu Z, Willis JH (2014). Mol Ecol 23: 2844-2860.
Sep 20, 2024 - Lead by Li Lei The genetic basis of climatic adaptation in cowpea
Akakpo R et al. (2024). .
Sep 13, 2024 - Lead by Luis Argeß GeneToCN: an alignment-free method for gene copy number estimation directly from next-generation sequencing reads
Pajuste FD & Remm M (2023). Sci Rep, 13(1).
Sep 6, 2024 - Lead by Peter Morrell Why is usefulness rarely useful
Wang F, Feldmann MJ, Runcie DE (2024). bioRxiv.
Aug 30, 2024 - Lead by Peter Morrell The population genetics of dN/dS
Kryazhimskiy, S, & Plotkin, JB (2008). PLoS Genet, 4(12).
Aug 23, 2024 - Lead by Luis Arge Cross-species modeling of plant genomes at single nucleotide resolution using a pre-trained DNA language model
Zhai, J, Gokaslan, A, Schiff, Y, Berthel, A, Liu, Z-Y, Miller, ZR, Scheben, A, Stitzer, MC, Romay, MC, Buckler, ES, & Kuleshov, V (2024). bioRxiv.
Aug 9, 2024 - Lead by Peter Morrell Beyond assembly: the increasing flexibility of single-molecule sequencing technology
Hook PW, Timp W (2023). Nat Rev Genet 24: 627-641.
Aug 2, 2024 - Lead by Li Lei Graph pangenome captures missing heritability and empowers tomato breeding
Zhou Y, Zhang Z, Bao Z, Li H, Lyu Y, Zan Y, Wu Y, Cheng L, Fang Y, Wu K, Zhang J, Lyu H, Lin T, Gao Q, Saha S, Mueller L, Fei Z, Städler T, Xu S, Zhang Z, Speed D, Huang S (2022). Nature 606: 527-534.
Jul 26, 2024 - Lead by Peter Morrell Introgression among North American wild grapes (Vitis) fuels biotic and abiotic adaptation
Morales-Cruz A, Aguirre-Liguori JA, Zhou Y, Minio A, Riaz S, Walker AM, Cantu D, Gaut BS (2021). Genome Biol 22: 27.
Jul 19, 2024 - Lead by Jacob Pacheco Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism
Novikova PY, Hohmann N, Nizhynska V, Tsuchimatsu T, Ali J, Muir G, Guggisberg A, Paape T, Schmid K, Fedorenko OM, Holm S, Säll T, Schlötterer C, Marhold K, Widmer A, Sese J, Shimizu KK, Weigel D, Krämer U, Koch MA, Nordborg M (2016). Nat Genet 48: 1077-1082.
Jul 12, 2024 - Lead by Luis Arge Keen on the tenure track job, are you? Know these things, you should
Voight BF (2019). Genome Biol 20: 6..
Jul 5, 2024 - Lead by Rolanda Akakpo Pervasive incomplete lineage sorting illuminates speciation and selection in primates
Rivas-González I, Rousselle M, Li F, Zhou L, Dutheil JY, Munch K, Shao Y, Wu D, Schierup MH, Zhang G (2023). Science 380: eabn4409.
Jun 28, 2024 - Lead by Jacob Pacheco Most Tibetan weedy barleys originated via recombination between Btr1 and Btr2 in domesticated barley
Gao G, Yan L, Cai Y, Guo Y, Jiang C, He Q, Tasnim S, Feng Z, Liu J, Zhang J, Komatsuda T, Mascher M, Yang P (2024). Plant Commun 5: 100828.
May 17, 2024 - Lead by Peter Morrell TRAILS: Tree reconstruction of ancestry using incomplete lineage sorting
Rivas-González I, Schierup MH, Wakeley J, Hobolth A (2024). PLoS Genet 20: e1010836.
May 10, 2024 - Lead by Roland Akakpo Inferring the geographic history of recombinant lineages using the full ancestral recombination graph
Deraje P, Kitchens J, Coop G, Osmond MM (2024). bioRxiv.
May 3, 2024 - Lead by Luis Arge Transposable element abundance subtly contributes to lower fitness in maize
Stitzer MC, Khaipho-Burch MB, Hudson AI, Song B, Valdez-Franco JA, Ramstein G, Feschotte C, Buckler ES (2023). bioRxiv.
Apr 26, 2024 - Lead by Roland Akakpo The era of the ARG: An introduction to ancestral recombination graphs and their significance in empirical evolutionary genomics
Lewanski AL, Grundler MC, Bradburd GS (2024). PLoS Genet 20: e1011110.
Apr 19, 2024 - Lead by Li Lei A geographic history of human genetic ancestry
Grundler MC, Terhorst J, Bradburd GS (2024). bioRxiv.
Apr 12, 2024 - Lead by Peter Morrell Prediction of deleterious mutations in coding regions of mammals with transfer learning
Plekhanova E, Nuzhdin SV, Utkin LV, Samsonova MG (2018). Evolutionary Applications.
Apr 5, 2024 - Lead by Luis Arge The impact of transposable elements on the structure, evolution and function of the rice genome
Akakpo R, Carpentier MC, Ie Hsing Y, Panaud O (2020). New Phytol 226: 44-49.
Mar 22, 2024 - Lead by Roland Akakpo The pattern of genetic variability in a core collection of 2,021 cowpea accessions
Fiscus CJ, Herniter IA, Tchamba M, Paliwal R, Muñoz-Amatriaín M, Roberts PA, Abberton M, Alaba O, Close TJ, Oyatomi O, Koenig D (2023). bioRxiv.
Mar 15, 2024 - Lead by Li Lei A super-pangenome of the North American wild grape species
Cochetel N, Minio A, Guarracino A, Garcia JF, Figueroa-Balderas R, Massonnet M, Kasuga T, Londo JP, Garrison E, Gaut BS, Cantu D (2023). Genome Biol 24: 290.
Mar 8, 2024 - Lead by Peter Morrell Quantifying the role of genome size and repeat content in adaptive variation and the architecture of flowering time in Amaranthus tuberculatus
Kreiner JM, Hnatovska S, Stinchcombe JR, Wright SI (2023). Plos Genetics.
Mar 1, 2024 - Lead by Roland Akakpo The evolution of selfing in Arabidopsis thaliana
Tang CL, Toomajian C, Sherman-Broyles S, Plagnol V, Guo YL, Hu TT, Clark RM, Nasrallah JB, Weigel D, Nordborg M (2007). Science 317: 1070-1072.
Feb 23, 2024 - Lead by Luis Arge Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza
Stein JC et al. (2018). Nat Genet 50: 285-296.
Feb 16, 2024 - Lead by Li Lei Indel-associated mutation rate varies with mating system in flowering plants
Hollister JD, Ross-Ibarra J, Gaut BS (2010). Mol Biol Evol 27: 409-416.
Feb 9, 2024 - Lead by Peter Morrell A how-to guide for code-sharing in biology
Abdill RJ, Talarico E, Grieneisen L (2024). arXiv preprint arXiv:240103068.
Feb 2, 2024 - Lead by Luis Arge Regional differences in the abiotic environment contribute to genomic divergence within a wild tomato species
Gibson MJS, Moyle LC (2020). Mol Ecol 29: 2204-2217.
Jan 26, 2024 - Lead by Roland Akakpo Pervasive selective sweeps across human gut microbiomes
Wolff R, Garud NR (2023). bioRxiv.
Jan 19, 2024 - Lead by Peter Morrell Redundancy analysis: A Swiss Army Knife for landscape genomics
Capblancq T, Forester BR (2021). Methods in Ecology and Evolution 12: 2298-2309.
Jan 12, 2024 - Lead by Luis Arge Functional neighborhood in plant genomes: High conservation of essential genes in clusters
Arge et al. (2024). .
Jan 5, 2024 - Lead by Li Lei Two teosintes made modern maize
Yang et al. (2023). Science.
Dec 22, 2023 - Lead by Peter Morrell Sodium azide induces a unique pattern of mutations in barley
Liu C, Frascarelli G, Stec A, Heinen S, Lei L, Wyant SR, Legg E, Spiller M, Muehlbauer GJ, Smith KP, Fay JC, Morrell PL (2023). .
Dec 8, 2023 - Lead by Luis Arge Prospects for whole-genome linkage disequilibrium mapping of common disease genes
Kruglyak L (1999). Nature Genet.
Dec 1, 2023 - Lead by Peter Morrell The future of genetic studies of complex human diseases
Risch N, Merikangas K (1996). Science.
Oct 13, 2023 - Lead by Luis Arge Natural selection drives emergent genetic homogeneity in a century-scale experiment with barley
Landis JB, Guercio AM, Brown KE, Fiscus CJ, Morrell PL, Koenig D (2023). bioRxiv.
Sep 29, 2023 - Lead by Luis Arge Exploring impact of recombination landscapes on breeding outcomes
Epstein R, Sajai N, Zelkowski M, Zhou A, Robbins KR, Pawlowski WP (2023). Proc Natl Acad Sci USA 120: e2205785119.
Sep 22, 2023 - Lead by Roland Akakpo The genomic scale of fluctuating selection in a natural plant population
Kelly JK (2022). Evol Lett 6:506-521.
Sep 15, 2023 - Lead by Peter Morrell On the tendency of species to form varieties; and on the perpetuation of varieties and species by natural means of selection
Darwin C, Wallace AR (1858). Proc. Linn. Soc.
Sep 8, 2023 - Lead by Peter Morrell Inversion invasions: when the genetic basis of local adaptation is concentrated within inversions in the face of gene flow
Schaal SM, Haller BC, Lotterhos KE (2022). Philos. Trans. R. Soc. Lond., B, Biol. Sci. 377.
Aug 25, 2023 - Lead by Li Lei Detecting adaptive differentiation in structured populations with genomic data and common gardens
Josephs EB, Berg JJ, Ross-Ibarra J, Coop G (2019). Genetics 211: 989-1004.
Aug 11, 2023 - Lead by Willian Arge UMAP reveals cryptic population structure and phenotype heterogeneity in large genomic cohorts
Diaz-Papkovich A, Anderson-Trocmé L, Ben-Eghan C, Gravel S (2019). PLoS Genet 15: e1008432.
Aug 4, 2023 - Lead by Roland Akakpo The paradox of adaptive trait clines with nonclinal patterns in the underlying genes
Lotterhos KE (2023). Proc Natl Acad Sci USA 120: e2220313120.
Jul 29, 2023 - Lead by Roland Akakpo Single-gene resolution of locally adaptive genetic variation in Mexican maize
Gates DJ, Runcie D, Janzen GM, Navarro AR, Willcox M, Sonder K, Snodgrass SJ, Rodríguez-Zapata F, Sawers RJH, Rellán-Álvarez R, Buckler ES, Hearne S, Hufford MB, Ross-Ibarra J (2019). bioRxiv.
Jul 21, 2023 - Lead by Peter Morrell ABLE: blockwise site frequency spectra for inferring complex population histories and recombination
Beeravolu CR, Hickerson MJ, Frantz LAF, Lohse K (2018). Genome Biol 19: 145.
Jul 14, 2023 - Lead by Peter Morrell From molecules to populations: appreciating and estimating recombination rate variation
Peñalba JV, Wolf JBW (2020). Nat Rev Genet 21: 476-492.
Jul 7, 2023 - Lead by Roland Akakpo Low-pass sequencing plus imputation using avidity sequencing displays comparable imputation accuracy to sequencing by synthesis while reducing duplicates
Li JH, Findley K, Pickrell JK, Blease K, Zhao J, Kruglyak S (2022). bioRxiv.
Jun 30, 2023 - Lead by Roland Akakpo Low-pass sequencing plus imputation using avidity sequencing displays comparable imputation accuracy to sequencing by synthesis while reducing duplicates
Li JH, Findley K, Pickrell JK, Blease K, Zhao J, Kruglyak S (2022). bioRxiv.
Jun 23, 2023 - Lead by Peter Morrell Yam genomics supports West Africa as a major cradle of crop domestication
Scarcelli N, Cubry P, Akakpo R, Thuillet AC, Obidiegwu J, Baco MN, Otoo E, Sonké B, Dansi A, Djedatin G, Mariac C, Couderc M, Causse S, Alix K, Chaïr H, François O, Vigouroux Y (2019). Sci Adv 5: eaaw1947.
Jun 9, 2023 - Lead by Roland Akakpo Barley crossovers
Liu C, Xu S, Fay JC, Smith KP, Morrell PL (in preparation). bioRxiv.
Jun 2, 2023 - Lead by Li Lei Genomic approaches to identify hybrids and estimate admixture times in European wildcat populations
Mattucci F, Galaverni M, Lyons LA, Alves PC, Randi E, Velli E, Pagani L, Caniglia R (2019). Sci Rep 9: 11612.
Jun 2, 2023 - Lead by Li Lei Genomic approaches to identify hybrids and estimate admixture times in European wildcat populations
Mattucci F, Galaverni M, Lyons LA, Alves PC, Randi E, Velli E, Pagani L, Caniglia R (2019). Sci Rep 9: 11612.
May 26, 2023 - Lead by Li Lei A draft human pangenome reference
Liao WW, Asri M, Ebler J, et al. (2023). Nature 617: 312-324.
May 12, 2023 - Lead by Chaochih Liu Identification of deleterious mutations within three human genomes
Chun S, Fay JC (2009). Genome Res 19: 1553-1561.
May 5, 2023 - Lead by Peter Morrell Evaluating the use of ABBA-BABA statistics to locate introgressed loci
Martin SH, Davey JW, Jiggins CD (2015). Mol Biol Evol 32: 244-257.
Apr 28, 2023 - Lead by Roland Akakpo Heterozygous inversion breakpoints suppress meiotic crossovers by altering recombination repair outcomes
Li H, Berent E, Hadjipanteli S, Galey M, Muhammad-Lahbabi N, Miller DE, Crown KN (2023). PLoS Genet 19: e1010702.
Apr 21, 2023 - Lead by Peter Morrell An efficient exact algorithm for identifying hybrids using population genomic sequences
Chakraborty S, Rannala B (2023). Genetics 223: iyad011.
Apr 14, 2023 - Lead by Peter Morrell A test of neutral molecular evolution based on nucleotide data
Hudson RR, Kreitman M, Aguade M (1987). Genetics 116: 153-159.
Apr 7, 2023 - Lead by Peter Morrell Good enough practices in scientific computing
Wilson G, Bryan J, Cranston K, Kitzes J, Nederbragt L, Teal TK (2017). PLoS Comput Biol e1005510.
Mar 22, 2023 - Lead by Giulia Frascarelli - Note: Special date & time, Wednesday 10:00 am CT Local PCA shows how the effect of population structure differs along the genome
Li H, Ralph P (2019). Genetics 211: 289-304.
Mar 17, 2023 - Lead by Peter Morrell Ten simple rules for quick and dirty scientific programming
Balaban G, Grytten I, Rand KD, Scheffer L, Sandve GK (2021). PLoS Comput Biol 17: e1008549.
Mar 10, 2023 - Lead by Peter Morrell Linkage disequilibrium: what history has to tell us
Nordborg M, Tavaré S (2002). Trends in Genetics 18: 83-90.
Mar 3, 2023 - Lead by Peter Morrell Fast, accurate local ancestry inference with FLAREs
Browning SR, Waples RK, Browning BL (2023). The American Journal of Human Genetics.
Feb 17, 2023 - Lead by Chaochih Liu RecombineX: A generalized computational framework for automatic high-throughput gamete genotyping and tetrad-based recombination analysis
Li J, Llorente B, Liti G, Yue JX (2022). PLoS Genet 18: e1010047.
Feb 10, 2023 - Lead by Roland Akakpo Six-rowed wild-growing barleys are hybrids of diverse origins
Guo Y, Himmelbach A, Weiss E, Stein N, Mascher M (2022). Plant J 111: 849-858.
Feb 3, 2023 - Lead by Peter Morrell The nature of variants in sodium azide-treated barley lines
Liu C, Frascarelli G, Stec AO, Heinen S, Lei L, Wyant SR, Legg E, Spiller M, et al. (2023). .
Jan 27, 2023 - Lead by Peter Morrell The genome of cowpea (**Vigna unguiculata** [L.] Walp.).
Lonardi S, Muñoz-Amatriaín M, Liang Q, Shu S, Wanamaker SI, Lo S, Tanskanen J, Schulman AH, Zhu T, Luo MC, Alhakami H, Ounit R, Hasan AM, Verdier J, Roberts PA, Santos JRP, Ndeve A, Doležel J, Vrána J, Hokin SA, Farmer AD, Cannon SB, Close TJ (2019). Plant J 98: 767-782.
Jan 20, 2023 - Lead by Peter Morrell Ten simple rules and a template for creating workflows-as-applications
Roach MJ, Pierce-Ward NT, Suchecki R, Mallawaarachchi V, Papudeshi B, Handley SA, Brown CT, Watson-Haigh NS, Edwards RA (2022). PLOS Computational Biology 18: e1010705.
Jan 6, 2023 - Lead by Chaochih Liu FIND-IT: Accelerated trait development for a green evolution
Knudsen S, Wendt T, Dockter C, Thomsen HC, Rasmussen M, Egevang Jørgensen M, Lu Q, Voss C, Murozuka E, Østerberg JT, Harholt J, Braumann I, Cuesta-Seijo JA, Kale SM, Bodevin S, Tang Petersen L, Carciofi M, Pedas PR, Opstrup Husum J, Nielsen MTS, Nielsen K, Jensen MK, Møller LA, Gojkovic Z, Striebeck A, Lengeler K, Fennessy RT, Katz M, Garcia Sanchez R, Solodovnikova N, Förster J, Olsen O, Møller BL, Fincher GB, Skadhauge B (2022). Sci Adv 8: eabq2266.
Dec 23, 2022 - Lead by Peter Morrell Dysgu: efficient structural variant calling using short or long reads
Cleal K, Baird DM (2022). Nucleic Acids Res 50: e53.
Dec 16, 2022 - Lead by Li Lei - Note: Special time, Friday 1:00 pm CT The relative power of genome scans to detect local adaptation depends on sampling design and statistical method
Lotterhos KE, Whitlock MC (2015). Mol Ecol 24: 1031-1046.
Dec 9, 2022 - Lead by Rolanda Akakpo Genome-wide polymorphism and genic selection in feral and domesticated lineages of Cannabis sativa
Woods P, Price N, Matthews P, McKay JK (2022). G3: jkac209.
Dec 2, 2022 - Lead by Peter Morrell Demes: a standard format for demographic models
Gower G, Ragsdale AP, Bisschop G, Gutenkunst RN, Hartfield M, Noskova E, Schiffels S, Struck TJ, Kelleher J, Thornton KR (2022). Genetics 222: iyac131.
Nov 25, 2022 - Lead by University of Minnesota No lab meeting this week
Thanksgiving (2022). East some good food.
Nov 18, 2022 - Lead by Peter Morrell ITALLIC: A tool for identifying and correcting errors in location based plant breeding data
Onsongo G, Fritsche S, Nguyen T, Belemlih A, Thompson J, Silverstein KAT (2022). Computers and Electronics in Agriculture 197: 106947.
Nov 11, 2022 - Lead by Li Lei Maximum SNP FST outperforms full-window statistics for detecting soft sweeps in local adaptation
da Silva Ribeiro T, Galván JA, Pool JE (2022). Genome Biol Evol.
Nov 4, 2022 - Lead by Peter Morrell Re-evaluating homoploid reticulate evolution in the annual sunflowers
Owens GL, Huang K, Todesco M, Rieseberg LH (2022). bioRxiv.
Oct 21, 2022 - Lead by Peter Morrell Prediction of evolutionary constraint by genomic annotations improves functional prioritization of genomic variants in maize
Ramstein GP, Buckler ES (2022). Genome Biol 23: 183.
Oct 21, 2022 - Lead by Peter Morrell Prediction of evolutionary constraint by genomic annotations improves functional prioritization of genomic variants in maize
Ramstein GP, Buckler ES (2022). Genome Biol 23: 183.
Oct 14, 2022 - Lead by Skylar Wyant Detection of domestication signals through the analysis of the full distribution of fitness effects using forward simulations and polygenic adaptation
Vourlaki I-T, Castellano D, Gutenkunst RN, Ramos-Onsins SE (2022). bioRxiv.
Oct 7, 2022 - Lead by Roland Akakpo A spectrum of free software tools for processing the VCF variant call format: vcflib, bio-vcf, cyvcf2, hts-nim and slivar
Garrison E, Kronenberg ZN, Dawson ET, Pedersen BS, Prins P (2022). PLOS Computational Biology 18: e1009123.
Sep 30, 2022 - Lead by Peter Morrell Quantifying hierarchy and dynamics in US faculty hiring and retention
Wapman KH, Zhang S, Clauset A, Larremore DB (2022). Nature.
Sep 16, 2022 - Lead by Emily Dittmar Quantifying the fraction of new mutations that are recessive lethal
Wade EE, Kyriazis CC, Cavassim MIA, Lohmueller KE (2022). bioRxiv.
Sep 9, 2022 - Lead by Peter Morrell Distinguishing among modes of convergent adaptation using population genomic data
Lee KM, Coop G (2017). Genetics.
Sep 2, 2022 - Lead by Roland Akakop Not so local: the population genetics of convergent adaptation in maize and teosinte.
Tittes S, Lorant A, McGinty S, Doebley JF, Holland JB, Sánchez-González JDJ, Seetharam A, Tenaillon M, Ross-Ibarra J (2021). bioRxiv.
Aug 12, 2022 - Lead by Chaochih Liu The megabase-scale crossover landscape is largely independent of sequence divergence
Lian Q, Solier V, Walkemeier B, Durand S, Huettel B, Schneeberger K, Mercier R (2022). Nat Commun.
Aug 5, 2022 - Lead by Emily Dittmar Instant appropriation–Heinz Bücher and the SS botanical collection commando to Russia 1943
Thronström CG, Hossfeld U (2002). Plant Genetic Resources Newsletter.
Jul 29, 2022 - Lead by Peter Morrell Pearl millet genomic vulnerability to climate change in West Africa highlights the need for regional collaboration
Rhoné B, Defrance D, Berthouly-Salazar C, Mariac C, Cubry P, Couderc M, Dequincey A, Assoumanne A, Kane NA, Sultan B, Barnaud A, Vigouroux Y (2020). Nat Commun.
Jul 15, 2022 - Lead by Peter Morrell Quantitative modelling of fine-scale variations in the Arabidopsis thaliana crossover landscape
Hsu Y-M, Falque M, Martin OC (2022). Quantitative Plant Biology.
Jul 1, 2022 - Lead by Summer Travel Summer Travel
(2022). European Time Zone.
Jul 1, 2022 - Lead by Peter Morrell Hard versus soft selective sweeps during domestication and improvement in soybean
Zhong L, Zhu Y, Olsen KM (2022). Mol Ecol.
Jun 27, 2022 - Lead by Giulia Frascarelli - Note: Special date and time, Monday 9:30 am Mutational load in sunflower
Dittmar E, Liu C, Burke JM, Morrell PL (2022). in preparation.
Jun 24, 2022 - Lead by Peter Morrell SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies
Goel M, Sun H, Jiao WB, Schneeberger K (2019). Genome Biol.
Jun 17, 2022 - Lead by Peter Morrell The evolutionary history of *Phaseolus vulgaris* as revealed by chloroplast and nuclear genomes
Frascarelli et al. (2022). .
Jun 10, 2022 - Lead by Peter Morrell Insights into the pan-genome of domesticated cowpea (Vigna unguiculata [L.] Walp.)
Close et al. (2022). in preparation.
Jun 3, 2022 - Lead by Li Lei Inference and analysis of population-specific fine-scale recombination maps across 26 diverse human populations
Spence JP, Song YS (2019). Sci Adv.
May 27, 2022 - Lead by Peter Morrell The emergence and development of genetics in Mexico.
Barahona A, Ayala FJ (2005). Nat Rev Genet.
May 20, 2022 - Lead by Penny Kianian Environmental resilience in crop wild relatives
Dittmar E, et al. (2022). .
May 13, 2022 - Lead by Giulia Frascarelli - Note: Special time, 11:30 am CT Genomic structural variants constrain and facilitate adaptation in natural populations of Theobroma cacao, the chocolate tree
Hämälä T, Wafula EK, Guiltinan MJ, Ralph PE, dePamphilis CW, Tiffin P (2021). Proc Natl Acad Sci USA.
May 4, 2022 - Lead by Peter Morrell - Note: Special day, Wed at 9:30 am CT Informativeness of genetic markers for inference of ancestry
Rosenberg NA, Li LM, Ward R, Pritchard JK (2003). Am J Hum Genet.
Apr 29, 2022 - Lead by Emily Dittmar - Note: Special time, 1:30 pm CT Clines, clusters, and the effect of study design on the inference of human population structure
Rosenberg NA, Mahajan S, Ramachandran S, Zhao C, Pritchard JK, Feldman MW (2005). PLoS Genetics.
Apr 22, 2022 - Lead by Penny Kianian Barley genomics
Lei, L, Liu C, Morrell PL (2022). in review.
Apr 15, 2022 - Lead by Chaochih Liu Physical geography, isolation by distance and environmental variables shape genomic variation of wild barley (*Hordeum vulgare* L. ssp. *spontaneum*) in the Southern Levant.
Chang CW, Fridman E, Mascher M, Himmelbach A, Schmid K (2022). Heredity.
Apr 8, 2022 - Lead by Li Lei Ten simple rules for better figures
Rougier NP, Droettboom M, Bourne PE (2014). PLoS Comput Biol.
Apr 5, 2022 - Lead by Giulia Frascarelli Chromosome-scale assembly of wild barley accession “OUH602”
Sato, K, Mascher, M, Himmelbach, A, Haberer, G, Spannagl, M, & Stein, N (2021). G3.
Apr 1, 2022 - Lead by Emily Dittmar - Note: Special date and time, Friday 10:00 am Rapid adaptation and range expansion in response to agriculture over the last two centuries
Kreiner J, Latorre SM, Burbano HA, Stinchcombe JR, Otto SP, Weigel D, Wright SI (2022). bioRxiv.
Mar 22, 2022 - Lead by Peter Morrell Using landscape genomics to infer genomic regions involved in environmental adaptation of soybean genebank accessions
Haupt, M, Schmid, K (2022). bioRxiv.
Mar 15, 2022 - Lead by Skylar Wyant Efficiently summarizing relationships in large samples: a general duality between statistics of genealogies and genomes
Ralph P, Thornton K, Kelleher, J (2020). Genetics.
Mar 8, 2022 - Lead by Penny Kianian Mutation saturation for fitness effects at human CpG sites
Agarwal I, Przeworski M (2021). eLife.
Mar 1, 2022 - Lead by Peter Morrell A unified genealogy of modern and ancient genomes
Wohns AW, Wong Y, Jeffery B, Akbari A, Mallick S, Pinhasi R, Patterson N, Reich D, Kelleher J, McVean G (2022). Science.
Feb 22, 2022 - Lead by Li Lei Mutation bias reflects natural selection in Arabidopsis thaliana
Monroe JG, Srikant T, Carbonell-Bejerano P, Becker C, Lensink M, Exposito-Alonso M, Klein M, Hildebrandt J, Neumann M, Kliebenstein D, Weng M, Imbert E, Ågren J, Rutter MT, Fenster CG, Weigel D (2022). Nature.
Feb 15, 2022 - Lead by Peter Morrell Genomic patterns of structural variation among diverse genotypes of Sorghum bicolor and a potential role for deletions in local adaptation
Songsomboon K, Brenton Z, Heuser J, Kresovich S, Shakoor N, Mockler T, Cooper EA (2021). G3.
Feb 8, 2022 - Lead by Emily Dittmar Statistical inference in population genomics
Johri P, Aquadro CF, Beaumont M, Charlesworth B, Excoffier L, Eyre-Walker A, Keightley PD, Lynch M, McVean P, Payseur BA, Pfeifer SP, Stephan W, Jensen JD (2021). bioRxiv.
Feb 1, 2022 - Lead by Li Lei Lottery, luck, or legacy?
Coop G, Przeworski M (2022). Book Chapter.
Jan 28, 2022 - Lead by Chaochih Liu Genomic prediction of the recombination rate variation in barley – A route to highly recombinogenic genotypes
Casale F, Inghelandt DV, Weisweiler M, Li J, Stich B (2021). Plant Biotechnology Journal.
Jan 21, 2022 - Lead by Peter Morrell - Note special date, Friday 9:15 am Prospects of telomere-to-telomere assembly in barley: analysis of sequence gaps in the MorexV3 reference genome
Navrátilová P, Toegelová H, Tulpová Z, Kuo Y, Stein N, Doležel J, Houben A, Šimková H, Mascher M (2021). bioRxiv.
Jan 10, 2022 - Lead by None Break for Virtual PAG Meeting
PAG Speakers (2022). PAG.
Jan 3, 2022 - Lead by the holidays Break! Happy holidays!
Break this week (2021). .
Dec 27, 2021 - Lead by the holidays Break! Happy holidays!
Break this week (2021). .
Dec 20, 2021 - Lead by Emily Dittmar Genomic conservation of citrus wild relatives
Wang et al. (2021). Manuscript draft will be sent out to lab members only.
Dec 13, 2021 - Lead by Li Lei Mutational load in domesticated sunflower
Dittmar EL et al. (2021). Manuscript draft will be sent out to lab members only.
Dec 6, 2021 - Lead by Peter Morrell Genome-wide survey of artificial mutations induced by ethyl methanesulfonate, sodium azide, and fast neutron radiation in Brachypodium
Lei L et al. (2021). Manuscript draft will be sent out to lab members only.
Nov 29, 2021 - Lead by Giulia Frascarelli Darwinian evolution can follow only very few mutational paths to fitter proteins
Weinreich DM, Delaney NF, DePristo MA, Hartl DL (2006). Science.
Nov 22, 2021 - Lead by Emily Dittmar Weighing the evidence for adaptation at the molecular level
Fay JC (2011). Trends in Genetics.
Nov 15, 2021 - Lead by Peter Morrell Mapping of transgenic alleles in soybean using a nanopore-based sequencing strategy
Li S, Jia S, Hou L, Nguyen H, Sato S, Holding D, Cahoon E, Zhang C, Clemente T, Yu B (2019). Journal of Experimental Botany.
Nov 5, 2021 - Lead by Chaochih Liu Molecular spandrels: tests of adaptation at the genetic level
Barrett RDH, Hoekstra HE (2011). Nature Reviews Genetics.
Oct 29, 2021 - Lead by Emily Dittmar Domestication shapes recombination patterns in tomato
Fuentes RR, de Ridder D, van Dijk ADJ, Peters SA (2021). Molecular Biology and Evolution.
Oct 22, 2021 - Lead by Peter Morrell Homology: a personal view on some of the problems
Fitch WM (2000). Trends in Genetics.
Oct 15, 2021 - Lead by Li Lei Population genetic models of GERP scores suggest pervasive turnover of constrained sites across mammalian evolution
Huber CD, Kim BY, Lohmueller KE (2020). PLOS Genetics.
Oct 8, 2021 - Lead by Chaochih Liu Hunting for beneficial mutations: conditioning on SIFT scores when estimating the distribution of fitness effect of new mutations
Chen J, Bataillon T, Glemin S, Lascous M (2021). Genome Biology and Evolution.
Oct 1, 2021 - Lead by Giulia Frascarelli Deleterious mutations accumulate faster in allopolyploid than diploid cotton (Gossypium) and unequally between subgenomes
Conover JL and Wendel JF (2021). bioRxiv.
Sep 24, 2021 - Lead by Peter Morrell Vcfanno: fast, flexible annotation of genetic variants
Pedersen BS, Layer RM, Quinlan AR (2016). Genome Biology.
Sep 17, 2021 - Lead by Emily Dittmar The utility of genomic prediction models in evolutionary genetics
McGaugh SE, Lorenz AJ, Flagel LE (2021). Proceedings of the Royal Society B.
Sep 10, 2021 - Lead by Chaochih Liu De novo assembly, annotation, and comparativeanalysis of 26 diverse maize genomes
Hufford MB, Seetharam AS, Woodhouse MR, Chougule KM, Ou S, Liu J, Ricci WA, Guo T, Olson A, Qiu Y, Coletta RD, Tittes S, Hudson AI, Marand AP, Wei S, Lu Z, Wang B, Tello-Ruiz MK, Piri RD, Wang N, won Kim D, Zeng Y, O’Connor CH, Li X, Gilbert AM, Baggs E, Krasileva KV, Portwood II JL, Cannon EKS, Andorf CM, Manchanda N, Snodgrass SJ, Hufnagel DE, Jiang Q, Pedersen S, Syring ML, Kudrna DA, Llaca V, Fengler K, Schmitz RJ, Ross-Ibarra J, Yu J, Gent JI, Hirsch CN, Ware D, Dawe RK (2021). Science.
Sep 3, 2021 - Lead by Li Lei From breeding to genome design: A genomic makeover for potatoes
Markel K, Shih PM (2021). Cell.
Sep 3, 2021 - Lead by Li Lei Genome design of hybrid potato
Zhang C, Yang Z, Tang D, Zhu Y, Wang P, Li D, Zhu G, Xiong X, Shang Y, Li C, Huang S (2021). Cell.
Aug 27, 2021 - Lead by Peter L. Morrell Referee: Reference Assembly Quality Scores
Thomas GWC, Hahn MW (2019). Genome Biol Evol 11: 1483-1486.
Aug 20, 2021 - Lead by Peter Morrell Multiple reference genomes and transcriptomes for Arabidopsis thaliana
Gan X, Stegle O, Behr J, Steffen JG, Drewe P, Hildebrand KL, Lyngsoe R, Schultheiss SJ, Osborne EJ, Sreedharan VT, Kahles A, Bohnert R, Jean G, Derwent P, Kersey P, Belfied EJ, Harberd NP, Kemen E, Toomajian C, Kover PX, Clark RM, Ratsch G, Mott R (2011). Nature.
Aug 13, 2021 - Lead by Li Lei - Special time 9:00 AM CT Optimal sequencing strategies for surveying molecular genetic diversity
Pluzhnikov A, Donnelly P (1996). Genetics.
Aug 6, 2021 - Lead by No discussion leader Break this week due to travel schedules
(2021). No Meeting.
Jul 30, 2021 - Lead by Peter Morrell Effective variant filtering and expected candidate variant yield in studies of rare human disease
Pedersen BS, Brown JM, Dashnow H, Wallace AD, Velinder M, Tristani-Firouzi M, Schiffman JD, Tvrdik T, Mao R, Best DH, Bayrak-Toydemir P, Quinlan AR (2021). npj Genomic Medicine.
Jul 23, 2021 - Lead by Emily Dittmar Evolutionary Biology Vol. 32. Ch 12. The limits to knowledge in quantitative genetics
Lynch M (2000). Springer.
Jul 16, 2021 - Lead by Skylar Wyant Genetic load may increase or decrease with selfing depending upon the recombination environment
Sianta SA, Peischl S, Moeller DA, Brandvain Y (2021). bioRxiv.
Jul 9, 2021 - Lead by Chaochih Liu - Special meeting time 9:00 AM Evolutionary Biology Vol. 32. Ch 11. Limits to prediction of phenotypes from knowledge of genotypes
Clark AG (2000). Springer.
Jul 2, 2021 - Lead by Li Lei Genetic and pharmacological causes of germline hypermutation
Kaplanis J, Ide B, Sanghvi R, Neville M, Danecek P, Prigmore E, Short P, Gallone G, McRae J, Odhams C, Moutsianas L, Genomics England Research Consortium, Carmichael J, Barnicoat A, Firth H, O'Brien P, Rahbari R, Hurles M (2021). bioRxiv.
Jun 25, 2021 - Lead by Peter Morrell The effect of neutral recombination variation on genome scans for selection
Lotterhos KE (2019). G3.
Jun 18, 2021 - Lead by Giulia Frascarelli Evolutionary Biology Vol. 32. Ch 2. Limits to knowledge in population genetics
Clegg MT (2000). Springer.
Jun 11, 2021 - Lead by Emily Dittmar - Note: Special Time 10:00 AM Nonparametric coalescent inference of mutation spectrum history and demography
DeWitt WS, Harris KD, Ragsdale AP, Harris K (2021). PNAS.
Jun 4, 2021 - Lead by Chaochih Liu Molecular evolution and the decline of purifying selection with age
Cheng C, Kirkpatrick M (2021). Nature Communications.
May 28, 2021 - Lead by Ruth Shaw (the talk is by invitation only) Entanglement of genomic and environmental influences on organismal fitness: its relevance to two research programs
Shaw RG (2021). Joint Lab Meeting.
May 21, 2021 - Lead by Li Lei Benchmarking variant identification tools for plant diversity discovery
Wu X, Heffelfinger C, Zhao H, Dellaporta SL (2019). BMC Genomics.
May 14, 2021 - Lead by Peter Morrell Systematic benchmark of state-of-the-art variant calling pipelines identifies major factors affecting accuracy of coding sequence variant discovery
Abasov R, Tvorogova VE, Glotov AS, Predeus AV, Barbitoff YA (2021). bioRxiv.
May 7, 2021 - Lead by Sam Hamann - Special Edition Does[0]Compute? Discussion Unit testing, model validation, and biological simulation
Sarma GP, Jacobs TW, Watts MD, Ghayoomie SV, Larson SD, Gerkin RC (2016). F1000 Research.
Apr 30, 2021 - Lead by Giulia Frascarelli Strongly deleterious mutations are a primary determinant of extinction risk due to inbreeding depression
Kyriazis CC, Wayne RK, Lohmueller KE (2020). Evolution Letters.
Apr 23, 2021 - Lead by Chaochih Liu Making science meaningful for broad audiences through stories
ElShafie SJ (2018). Integrative and Comparative Biology.
Apr 16, 2021 - Lead by Li Lei - Note: special time, 10:00 AM CT Evolutionary genomics of structural variation in Asian rice (Oryza sativa) domestication
Kou Y, Liao Y, Toivainen T, Lv Y, Tian X, Emerson JJ, Gaut BS, Zhou Y (2020). Molecular Biology and Evolution.
Apr 9, 2021 - Lead by Ellie Taagen Mutation load at a mimicry supergene sheds new light on the evolution of inversion polymorphisms
Jay P, Chouteau M, Whibley A, Bastide H, Parrinello H, Llaurens V, Joron M (2021). Nature Genetics.
Apr 2, 2021 - Lead by Emily Dittmar A quantitative genomics map of rice provides genetic insights and guides breeding
Wei X, Qiu J, Yong K, Fan J, Zhang Q, Hua H, Liu J, Wang Q, Olsen KM, Han B, Huang X (2021). Nature Genetics.
Mar 26, 2021 - Lead by Group Discussion Discuss 3/24 talk: Sex chromosome, introgression, & speciation of sticklebacks
Kirkpatrick M (2021). Speciation and Introgression Discussion, hosted by Silu Wang at UC Berkeley.
Mar 19, 2021 - Lead by Peter Morrell Long-read sequence assembly: a technical evaluation in barley
Mascher M, Wicker T, Jenkins J, Plott C, Lux T, Koh CS, Ens J, Gundlach H, Boston LB, Tulpova Z, Holden S, Hernandez-Pinzon I, Scholz U, Mayer KFX, Spannagl M, Pozniak CJ, Sharpe AG, Simkova H, Moscou MJ, Grimwood J, Schmutz J, Stein N (2021). The Plant Cell.
Mar 12, 2021 - Lead by Sam Hamann Structural variant calling: the long and the short of it
Mahmoud M, Gobet N, Cruz-Dávalos DI, Mounier N, Dessimoz C, Sedlazeck FJ (2019). Genome Biology.
Mar 5, 2021 - Lead by Chaochih Liu Why do species get a thin slice of π? Revisiting Lewontin’s Paradox of Variation
Buffalo V (2021). bioRxiv.
Feb 26, 2021 - Lead by Ellie Taagen Comparative evolutionary genetics of deleterious load in sorghum and maize
Lozano R, Gazave E, dos Santos JPR, Stetter MG, Valluru R, Bandillo N, Fernandes SB, Brown PJ, Shakoor N, Mockler TC, Cooper EA, Perkins MT, Buckler ES, Ross-Ibarra J, Gore MA (2021). Nature Plants.
Feb 19, 2021 - Lead by Li Lei Wheat eQTL
Akhunov E, et al (2021). In Preparation (will be emailed to attendees).
Feb 12, 2021 - Lead by Giulia Frascarelli Assessing runs of Homozygosity: a comparison of SNP Array and whole genome sequence low coverage data
Ceballos FC, Hazelhurst S, Ramsay M (2018). BMC Genomics.
Feb 5, 2021 - Lead by Penny Kianian Pan-genome of wild and cultivated soybeans
Liu Y, Du H, Li P, Shen Y, Peng H, Liu S, Zhou G, Zhang H, Liu Z, Shi M, Huang X, Li Y, Zhang M, Wang Z, Zhu B, Han B, Liang C, Tian Z (2020). Cell.
Jan 29, 2021 - Lead by Peter Morrell The impact of identity-by-descent on fitness and disease in natural and domesticated Canid populations
Mooney JA, Yohannes A, Lohmueller KE (2020). bioRxiv.
Jan 22, 2021 - Lead by Emily Dittmar Dating genomic variants and shared ancestry in population-scale sequencing data
Albers PK, McVean G (2020). PLOS Biology.
Jan 15, 2021 - Lead by Li Lei The barley pan-genome reveals the hidden legacy of mutation breeding
Jayakodi M, Padmarasu S, Haberer G, Bonthala VS, Gundlach H, Monat C, Lux T, Kamal N, Lang D, Himmelbach A, Ens J, Zhang X, Angessa TT, Zhou G, Tan C, Hill C, Wang P, Schreiber M, Boston LB, Plott C, Jenkins J, Guo Y, Fiebig A, Budak H, Xu D, Zhang J, Wang C, Grimwood J, Schmutz J, Guo G, Zhang G, Mochida K, Hirayama T, Sato K, Chalmers KJ, Langridge P, Waugh R, Pozniak C, Scholz U, Mayer KFX, Spannagl M, Li C, Mascher M, Stein N (2020). Nature.
Jan 8, 2021 - Lead by Peter Morrell African Americans in evolutionary science: where we have been, and what’s next
Graves Jr. JL (2019). Evolution: Education and Outreach.
Jan 1, 2021 - Lead by University of Minnesota Happy New Year! No lab meeting this week
New Year (2020). Celebrate the new year!.
Dec 25, 2020 - Lead by University of Minnesota Happy holidays! No lab meeting this week
Christmas (2020). Eat lots of yummy food.
Dec 18, 2020 - Lead by Chaochih Liu A community-maintained standard library of population genetic models
Adrion JR, Cole CB, Dukler N, Galloway JG, Gladstein AL, Gower G, Kyriazis CC, Ragsdale AP, Tsambos G, Baumdicker F, Carlson J, Cartwright RA, Druvasula A, Gronau I, Kim BY, McKenzie P, Messer PW, Noskova E, Vecchyo DO, Racimo F, Struck TJ, Gravel S, Gutenkunst RN, Lohmueller KE, Ralph PL, Schrider DR, Siepel A, Kelleher J, Kern AD (2020). eLife.
Dec 11, 2020 - Lead by Sam Hamann Samplot: A platform for structural variant visual validation and automated filtering
Belyeu JR, Chowdhury M, Brown J, Pedersen BS, Cormier MJ, Quinlan AR, Layer RM (2020). bioRxiv.
Dec 4, 2020 - Lead by Giulia Frascarelli Estimation of the SNP mutation rate in two vegetatively propagating species of duckweed
Sandler G, Bartkowska M, Agrawal AF, Wright SI (2020). G3.
Nov 27, 2020 - Lead by University of Minnesota No lab meeting this week
Thanksgiving (2020). Eat lots of yummy food.
Nov 20, 2020 - Lead by Li Lei Recurrent loss of sex is associated with accumulation of deleterious mutations in Oenothera
Hollister JD, Greiner S, Wang W, Wang J, Zhang Y, Wong GK, Wright SI, Johnson MTJ (2014). Molecular Biology Evolution.
Nov 13, 2020 - Lead by No discussion leader Break this week due to schedule conflicts
(2020). No Meeting.
Nov 6, 2020 - Lead by Peter Morrell High-resolution crossover mapping reveals similarities and differences of male and female recombination in maize
Kianian PMA, Wang M, Simons K, Ghavami F, He Y, Dukowic-Schulze S, Sundararajan A, Sun Q, Pillardy J, Mudge J, Chen C, Kianian SF, Pawlowski WP (2018). Nature Communications.
Oct 30, 2020 - Lead by Skylar Wyant Changing local recombination patterns in Arabidopsis by CRISPR/Cas mediated chromosome engineering
Schmidt C, Fransz P, Ronspies M, Dreissig S, Fuchs J, Heckmann S, Houben A, Puchta H (2020). Nature Communications.
Oct 23, 2020 - Lead by Emily Dittmar (Note: Special meeting time, 11:30 AM) Plant pan-genomics comes of age
Lei L, Goltsman EE, Goodstein D, Wu GA, Rokhsar D, Vogel JP (2020). Annual Review Plant Biology. (Will be emailed out).
Oct 16, 2020 - Lead by Chaochih Liu The distribution of common-variant effect sizes
O'Connor LJ (2020). bioRxiv.
Oct 9, 2020 - Lead by Giulia Frascarelli Population genomics of the Viking world
Margaryan A, Lawson DJ, Sikora M, Racimo F, Rasmussen S, Moltke I, Cassidy L, Jorsboe E, Ingason A, Willerslev E, et al. (2020). Nature.
Oct 2, 2020 - Lead by Li Lei Molecular parallelism underlies convergent highland adaptation of maize landraces
Wang L, Josephs EB, Lee KM, Roberts LM, Rellan-Alvarez R, Ross-Ibarra J, Hufford MB (2020). bioRxiv.
Sep 25, 2020 - Lead by Emily Dittmar Evaluating the cost of domestication in sunflower
Dittmar EL (2020). Talk.
Sep 18, 2020 - Lead by Peter Morrell Counting on crossovers: controlled recombination for plant breeding
Taagen E, Bogdanove AJ, Sorrells ME (2020). Trends in Plant Science.
Sep 11, 2020 - Lead by Sam Hamann A common inversion under selection in Europeans
Stefansson H, Helgason A, Thorleifsson G, Steinthorsdottir V, Masson G, Barnard J, Baker A, Jonasdottir A, Ingason A, Gudnadottir VG, Desnica N, Hicks A, Gylfason A, Gudbjartsson DF, Jonsdottir GM, Sainz J, Agnarsson K, Birgisdottir B, Ghosh S, Olafsdottir A, Cazier J, Kristjansson K, Frigge ML, Thorgeirsson TE, Gulcher JR, Kong A, Stefansson K (2005). Nature Genetics.
Sep 4, 2020 - Lead by Chaochih Liu Identifying genetic variants underlying phenotypic variation in plants without complete genomes
Voichek Y, Weigel D (2020). Nature Genetics.
Aug 28, 2020 - Lead by Li Lei Predicting the landscape of recombination using deep learning
Adrion JR, Galloway JG, Kern AD (2020). Molecular Biology Evolution.
Aug 21, 2020 - Lead by Giulia Frascarelli Ratatosk – Hybrid error correction of long reads enables accurate variant calling and assembly
Holley G, Beyter D, Ingimundardottir H, Kristmundsdottir S, Eggertsson HP, Halldorsson BV (2020). bioRxiv.
Aug 14, 2020 - Lead by Li Lei News & Views piece on the Todesco et al. 2020 paper: Large chromosomal variants drive adaptation in sunflowers
Zhou Y, Gaut BS (2020). Nature Plants.
Aug 14, 2020 - Lead by Li Lei Massive haplotypes underlie ecotypic differentiation in sunflowers
Todesco M, Owens GL, Bercovich N, Legare J, Soudi S, Burge D, Huang K, Ostevik KL, Drummond EBM, Imerovski I, Lande K, Pascual-Robles MA, Nanavati M, Johani M, Cheung W, Staton SE, Munos S, Nielsen R, Donovan LA, Burke JM, Yeaman S, Rieseberg LH (2020). Nature.
Aug 7, 2020 - Lead by Skylar Wyant Evolutionary genomics of structural variation in Asian rice (Oryza sativa) domestication
Kou Y, Liao Y, Toivainen T, Lv Y, Tian X, Emerson JJ, Gaut BS, Zhou Y (2020). Molecular Biology and Evolution.
Jul 31, 2020 - Lead by Sam Hamann USDA Agriculture and Food Research Initiative grant proposal discussion
Liu C et al (2020). Will be emailed to lab members.
Jul 24, 2020 - Lead by Peter Morrell pixy: Unbiased estimation of nucleotide diversity and divergence in the presence of missing data
Korunes KL, Samuk K (2020). bioRxiv.
Jul 17, 2020 - Lead by Giulia Frascarelli News item about the Antonio et al. 2019 paper: Many imperial Romans had roots in the Middle East, genetic history shows
Wade L (2019). Science.
Jul 17, 2020 - Lead by Giulia Frascarelli Ancient Rome: A genetic crossroads of Europe and the Mediterranean
Antonio ML, Gao Z, Moots HM, Lucci M, Candilio F, Sawyer S, Oberreiter V, Calderon D, Devitofranceschi K, Pritchard JK, et al (2019). Science.
Jul 9, 2020 - Lead by Li Lei - Note: Special meeting day, Thursday 11:00 am Machine learning techniques for classifying the mutagenic origins of point mutations
Zhu Y, Ong CS, Huttley GA (2020). Genetics.
Jul 3, 2020 - Lead by No one Happy July 4th!
No meeting today (2020). Holiday.
Jun 26, 2020 - Lead by No one RECOMB-GENETICS 2020 Conference, June 25-26
RECOMB (2020). No meeting today due to conference.
Jun 21, 2024 - Lead by Li Lei The ecological genetics of domestication and the origins of agriculture
Blumler MA & Byrne R (1991). Curr Anthropol 32.
Jun 19, 2020 - Lead by Peter Morrell Lab grant proposal discussion
Morrell PL et al (2020). Will be emailed to lab members.
Jun 14, 2024 - Lead by Peter Morrell DNA language models are powerful predictors of genome-wide variant effects
Benegas G, Batra SS, Song YS (2023). Proc Natl Acad Sci USA 120: e2311219120.
Jun 12, 2020 - Lead by Chaochih Liu The mutational constraint spectrum quantified from variation in 141,456 humans
Karczewski KJ, Francioli LC, Tiao G, Cummings BB, Alfoldi J, Wang Q, Collins RL, Laricchia KM, Ganna A, MacArthur DG, et al. (2020). Nature.
Jun 7, 2024 - Lead by Luis Arge Prediction of crossover recombination using parental genomes
Peñuela M, Riccio-Rengifo C, Finke J, Rocha C, Gkanogiannis A, Wing RA, Lorieux M (2023). PLoS One 18: e0281804.
Jun 5, 2020 - Lead by Giulia Frascarelli L. Luca Cavalli-Sforza: a Renaissance scientist
Feldman MW (2020). Theoretical Population Biology.
May 31, 2024 - Lead by Peter Morrell Enhancers in plants
Lei et al. (2024). .
May 29, 2020 - Lead by Skylar Wyant Dominance of deleterious alleles controls the response to a population bottleneck
Balick DJ, Do R, Cassa CA, Reich D, Sunyaev SR (2015). PLOS Genetics.
May 25, 2020 - Lead by No meeting today. Happy Memorial Day!
(2020). .
May 23, 2024 - Lead by Roland Akakpo - Note special date and time, Thursday 12:00 pm Wild barley introgression
Liu et al. (2024). .
May 18, 2020 - Lead by Emily Dittmar Gene body methylation is conserved between plant orthologs and is of evolutionary consequence
Takuno S, Gaut BS (2013). Proceedings of the National Academy of Sciences.
May 11, 2020 - Lead by Peter Morrell Structural variants exhibit widespread allelic heterogeneity and shape variation in complex traits
Chakraborty M, Emerson JJ, Macdonald SJ, Long AD (2019). Nature Communications.
May 4, 2020 - Lead by Chaochih Liu Using next-generation sequencing to isolate mutant genes from forward genetic screens
Schneeberger K (2014). Nature Reviews Genetics.
Apr 27, 2020 - Lead by Sam Hamann Geneticists and race
Provine WB (1986). American Zoologist.
Apr 20, 2020 - Lead by Giulia Frascarelli Phylogenetic shifts in gene body methylation correlate with gene expression and reflect trait conservation
Seymour DK, Gaut BS (2020). Molecular Biology Evolution.
Apr 13, 2020 - Lead by Skylar Wyant Evidence for positive selection in the superoxide dismutase (Sod) region of Drosophila melanogaster
Hudson RR, Bailey K, Skarecky D, Kwiatowski J, Ayala FJ (1994). Genetics.
Apr 6, 2020 - Lead by Emily Dittmar Recent selective sweeps in North American Drosophila melanogaster show signatures of soft sweeps
Garud NR, Messer PW, Buzbas EO, Petrov DA (2015). PLOS Genetics.
Apr 3, 2020 - Lead by Li Lei - Note: Special day and time, Friday 3:00 PM Fast neutron mutagenesis in soybean: biological, breeding, and safety consequences.
Wyant SR, Rodriguez MF, Carter CK, Parrott WA, Jackson SA, Stupar RM, Morrell PL (2020). Draft, will be distributed internally..
Mar 23, 2020 - Lead by Peter Morrell CADD: predicting the deleteriousness of variants throughout the human genome
Rentzsch P, Witten D, Cooper GM, Shendure J, Kircher M (2018). Nucleic Acids Research.
Mar 20, 2020 - Lead by Chaochih Liu - Note: Special day, Friday at 1:00 PM Properties of different selection signature statistics and a new strategy for combining them
Ma Y, Ding X, Qanbari S, Weigend S, Zhang Q, Simianer H (2015). Heredity.
Mar 9, 2020 - Lead by Giulia Frascarelli Patterns and processes in crop domestication: an historical review and quantitative analysis of 203 global food crops
Meyer RS, DuVal AE, Jensen HR (2012). New Phytologist.
Mar 2, 2020 - Lead by No discussion leader Break this week due to schedule conflicts
(2020). No Meeting.
Feb 24, 2020 - Lead by Li Lei The genomics of speciation in Drosophila: diversity, divergence, and introgression estimated using low-coverage genome sequencing
Kulathinal RJ, Stevison LS, Noor MAF (2009). PLOS Genetics.
Feb 17, 2020 - Lead by Emily Dittmar Linked-read sequencing of gametes allows efficient genome-wide analysis of meiotic recombination
Sun H, Rowan BA, Flood PJ, Brandt R, Fuss J, Hancock AM, Michelmore RW, Huettel B, Schneeberger K (2019). Nature Communications.
Feb 10, 2020 - Lead by Peter Morrell Effects of inversions on within- and between-species recombination and divergence
Stevison LS, Hoehn KB, Noor MAF (2011). Genome Biology and Evolution.
Feb 3, 2020 - Lead by Chaochih Liu An ultra high-density Arabidopsis thaliana crossover map that refines the influences of structural variation and epigenetic features
Rowan BA, Heavens D, Feuerborn TR, Tock AJ, Henderson IR, Weigel D (2019). Genetics.
Jan 27, 2020 - Lead by Giulia Frascarelli Human origins in a southern African palaeo-wetland and first migrations
Chan EKF, Timmermann A, Baldi BF, Moore AE, Lyons RJ, Lee S, Kalsbeek AMF, Petersen DC, Rautenbach H, Fortsch HEA, Bornman MSR, Hayes VM (2019). Nature.
Jan 24, 2020 - Lead by Li Lei - Note: Special day and time, 3:00 PM Friday Constructing genomic maps of positive selection in humans: where do we go from here?
Akey JM (2009). Genome Research.
Jan 13, 2020 - Lead by No one PAG Conference. No lab meeting this week
Break! (2019). UMN.
Jan 8, 2020 - Lead by Emily Dittmar - Note: Special day and time, 3:00 PM Wednesday Resequencing data indicate a modest effect of domestication on diversity in barley: a cultigen with multiple origins
Morrell PL, Gonzales AM, Meyer KKT, Clegg MT (2014). Journal of Heredity.
Dec 30, 2019 - Lead by No one No lab meeting this week
Winter Break! (2019). UMN.
Dec 23, 2019 - Lead by No one No lab meeting this week
Winter Break! (2019). UMN.
Dec 16, 2019 - Lead by Peter Morrell Two evolutionary histories in the genome of rice: the roles of domestication genes
He Z, Zhai W, Wen H, Tang T, Wang Y, Lu X, Greenberg AJ, Hudson RR, Wu C, Shi S (2011). PLOS Genetics.
Dec 9, 2019 - Lead by No one No lab meeting this week
Break due to travel schedules (2019). UMN.
Dec 4, 2019 - Lead by Chaochih Liu - NOTE: Special day and time, Wednesday at 11:00 AM Understanding the factors that shape patterns of nucleotide diversity in the house mouse genome
Booker TR, Keightley PD (2018). Molecular Biology and Evolution.
Nov 25, 2019 - Lead by Skylar Wyant Polygenic adaptation to an environmental shift: temporal dynamics of variation under Gaussian stabilizing selection and additive effects on a single trait
Thornton KR (2019). Genetics.
Nov 18, 2019 - Lead by Peter Morrell Analysis of author gender in TPB, 1991–2018
Severson AL, Uricchio LH, Arbisser IM, Glassberg EC, Rosenberg NA (2019). Theoretical Population Biology.
Nov 11, 2019 - Lead by Emily Dittmar Polygenic adaptation after a sudden change in environment
Hayward LK, Sella G (2019). bioRxiv.
Nov 4, 2019 - Lead by Peter Morrell Efficiently summarizing relationships in large samples: a general duality between statistics of genealogies and genomes
Ralph PL, Thornton K, Kelleher J (2019). bioRxiv.
Oct 28, 2019 - Lead by Skylar Wyant - Part II: pgs 476-end Thinking about the evolution of complex traits in the era of genome-wide association studies
Sella G, Barton NH (2019). Annual Review of Genomics and Human Genetics.
Oct 21, 2019 - Lead by Chaochih Liu - Part I: pgs 461-475 (through section 3.2.2) Thinking about the evolution of complex traits in the era of genome-wide association studies
Sella G, Barton NH (2019). Annual Review of Genomics and Human Genetics.
Oct 14, 2019 - Lead by Peter Morrell Global adaptation confounds the search for local adaptation
Booker TR, Yeaman S, Whitlock MC (2019). bioRxiv.
Oct 7, 2019 - Lead by Li Lei Comparative evolutionary analysis and prediction of deleterious mutation patterns between sorghum and maize
Lozano R, Gazave E, dos Santos JPR, Stetter M, Valluru R, Bandillo N, Fernandes SB, Brown PJ, Shakoor N, Mockler TC, Ross-Ibarra J, Buckler ES, Gore MA (2019). bioRxiv.
Oct 1, 2019 - Lead by Emily Dittmar - Note: Special time (2:00 PM) and date (10/1) What can genome‐wide association studies tell us about the evolutionary forces maintaining genetic variation for quantitative traits?
Josephs EB, Stinchcombe JR, Wright SI (2017). New Phytologist.
Sep 23, 2019 - Lead by No one Lab meeting rescheduled to next week
No one (2019). UMN.
Sep 20, 2019 - Lead by Chaochih Liu Recombination rate variation shapes barriers to introgression across butterfly genomes
Martin SH, Davey JW, Salazar C, Jiggins CD (2019). PLoS Biol 17(2): e2006288.
Sep 13, 2019 - Lead by No one Lab meeting rescheduled to next week
No one (2019). UMN.
Sep 6, 2019 - Lead by Peter Morrell Analysis of the recombination landscape of hexaploid bread wheat reveals genes controlling recombination and gene conversion frequency
Gardiner L, Wingen LU, Bailey P, Joynson R, Brabbs T et al. (2019). Genome Biology 20.
Aug 30, 2019 - Lead by Skylar Wyant Plant genome editing and the relevance of off-target changes
Graham N, Patil GB, Bubeck DM, Dobert RC, Glenn KC et al. (2019). In review - will be emailed to lab members.
Aug 23, 2019 - Lead by Chaochih Liu DFEnitely different: Genome-wide characterization of differences in mutation fitness effects between populations
Fortier AL, Coffman AJ, Struck TJ, Irby MN, Burguete JEL et al. (2019). bioRxiv.
Aug 16, 2019 - Lead by Peter Morrell The architecture of intra-organism mutation rate variation in plants
Wang L, Ji Y, Hu Y, Hu H, Jia X et al. (2019). PLoS Biol 17(4): e3000191.
Aug 9, 2019 - Lead by Emily Dittmar High genetic diversity can contribute to extinction in small populations
Kyriazis CC, Wayne RK, Lohmueller KE (2019). bioRxiv.
Aug 2, 2019 - Lead by Skylar Wyant Development of a multi-parent population for genetic mapping and allele discovery in six-row barley
Hemshrot A, Poets AM, Tyagi P, Lei L, Carter CK, Hirsch CN, Li L, Brown-Guedira G, Morrell PL, Muehlbauer GJ, Smith KP (2019). Genetics.
Jul 18, 2019 - Lead by Joint lab meeting with Irvine labs - special time: 2 PM Pacific Time From drift to draft: How much do beneficial mutations actually contribute to predictions of Ohta’s slightly deleterious model of molecular evolution?
Chen J, Glémin S, Lascoux M (2019). bioRxiv.
Jul 11, 2019 - Lead by Chaochih Liu - Special time: Thursday at 1:00 PM Standing genetic variation drives repeatable experimental evolution in outcrossing populations of Saccharomyces cerevisiae
Burke MK, Liti G, Long AD (2014). MBE.
Jul 5, 2019 - Lead by Peter Morrell Joint estimates of quantitative trait locus effect and frequency using synthetic recombinant populations of Drosophila melanogaster
Macdonald and Long (2007). Genetics.
Jun 28, 2019 - Lead by Li Lei TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools
Monat C, Padmarasu S, Lux T, Wicker T, Gundlach H et al. (2019). bioRxiv.
Jun 21, 2019 - Lead by Emily Dittmar Inferring the probability of the derived vs. the ancestral allelic state at a polymorphic site
Keightley PD, Jackson BC (2018). Genetics.
Jun 14, 2019 - Lead by Chaochih Liu Population differentiation as a test for selective sweeps
Chen H, Patterson N, Reich D (2010). Genome Research.
Jun 7, 2019 - Lead by Corey Carter Comparative analyses identify the contributions of exotic donors to disease resistance in a barley experimental population
Fang Z, Eule-Nashoba A, Powers C, Kono TY, Takuno S, Morrell P, Smith KP (2013). G3.
May 31, 2019 - Lead by Skylar Wyant Revisiting an old riddle: what determines genetic diversity levels within species?
Leffler EM, Bullaughey K, Mutate DR, Meyer WK, Ségurel L et al. (2012). PLoS Biology.
May 24, 2019 - Lead by Emily Dittmar From the past to the future: considering the value and limits of evolutionary prediction
Shaw RG (2019). The American Naturalist.
May 17, 2019 - Lead by Chaochih Liu Weighing the evidence for adaptation at the molecular level
Justin Fay (2011). Trends in Genetics.
May 10, 2019 - Lead by Li Lei Muller's ratchet and the long-term fate of chromosomal inversions
Berdan EL, Blanckaert A, Butlin RK, Bank C (2019). bioRxiv.
May 2, 2019 - Lead by Skylar Wyant - Special time and place: Thursday at 3:00 PM in Hayes 408 The genomics of selfing in maize (Zea mays ssp. mays): catching purging in the act
Roessler K, Muyle A, Diez CM, Gaut GRJ, Bousios A et al. (2019). bioRxiv.
Apr 26, 2019 - Lead by Peter Morrell The interplay of demography and selection during maize domestication and expansion
Wang L, Beissinger TM, Lorant A, Ross-Ibarra C, Ross-Ibarra J et al. (2017). Genome Biology.
Apr 19, 2019 - Lead by Ron Okagaki A critical assessment of 60 years of maize intragenic recombination
Okagaki R, Dukowic-Schulze S, Eggleston WB, Muehlbauer GJ (2018). Frontiers in Plant Science.
Apr 12, 2019 - Lead by Fernanda Rodriguez Landscape of genomic diversity and trait discovery in soybean
Valliyodan B, Qiu D, Patil G, Zeng P, Huang J et al. (2016). Scientific Reports.
Apr 5, 2019 - Lead by Skylar Wyant The Aquilegia genome provides insight into adaptive radiation and reveals an extraordinarily polymorphic chromosome with a unique history
Filiault DL, Ballerini ES, Mandáková T, Aköz G, Derieg NJ et al. (2018). eLIFE.
Mar 29, 2019 - Lead by Emily Dittmar The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution
Badouin H, Gouzy J, Grassa CJ, Murat F, Staton SE et al. (2017). Nature.
Mar 20, 2019 - Lead by Peter Morrell - Note: special day, Wednesday 1:00 PM Natural selection interacts with recombination to shape the evolution of hybrid genomes
Schumer M, Xu C, Powell DL, Durvasula A, Skov L et al. (2018). Science.
Mar 15, 2019 - Lead by Chaochih Liu Wheat introgression paper - in review
TBD (2019). Will be distributed internally via email.
Mar 8, 2019 - Lead by Li Lei Structural variants, clonal propagation, and genome evolution in grapevine (Vitis vinifera)
Zhou YS, Minio A, Massonnet M, Solares EA, Lyu Y et al. (2019). bioRxiv.
Feb 27, 2019 - Lead by Y chromosome owners - Wednesday at 1:00 PM - Multiple papers! Illuminating women’s hidden contribution to historical theoretical population genetics
Dung SK, Lópex A, Barragan EL, Reyes RJ, Thu R et al. (2019). Genetics.
Feb 27, 2019 - Lead by Y chromosome owners - Wednesday at 1:00 PM - Multiple papers! Expectations of brilliance underlie gender distributions across academic disciplines
Leslie SJ, Cimpian A, Meyer M, Freeland E (2015). Science.
Feb 27, 2019 - Lead by Group Discussion - Wednesday at 1:00 PM - Multiple papers! Discuss PAG talks and posters
PAG (2019). PAG.
Feb 22, 2019 - Lead by Peter Morrell Fast, scalable prediction of deleterious noncoding variants from functional and population genomic data
Huang Y, Gulko B, Siepel A (2017). Nature Genetics.
Feb 15, 2019 - Lead by Skylar Wyant The population genetics of human disease: The case of recessive, lethal mutations
Amorim CEG, Gao Z, Baker Z, Diesel JF, Simons YB et al. (2017). PLoS Genetics.
Jan 22, 2019 - Lead by Peter Morrell SV-plaudit: A cloud-based framework for manually curating thousands of structural variants
Belyeu JR, Nicholas TJ, Pedersen BS, Sasani TA, Havrilla JM et al. (2018). GigaScience.
Jan 18, 2019 - Lead by no one No lab meeting this week - Enjoy PAG!
No one (2018). UMN.
Jan 9, 2019 - Lead by Li Lei - Note special date! (Wednesday at 1 PM) PAG Talk & Poster Critique
Lei L, Poets AM, Liu C, Wyant SR, Hoffman PJ, Carter CK, Trantow RM, Li X, Muehlbauer GJ, Katagiri F, Morrell PL (2018). bioRxiv.
Jan 4, 2019 - Lead by Mike Shao Intraspecific variation of recombination rate in maize
Bauer E, Falque M, Walter H, Bauland C, Camisan C, et al. (2013). Genome Biology.
Dec 28, 2018 - Lead by No one No lab meeting this week
Winter break (2018). UMN.
Dec 21, 2018 - Lead by Fernanda Rodriguez Machine learning techniques for classifying the mutagenic origins of point mutations
Zhu Y, Soon CO, Huttley G (2018). bioRxiv.
Dec 7, 2018 - Lead by No one Lab meeting rescheduled to next week
No one (2018). UMN.
Dec 7, 2018 - Lead by No one Lab meeting rescheduled to next week
No one (2018). UMN.
Nov 30, 2018 - Lead by Peter Morrell Combining population genomics and fitness QTLs to identify the genetics of local adaptation in Arabidopsis thaliana
Price N, Moyers BT, Lopez L, Lasky JR, Monroe JG, et al. (2018). PNAS.
Nov 23, 2018 - Lead by University of Minnesota No lab meeting this week
Thanksgiving (2018). Eat lots of yummy food.
Nov 16, 2018 - Lead by Elise Tourrette Evidence of hitchhiking of deleterious mutations within the human genome
Chun S, Fay JC (2011). PLoS Genetics.
Nov 9, 2018 - Lead by Skylar Wyant - Note: Special time 3:30 PM Deleterious variation shapes the genomic landscape of introgression
Kim KY, Huber CD, Lohmueller KE (2018). PLoS Genetics.
Nov 2, 2018 - Lead by Li Lei A molecular approach to the study of genic heterozygosity in natural populations. II. Amount of variation and degree of heterozygosity in natural populations of Drosophila pseudoobscura
Lewontin RC, Hubby JL (1966). Genetics.
Oct 26, 2018 - Lead by Chaochih Liu The genetic architecture of natural variation in recombination rate in Drosophila melanogaster
Hunter CM, Huang W, Mackay TFC, Singh ND (2016). PLOS Genetics.
Oct 19, 2018 - Lead by Peter Morrell Bottlenecks and selective sweeps during domestication have increased deleterious genetic variation in dogs
Marsden CD, Vecchyo DO, O'Brien DP, Taylor JF, Ramirez O, Vila C, et al (2016). PNAS.
Oct 12, 2018 - Lead by Elise Tourrette - Note: Special time 3:30 PM Removal of alleles by genome editing — RAGE against the deleterious load
Johnsson M, Gaynor RC, Jenko J, Gorjanc G, de Koning D, Hickey JM (2018). bioRxiv.
Oct 5, 2018 - Lead by Skylar Wyant - Note: weekly meeting time changed to 1:00 PM Fridays The evolutionary advantage of recombination. II. individual selection for recombination
Felsenstein J & Yokoyama S (1976). Genetics.
Sep 28, 2018 - Lead by No meeting this week Break this week.
(). .
Sep 21, 2018 - Lead by Group Discussion Path to success: an analysis of US educated elite academics in the United States
Yuret T (2018). Scientometrics.
Sep 14, 2018 - Lead by Fernanda Rodriguez - Note: Special time 10:00 AM Connected populations for detecting quantitative trait loci and testing for epistasis: an application in maize
Blanc G, Charcosset A, Mangin B, Gallais A, Moreau L (2006). Theoretical and Applied Genetics.
Sep 7, 2018 - Lead by Peter Morrell - Note: Special day Wednesday at 2:00 PM Genome-scale sequence disruption following biolistic transformation in rice and maize
Liu J, Nannas NJ, Fu F, Shi J, Aspinwall B, Parrott WA et al. (2018). bioRxiv.
Aug 24, 2018 - Lead by Group Discussion 5th Midwest Population Genetics Meetings
No lab meeting this week (2018). .
Aug 17, 2018 - Lead by Li Lei Factors influencing the effect size distribution of adaptive substitutions
Dittmar EL, Oakley CG, Conner JK, Gould BA, Schemske DW (2016). Proceedings of the Royal Society B.
Aug 10, 2018 - Lead by Chaochih Liu The genetic architecture of genome‐wide recombination rate variation in allopolyploid wheat revealed by nested association mapping
Jordan KW, Wang S, et al. (2018). The Plant Journal.
Aug 2, 2018 - Lead by Peter Morrell - Note special date and time, Thursday 1:00 pm Evaluation and retrospective optimization of genomic selection for yield and disease resistance in spring barley
Tiede T & Smith KP (2018). Molecular Breeding.
Jul 27, 2018 - Lead by Peter Morrell Leveraging mutational burden for complex trait prediction in sorghum
Valluru R, Gazave EE, et al. (2018). bioRxiv.
Jul 13, 2018 - Lead by Corey Carter Environmental association in barley landraces: Identifying the genetic basis of low temperature and drought tolerance
Distributed internally only (in preparation). Email Li for manuscript.
Jul 6, 2018 - Lead by Li Lei The impact of recent population history on the deleterious mutation load in humans and close evolutionary relatives
Simons YB & Sella G (2016). Current Opinion in Genetics & Development.
Jun 22, 2018 - Lead by Peter Morrell - 2:00 PM Evaluating methods to visualize patterns of genetic differentiation on a landscape
House GL & Hahn MW (2017). Molecular Ecology Resources.
Jun 14, 2018 - Lead by Corey Carter The repetitive landscape of the 5100 Mbp barley genome
Wicker T, Schulman AH, Tanskanen J, Spannagl M, Twardziok S, Mascher M et al. (2017). Mobile DNA.
Jun 7, 2018 - Lead by Fernanda Rodriguez Assembly and annotation of a draft genome sequence for Glycine latifolia, a perennial wild relative of soybean
Liu Q, Chang S, Hartman GL, Domier LL (2018). The Plant Journal.
May 31, 2018 - Lead by Chaochih Liu Independent molecular basis of convergent highland adaptation in maize
Takuno S, Ralph P, Swarts K, Elshire RJ, Glaubitz JC, Buckler ES et al. (2015). Genetics.
May 24, 2018 - Lead by Li Lei Overlooked roles of DNA damage and maternal age in generating human germline mutations
Gao Z, Moorjani P, Amster G, Przeworski M (2018). bioRxiv.
May 17, 2018 - Lead by Genetics Society of America Population, Evolutionary and Quantitative Genetics Conference (PEQG) Conference
(2018). .
May 10, 2018 - Lead by Peter Morrell, Le Lei, Chaochih Liu Poster peer review for PEQG conference
Distributed internally only (2018). .
May 3, 2018 - Lead by Peter Morrell A population genetic interpretation of GWAS findings for human quantitative traits
Simons YB, Bullaughey K, Hudson RR, Sella G (2018). PLOS Biology.
Apr 19, 2018 - Lead by Li Lei An expanded view of complex traits: From polygenic to omnigenic
Boyl EA, Li YI, and Pritchard JK (2017). Cell.
Apr 12, 2018 - Lead by Peter Morrell Evolutionary genomics of grape (Vitis vinifera ssp. vinifera) domestication
Zhou Y, Massonnet M, Sanjak JS, Cantu D, and Gaut BS (2017). PNAS.
Apr 5, 2018 - Lead by Li Lei Genome graphs
Novak AM, Hickey G, Garrison E, Blum S, Connelly A, Dilthey A et al. (2017). bioRxiv 101378.
Mar 29, 2018 - Lead by Chaochih Liu Genome graphs and the evolution of genome inference
Paten B, Novak AM, Eizenga JM, Garrison E (2017). Genome Research 27: 665-676.
Mar 23, 2018 - Lead by Li Lei - 3:00 PM - Note special date and time Estimating the relative contribution of deleterious and neutral SNPs to agronomic phenotypes
Kono TJY, Liu C, Vonderharr EE, Koenig D, Fay JC et al. (preprint). Will be distributed internally only.
Mar 8, 2018 - Lead by Corey Carter Genome-wide nucleotide patterns and potential mechanisms of genome divergence following domestication
Wang J, Li X, Kim KD, Scanlon MJ, Jackson SA et al. (preprint). bioRxiv - Will be distributed internally only.
Mar 1, 2018 - Lead by Peter Morrell Evolutionary patterns of DNA base composition and correlation to polymorphisms in DNA repair systems
Li X, Scanlon MJ, Yu J (2015). Nucleic Acids Research 43: 3614–3625.
Feb 22, 2018 - Lead by Xin Li Inferring selective constraint from population genomic data suggests recent regulatory turnover in the human brain
Schrider DR, Kern AD (2015). Genome Biol Evol 7(12): 3511–3528.
Feb 15, 2018 - Lead by Fernanda Rodriguez Genome-wide association study of extreme longevity in Drosophila melanogaster
Burke MK, King EG, Shahrestani P, Rose MR, Long AD (2014). Genome Biol Evol 6(1): 1-11.
Feb 8, 2018 - Lead by Fernanda Rodriguez Genome-wide association study of extreme longevity in Drosophila melanogaster
Burke MK, King EG, Shahrestani P, Rose MR, Long AD (2014). Genome Biol Evol 6(1): 1-11.
Feb 1, 2018 - Lead by Chaochih Liu S/HIC: Robust identification of soft and hard sweeps using machine learning
Schrider DR, Kern AD (2016). PLoS Genet 12(3): e1005928.
Jan 25, 2018 - Lead by Xin Li Standing genetic variation drives repeatable experimental evolution in outcrossing populations of Saccharomyces cerevisiae
Burke MK, Liti G, Long AD (2014). Mol Biol Evol 31(12): 3228–3239.
Jan 19, 2018 - Lead by Skylar Wyant - 1:00 PM - Note special date and time African genomes illuminate the early history and transition to selfing in Arabidopsis thaliana
Durvasula A, Fulgione A, Gutaker RM, Alacakaptan SI, Flood PJ, Neto C et al. (2017). Proc Natl Acad Sci USA 114: 5213-5218.
Jan 11, 2018 - Lead by Connor Depies Terminal Pleistocene Alaskan genome reveals first founding population of Native Americans
Moreno-Mayar JV, Potter BA, Vinner L, Steinrücken M, Rasmussen S, Terhorst J et al. (2018). Nature.
Jul 13, 2018 - Lead by Corey Carter Environmental association in barley landraces: Identifying the genetic basis of low temperature and drought tolerance
Distributed internally only (in preparation). Email Li for manuscript.
Dec 14, 2017 - Lead by Peter Morrell Applications of population genetics to animal breeding, from wright, fisher and lush to genomic prediction
Will WG (2014). Genetics 196: 1-16.
Dec 7, 2017 - Lead by Li Lei Resequencing data indicate a modest effect of domestication on diversity in barley: a cultigen with multiple origins
Morrell PL, Gonzales AM, Meyer KKT, Clegg MT (2014). Journal of Heredity.
Nov 30, 2017 - Lead by Chaochih Liu Machine learning for population genetics: a new paradigm
Schrider DR, Kern AD (2017). bioRxiv.
Nov 23, 2017 - Lead by Morrell Lab Thanksgiving Holiday
University holiday (2017). Eat lots of turkey.
Nov 16, 2017 - Lead by Colin Pierce Prospective targeted recombination and genetic gains for quantitative traits in maize
Bernardo R (2017). The Plant Genome.
Nov 9, 2017 - Lead by Chaochih Liu Sequencing of single pollen nuclei reveals meiotic recombination events at megabase resolution and circumvents segregation distortion caused by postmeiotic processes
Dreissig S, Fuchs J, Himmelbach A, et al. (2017). Frontiers.
Nov 2, 2017 - Lead by Ron Okagaki Intense and highly localized gene conversion activity in human meiotic crossover hot spots
Jeffreys AJ, May CA (2004). Nature Genetics.
Oct 26, 2017 - Lead by Peter Morrell Inference of the distribution of selection coefficients for new nonsynonymous mutations using large samples
Kim BY, Huber CD, Lohmueller KE (2017). Genetics.
Sep 26, 2017 - Lead by Colin Pierce Determining the factors driving selective effects of new nonsynonymous mutations
Huber CD, Kim BY, Marsden CD, Lohmueller KE (2017). PNAS.
Oct 19, 2017 - Lead by Li Lei Linkage disequilibrium–dependent architecture of human complex traits shows action of negative selection
Gazal S, Finucane HK, Furlotte NA, Loh PR, Palamara PF, et al. (2017). Nature genetics.
Oct 12, 2017 - Lead by Fernanda Rodriguez Plant phenomics, from sensors to knowledge
Tardieu F, Cabrera-Bosquet L, Peidmore T, Bennet M (2017). Current Biology.
Oct 5, 2017 - Lead by Chaochih Liu Genetic Characterization of the Soybean Nested Association Mapping Population
Song Q, Yan L, Quigley C, Jordan BD, Fickus E, et al. (2017). Alliance of Crop, Soil, and Environmental Science Socities.
Sep 28, 2017 - Lead by Peter Morrell - Note special meeting time (2:30 PM) Limited role of differential fractionation in genome content variation and function in maize (Zea mays L.) inbred lines
Brohammer AB, Kono TJY, Springer NM, McGaugh SE, Hirsch CN (2017). BioRxiv.
Sep 21, 2017 - Lead by Skylar Wyant Defining the role of the MADS-box gene, Zea agamous like1, a target of selection during maize domestication
Wills DM, Fang Z, York AM, Holland JB, Doebley JF (2017). Journal of Heredity.
Sep 14, 2017 - Lead by Colin Pierce Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution
Drummond DA, Wilke CO (2008). Cell.
Sep 7, 2017 - Lead by Chaochih Liu Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA
Huerta-Sánchez E, Jin X, Asan, Bianba Z, Peter BM et al. (2014). Nature.
Aug 30, 2017 - Lead by Peter Morrell and Li Lei - two papers Epistasis between deleterious mutations and the evolution of recombination
Kouyos RD, Silander OK, Bonhoeffer S (2007). Trends in Ecology & Evolution.
Aug 30, 2017 - Lead by Peter Morrell and Li Lei - two papers Negative selection in humans and fruit flies involves synergistic epistasis
Sohail et al. (2017). Science.
Aug 23, 2017 - Lead by Peter Morrell The draft genome of Tibetan hulless barley reveals adaptive patterns to the high stressful Tibetan Plateau
Zeng W, Long H, Zhao S, Tang Y, Huang Z et al. (2015). PNAS.
Aug 9, 2017 - Lead by Li Lei Molecular ecology, epistasis, and adaptive convergence
Colin Pierce - Masters Thesis (2017). Will be distributed to lab.
Jul 26, 2017 - Lead by Colin Pierce Deep learning for population genetic inference
Sheehan S, Song YS (2016). PLOS Computational Biology.
Jul 19, 2017 - Lead by Li Lei - Optional reading Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.
Beier et al. (2017). Nature.
Jul 19, 2017 - Lead by Li Lei A chromosome conformation capture ordered sequence of the barley genome
Mascher et al. (2017). Nature.
Jul 12, 2017 - Lead by Tom Kono The QTN program and the alleles that matter for evolution: all that's gold does not glitter
Matthew Rockman (2011). Evolution.
Jul 5, 2017 - Lead by Morrell Lab Society of Molecular Biology and Evolution
Austin, TX (2017). No lab meeting this week.
Jun 28, 2017 - Lead by Chaochih Liu and Li Lei - Two papers this week POPBAM: Tools for evolutionary analysis of short read sequence alignments
Daniel Garrigan (2013). Evolutionary Bioinformatics Online.
Jun 28, 2017 - Lead by Chaochih Liu and Li Lei - Two papers this week PopGenome: An efficient Swiss army knife for population genomic analyses in R
Pfeifer B, Wittelsbürger U, Ramos-Onsins SE, Lercher MJ (2014). MBE.
Jun 21, 2017 - Lead by Skylar Wyant Genome-wide analysis of mutations in mutant lineages selected following fast-neutron irradiation mutagenesis of Arabidopsis thaliana
Belfield et al. (2012). Genome Research.
Jun 14, 2017 - Lead by Connor Depies The distribution of deleterious genetic variation in human populations
Lohmueller KE (2014). Current Opinion in Genetics & Development.
Jun 7, 2017 - Lead by Chaochih Liu A model of compound heterozygous, loss-of-function alleles is broadly consistent with observations from complex-disease GWAS datasets
Sanjak et al. (2017). PLOS Genetics.
May 31, 2017 - Lead by Peter Morrell Association mapping and the genomic consequences of selection in sunflower
Mandel et al. (2013). PLOS Genetics.
May 24, 2017 - Lead by Li Lei - Note special meeting time (3:00 PM) and room (401 Hayes) Genomic prediction manuscript
Kono et al. (TBD). Will be distributed to lab only.
May 18, 2017 - Lead by Skylar Wyant - Note special meeting date (Thursday) Domestication history and geographical adaptation inferred from a SNP map of African rice
Meyer et al. (2016). Nature Genetics.
May 12, 2017 - Lead by Corey Carter - Note special meeting time (2:00 PM) and room (401 Hayes) The interplay of demography and selection during maize domestication and expansion
Wang et al. (2017). bioRxiv.
May 4, 2017 - Lead by Chaochih Liu - Note Special Meeting Date (Thursday) and Time (4:15 pm) The pseudo-response regulator Ppd-H1 provides adaptation to photoperiod in barley
Turner et al. (2005). Science.
Apr 28, 2017 - Lead by Connor Depies PopVar: a genome-wide procedure for predicting genetic variance and correlated response in biparental breeding populations
Mohammadi, Tiede, and Smith (2015). Crop Science.
Apr 21, 2017 - Lead by Erica Sun Genetic costs of domestication and improvement
Moyers, Morrell, and McKay (2017). bioRxiv.
Apr 14, 2017 - Lead by Li Lei Deep sequencing of natural and experimental populations of Drosophila melanogaster reveals biases in the spectrum of new mutations
Assaf, Tilk, Park, Siegal, and Petrov (preprint). bioRxiv.
Apr 7, 2017 - Lead by Chaochih Liu 1,135 genomes reveal the global pattern of polymorphism in Arabidopsis thaliana
The 1001 Genomes Consortium (2016). Cell.
Mar 31, 2017 - Lead by Skylar Wyant Estimating the rate of adaptive molecular evolution in the presence of slightly deleterious mutations and population size change
Eyre-Walker, A and Keightley, PD (2009). MBE.
Mar 10, 2017 - Lead by Danelle Seymour The genetic architecture of freezing tolerance varies across the range of Arabidopsis thaliana
Horton, Willems, Sasaki, Koornneef, and Nordborg (2016). PLant, Cell, and Environment.
Mar 3, 2017 - Lead by Paul Hoffman Genomic Prediction in Barley
Thomas Kono et al (2017). Will be distributed to lab only.
Feb 24, 2017 - Lead by Chaochih Liu Genomic variation across landscapes: insights and applications
Bragg, et al. (2015). New Phytologist.
Feb 17, 2017 - Lead by Li Lei Developing maps of fitness consequences for plant genomes
Zoé Joly-Lopez, Jonathan M Flowers, Michael D Purugganan (2016). Current Opinion in Plant Biology.
Feb 10, 2017 - Lead by Peter Morrell Robust and scalable inference of population history from hundreds of unphased whole genomes
Jonathan Terhorst, John A Kamm, Yun S Song (2016). Nature Genetics.
Feb 3, 2017 - Lead by Danelle Seymour Molecular, genetic and evolutionary analysis of a paracentric inversion in Arabidopsis thaliana.
Paul Fransz, et al. (2016). The Plant Journal.
Jan 27, 2017 - Lead by Chaochih Liu More about deleterous mutations!
Thomas J.Y. Kono, Li Lei, Ching-Hua Shih, Paul J. Hoffman, Skylar R. Wyant, Peter L. Morrell, Justin C. Fay (2017). Will be distributed to lab only.
Jan 20, 2017 - Lead by Marisa Miller Statistical methods for identifying sequence motifs affecting point mutations
Yicheng Zhu, Teresa Neeman, Von Bing Yap, and Gavin A. Huttley (2016). Genetics.
Jan 13, 2017 - Lead by Li Lei Detection of human adaptation during the past 2000 years
Yair Field, Evan A Boyle, Natalie Telis, Ziyue Gao1, Kyle J. Gaulton, et al. (2016). Science.
Jan 6, 2017 - Lead by Colin Pierce Genetic architecture of nonadditive inheritance in Arabidopsis thaliana hybrids
Danelle K. Seymour, Eunyoung Chae, Dominik G. Grimm, Carmen Martín Pizarro, Anette Habring-Müller, et al. (2016). Proceedings of the National Academy of Sciences.
Dec 16, 2016 - Lead by Peter Morrell Incomplete dominance of deleterious alleles contribute substantially to trait variation and heterosis in maize
Jinliang Yang, Sofiane Mezmouk, Andy Baumgarten, Edward S Buckler, Katherine E Guill, et al. (preprint). bioRxiv.
Dec 9, 2016 - Lead by Paul Hoffman Variation in mutation dynamics across the maize genome as a function of regional and flanking base composition
Morton B, Bi I, McMullen M, and Gaut B (2006). Genetics.
Dec 2, 2016 - Lead by Colin Pierce Transposable elements contribute to activation of maize genes in response to abiotic stress
Makarevitch I, Waters AJ, West PT, Stitzer M, Hirsch CN et al. (2015). PLoS Genetics 11(1): e1004915.
Nov 25, 2016 - Lead by the University of Minnesota Thanksgiving Break
(November 24^th & 25^th 2016). Eat lots of turkey.
Nov 17, 2016 - Lead by Li Lei — Note special time (11:00 AM) and date The influence of genomic context on mutation patterns in the human genome inferred from rare variants
Schaibley et al (2013). Genome Research.
Nov 11, 2016 - Lead by Danelle Seymour Epigenetic silencing of transposable elements: A trade-off between reduced transposition and deleterious effects on neighboring gene expression
Jesse D. Hollister and Brandon S. Gaut (2009). Genome Research.
Nov 4, 2016 - Lead by Ana Poets Genomic analysis of 6,000-year-old cultivated grain illuminates the domestication history of barley
Mascher M, Schuenemann VJ, Davidovich U, Marom N, Himmelbach A et al. (2016). Nature Genetics.
Oct 28, 2016 - Lead by Corey Carter and Skylar Wyant Deleterious variants in Asian rice and the potential cost of domestication
Qingpo Liu, Yongfeng Zhou, Peter L. Morrell, Brandon S. Gaut (2016). BioRxiv.
Oct 21, 2016 - Lead by Marisa Miller Barley Inversions
Chaochih Liu and Li Lei (2016). Will be distributed to lab only.
Oct 14, 2016 - Lead by Tom Kono and Richard Trantow Exome sequencing of geographically diverse barley landraces and wild relatives gives insights into environmental adaptation
Russell J, Mascher M, Dawson IK, Kyriakidis S, Calixto C et al. (2016). Nature Genetics.
Oct 7, 2016 - Lead by Li Lei Population genetics and the evolution of geographic range limits in the annual plant
Moeller DA, Geber MA, Tiffin P (2011). The American Naturalist 178: S44-S61.
Sep 30, 2016 - Lead by Peter Morrell Efficient genome-wide detection and cataloging of EMS-induced mutations using exome capture and next-generation sequencing
Henry IM, Nagalakshmi U, Lieberman MC, Ngo KJ, Krasileva KV et al. (2014). The Plant Cell 26: 1382–1397.
Sep 23, 2016 - Lead by Tom Kono Special Event - Dissertation Defense - Thomas Kono
Note Special Date and Time (1:00pm). 306 Borlaug Hall.
Sep 16, 2016 - Lead by Colin Pierce A tutorial on how (not) to over-interpret STRUCTURE/ADMIXTURE bar plots
Falush D, van Dorp L, Lawson D (2016). bioRxiv.
Sep 9, 2016 - Lead by Skylar Wyant ANGSD-wrapper: utilities for analyzing next generation sequencing data
Durvasula A, Hoffman PJ, Kent TV, Liu C, Kono TJY, Morrell PL, Ross-Ibarra J (2016). Molecular Ecology Resources.
Aug 29, 2016 - Lead by Li Lei Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism
Novikova PY, Hohmann N, Nizhynska V, Tsuchimatsu JA, Muir G, et al. (2016). Nature Genetics.
Aug 22, 2016 - Lead by Corey Carter Coming of age: ten years of next-generation sequencing technologies
Goodwin S, McPherson JD, McCombie WR (2016). Nature Reviews Genetics 17: 333–351.
Aug 15, 2016 - Lead by Paul Hoffman Heterogeneous geographic patterns of nucleotide sequence diversity between two alcohol dehydrogenase genes in wild barley (Hordeum vulgare subspecies spontaneum)
Jing-Zhong L, Brown AHD, Clegg MT (2001). Proceedings of the National Academy of Sciences of the United States of America 98: 531–536.
Aug 8, 2016 - Lead by Chaochih Liu Population genetics from 1966 to 2016
Charlesworth B, Charlesworth D (2016). Heredity.
Aug 3, 2016 - Lead by Li Lei - Joint meeting with the Tiffin, Brandvain, and McGaugh Labs at 11:00 Detection of human adaptation during the past 2,000 years
Field Y, Boyle EA, Telis N, Gao Z, Gaulton KJ et al. (2016). bioRxiv.
Jul 25, 2016 - Lead by Colin Pierce A C++ template library for efficient forward-time population genetic simulation of large populations
Thornton, KR (2014). Genetics 198: 157-166.
Jul 18, 2016 - Lead by Skylar Wyant Genomic evidence of rapid and stable adaptive oscillations over seasonal time scales in Drosophila
Bergland AO, Behrman EL, O'Brien KR, Schmidt PS, Petrov DA (2014). PLoS Genetics 10:e1004775.
Jul 11, 2016 - Lead by Li Lei BAD_Mutations: Blast aligned deleterious mutation annotation
Kono et al. (2016). Github.
Jul 5, 2016 - Lead by Ana Poets Using crossover breakpoints in recombinant inbred lines to identify quantitative trait loci controlling the global recombination frequency
Esch E, Szymaniak JM, Yates H, Pawlowski WP, Buckler ES (2007). Genetics 177: 1851-1858.
Jun 27, 2016 - Lead by the University of Minnesota International Barley Genetics Symposium
No lab meeting this week. (IBGS). .
Jun 20, 2016 - Lead by Richard Trantow and Felipe Reyes A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes
Jordan KW, Wang S, Lun Y, Gardiner LJ, MacLachlan R et al. (2015). Genome Biology 16: 48.
Jun 13, 2016 - Lead by Chaochih Liu Deleterious variants in Asian rice and the potential cost of domestication
Liu Q, Zhou Y, Morrell PL, Gaut BS (2016). bioRxiv.
Jun 6, 2016 - Lead by Tom Kono Genomic prediction in barley
Kono et al. (2016). Manuscript.
May 31, 2016 - Lead by Paul Hoffman GBStools: A statistical method for estimating allelic dropout in reduced representation sequencing data
Cooke TF, Yee M-C, Muzzio M, Sockell A, Bell R et al. (2016). PLOS Genetics 12: e1005631.
May 23, 2016 - Lead by Skylar Wyant The limits of natural selection in a nonequilibrium world
Brandvain Y, Wright SI (2016). Trends Genetics 32: 201-210.
May 16, 2016 - Lead by Felipe Reyes Good enough practices for scientific computing
Bryan J, Cranston K, Kitzes J, Nederbragt L, Teal T et al. (2016). The Internet.
May 9, 2016 - Lead by Shawn Goggins Landscape of standing variation for tandem duplications in Drosophila yakuba and Drosophila simulans
Rogers RL, Cridland JM, Shao L, Hu TT, Andolfatto P et al. (2014). Molecular Biology and Evolution 31: 1750-1766.
May 2, 2016 - Lead by Li Lei Molecular evolution in nonrecombining regions of the Drosophila melanogaster genome
Campos JL, Charlesworth B, Haddrill PR (2012). Genome Biology and Evolution 4: 278-288.
Apr 25, 2016 - Lead by Alex Ollhoff Genetic properties of the maize nested association mapping population
McMullen MD, Kresovich S, Villeda HS, Bradbury P, Li H et al. (2009). Science 325: 737-740.
Apr 18, 2016 - Lead by Alex Susko Genomewide analysis of epistatic effects for quantitative traits in barley
Xu S, Jia Z (2007). Genetics 175: 1955-1963.
Apr 11, 2016 - Lead by Chaochih Liu Genome-wide identification of evolutionarily conserved alternative splicing events in flowering plants
Chamala S, Feng G, Chavarro C, Barbazuk WB (2015). Frontiers in Bioengineering and Biotechnology 3: 33.
Apr 4, 2016 - Lead by Tom Kono Divergence and functional degradation of a sex chromosome-like supergene
Tuttle EM, Bergland AO, Korody ML, Brewer MS, Newhouse DJ et al. (2016). Current Biology 26: R105-7.
Mar 28, 2016 - Lead by Paul Hoffman Recombination in diverse maize is stable, predictable, and associated with genetic load
Rodgers-Melnick E, Bradbury PJ, Elshire RJ, Glaubitz JC, Acharya CB et al. (2015). Proceedings of the National Academy of Sciences of the United States of America 112: 3823–3828.
Mar 21, 2016 - Lead by Shawn Goggins Evolutionary patterns of genic DNA methylation vary across land plants
Takuno S, Ran J-H, Gaut BS (2016). Nature Plants 2: 15222.
Mar 21, 2016 - Lead by Shawn Goggins Plant genic methylation: Conserved for 400 million years
Schneeberger K (2016). Nature Plants 2: 16003.
Mar 7, 2016 - Lead by Ana Poets The Capsella rubella genome and the genomic consequences of rapid mating system evolution
Slotte T, Hazzouri KM, Ågren JA, Koenig D, Maumus F et al. (2013). Nature Genetics 45: 831-835.
Feb 29, 2016 - Lead by Li Lei Estimating the contribution of mutation, recombination and gene conversion in the generation of haplotypic diversity
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Feb 22, 2016 - Lead by Skylar Wyant Is the gene the unit of selection? Evidence from two experimental plant populations
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Feb 15, 2016 - Lead by Chaochih Liu Genome resilience and prevalence of segmental duplications following fast neutron irradiation of soybean
Bolon YT, Stec AO, Michno JM, Roessler J, Bhaskar PB et al. (2014). Genetics 198: 967-981.
Feb 8, 2016 - Lead by Tom Kono Two-locus sampling distributions and their application
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Feb 1, 2016 - Lead by Jeff Neyhart GCTA: a tool for genome-wide complex trait analysis
Yang J, Lee SH, Goddard ME, Visscher PM (2011). American Society of Human Genetics 88: 76-82.
Feb 1, 2016 - Lead by Jeff Neyhart Genome-wide complex trait analysis (GCTA): methods, data analyses, and interpretations
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Jan 25, 2016 - Lead by Colin Pierce Gene duplication and divergence affecting drug content in Cannabis sativa
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Jan 22, 2016 - Lead by Li Lei Distance from sub-Saharan Africa predicts mutational load in diverse human genomes
Henn BM, Botigué LR, Peischl S, Dupanloup I, Lipatov M et al. (2015). Proceedings of the National Academy of Sciences of the United States of America 113: E440–E449.
Jan 5, 2016 - Lead by Alex Susko The evolution of self-fertilization and inbreeding depression in plants. I. Genetic models
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Dec 15, 2015 - Lead by Paul Hoffman Evolution of the grain dispersal system in barley
Pourkheirandish M, Hensel G, Kilian B, Senthil N, Chen G, Sameri M, Azhaguvel P, Sakuma S, Dhanagond S, Sharma R et al. (2015). Cell 162: 527–539.
Dec 10, 2015 - Lead by Felipe Reyes Evolution of Darwin’s finches and their beaks revealed by genome sequencing
Lamichhaney S, Berglund J, Almén MS, Maqbool K, Grabherr M, Martinez-Barrio A, Promerová M, Rubin CJ, Wang C, Zamani N et al. (2015). Nature 518: 371–375.
Dec 1, 2015 - Lead by Benjamin Campbell Identification of markers linked to disease-resistance genes by bulked segregant analysis - a rapid method to detect markers in specific genomic regions by using segregating populations
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Nov 24, 2015 - Lead by Li Lei Network properties of robust immunity in plants
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Nov 17, 2015 - Lead by Ana Poets Power analysis of artificial selection experiments using efficient whole genome simulation of quantitative traits
Kessner D, Novembre J (2015). Genetics 199: 991–1005.
Nov 10, 2015 - Lead by Tom Kono Genome-wide variation in polyadenylation site usage and association mapping in Arabidopsis MAGIC founders
Li Lei, Joshua G. Steffen, Robert Greenhalgh, Edward J. Osborne, Philipp Drewe, Andre Kahles, Gunnar Raetsch, Richard Mott, Richard M. Clark, Christopher Toomajian (2015). Plant and Animal Genome XXIII Conference P0145.
Nov 3, 2015 - Lead by Shawn Goggins The accumulation of deleterious mutations as a consequence of domestication and improvement in sunflowers and other compositae crops
Renaut S, Rieseberg LH (2015). Molecular Biology and Evolution 32: 2273–2283.
Oct 27, 2015 - Lead by Jeff Neyhart Whole-genome nucleotide diversity, recombination, and linkage disequilibrium in the model legume Medicago truncatula
Branca A, Paape TD, Zhou P, Briskine R, Farmer AD, Mudge J, Bharti AK, Woodward JE, May GD, Gentzbittel L et al. (2011). Proceedings of the National Academy of Sciences of the United States of America 108: E864–70.
Oct 20, 2015 - Lead by Alex Susko and Fumi Katagiri Inference of population structure using multilocus genotype data
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Oct 13, 2015 - Lead by Chaochih Liu The effects of both recent and long-term selection and genetic drift are readily evident in North American barley breeding populations
Poets AM, Mohammadi M, Seth K, Wang H, Kono TJY et al. (2015). G3 115.024349.
Oct 8, 2015 - Lead by Lex Flagel Multiple instances of ancient balancing selection shared between humans and chimpanzees
Leffler EM, Gao Z, Pfeifer S, Segurel L, Auton A, Venn O, Bowden R, Bontrop R, Wall JD, Sella G et al. (2013). Science 339: 1578–1582.
Sep 29, 2015 - Lead by Peter Morrell The number of alleles that can be maintained in a finite population
Kimura M, Crow JF (1964). Genetics 49: 725–738.
Sep 22, 2015 - Lead by Benjamin Campbell MAGIC populations in crops: current status and future prospects
Huang BE, Verbyla KL, Verbyla AP, Raghavan C, Singh VK et al. (2015). Theoretical and Applied Genetics 128: 999-1017.
Sep 15, 2015 - Lead by Tom Kono Transposable elements contribute to activation of maize genes in response to abiotic stress
Makarevitch I, Waters AJ, West PT, Stitzer M, Hirsch CN et al. (2015). PLOS Genetics 11: e1004915.
Sep 8, 2015 - Lead by Shawn Goggins A spatial framework for understanding population structure and admixture
Bradburd G, Ralph PL, Coop G (2015). PLOS Genetics 12: e1005703.
Sep 2, 2015 - Lead by Alex Susko Q(ST)-F(ST) comparisons: evolutionary and ecological insights from genomic heterogeneity
Leinonen T, McCairns RJ, O’Hara RB, Merilä J (2013). Nature Reviews Genetics 14: 179-190.
Aug 26, 2015 - Lead by Chaochih Liu and Yaniv Brandvain Genome-wide inference of ancestral recombination graphs
Rasmussen MD, Hubisz MJ, Gronau I, Siepel A (2014). PLOS Genetics 10: e1004342.
Aug 19, 2015 - Lead by Paul Hoffman Genomics and the contrasting dynamics of annual and perennial domestication
Gaut BS, Diez CM, Morrell PL (2015). Trends in Genetics 31: 709-719.
Aug 12, 2015 - Lead by Tom Kono Obstruction of adaptation in diploids by recessive, strongly deleterious alleles
Assaf ZJ, Petrov DA, Blundell JR (2015). Proceedings of the National Academy of Sciences of the United States of America 112: E2658-E2666.
Aug 5, 2015 - Lead by Peter Morrell Confounding between recombination and selection, and the Ped/Pop method for detecting selection
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Jul 29, 2015 - Lead by Fengli Fu PopGenome: an efficient Swiss army knife for population genomic analyses in R
Pfeifer B, Wittelsbürger U, Ramos-Onsins SE, Lercher MJ (2014). Molecular Biology and Evolution 31: 1929-1936.
Jul 24, 2015 - Lead by Peter Morrell Standing genetic variation drives repeatable experimental evolution in outcrossing populations of Saccharomyces cerevisiae
Burke MK, Liti G, Long AD (2014). Molecular Biology and Evolution 31: 3228-3239.
Jul 10, 2015 - Lead by Paul Hoffman Olive domestication and diversification in the Mediterranean Basin
Diez CM, Trujillo I, Martinez-Urdiroz N, Barranco D, Rallo L et al. (2015). New Phytologist 206: 436-447.
Jul 1, 2015 - Lead by Tom Kono Identifying adaptive genetic divergence among populations from genome scans
Beaumont MA, Balding DJ (2004). Molecular Ecology 13: 969-980.
Jun 24, 2015 - Lead by Jean-Michel Michno A roadmap for functional structural variants in the soybean genome
Anderson JE, Kantar MB, Kono TY, Fu F, Stec AO et al. (2014). G3 4: 1307-1318.
Jun 17, 2015 - Lead by Chaochih Liu and Tom Kono Detection and polarization of introgression in a five-taxon phylogeny
Pease JB, Hahn MW (2015). Systematic Biology 64: 651-662.
Jun 10, 2015 - Lead by Justin Anderson Prehistoric genomes reveal the genetic foundation and cost of horse domestication
Schubert M, Jonsson H, Chang D, Der Sarkissian C, Ermini L et al. (2014). Proceedings of the National Academy of Sciences of the United States of America 111: E5661-E5669.
Jun 3, 2015 - Lead by Alex Susko Seven common mistakes in population genetics and how to avoid them
Meirmans PG (2015). Molecular Ecology 24: 3223-3231.
May 27, 2015 - Lead by Austin Dobbels Natural variation in teosinte at the domestication locus teosinte branched1 (tb1)
Vann L, Kono T, Pyhajarvi T, Hufford MB, Ross-Ibarra J (2015). PeerJ 3: e900.
May 20, 2015 - Lead by Alex Susko Advances and limits of using population genetics to understand local adaptation
Tiffin P, Ross-Ibarra J (2014). Trends in Ecology and Evolution 29: 673-680.
May 13, 2015 - Lead by Fengli Fu A genetic atlas of human admixture history
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May 6, 2015 - Lead by Diana Trujillo Improved data analysis for the MinION nanopore sequencer
Jain M, Fiddes IT, Miga KH, Olsen HE, Paten B, Akeson M (2015). Nature Methods 12: 351-356.
Apr 29, 2015 - Lead by Tom Kono Barley landraces are characterized by geographically heterogeneous genomic origins
Poets AM, Fang Z, Clegg MT, Morrell PL (2015). Genome Biology 16: 173.
Apr 22, 2015 - Lead by Mikey Kantar The strategy of model building in population biology
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Apr 15, 2015 - Lead by Justin Anderson Precision genome engineering and agriculture: opportunities and regulatory challenges
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Apr 8, 2015 - Lead by Mikey Kantar Second-generation PLINK: rising to the challenge of larger and richer datasets
Chang CC, Chow CC, Tellier LC, Vattikuti S, Purcell SM et al. (2015). Gigascience 4: 7.
Apr 1, 2015 - Lead by Kyungsoo Yoo Potential of DNA barcoding for earthworm research in taxonomy and ecology
Decaens T, Porco D, Rougerie R, Brown GG, James SW (2013). Applied Soil Ecology 65: 35-42.
Mar 25, 2015 - Lead by Alex Susko Epistasis and its contribution to genetic variance components
Cheverud JM, Routman EJ (1995). Genetics 139: 1455-1461.
Mar 11, 2015 - Lead by Chaochih Liu Contrasting population genetic patterns within the white-throated sparrow genome (Zonotrichia albicollis)
Huynh LY, Maney DL, Thomas JW (2010). BioMed Central Genetics 11: 96.
Mar 6, 2015 - Lead by Peter Morrell Estimating and interpreting FST: the impact of rare variants
Bhatia G, Patterson N, Sankararaman S, Price AL (2013). Genome Research 23: 1514-1521.
Feb 25, 2015 - Lead by Tom Kono When is selection effective?
Gravel S (2016). Genetics 202.
Feb 18, 2015 - Lead by Ana Gonzales Linkage disequilibrium: what history has to tell us
Nordborg M, Tavaré S (2002). Trends in Genetics 18: 83-90.
Feb 11, 2015 - Lead by Kiran Seth Sex determination: why so many ways of doing it?
Bachtrog D, Mank JE, Peichel CL, Kirkpatrick M, Otto SP et al. (2014). PLOS Biology 12: e1001899.
Feb 2, 2015 - Lead by Justin Anderson Characteristics of neutral and deleterious protein-coding variation among individuals and populations
Fu W, Gittelman RM, Bamshad MJ, Akey JM (2014). The American Journal of Human Genetics 95: 421-436.
Jan 26, 2015 - Lead by Tom Kono and Peter Morrell ANGSD: Analysis of Next Generation Sequencing Data
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Jan 20, 2015 - Lead by Kiran Seth A population genetic signal of polygenic adaptation
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Jan 5, 2015 - Lead by Weidong Wang Haplotype-based genomic sequencing of a chromosomal polymorphism in the white-throated sparrow (Zonotrichia albicollis)
Davis JK, Mittel LB, Lowman JJ, Thomas PJ, Maney DL et al. (2011). Journal of Heredity 102: 380-390.
Dec 15, 2014 - Lead by Mikey Kantar “Patterns of Speciation in Drosophila” Revisited
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Dec 15, 2014 - Lead by Mikey Kantar Patterns of speciation in Drosophila
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Dec 8, 2014 - Lead by Yaniv Brandvain Measuring linkage disequilibrium by the partial correlation coefficient
Lin CY, Xing G, Xing (2012). Heredity (Edinb) 109: 401-402.
Dec 8, 2014 - Lead by Yaniv Brandvain Novel measures of linkage disequilibrium that correct the bias due to population structure and relatedness
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Dec 1, 2014 - Lead by Peter Morrell Discussion on the meeting on’Statistical modelling and analysis of genetic data’
Balding DJ, Carothers AD, Marchini JL, Cardon LR, Vetta A et al. (2002). Journal of the Royal Statistical Society: Series B (Statistical Methodology) 64: 737-775.
Dec 1, 2014 - Lead by Peter Morrell Assessing population differentiation and isolation from single-nucleotide polymorphism data
Nicholson G, Smith AV, Jónsson F, Gústafsson Ó, Stefánsson K et al. (2002). Journal of the Royal Statistical Society: Series B (Statistical Methodology) 64: 695-715.
Nov 24, 2014 - Lead by Chaochih Liu Error detection in SNP data by considering the likelihood of recombinational history implied by three-site combinations
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Nov 17, 2014 - Lead by Tom Kono The structure of linkage disequilibrium around a selective sweep
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Nov 10, 2014 - Lead by Ana Poets Notes on Population Genetics Chapter 1: Allele and genotype frequencies
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Nov 3, 2014 - Lead by Diana Trujillo Epigenetics and crop improvement
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Oct 27, 2014 - Lead by Justin Anderson Combining population genomics and quantitative genetics: finding the genes underlying ecologically important traits
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Oct 20, 2014 - Lead by Chaochih Liu Phylogenetics and the origin of species
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Oct 17, 2014 - Lead by Allison Haaning The USDA barley core collection: genetic diversity, population structure, and potential for genome-wide association studies
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Oct 6, 2014 - Lead by Peter Morrell Whole population, genome-wide mapping of hidden relatedness
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Sep 29, 2014 - Lead by Tom Kono Properties and modeling of GWAS when complex disease risk is due to non-complementing, deleterious mutations in genes of large effect
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Sep 26, 2014 - Lead by Ana Gonzales A unifying theory for general multigenic heterosis: energy efficiency, protein metabolism, and implications for molecular breeding
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Sep 15, 2014 - Lead by Kiran Seth The use of next generation sequencing and junction sequence analysis bioinformatics to achieve molecular characterization of crops improved through modern biotechnology
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Sep 10, 2014 - Lead by Diana Trujillo Human genetics. The genetics of Mexico recapitulates Native American substructure and affects biomedical traits
Moreno-Estrada A, Gignoux CR, Fernandez-Lopez JC, Zakharia F, Sikora M et al. (2010). Science 344: 1280-1285.
Sep 3, 2014 - Lead by Justin Anderson Local adaptation and the evolution of chromosome fusions
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Aug 20, 2014 - Lead by Chaochih Liu Assessing the accuracy and power of population genetic inference from low-pass next-generation sequencing data
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Aug 13, 2014 - Lead by Derek Nedveck and Mikey Kantar Prospects for whole-genome linkage disequilibrium mapping of common disease genes
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Aug 13, 2014 - Lead by Derek Nedveck and Mikey Kantar The future of genetic studies of complex human diseases
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Jul 30, 2014 - Lead by Ana Gonzales and Chaochih Liu The complex domestication history of the common bean
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Jul 30, 2014 - Lead by Ana Gonzales and Chaochih Liu A reference genome for common bean and genome-wide analysis of dual domestications
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Jul 23, 2014 - Lead by Mikey Kantar On the immortality of television sets: “function” in the human genome according to the evolution-free gospel of ENCODE
Graur D, Zheng Y, Price N, Azevedo RB, Zufall RA et al. (2013). Genome Biology and Evolution 5: 578-590.
Jul 16, 2014 - Lead by Kiran Seth Genomic signature of adaptation to climate in Medicago truncatula
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Jun 25, 2014 - Lead by Kiran Seth Genomic sequence diversity and population structure of Saccharomyces cerevisiae assessed by RAD-seq
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Jun 18, 2014 - Lead by Allison Haaning Gene body methylation is conserved between plant orthologs and is of evolutionary consequence
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Jun 12, 2014 - Lead by Ana Gonzales Quantifying population genetic differentiation from next-generation sequencing data
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Jun 3, 2014 - Lead by Justin Anderson Analysis of barley landrace provenance
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May 27, 2014 - Lead by Derek Nedveck Number of heterozygous nucleotide sites maintained in a finite population due to steady flux of mutations
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May 20, 2014 - Lead by Ana Gonzales Adaptive evolution of non-coding DNA in Drosophila
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May 13, 2014 - Lead by Justin Anderson Landscape of standing variation for tandem duplications in Drosophila yakuba and Drosophila simulans
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May 6, 2014 - Lead by Derek Nedveck and Mikey Kantar The cost of natural selection and the extent of enzyme polymorphism
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May 6, 2014 - Lead by Derek Nedveck and Mikey Kantar Roger Milkman-selection is the major determinant
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May 6, 2014 - Lead by Derek Nedveck and Mikey Kantar The neutral theory as a supplement to Darwinism
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04/29/2014
Kono TJY, Fu F, Mohammadi M et al. (in preparation) Bad mutations.
Discussion Leader: Amber Eule-Nashoba

04/24/2014
Joint Meeting Brandvain, Goldberg, Moeller, Morrell, & Tiffin Lab Groups
Mimura M, Ono K, Goka K, Hara T (2013) Standing variation boosted by multiple sources of introduction contributes to the success of the introduced species, Lotus corniculatus. Biol Invasions 15: 2743-2754.
Discussion Leader: Derek Nedveck

04/22/2014
Baldwin-Brown JG, Long AD, Thornton KR (2014) The power to detect quantitative trait loci using resequenced, experimentally evolved populations of diploid, sexual organisms. Mol Biol Evol
Discussion Leader: Diana Trujillo

04/15/2014
Ralph P, Coop G (2013) The geography of recent genetic ancestry across Europe. PLoS Biol 11: e1001555.
Discussion Leader: Tom Kono

04/08/2014
Crisci JL, Poh YP, Bean A, Simkin A, Jensen JD (2012) Recent progress in polymorphism-based population genetic inference. J Hered 103: 287-296.
Discussion Leader: Allison Haaning

04/01/2014
Xu S, Jia Z (2007) Genomewide analysis of epistatic effects for quantitative traits in barley. Genetics 175: 1955-1963.
Discussion Leader: Justin Anderson

03/28/2014
Joint Meeting Brandvain, Goldberg, Moeller, Morrell, & Tiffin Lab Groups
Chantha SC, Herman AC, Platts AE, Vekemans X, Schoen DJ (2013) Secondary evolution of a self-incompatibility locus in the Brassicaceae genus Leavenworthia. PLoS Biol 11: e1001560.
Discussion Leader: Emma Goldberg

03/25/2014
Reading the Classics
Lander ES, Botstein D (1989) Mapping mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121: 185-199.
Discussion Leader: Derek Nedveck

03/18/2014
Li H, Durbin R (2011) Inference of human population history from individual whole-genome sequences. Nature 475: 493-496.
Discussion Leader: Ana Gonzales

03/11/2014
Freedman AH, Gronau I, Schweizer RM, Ortega-Del V, Diego, Han E et al. (2014) Genome sequencing highlights the dynamic early history of dogs. PLoS Genet 10: e1004016.
Discussion Leader: Chaochih Liu & Peter Morrell

03/04/2014
Hollister JD, Ross-Ibarra J, Gaut BS (2010) Indel-associated mutation rate varies with mating system in flowering plants. Mol Biol Evol 27: 409-416.
Discussion Leader: Diana Trujillo

02/28/2014
Joint Meeting Brandvain, Goldberg, Moeller, Morrell, & Tiffin Lab Groups
Rasmussen M, Anzick SL, Waters MR, Skoglund P, DeGiorgio M et al. (2014) The genome of a Late Pleistocene human from a Clovis burial site in western Montana. Nature 506: 225-229.
Discussion Leader: Tom Kono

02/25/2014
Hartfield M, Glemin S (2014) Hitchhiking of deleterious alleles and the cost of adaptation in partially selfing species. Genetics 196: 281-293.
Discussion Leader: Ron Okagaki

02/18/2014
Arbiza L, Gronau I, Aksoy BA, Hubisz MJ, Gulko B et al. (2013) Genome-wide inference of natural selection on human transcription factor binding sites. Nat Genet 45: 723-729.
Discussion Leader: Allison Haaning

02/11/2014
Nielsen R, Korneliussen T, Albrechtsen A, Li Y, Wang J (2012) SNP calling, genotype calling, and sample allele frequency estimation from New-Generation Sequencing data. PLoS One 7: e37558.
Discussion Leader: Tom Kono

02/04/2014 - 2:30 pm - Note Special Time
Reading the Classics
Lewontin RC, Krakauer J (1973) Distribution of gene frequency as a test of the theory of the selective neutrality of polymorphisms. Genetics 74: 175-195.
Discussion Leader: Derek Nedveck

01/28/2014
Han E, Sinsheimer JS, Novembre J (2013) Characterizing bias in population genetic inferences from low coverage sequencing data. Mol Biol Eval
Discussion Leader: Ana Gonzales

01/24/2014
Joint Meeting Brandvain, Goldberg, Moeller, Morrell, & Tiffin Lab Groups
Skoglund P, Malmstrom H, Raghavan M, Stora J, Hall P et al. (2012) Origins and genetic legacy of Neolithic farmers and hunter-gatherers in Europe. Science 336: 466-469.
Discussion Leader: Yaniv Brandvain

01/21/2014
Slatkin M (2009) Epigenetic inheritance and the missing heritability problem. Genetics 182: 845-850.
Discussion Leader: Justin Anderson

01/14/2014
International Plant and Animal Genome Meeting

01/07/2014
Fay JC, Wyckoff GJ, Wu CI (2001) Positive and negative selection on the human genome. Genetics 158: 1227-1234.
Discussion Leader: Kiran Seth

12/31/2013
Christmas Holiday

12/24/2013
Christmas Holiday

12/17/2013
Gonzales AM, Fang Z, Clegg MT, Morrell PL (in prep) Barley landraces - SNP Analysis.
Discussion Leader: Tom Kono

12/12/2013 - Note Special Date
Guo M, Rupe MA, Wei J, Winkler C, Goncalves-Butruille M et al. (2013) Maize ARGOS1 (ZAR1) transgenic alleles increase hybrid maize yield. J Exp Bot
Discussion Leader: Peter Morrell

12/13/2013 - 10:30 am - Note Special Date & Time
Joint Meeting Moeller, Morrell, & Tiffin Lab Groups
Moreno-Estrada A, Gravel S, Zakharia F, McCauley JL, Byrnes JK et al. (2013) Reconstructing the population genetic history of the Caribbean. PLoS Genet 9: e1003925.
Discussion Leader: Dave Moeller

12/03/2013
Nicholson G, Smith AV, Jónsson F, Gústafsson Ó, Stefánsson K et al. (2002) Assessing population differentiation and isolation from single-nucleotide polymorphism data. J R Stat Soc Ser B Stat Methodol 64: 695-715.
Discussion Leader: Zhou Fang

11/26/2013
Epperson B.K., 1999. Gustave Malecot, 1911-1998. Population genetics founding father. Genetics 152: 477-484.
Discussion Leader: Ron Okagaki

11/19/2013
Berg J.J., Coop G., 2013. The population genetic signature of polygenic local adaptation. J arXiv preprint arXiv:1307.7759
Discussion Leader: Ana Gonzales

11/15/2013 - 2:30 pm - Note Special Date & Time
Joint Meeting with Blekham, McCue, Moeller, & Tiffin Lab Groups
Brandvain Y., Slotte T., Hazzouri K.M., Wright S.I., Coop G., 2013. Genomic identification of founding haplotypes reveals the history of the selfing species Capsella rubella. PLoS Genet 9: e1003754.
Discussion Leader: Tom Kono

11/12/2013
Reading the Classics
Hill WG, Robertson A (1966) The effect of linkage on limits to artificial selection. Genet Res 8: 269-294.
Discussion Leader: Ron Okagaki

11/05/2013
van Heerwaarden J, Hufford MB, Ross-Ibarra J (2012) Historical genomics of North American maize. Proc Natl Acad Sci U S A
Discussion Leader: Xin Li

10/29/2013
Rosenberg NA, Li LM, Ward R, Pritchard JK (2003) Informativeness of genetic markers for inference of ancestry. Am J Hum Genet 73: 1402-1422.
Discussion Leader: Zhou Fang

10/22/2013
Loh PR, Lipson M, Patterson N, Moorjani P, Pickrell JK et al. (2013) Inferring admixture histories of human populations using linkage disequilibrium. Genetics 193: 1233-1254.
Discussion Leader: Tom Kono

10/15/2013
Rosenberg NA, Mahajan S, Ramachandran S, Zhao C, Pritchard JK et al. (2005) Clines, clusters, and the effect of study design on the inference of human population structure. PLoS Genetics 1: e70.
Discussion Leader: Zhou Fang

10/08/2013
Fang Z, Gonzales AM, Clegg MT, Muehlbauer GJ, et al. (in preparation) Two genomic regions contribute disproportionately to population structure in wild barley.
Discussion Leader: Allison Haaning

10/04/2013 - 2:30 pm - Note Special Date & Time
Joint Meeting with Blekham, McCue, Moeller, & Tiffin Lab Groups
Long Q, Rabanal FA, Meng D, Huber CD, Farlow A et al. (2013) Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden. Nat Genet 45: 884-890.
Discussion Leader: Peter Tiffin

09/24/2013
King EG, Macdonald SJ, Long AD (2012) Properties and power of the Drosophila synthetic population resource for the routine dissection of complex traits. Genetics 191: 935-949.
Discussion Leader: Tom Kono

09/17/2013
Richman AD, Uyenoyama MK, Kohn JR (1996) Allelic diversity and gene genealogy at the self-incompatibility locus in the Solanaceae. Science 273: 1212-1216.
Discussion Leader: Kelly Tweito

09/10/2013
Flowers JM, Molina J, Rubinstein S, Huang P, Schaal BA, Purugganan MD (2012) Natural selection in gene-dense regions shapes the genomic pattern of polymorphism in wild and domesticated rice. Mol Biol Evol 29: 675-687.
Discussion Leader: Tom Kono

08/29/2013
King EG, Merkes CM, McNeil CL, Hoofer SR, Sen S et al. (2012) Genetic dissection of a model complex trait using the Drosophila Synthetic Population Resource. Genome Res
Discussion Leader: Vikram Vikus

08/22/2013
Beleza S, Johnson NA, Candille SI, Absher DM, Coram MA et al. (2013) Genetic architecture of skin and eye color in an African-European admixed population. PLoS Genet 9: e1003372.
Discussion Leader: Allison Haaning

08/14/2013 - 10:00 am - Note Special Date & Time
Hudson RR, Bailey K, Skarecky D, Kwiatowski J, Ayala FJ (1994) Evidence for positive selection in the superoxide dismutase (Sod) region of Drosophila melanogaster. Genetics 136: 1329-1340.
Discussion Leader: Justin Anderson

08/08/2013
Morrell, P.L., Rieseberg, L.H. 1998. Molecular tests of the proposed diploid hybrid origin of Gilia achilleifolia (Polemoniaceae). Am J Bot 85:1439–1453.
Discussion Leader: Zhou Fang

08/01/2013
Cutter AD, Payseur BA (2013) Genomic signatures of selection at linked sites: unifying the disparity among species. Nat Rev Genet 14: 262-274.
Discussion Leader: Ana Gonzales

07/26/2013 - Note Special Date
McVean G (2009) A genealogical interpretation of principal components analysis. PLoS Genet 5: e1000686.
Discussion Leader: Vikram Vikus

07/18/2013
Deleterious Mutations Jigsaw
Lopes AM, Aston KI, Thompson E, Carvalho F, Goncalves J et al. (2013) Human spermatogenic failure purges deleterious mutation load from the autosomes and both sex chromosomes, including the gene DMRT1. PLoS Genet 9: e1003349.
Discussion Leaders: Allison Haaning, Tom Kono

Peischl S, Dupanloup I, Kirkpatrick M, Excoffier L (2013) On the accumulation of deleterious mutations during range expansions. J arXiv preprint arXiv:13061652
Discussion Leaders: Kelly Tweito, Ana Gonzales

Simons YB, Turchin MC, Pritchard JK, Sella G (2013) The deleterious mutation load is insensitive to recent population history. J arXiv preprint arXiv:13052061
Discussion Leaders: Margie Stringfield, Justin Anderson

Szpiech ZA, Xu J, Pemberton TJ, Peng W, Zollner S et al. (2013) Long runs of homozygosity are enriched for deleterious variation. Am J Hum Genet
Discussion Leaders: Mikey Kantar, Diana Trujillo

07/11/2013
Society for Molecular Biology & Evolution (SMBE) Meeting 2013 - Chicago

07/04/2013
Independence Day

06/27/2013
Sousa V, Hey J (2013) Understanding the origin of species with genome-scale data: modelling gene flow. Nat Rev Genet 14: 404-414.
Discussion Leader: Diana Trujillo

06/20/2013
Petersen JL, Mickelson JR, Rendahl AK, Valberg SJ, Andersson LS et al. (2013) Genome-wide analysis reveals selection for important traits in domestic horse breeds. PLoS Genet 9: e1003211.
Discussion Leaders: Justin Anderson

06/13/2013
Reading the Classics
Smith JM, Haigh J (1974) The hitchhiking effect of a favorable gene. Genet Res 23: 23-35.
Discussion Leader: Mikey Kantar

06/06/2013
Charlesworth B 2012. The effects of deleterious mutations on evolution at linked sites. Genetics 190: 5–22.
Charlesworth B 2013. Background selection 20 years on: The Wilhelmine E. Key 2012 Invitational Lecture. J Hered 104: 161–171.
Discussion Leaders: Fengli Fu & Mohsen Mohammadi

05/30/2013
Lin Z, Li X, Shannon LM, Yeh CT, Wang ML et al. (2012) Parallel domestication of the Shattering1 genes in cereals. Nat Genet 44: 720-724.
Discussion Leader: Amber Eule-Nashoba

05/23/2013
Guerrero RF, Rousset F, Kirkpatrick M (2012) Coalescent patterns for chromosomal inversions in divergent populations. Philos Trans R Soc Lond B Biol Sci 367: 430-438.
Discussion Leader: Tom Kono

05/17/2013
Fuller DQ, Willcox G, Allaby RG (2012) Early agricultural pathways: moving outside the ‘core area’ hypothesis in Southwest Asia. J Exp Bot 63: 617-633.
Discussion Leader: Peter Morrell

05/10/2013
Takebayashi N, Morrell PL (2001) Is self-fertilization an evolutionary dead end? Revisiting an old hypothesis with genetic theories and a macroevolutionary approach. Am J Bot 88: 1143-1150.
Igic B, Busch JW (2013) Is self-fertilization an evolutionary dead end? New Phytol 198: 386-397.
Discussion Leaders: Ana Gonzales & Tom Kono

05/03/2013
Joint Meeting with McCue, Moeller, & Tiffin Lab Groups
Ober U, Ayroles JF, Stone EA, Richards S, Zhu D, Gibbs RA, Stricker C, Gianola D, Schlather M, Mackay TF, Simianer H (2012) Using whole-genome sequence data to predict quantitative trait phenotypes in Drosophila melanogaster. PLoS Genet 8: e1002685.
Discussion Leader: Vikram Vikus

04/26/2013
Fuller DQ, Willcox G, Allaby RG (2011) Cultivation and domestication had multiple origins: arguments against the core area hypothesis for the origins of agriculture in the Near East. World Archaeology 43: 628-652.
Discussion Leader: Tom Kono

04/19/2013
Reading the Classics
Felsenstein J (1974) The evolutionary advantage of recombination. Genetics 78: 737-756.
Discussion Leader: Mikey Kantar

04/12/2013
Parker GA, Smith JM (1990) Optimality theory in evolutionary biology. Nature 348: 27-33.
Shoval O, Sheftel H, Shinar G, Hart Y, Ramote O et al. (2012) Evolutionary trade-offs, Pareto optimality, and the geometry of phenotype space. Science 336: 1157-1160.
Discussion Leader: Ron Okagaki

04/05/2013
Fu W, O’Connor TD, Jun G, Kang HM, Abecasis G, Leal SM, Gabriel S, Altshuler D, Shendure J, Nickerson DA, Bamshad MJ, Akey JM (2013) Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants. Nature 493: 216-220.v Karakoc E, Alkan C, O’Roak BJ, Dennis MY, Vives L et al. (2012) Detection of structural variants and indels within exome data. Nat Methods 9: 176-178.
Discussion Leader: Ahmad Sallam

03/29/2013
Gan X, Stegle O, Behr J, Steffen JG, Drewe P et al. (2011) Multiple reference genomes and transcriptomes for Arabidopsis thaliana. Nature 477: 419-423.
Discussion Leader: Tom Kono

03/22/2013
Spring Break

03/15/2013
Yang S, Yuan Y, Wang L, Li J, Wang W et al. (2012) Great majority of recombination events in Arabidopsis are gene conversion events. Proc Natl Acad Sci USA
Discussion Leader: Amber Eule-Nashoba

03/08/2013
Reading the Classics
Watterson GA (1975) On the number of segregating sites in genetical models without recombination. Theor Popul Biol 7: 256-276.
Discussion Leader: Mikey Kantar

03/01/2013
Morrell PL, Gonzales AM, Meyer KKT, Clegg MT (in prep) Resequencing data indicate a modest effect of domestication on diversity in barley: a cultigen with multiple origins.
Discussion Leader: Zhou Fang

02/22/2013
Joint Meeting with McCue, Moeller, & Tiffin Lab Groups
Rockman MV (2012) The QTN program and the alleles that matter for evolution: all that’s gold does not glitter. Evolution 66: 1-17.
Discussion Leader: Peter Tiffin

02/15/2013
Lu J, Tang T, Tang H, Huang J, Shi S, Wu CI (2006) The accumulation of deleterious mutations in rice genomes: a hypothesis on the cost of domestication. Trends Genet 22: 126-131.
Discussion Leader: Amber Eule-Nashoba

02/08/2013
Reading the Classics
Gould SJ, Lewontin RC (1979) The spandrels of San Marco and the Panglossian paradigm: a critique of the adaptationist programme. Proceedings of the Royal Society B: Biological Sciences 205: 581-598.
Discussion Leader: Mikey Kantar

02/01/2013
Comeron JM, Ratnappan R, Bailin S (2012) The many landscapes of recombination in Drosophila melanogaster. PLoS Genet 8: e1002905.
Discussion Leader: Peter Morrell

01/24/2013
Turchin MC, Chiang CW, Palmer CD, Sankararaman S, Reich D et al. (2012) Evidence of widespread selection on standing variation in Europe at height-associated SNPs. Nat Genet 44: 1015-1019.
Discussion Leader: Ana Gonzales

01/17/2013
Pickrell JK, Pritchard JK (2012) Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genet 8: e1002967.
Discussion Leader: Tom Kono

01/10/2013
International Plant and Animal Genome Meeting

01/03/2013
Christmas Holiday

12/27/2013
Christmas Holiday

12/20/2012
Swanson-Wagner R, Briskine R, Schaefer R, Hufford MB, Ross-Ibarra J, Myers CL, Tiffin P, Springer NM (2012) Reshaping of the maize transcriptome by domestication. Proc Natl Acad Sci U S A 109: 11878-11883.
Discussion Leader: Zhou Fang

12/13/2012
Leffler EM, Bullaughey K, Matute DR, Meyer WK, Segurel L et al. (2012) Revisiting an old riddle: what determines genetic diversity levels within species? PLoS Biol 10: e1001388.
Sella G, Petrov DA, Przeworski M, Andolfatto P (2009) Pervasive natural selection in the Drosophila genome? Plos Genet 5: ARTN e1000495.
Discussion Leader: Ana Gonzales & Peter Morrell

12/06/2012
van Heerwaarden J, Hufford MB, Ross-Ibarra J (2012) Historical genomics of North American maize. Proc Natl Acad Sci USA
Discussion Leader: Emily Combs

11/28/2012
Kono TY, Seth K, Stupar RM, Morrell PL (in prep) SNP annotation and SNP metadata collection without a reference genome.
Discussion Leader: Zhou Fang

11/22/2012
Thanksgiving Holiday

11/16/2012
Hahn MW (2008) Toward a selection theory of molecular evolution. Evolution 62: 255-265.
Discussion Leader: Ron Okagaki

11/08/2012
Reading the Classics
Tajima F (1983) Evolutionary relationship of DNA sequences in finite populations. Genetics 105: 437-460.
Discussion Leader: Mikey Kantar

11/01/2012
Ralph P, Coop G (2012) The geography of recent genetic ancestry across Europe. J Arxiv preprint arXiv:12073815
Discussion Leader: Ron Okagaki

10/25/2012
Mayer KF, Waugh R, Langridge P, Close TJ, Wise RP et al. (2012) A physical, genetic and functional sequence assembly of the barley genome. Nature
Discussion Leader: Peter Morrell

10/19/2012
Joint Meeting with the Smith Lab
Fang Z, Eule-Nashoba A, Powers C, Kono TY, Morrell PL et al. (in prep) Multiple genomic regions indicate a response to selection for Fusarium head blight resistance in a barley experimental breeding population.
Discussion Leader: Vikram Vikus

10/11/2012
Fang Z, Gonzales AM, Durbin ML, Meyer KKT, Miller BH, Volz KM, Clegg MT, Morrell PL (in prep) Tracing the geographic origin of weedy Ipomoea purpurea in the Southeastern United States.
Discussion Leader: Tom Kono

10/04/2012
Lee CR, Mitchell-Olds T (2011) Quantifying effects of environmental and geographical factors on patterns of genetic differentiation. Mol Ecol 20: 4631-4642.
Discussion Leader: Ana Gonzales

09/27/2012
Gonzales AM, Fang Z, Durbin ML, Meyer KKT, Clegg MT et al. (in press) Nucleotide sequence diversity of floral pigment genes in Mexican populations of Ipomoea purpurea (morning glory) accord with a neutral model of evolution. J of Heredity
Discussion Leader: Amber Eule-Nashoba

09/21/2012
Joint Meeting with McCue, Moeller, & Tiffin Labs
Wang C, Zollner S, Rosenberg NA (2012) A quantitative comparison of the similarity between genes and geography in worldwide human populations. PLoS Genet 8: e1002886.
Discussion Leader: Jeremy Yoder

09/13/2012
Whittington HR, Deede L, Powers JS (2012) Growth responses, biomass partitioning, and nitrogen isotopes of prairie legumes in response to elevated temperature and varying nitrogen source in a growth chamber experiment. Am J Bot 99: 838-846.
Discussion Leader: Peter Morrell

09/06/2012
Morrell PL, Buckler ES, Ross-Ibarra J (2012) Crop genomics: advances and applications. Nat Rev Genet 13: 85-96.
Discussion Leader: Zhou Fang

08/30/2012
Microbial and Plant Genomics Institute
3rd Annual Fall Symposium

08/23/2012
Eichten SR, Swanson-Wagner RA, Schnable JC, Waters AJ, Hermanson PJ, Liu S, Yeh CT, Jia Y, Gendler K, Freeling M, Schnable PS, Vaughn MW, Springer NM (2011) Heritable epigenetic variation among maize inbreds. PLoS Genet 7: e1002372.
Discussion Leader: Peter Morrell

08/16/2012
Warmuth V, Eriksson A, Bower MA, Canon J, Cothran G et al. (2011) European domestic horses originated in two holocene refugia.PLoS One 6: e18194.
Warmuth V, Eriksson A, Bower MA, Barker G, Barrett E et al. (2012) Reconstructing the origin and spread of horse domestication in the Eurasian steppe. Proc Natl Acad Sci U S A 109: 8202-8206.
Discussion Leader: Tom Kono

08/09/2012
Zhong SQ, Dekkers JCM, Fernando RL, Jannink JL (2009) Factors affecting accuracy from genomic selection in populations derived from multiple inbred lines: A barley case study. Genetics 182: 355-364.
Discussion Leader: Vikram Vikus

08/02/2012
Hoban S, Bertorelle G, Gaggiotti OE (2011) Computer simulations: tools for population and evolutionary genetics. Nat Rev Genet 13: 110-122.
Discussion Leader: Emily Combs

07/26/2012
Reading the Classics
Kreitman M (1983) Nucleotide polymorphism at the alcohol dehydrogenase locus of Drosophila melanogaster. Nature 304: 412-417.
Discussion Leader: Mikey Kantar

07/19/2012
Mackay TF, Richards S, Stone EA, Barbadilla A, Ayroles JF et al. (2012) The Drosophila melanogaster Genetic Reference Panel. Nature 482: 173-178.
Discussion Leader: Peter Morrell

07/12/2012
Novembre J, Ramachandran S (2011) Perspectives on human population structure at the cusp of the sequencing era. Annu Rev Genomics Hum Genet 12: 245-274.
Discussion Leader: Tom Kono

07/05/2012
Wegmann D, Kessner DE, Veeramah KR, Mathias RA, Nicolae DL et al. (2011) Recombination rates in admixed individuals identified by ancestry-based inference. Nat Genet 43: 847-853.
Discussion Leader: Ron Okagaki

06/28/2012
Horton MW, Hancock AM, Huang YS, Toomajian C, Atwell S et al. (2012) Genome-wide patterns of genetic variation in worldwide Arabidopsis thaliana accessions from the RegMap panel. Nat Genet 44: 212-216.
Gaut BS (2012) _Arabidopsis thaliana_ as a model for the genetics of local adaptation. Nat Genet 44: 115-116.
Discussion Leader: Amber Eule-Nashoba

06/21/2012
Engelhardt BE, Stephens M (2010) Analysis of population structure: a unifying framework and novel methods based on sparse factor analysis. PLoS Genet 6:
Yang WY, Novembre J, Eskin E, Halperin E (2012) A model-based approach for analysis of spatial structure in genetic data. Nat Genet 44: 725-731.
Discussion Leader: Vikram Vikus & Ana Gonzales

06/14/2012
Moeller DA, Geber MA, Tiffin P (2011) Population genetics and the evolution of geographic range limits in an annual plant. Am Nat 178 Suppl 1: S44-57.
Discussion Leader: Peter Morrell

06/07/2012
Hufford MB, Xun X, van Heerwaarden J, Pyhäjärvi T, Chia J-M, Cartwright RA, Elshire RJ, Glaubitz JC, Guill KE, Kaeppler SM, Lai J, Morrell PL, Shannon LM, Song C, Springer NM, Swanson-Wagner RA, Tiffin P, Wang J, Zhang G, Doebley J, McMullen MD, Ware D, Buckler ES, Yang S, Ross-Ibarra J (in press) Population genomics of domestication and improvement in maize. Nature Genetics
Discussion Leader: Mikey Kantar

05/31/2012
Otto SP, Whitlock MC (1997) The probability of fixation in populations of changing size. Genetics 146: 723-733.
Discussion Leader: Amber Eule-Nashoba

05/24/2012
Tang H, Choudhry S, Mei R, Morgan M, Rodriguez-Cintron W et al. (2007) Recent genetic selection in the ancestral admixture of Puerto Ricans. Am J Hum Genet 81: 626-633.
Discussion Leader: Ana Gonzales

05/17/2012
Ng PC, Henikoff S (2003) SIFT: Predicting amino acid changes that affect protein function. Nucleic Acids Res 31: 3812-3814.
Ng PC, Nickerson DA, Bamshad MJ, Shendure J (2010) Massively parallel sequencing and rare disease. Hum Mol Genet 19: R119-24.
Discussion Leader: Tom Kono

05/10/2012
Lawson DJ, Hellenthal G, Myers S, Falush D (2012) Inference of population structure using dense haplotype data. PLoS Genet 8: e1002453.
Gattepaille LM, Jakobsson M (2012) Combining markers into haplotypes can improve population structure inference. Genetics 190: 159-174.
Discussion Leaders: Ana Gonzales & Peter Morrell

05/03/2012
Haun WJ, Hyten DL, Xu WW, Gerhardt DJ, Albert TJ et al. (2011) The composition and origins of genomic variation among individuals of the soybean reference cultivar Williams 82. Plant Physiol 155: 645-655.
Discussion Leader: Mikey Kantar

04/26/2012
Fournier-Level A, Korte A, Cooper MD, Nordborg M, Schmitt J et al. (2011) A map of local adaptation in Arabidopsis thaliana. Science 334: 86-89.
Discussion Leader: Amber Eule-Nashoba

04/19/2012
Marth GT, Yu F, Indap AR, Garimella K, Gravel S et al. (2011) The functional spectrum of low-frequency coding variation. Genome Biol 12: R84.
Discussion Leader: Zhou Fang

04/12/2012
Pyhäjärvi T, Kujala ST, Savolainen O (2011) Revisiting protein heterozygosity in plants—nucleotide diversity in allozyme coding genes of conifer Pinus sylvestris. Tree Genetics & Genomes 7: 385-397.
Discussion Leader: Tom Kono

04/05/2012
Dumont BL, Payseur BA (2011) Genetic analysis of genome-scale recombination rate evolution in house mice. PLoS Genet 7: e1002116.
Discussion Leader: Mikey Kantar

03/29/2012
Tenaillon O, Rodriguez-Verdugo A, Gaut RL, McDonald P, Bennett AF et al. (2012) The molecular diversity of adaptive convergence. Science 335: 457-461.
Discussion Leader: Ron Okagaki

03/22/2012
Blackman BK, Rasmussen DA, Strasburg JL, Raduski AR, Burke JM et al. (2011) Contributions of flowering time genes to sunflower domestication and improvement. Genetics 187: 271-287.
Discussion Leader: Mikey Kantar

03/15/2012
Spring Break

03/08/2012 (location - 138 Cargill)
Joint Meeting with the Smith Lab
Illumina Genotyping - GenomeStudio and Alchemy
Wright MH, Tung CW, Zhao K, Reynolds A, McCouch SR et al. (2010) ALCHEMY: a reliable method for automated SNP genotype calling for small batch sizes and highly homozygous populations. Bioinformatics 26: 2952-2960.
Discussion Leaders: Karen Beaubien, Ana Gonzales, and Maria Munoz
If you need an Minnesota Supercomputing Institute (MSI) account to participate, register here: https://www.msi.umn.edu/tutorial/802

03/01/2012
Zhao K, Tung CW, Eizenga GC, Wright MH, Ali ML et al. (2011) Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa. Nat Commun 2: 467.
Discussion Leader: Ana Gonzales

02/23/2012
Macdonald SJ, Long AD (2007) Joint estimates of quantitative trait locus effect and frequency using synthetic recombinant populations of Drosophila melanogaster. Genetics 176: 1261-1281.
Discussion Leader: Vikram Vikus

02/16/2012
Albrechtsen A, Nielsen FC, Nielsen R (2010) Ascertainment biases in SNP chips affect measures of population divergence. Mol Biol Evol 27: 2534-2547.
Discussion Leader: Zhou Fang

02/09/2012
Reading the Classics
Lewontin RC, Hubby JL (1966) A molecular approach to the study of genic heterozygosity in natural populations. II. Amount of variation and degree of heterozygosity in natural populations of Drosophila pseudoobscura. Genetics 54: 595-609.
Discussion Leader: Amber Eule-Nashoba

02/02/2012
Saintenac C, Jiang D, Akhunov ED (2011) Targeted analysis of nucleotide and copy number variation by exon capture in allotetraploid wheat genome. Genome Biol 12: R88.
Discussion Leader: Zhou Fang

01/26/2012
Reading the Classics
Lewontin RC, Krakauer J (1973) Distribution of gene frequency as a test of the theory of the selective neutrality of polymorphisms. Genetics 74: 175-195.
Discussion Leader: Mikey Kantar

01/19/2012
International Plant and Animal Genome Meeting

01/13/2012
International Plant and Animal Genome Meeting

01/06/2012
Christmas Holiday

12/29/2011
Christmas Holiday

12/22/2011
Nair, S.K., Wang, N., Turuspekov, Y., Pourkheirandish, M., Sinsuwongwat, S., Chen, G., Sameri, M., Tagiri, A., Honda, I., Watanabe, Y., Kanamori, H., Wicker, T., Stein, N., Nagamura, Y., Matsumoto, T., Komatsuda, T. 2010. Cleistogamous flowering in barley arises from the suppression of microRNA-guided HvAP2 mRNA cleavage. Proc Natl Acad Sci U S A 107:490–495.
Discussion Leader: Ana Gonzales

12/15/2011
Wakeley J (2005) The limits of theoretical population genetics. Genetics 169: 1-7.
Discussion Leader: Peter Morrell

12/08/2011 (location - 138 Cargill)
Joint Meeting with the Smith Lab
UNIX Shell Scripting and Job Queueing on Linux Clusters
http://manuals.bioinformatics.ucr.edu/home/linux-basics
Discussion Leader: Tom Kono and Erin Treiber
If you need an Minnesota Supercomputing Institute (MSI) account to participate, register here: https://www.msi.umn.edu/tutorial/786

11/30/2011
Joint Meeting with McCue, Moeller, & Tiffin Labs
Studer A, Zhao Q, Ross-Ibarra J, Doebley J (2011) Identification of a functional transposon insertion in the maize domestication gene tb1. Nat Genet 43: 1160-1163.
Discussion Leader: Tom Kono

11/24/2010
Thanksgiving Holiday

11/17/2011
Fay JC (2011) Weighing the evidence for adaptation at the molecular level. Trends Genet
Discussion Leader: Raffa Teixera

11/10/2011
Macdonald SJ, Long AD (2007) Joint estimates of quantitative trait locus effect and frequency using synthetic recombinant populations of Drosophila melanogaster. Genetics 176: 1261-1281.
Discussion Leader: Peter Morrell

11/03/2011
Ju YS, Kim JI, Kim S, Hong D, Park H et al. (2011) Extensive genomic and transcriptional diversity identified through massively parallel DNA and RNA sequencing of eighteen Korean individuals. Nat Genet 43: 745-752.
Discussion Leader: Mikey Kantar

10/26/2011 (note date, time, and location 371 Bioscience - 12:30 pm)
Joint Meeting with McCue, Moeller, & Tiffin Lab Groups
Cao, J., Schneeberger, K., Ossowski, S., Gunther, T., Bender, S., Fitz, J., Koenig, D., Lanz, C., Stegle, O., Lippert, C., Wang, X., Ott, F., Muller, J., Alonso-Blanco, C., Borgwardt, K., Schmid, K.J., Weigel, D. 2011. Whole-genome sequencing of multiple Arabidopsis thaliana populations. Nat Genet
Discussion Leader: John Stanton-Geddes

10/20/2011
Emasculation and pollination of barley
Discussion Leader: Kevin Smith

10/13/2011
McHale LK, Huan WJ, Xu WW, Bhaskar PB, Hyten DL et al. (in review) Structural variation hotspots in the soybean genome localize to clusters of biotic stress response genes. - see email for weblink
Discussion Leader: Tom Kono

10/06/2011
Kover PX, Valdar W, Trakalo J, Scarcelli N, Ehrenreich IM et al. (2009) A multiparent advanced generation inter-cross to fine-map quantitative traits in Arabidopsis thaliana. Plos Genet 5: ARTN e1000551.
Discussion Leader: Ana Gonzales

09/28/2011 (note date)
Joint Meeting with McCue, Moeller, & Tiffin Lab Groups
Vonholdt BM, Pollinger JP, Earl DA, Knowles JC, Boyko AR et al. (2011) A genome-wide perspective on the evolutionary history of enigmatic wolf-like canids. Genome Res 21: 1294-1305.
Discussion Leader: Tim Paape

09/22/2011
McHale LK, Huan WJ, Xu WW, Bhaskar PB, Hyten DL et al. (in review) Stuctural variation hotspots in the soybean genome localize to clusters of biotic stress response genes. - see email for weblink
Discussion Leader: Tom Kono

09/15/2011
Coop G, Pickrell JK, Novembre J, Kudaravalli S, Li J et al. (2009) The role of geography in human adaptation. PLoS Genet 5: e1000500.
Discussion Leader: Mikey Kantar

09/08/2011
Ossowski S, Schneeberger K, Lucas-Lledo JI, Warthmann N, Clark RM et al. (2010) The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana. Science 327: 92-94.
Discussion Leader: Emily Combs

09/01/2011
Microbial and Plant Genomics Institute
2nd Annual Fall Symposium

08/25/2011
Coop G, Witonsky D, Di Rienzo A, Pritchard JK (2010) Using environmental correlations to identify loci underlying local adaptation. Genetics 185: 1411-1423.
Discussion Leader: Hongyun Wang

08/18/2011
Sakai AK, Lane MJ (1996) National Science Foundation funding patterns of women and minorities in biology. BioScience 46: 621-625.
Discussion Leader: Kiran Seth

08/11/2011
Moyle LC, Nakazato T (2010) Hybrid incompatibility “snowballs” between Solanum species. Science 329: 1521-1523.
Discussion Leader: Ana Gonzales

08/04/2011
Rothberg JM, Hinz W, Rearick TM, Schultz J, Mileski W et al. (2011) An integrated semiconductor device enabling non-optical genome sequencing. Nature 475: 348-352.
Discussion Leader: Peter Morrell

07/28/2011
Altshuler DL, Durbin RM, Abecasis GR, Bentley DR, Chakravarti A et al. (2010) A map of human genome variation from population-scale sequencing. Nature 467: 1061-1073.
Discussion Leader: Ana Gonzales

07/21/2011
Li H, Ruan J, Durbin R (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 18: 1851-1858.
Discussion Leader: Robert Schaefer

07/14/2011
Haasl RJ, Payseur BA (2011) Multi-locus inference of population structure: a comparison between single nucleotide polymorphisms and microsatellites. Heredity 106: 158-171.
Discussion Leader: Zhou Fang

07/07/2011
Wade CM, Giulotto E, Sigurdsson S, Zoli M, Gnerre S et al. (2009) Genome sequence, comparative analysis, and population genetics of the domestic horse. Science 326: 865-867.
Discussion Leader: Ron Okagaki

06/30/2011
Yang Z, Rannala B (2010) Bayesian species delimitation using multilocus sequence data. Proc Natl Acad Sci U S A 107: 9264-9269.
Discussion Leader: Beau Miller

06/23/2011
Molina J, Sikora M, Garud N, Flowers JM, Rubinstein S et al. (2011) Molecular evidence for a single evolutionary origin of domesticated rice. Proc Natl Acad Sci U S A 108: 8351-8356.
Discussion Leader: Ana Gonzales

06/16/2011
Evolution Meeting 2011

06/09/2011
Mackay TF, Stone EA, Ayroles JF (2009) The genetics of quantitative traits: challenges and prospects. Nat Rev Genet 10: 565-577.
Discussion Leader: Kiran Seth

06/02/2011
Nielsen R, Paul JS, Albrechtsen A, Song YS (2011) Genotype and SNP calling from next-generation sequencing data. Nat Rev Genet 12: 443-451.
Discussion Leader: Jessica Petersen

05/26/2011
Morrell PL, Toleno DM, Lundy KE, Clegg MT (2006) Estimating the contribution of mutation, recombination and gene conversion in the generation of haplotypic diversity. Genetics 173: 1705-1723.
Discussion Leader: Peter Morrell

05/19/2011
Guo F, Dey DK, Holsinger KE (2009) A Bayesian hierarchical model for analysis of SNP diversity in multilocus, multipopulation samples. J Am Stat Assoc 104: 142-154.
Discussion Leader: Amber Eule-Nashoba

05/12/2011
Reading the Classics
Cavalli-Sforza LL (1966) Population structure and human evolution. Proc R Soc Lond B Biol Sci 164: 362-379.
Discussion Leader: Ron Okagaki

05/05/2011
Huynh LY, Maney DL, Thomas JW (2010) Chromosome-wide linkage disequilibrium caused by an inversion polymorphism in the white-throated sparrow (Zonotrichia albicollis). Heredity 106: 537-546.
Discussion Leader: Zhou Fang

04/28/2011
Macdonald SJ, Long AD (2007) Joint estimates of quantitative trait locus effect and frequency using synthetic recombinant populations of Drosophila melanogaster. Genetics 176: 1261-1281.
Discussion Leader: Nichol Schultz

04/21/2011
Ralph P, Coop G (2010) Parallel adaptation: one or many waves of advance of an advantageous allele? Genetics 186: 647-668.
Discussion Leader: Jessica Petersen

04/14/2011
Burke MK, Dunham JP, Shahrestani P, Thornton KR, Rose MR et al. (2010) Genome-wide analysis of a long-term evolution experiment with Drosophila. Nature 467: 587-590.
Discussion Leader: Margaret Taylor

04/07/2011
Joint Meeting with McCue, Moeller, & Tiffin Lab Groups
Tenaillon MI, Hufford MB, Gaut BS, Ross-Ibarra J (2011) Genome size and transposable element content as determined by high-throughput sequencing in maize and Zea luxurians. Genome Biol Evol
Discussion Leader: Ana Gonzales

03/31/2011
Cuesta-Marcos A, Szucs P, Close TJ, Filichkin T, Muehlbauer GJ, Smith KP, Hayes PM (2010) Genome-wide SNPs and re-sequencing of growth habit and inflorescence genes in barley: implications for association mapping in germplasm arrays varying in size and structure. BMC Genomics 11: ARTN 707
Discussion Leader: Emily Combs

03/24/2011
Barley diversity manuscript - see email for weblink
Discussion Leader: Ana Gonzales

03/17/2011
Spring Break

03/10/2011
Li Y, Vinckenbosch N, Tian G, Huerta-Sanchez E, Jiang T et al. (2010) Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants. Nat Genet 42: 969-972.
Discussion Leader: Krista Fritz

03/03/2011
Lohmueller KE, Indap AR, Schmidt S, Boyko AR, Hernandez RD et al. (2008) Proportionally more deleterious genetic variation in European than in African populations. Nature 451: 994-997.
Discussion Leader: Peter Morrell

02/24/2011
Chun S, Fay JC (2009) Identification of deleterious mutations within three human genomes. Genome Res 19: 1553-1561.
Discussion Leader: Beau Miller

02/17/2011
Joint Meeting with McCue, Moeller, & Tiffin Lab Groups
Casto AM, Feldman MW__ (2011) Genome-wide association study SNPs in the Human Genome Diversity Project populations: does selection affect unlinked SNPs with shared trait associations? PLoS Genet 7:__ e1001266
Discussion Leader: Tim Paape

02/10/2011
Sabeti PC, Walsh E, Schaffner SF, Varilly P, Fry B et al. (2005) The case for selection at CCR5-Delta 32. Plos Biol 3: 1963-1969-ARTN e378.
Discussion Leader: Annette McCoy

02/03/2011
To Be Determined (Maize LD manuscript)
Discussion Leader: Zhou Fang

01/27/2011
Joint Meeting with McCue, Moeller, & Tiffin Lab Groups
Lam HM, Xu X, Liu X, Chen W, Yang G et al. (2010) Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nat Genet 42: 1053-1059.
Discussion Leader: Emily Combs

01/20/2011
Albrechtsen A, Moltke I, Nielsen R (2010) Natural selection and the distribution of identity-by-descent in the human genome. Genetics 186: 295-308.
Discussion Leader: Amber Eule-Nashoba/Ron Okagaki

01/13/2011
Kirkpatrick M, Barton N (2006) Chromosome inversions, local adaptation and speciation. Genetics 173: 419-434.
Discussion Leader: Zhou Fang

01/06/2011
Pluzhnikov A, Donnelly P (1996) Optimal sequencing strategies for surveying molecular genetic diversity. Genetics 144: 1247-1262.
Discussion Leader: Peter Morrell

12/30/2010
Christmas Holiday

12/23/2010
Christmas Holiday

12/16/2010
Coalescent Simulation
http://home.uchicago.edu/~rhudson1/source/mksamples.html
Discussion Leader: Ana Gonzales

12/09/2010
Padhukasahasram B, Marjoram P, Wall JD, Bustamante CD, Nordborg M (2008) Exploring population genetic models with recombination using efficient forward-time simulations. Genetics 178: 2417-2427.
Discussion Leader: Peter Morrell

12/02/2010
Joint Meeting with McCue, Moeller, & Tiffin Lab Groups
Dickson SP, Wang K, Krantz I, Hakonarson H, Goldstein DB (2010) Rare variants create synthetic genome-wide associations. PLoS Biol 8: e1000294.
Discussion Leader: Peter Tiffin

11/25/2010
Thanksgiving Holiday

11/18/2010
Komatsuda T, Pourkheirandish M, He C, Azhaguvel P, Kanamori H et al. (2007) Six-rowed barley originated from a mutation in a homeodomain-leucine zipper I-class homeobox gene. Proc Natl Acad Sci USA 104: 1424-1429.
Discussion Leader: Ron Okagaki

11/11/2010
Hancock AM, Witonsky DB, Gordon AS, Eshel G, Pritchard JK et al. (2008) Adaptations to climate in candidate genes for common metabolic disorders. Plos Genet 4: ARTN e32.
Discussion Leader: Jessica Petersen

11/04/2010
Li H, Homer N (2010) A survey of sequence alignment algorithms for next-generation sequencing. Brief Bioinform 11: 473-483.
Discussion Leader: Peter Morrell

10/29/2010
Clark RM, Linton E, Messing J, Doebley JF (2004) Pattern of diversity in the genomic region near the maize domestication gene tb1. Proc Natl Acad Sci U S A 101: 700-707.
Discussion Leader: Zhou Fang

10/21/2010
Joint Meeting with McCue, Moeller, & Tiffin Lab Groups Gossmann TI, Song BH, Windsor AJ, Mitchell-Olds T, Dixon CJ et al. (2010) Genome wide analyses reveal little evidence for adaptive evolution in many plant species. Mol Biol Evol 27: 1822-1832.
Discussion Leader: Tim Paape

10/14/2010
Haddrill PR, Thornton KR, Charlesworth B, Andolfatto P (2005) Multilocus patterns of nucleotide variability and the demographic and selection history of Drosophila melanogaster populations. Genome Res 15: 790-799.
Discussion Leader: Peter Morrell

10/07/2010
Hudson RR (1990) Gene genealogies and the coalescent process. Oxford Surveys in Evolutionary Biology 7: 1-42. Second half of the chapter.
Discussion Leader: Peter Morrell

09/30/2010
Durand E, Tenaillon MI, Ridel C, Coubriche D, Jamin P et al. (2010) Standing variation and new mutations both contribute to a fast response to selection for flowering time in maize inbreds. Bmc Evol Biol 10: ARTN 2.
Discussion Leader: Vikram Vikus

09/23/2010
Andolfatto P, Nordborg M (1998) The effect of gene conversion on intralocus associations. Genetics 148: 1397-1399.
Jeffreys AJ, May CA (2004) Intense and highly localized gene conversion activity in human meiotic crossover hot spots. Nat Genet 36: 151-156.
Discussion Leader: Peter Morrell

09/16/2010
Atwell S, Huang YS, Vilhjalmsson BJ, Willems G, Horton M et al. (2010) Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature 465: 627-631.
Discussion Leader: Nichol Schultz

09/09/2010
Zhai W, Nielsen R, Slatkin M (2009) An investigation of the statistical power of neutrality tests based on comparative and population genetic data. Mol Biol Evol 26: 273-283.
Discussion Leader: Ana Gonzales

09/03/2010
Lockton S, Ross-Ibarra J, Gaut BS (2008) Demography and weak selection drive patterns of transposable element diversity in natural populations of Arabidopsis lyrata. P Natl Acad Sci Usa 105: 13965–13970
Discussion Leader: Peter Morrell

08/27/2010
Albrechtsen A, Nielsen FC, Nielsen R (2010) Ascertainment biases in SNP chips affect measures of population divergence. Mol Biol Evol 27: 2534-2547.
Discussion Leaders: Zhou Fang

08/20/2010
Karasov T, Messer PW, Petrov DA (2010) Evidence that adaptation in Drosophila is not limited by mutation at single sites. Plos Genet 6: ARTN e1000924.
Discussion Leader: Krista Fritz

08/13/2010
Baudat F, Buard J, Grey C, Fledel-Alon A, Ober C et al. (2010) PRDM9 is a major determinant of meiotic recombination hotspots in humans and mice. Science 327: 836-840.
Discussion Leader: Peter Morrell

08/06/2010
No Meeting

07/30/2010
No Meeting

07/23/2010
Yang J, Benyamin B, McEvoy BP, Gordon S, Henders AK et al. (2010) Common SNPs explain a large proportion of the heritability for human height. Nat Genet 42: 565-569.
Discussion Leader: Molly McCue

07/16/2010
Hudson RR (1990) Gene genealogies and the coalescent process. Oxford Surveys in Evolutionary Biology 7: 1-42.
Discussion Leader: Diego Coelho

07/09/2010
An introduction to libsequence & phred/phrap/consed/polyphred
Thornton K (2003) Libsequence: a C++ class library for evolutionary genetic analysis. Bioinformatics 19: 2325-2327.
Discussion Leaders: Ana Gonzales / Zhou Fang

07/02/2010
Fay JC, Wu CI (2000) Hitchhiking under positive Darwinian selection. Genetics 155: 1405-1413.
Discussion Leader: Jessica Petersen

06/25/2010
Morrell PL, Clegg MT (2007) Genetic evidence for a second domestication of barley (Hordeum vulgare) east of the Fertile Crescent. Proc Natl Acad Sci USA 104: 3289-3294.
Discussion Leader: Godwin Macharia

06/18/2010
Eckert AJ, van Heerwaarden J, Wegrzyn JL, Nelson CD, Ross-Ibarra J et al. (2010) Patterns of population structure and environmental associations to aridity across the range of loblolly pine (Pinus taeda L., Pinaceae). Genetics 185: 969-982.
Discussion Leaders: Diego Coelho / Kevin Volz

06/11/2010
Ross-Ibarra J, Tenaillon M, Gaut BS (2009) Historical divergence and gene flow in the genus Zea. Genetics 181: 1399-1413.
Discussion Leader: Zhou Fang

06/04/2010
Plagnol V, Padhukasahasram B, Wall JD, Marjoram P, Nordborg M (2006) Relative influences of crossing over and gene conversion on the pattern of linkage disequilibrium in Arabidopsis thaliana. Genetics 172: 2441-2448.
Discussion Leader: Ana Gonzales

05/28/2010
Price AL, Tandon A, Patterson N, Barnes KC, Rafaels N et al. (2009) Sensitive detection of chromosomal segments of distinct ancestry in admixed populations. PLoS Genet 5: e1000519.
Discussion Leader: Zhou Fang

05/21/2010
Gaut BS, Long AD (2003) The lowdown on linkage disequilibrium. Plant Cell 15: 1502-1506.
Discussion Leaders: Peter Morrell

05/14/2010
Green RE, Krause J, Briggs AW, Maricic T, Stenzel U et al. (2010) A draft sequence of the Neandertal genome. Science 328: 710-722.
Discussion Leaders: Ana Gonzales / Diego Coelho

05/07/2010
Linux Basics
http://manuals.bioinformatics.ucr.edu/home/linux-basics
Discussion Leaders: Ana Gonzales / Zhou Fang

04/30/2010
Feng L, Sebastian S, Smith S, Cooper M (2006) Temporal trends in SSR allele frequencies associated with long-term selection for yield of maize. Maydica 51: 293-300.
Discussion Leader: Godwin Macharia

04/23/2010
Charlesworth D, Willis JH (2009) FUNDAMENTAL CONCEPTS IN GENETICS The genetics of inbreeding depression. Nat Rev Genet 10: 783-796.
Discussion Leader: Hao Zhou

04/16/2010
Pickrell JK, Coop G, Novembre J, Kudaravalli S, Li JZ et al. (2009) Signals of recent positive selection in a worldwide sample of human populations. Genome Res 19: 826-837.
Discussion Leader: Zhou Fang

04/09/2010
Metzker ML (2010) APPLICATIONS OF NEXT-GENERATION SEQUENCING Sequencing technologies - the next generation. Nat Rev Genet 11: 31-46.
Discussion Leader: Vikram Vikus

04/02/2010
Vonholdt BM, Pollinger JP, Lohmueller KE, Han E, Parker HG et al. (2010) Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication. Nature 464: 898-902. - Supplemental Information & analytical methods
Discussion Leader: Peter Morrell

03/26/2010
Vonholdt BM, Pollinger JP, Lohmueller KE, Han E, Parker HG et al. (2010) Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication. Nature 464: 898-902.
Discussion Leader: Peter Morrell

03/19/2010
Spring Break

03/12/2010
Chen H, Morrell PL, Ashworth VE, de la Cruz M, Clegg MT (2009) Tracing the geographic origins of major avocado cultivars. J Hered 100: 56-65.
Discussion Leader: Ana Gonzales

03/05/2010
Chen H, Morrell PL, de la Cruz M, Clegg MT (2008) Nucleotide diversity and linkage disequilibrium in wild avocado (Persea americana Mill.). J Hered 99: 382-389.
Discussion Leader: Ana Gonzales

02/26/2010
Long AD, Langley CH (1999) The power of association studies to detect the contribution of candidate genetic loci to variation in complex traits. Genome Res 9: 720-731.
Discussion Leader: Liana Nice

02/19/2010
Rockman MV, Kruglyak L (2008) Breeding designs for recombinant inbred advanced intercross lines. Genetics 179: 1069-1078.
Discussion Leader: Peter Morrell

02/12/2010
Buckler ES, Holland JB, Bradbury PJ, Acharya CB, Brown PJ et al. (2009) The genetic architecture of maize flowering time. Science 325: 714-718.
Discussion Leader: Peter Morrell

02/05/2010
Zhao KY, Aranzana MJ, Kim S, Lister C, Shindo C et al. (2007) An Arabidopsis example of association mapping in structured samples. Plos Genet 3: ARTN e4.
Discussion Leaders: Vikram Vikus / Stephanie Nevara

01/29/2010
Nordborg M, Hu TT, Ishino Y, Jhaveri J, Toomajian C et al. (2005) The pattern of polymorphism in Arabidopsis thaliana. PLos Biol 3: e196.
Discussion Leader: Zhou Fang

01/22/2010
Wright SI, Bi IV, Schroeder SG, Yamasaki M, Doebley JF et al. (2005) The effects of artificial selection on the maize genome. Science 308: 1310-1314.
Discussion Leader: Chris Taylor

01/12/2010
Plant & Animal Genome Meeting

01/05/2010
Rosenberg NA, Pritchard JK, Weber JL, Cann HM, Kidd KK et al. (2002) Genetic structure of human populations. Science 298: 2381-2385.
Discussion Leader: Peter Morrell

12/23/2009
Rosenberg NA, Nordborg M (2002) Genealogical trees, coalescent theory and the analysis of genetic polymorphisms. Nat Rev Genet 3: 380-390.
Discussion Leader: Peter Morrell

12/17/2009
Voelkerding KV, Dames SA, Durtschi JD (2009) Next-generation sequencing: from basic research to diagnostics. Clin Chem 55: 641-658.
Discussion Leader: Zhou Fang

12/10/2009
Gore MA, Chia JM, Elshire RJ, Sun Q, Ersoz ES et al. (2009) A first-generation haplotype map of maize. Science 326: 1115-1117.
Discussion Leader: Peter Morrell

12/03/2009
Wakeley J (2008) Coalescent Theory: An Introduction. Roberts & Company Publishers. Chapter 1 (continued).
Discussion Leader: Chris Taylor

11/26/2009
Thanksgiving Holiday

11/19/2009
Wakeley J (2008) Coalescent Theory: An Introduction. Roberts & Company Publishers. Chapter 1.
Discussion Leader: Ana Gonzales

11/12/2009
Tenaillon MI, Sawkins MC, Long AD, Gaut RL, Doebley JF et al. (2001) Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. mays L.). Proc Natl Acad Sci USA 98: 9161-9166.
Discussion Leader: Ana Gonzales

11/05/2009
Stumpf MP, McVean GA (2003) Estimating recombination rates from population-genetic data. Nat Rev Genet 4: 959-968.
Discussion Leader: Peter Morrell