Article
Biochemistry & Molecular Biology
Vikas Kumar, E. Andrew Bennett, Dongyue Zhao, Yun Liang, Yunpeng Tang, Meng Ren, Qinyan Dai, Xiaotian Feng, Peng Cao, Ruowei Yang, Feng Liu, Wanjing Ping, Ming Zhang, Manyu Ding, Melinda A. Yang, Berdimurodov Amridin, Hasanov Muttalib, Jianxin Wang, Qiaomei Fu
Summary: Despite the continuation of Bronze Age ancestry into the Iron Age in Uzbekistan, individuals from the Iron Age show diverse ancestries related to Iranian farmers, Anatolian farmers, and Steppe herders, along with a small amount of West European Hunter Gatherer, East Asian, and South Asian Hunter Gatherer ancestry. An increase in Anatolian farmer-like ancestry and a decrease in Iranian farmer-like ancestry were observed in Uzbekistan Iron Age individuals compared to BMAC populations from Uzbekistan, indicating increased admixture played a significant role in the transition from Bronze to Iron Age. This mixed ancestry is also observed in other parts of the Steppe and Central Asia, suggesting widespread admixture among local populations.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Editorial Material
Multidisciplinary Sciences
Charles N. Rotimi, Adebowale A. Adeyemo
Summary: Over the past 20 years, the increasing diversity in genomic sequencing has provided valuable insights into our evolutionary history and health status.
Article
Multidisciplinary Sciences
Monica H. Keith, Mark Flinn, Harly J. Durbin, Troy N. Rowan, Gregory E. Blomquist, Kristen H. Taylor, Jeremy F. Taylor, Jared E. Decker
Summary: The Caribbean region is genetically diverse, with Dominica showing unique patterns of migration, mixture, and isolation. African ancestry is the predominant component, followed by European and indigenous components. The genetic results support local narratives about the community's history and founding.
Article
Genetics & Heredity
Lucia Spangenberg, Maria Ines Fariello, Dario Arce, Gabriel Illanes, Gonzalo Greif, Jong-Yeon Shin, Seong-Keun Yoo, Jeong-Sun Seo, Carlos Robello, Changhoon Kim, John Novembre, Monica Sans, Hugo Naya
Summary: The Charruas, an Amerindian group in Uruguay, were extinguished as an ethnic group due to genocide, but their heritage still plays a significant role in the identity of Uruguayans. Genetic studies of Uruguayan individuals with Charruan heritage show evidence of indigenous ancestry, with specific genetic markers indicating interactions with other Amerindian groups. The genomic similarity between Charruas and other Amerindians, as well as their European admixture history, reveal a complex genetic and historical background of Uruguay.
FRONTIERS IN GENETICS
(2021)
Article
Pharmacology & Pharmacy
Heidi E. Steiner, Kelvin Carrasquillo Carrion, Jason B. Giles, Abiel Roche Lima, Kevin Yee, Xiaoxiao Sun, Larisa H. Cavallari, Minoli A. Perera, Jorge Duconge, Jason H. Karnes
Summary: The accuracy of warfarin dose prediction algorithms can be improved by including data from diverse populations in genetic studies, as demonstrated by this study. It also highlights the technical challenges of including diverse, especially admixed populations in pharmacogenomic research.
CLINICAL PHARMACOLOGY & THERAPEUTICS
(2023)
Article
Multidisciplinary Sciences
D. Truelsen, T. Tvedebrink, H. S. Mogensen, M. S. Farzad, M. A. Shan, N. Morling, V Pereira, C. Borsting
Summary: This study used a custom EUROFORGEN NAME panel and Precision ID Ancestry panel to sequence 1098 individuals from 14 populations. The results showed that the two panels could accurately differentiate individuals from Europe and the Middle East, while the Precision ID Ancestry panel could separate North African individuals from European and Middle Eastern individuals, with added improvement from the EUROFORGEN NAME panel. However, the separation of Middle Eastern populations from European and South-Central Asian populations remains challenging even with the use of both panels.
SCIENTIFIC REPORTS
(2021)
Article
Cell Biology
William E. E. Gundling Jr, Sasha Post, Nicholas P. Illsley, Lourdes Echalar, Stacy Zamudio, Derek E. Wildman
Summary: The placenta mediates fetal growth and the cell type involved in nutrient exchange is called syncytiotrophoblast. Residence at high-altitude is associated with reduced fetal growth and complications. Altitude-related differences in placental gene expression can be attributed to DNA methylation, and a gene called DYSF shows higher expression in high-altitude placentas. A single nucleotide variant of DYSF can influence DNA methylation and this gene is under balancing selection in Andeans and Europeans living at high-altitude.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2023)
Article
Neurosciences
Rachel L. Kember, Alison K. Merikangas, Shefali S. Verma, Anurag Verma, Renae Judy, Scott M. Damrauer, Marylyn D. Ritchie, Daniel J. Rader, Maja Bucan
Summary: By studying over 10,000 individuals, it was found that PRSs for psychiatric disorders are moderately associated with their primary phenotypes, but lack clinical predictive value in naive patients. Cross-trait associations indicate a broader effect of genetic liability beyond traditional diagnostic boundaries.
BIOLOGICAL PSYCHIATRY
(2021)
Article
Medicine, General & Internal
Elizabeth Jordan, Daniel D. Kinnamon, Garrie J. Haas, Mark Hofmeyer, Evan Kransdorf, Gregory A. Ewald, Alanna A. Morris, Anjali Owens, Brian Lowes, Douglas Stoller, W. H. Wilson Tang, Sonia Garg, Barry H. Trachtenberg, Palak Shah, Salpy V. Pamboukian, Nancy K. Sweitzer, Matthew T. Wheeler, Jane E. Wilcox, Stuart Katz, Stephen Pan, Javier Jimenez, Daniel P. Fishbein, Frank Smart, Jessica Wang, Stephen S. Gottlieb, Daniel P. Judge, Charles K. Moore, Jonathan O. Mead, Natalie Hurst, Jinwen Cao, Gordon S. Huggins, Jason Cowan, Hanyu Ni, Heidi L. Rehm, Gail P. Jarvik, Matteo Vatta, Wylie Burke, Ray E. Hershberger
Summary: This study compares the rare variant genetic architecture of dilated cardiomyopathy (DCM) among patients with DCM who are of African ancestry compared with European ancestry. The study found that African patients with DCM were less likely to have clinically actionable variants in DCM genes than those of European ancestry due to differences in genetic architecture and a lack of representation of African ancestry in clinical data sets.
JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION
(2023)
Article
Genetics & Heredity
Paul S. Appelbaum, Wylie Burke, Erik Parens, David A. Zeevi, Laura Arbour, Nanibaa A. Garrison, Vence L. Bonham, Wendy K. Chung
Summary: The underrepresentation of non-European ancestry groups in genomic databases complicates the interpretation of their genetic test results. Efforts are being made to address this issue through broad-based recruitment, but some underrepresented groups may have concerns that hinder their participation. Two initiatives, targeting the Sephardi Jewish community in New York and the First Peoples of Canada, have been developed to meet the needs of underrepresented ancestry groups. These initiatives aim to address the specific concerns of each group and ensure the data are used primarily for clinical test analyses.
AMERICAN JOURNAL OF HUMAN GENETICS
(2022)
Article
Multidisciplinary Sciences
Brieuc Lehmann, Maxine Mackintosh, Gil McVean, Chris Holmes
Summary: Polygenic scores (PGSs) are individual-level measures that aggregate the genome-wide genetic predisposition to a given trait. Trait prediction using European ancestry-derived PGS is less accurate in non-European ancestry individuals. The effect of sample size and ancestry composition on PGS performance is investigated in this study.
NATURE COMMUNICATIONS
(2023)
Article
Ecology
Megan E. Frayer, Bret A. Payseur
Summary: Demographic factors such as migration rate and population size play a significant role in influencing speciation and hybrid zones. Through individual-based simulations, it was found that the number of ancestry junctions and heterogenicity are closely connected to demographic history in structured hybrid zones.
ECOLOGY AND EVOLUTION
(2021)
Article
Evolutionary Biology
Kelsey E. Witt, Alyssa Funk, Valeria Anorve-Garibay, Lesly Lopez Fang, Emilia Huerta-Sanchez
Summary: Admixture has frequently occurred in human history and shaped genetic ancestry in modern humans. This study analyzes admixed populations in the Americas and identifies a positive correlation between non-African ancestry and archaic alleles. The results also indicate a slight increase of Denisovan alleles in Indigenous American segments compared to European segments in admixed genomes.
GENOME BIOLOGY AND EVOLUTION
(2023)
Article
Genetics & Heredity
Anthony Caragiulo, Stephen J. Gaughran, Neil Duncan, Christopher Nagy, Mark Weckel, Bridgett M. VonHoldt
Summary: This study explored the genomic composition of coyotes in the New York metropolitan area and found a relatively small population of coyotes with moderate-to-high relatedness. Hybridization between coyotes and dogs was also detected, with one male coyote-dog hybrid and his offspring carrying significant dog ancestry. Genetic variations associated with human-directed hypersociability were found in these hybrid individuals and an unrelated coyote, suggesting that gene flow from domestic dogs could be an important factor in urban coyote populations.
Article
Oncology
Minoru Miyashita, Joshua S. K. Bell, Stephane Wenric, Ezgi Karaesmen, Brooke Rhead, Matthew Kase, Kristiyana Kaneva, Francisco M. M. de la Vega, Yonglan Zheng, Toshio F. F. Yoshimatsu, Galina Khramtsova, Fang Liu, Fangyuan Zhao, Frederick M. M. Howard, Rita Nanda, Nike Beaubier, Kevin P. P. White, Dezheng Huo, Olufunmilayo I. I. Olopade
Summary: This study compared the molecular features of HR+/HER2- breast cancer and TNBC subtypes between patients of African and European ancestries, and found significant differences in genetic mutations, gene expression, and transcriptional signatures. These findings contribute to promoting equity in personalized cancer treatment by providing more accurate treatment strategies for diverse populations.
BREAST CANCER RESEARCH
(2023)
Article
Plant Sciences
Zoe Migicovsky, Kyle M. Gardner, Christopher Richards, C. Thomas Chao, Heidi R. Schwaninger, Gennaro Fazio, Gan-Yuan Zhong, Sean Myles
Summary: The study reveals the close genetic relationship between modern apple cultivars and the primary progenitor species from Central Asia, as well as the European crabapple's influence on cider apples. The USDA apple collection forms a large complex pedigree with many interconnected relationships, including with top cultivars produced in the USA. Intense selection for traits like red skin and increased firmness has been observed, along with the potential benefits of exploiting the natural genetic diversity of apples for future improvements.
HORTICULTURE RESEARCH
(2021)
Article
Multidisciplinary Sciences
Karim Karimi, A. Hossain Farid, Sean Myles, Younes Miar
Summary: This study identified genomic regions in American mink that are under selection in response to infection with Aleutian mink disease virus (AMDV), revealing genes related to immune response, liver development, and reproduction. Two strongly selected regions containing candidate genes related to immune response, virus-host interaction, reproduction, and liver regeneration were supported by hapFLK test.
SCIENTIFIC REPORTS
(2021)
Article
Ecology
Kelly Swarts, Eva Bauer, Jeffrey C. Glaubitz, Tiffany Ho, Lynn Johnson, Yongxiang Li, Yu Li, Zachary Miller, Cinta Romay, Chris-Carolin Schon, Tianyu Wang, Zhiwu Zhang, Edward S. Buckler, Peter Bradbury
Summary: This study explores the biological basis of temperate adaptation in maize populations from different regions, revealing differences in predictive ability among populations. By analyzing the genetic characteristics of different maize populations in temperate and tropical regions, the study provides insights into adaptive differences in different geographical areas.
Article
Multidisciplinary Sciences
Baoxing Song, Santiago Marco-Sola, Miquel Moreto, Lynn Johnson, Edward S. Buckler, Michelle C. Stitzer
Summary: This study introduces a genome alignment method called AnchorWave, which shows significant improvement when applied to species with complex genomes. It can accurately identify multikilobase indels and improve the recall rate of transcription factor-binding sites.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Genetics & Heredity
Evan M. Long, Peter J. Bradbury, M. Cinta Romay, Edward S. Buckler, Kelly R. Robbins
Summary: Genomic applications such as genomic selection and genome-wide association have become more common since the advent of genome sequencing, but genotyping costs remain high. Genotype imputation allows for inferring whole-genome information from limited input data, making large-scale genomic applications more feasible. The practical haplotype graph (PHG) is a tool developed to accurately impute genotypes, showcasing high imputation accuracy especially in predicting rare alleles in highly heterozygous species like cassava.
G3-GENES GENOMES GENETICS
(2022)
Article
Multidisciplinary Sciences
Thomas Davies, Sophie Watts, Kendra McClure, Zoe Migicovsky, Sean Myles
Summary: This study investigated the relationship between cultivated apple (Malus domestica) and its wild progenitor species (M. sieversii), and found significant differences in phenotypic space. Cultivated apples had a shorter juvenile phase, flowered and produced ripe fruit later, were heavier, less acidic, and had lower phenolic content compared to wild apples. Historical records also showed that apple breeding over the past 200 years led to continued changes in apple phenotype.
Article
Multidisciplinary Sciences
Joseph L. Gage, Sujina Mali, Fionn McLoughlin, Merritt Khaipho-Burch, Brandon Monier, Julia Bailey-Serres, Richard D. Vierstra, Edward S. Buckler
Summary: The study found that rare variants in the 5' UTR can dysregulate maize protein abundance, and rare variants near the start codon of uORFs can repress or derepress mORF translation. Common variants that modify uORF start codons also disproportionately affect metabolic and whole-plant phenotypes.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Plant Sciences
Yaoyao Wu, Lynn Johnson, Baoxing Song, Cinta Romay, Michelle Stitzer, Adam Siepel, Edward Buckler, Armin Scheben
Summary: The study developed the msa_pipeline workflow for practical and sensitive multiple alignment of diverged plant genomes. Different masking approaches and parameters of the LAST aligner were explored, and parameter tuning was found to improve alignment rate and conservation scores.
Article
Biochemical Research Methods
Carolyn J. Lawrence-Dill, Robyn L. Allscheid, Albert Boaitey, Todd Bauman, Edward S. Buckler, Jennifer L. Clarke, Christopher Cullis, Jack Dekkers, Cassandra J. Dorius, Shawn F. Dorius, David Ertl, Matthew Homann, Guiping Hu, Mary Losch, Eric Lyons, Brenda Murdoch, Zahra-Katy Navabi, Somashekhar Punnuri, Fahad Rafiq, James M. Reecy, Patrick S. Schnable, Nicole M. Scott, Moira Sheehan, Xavier Sirault, Margaret Staton, Christopher K. Tuggle, Alison Van Eenennaam, Rachael Voas
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Plant Sciences
Travis Wrightsman, Alexandre P. Marand, Peter A. Crisp, Nathan M. Springer, Edward S. Buckler
Summary: Accessible chromatin regions are critical for gene regulation, and predicting them from sequence in plants has been challenging. By training a deep learning model, we successfully predicted chromatin accessibility and methylation levels across multiple angiosperm species, revealing the conservation of chromatin mechanisms. We also identified important transcription factor families.
Correction
Multidisciplinary Sciences
Xiaoyu Tu, Maria Katherine Mejia-Guerra, Jose A. Valdes Franco, David Tzeng, Po-Yu Chu, Wei Shen, Yingying Wei, Xiuru Dai, Pinghua Li, Edward S. Buckler, Silin Zhong
NATURE COMMUNICATIONS
(2023)
Article
Biodiversity Conservation
Tayab Soomro, Sophie Watts, Zoe Migicovsky, Sean Myles
Summary: This article examines the differences between dessert apples and cider apples, and finds that they are mostly indistinguishable across 10 traits.
PLANTS PEOPLE PLANET
(2022)
Article
Plant Sciences
Charles P. Pignon, Samuel B. Fernandes, Ravi Valluru, Nonoy Bandillo, Roberto Lozano, Edward Buckler, Michael A. Gore, Stephen P. Long, Patrick J. Brown, Andrew D. B. Leakey
Summary: This study used high-throughput thermal imaging to assess stomatal conductance traits in a diverse population of sorghum accessions, revealing significant correlations with photosynthetic gas exchange measurements. The study identified key candidate genes related to stomatal conductance traits that could help understand the genetic basis of water-use efficiency in C-4 grasses for bioenergy, food, and forage production.
Article
Plant Sciences
John N. Ferguson, Samuel B. Fernandes, Brandon Monier, Nathan D. Miller, Dylan Allen, Anna Dmitrieva, Peter Schmuker, Roberto Lozano, Ravi Valluru, Edward S. Buckler, Michael A. Gore, Patrick J. Brown, Edgar P. Spalding, Andrew D. B. Leakey
Summary: This study addressed the association between water use efficiency and biomass production in sorghum through advanced methods, revealing key genes related to these traits and their complex genetic relationships.
Article
Plant Sciences
Sophie Watts, Michel McElroy, Zoe Migicovsky, Hugo Maassen, Robin van Velzen, Sean Myles
Summary: The study found that Cannabis labelling is associated with genetic variations in terpene synthase genes.