Editorial Material
Biochemistry & Molecular Biology
Brian Charlesworth, Jeffrey D. Jensen
Summary: This article addresses recent claims regarding the importance of indirect selection, arguing that it is not a new or poorly studied phenomenon and that alternative explanations exist for the patterns described by the authors.
Article
Agriculture, Dairy & Animal Science
Abbas Hajihosseinlo, Ardeshir Nejati-Javaremi, Seyed Reza Miraei-Ashtiani
Summary: This research measured the extent of linkage disequilibrium, effective population size, haplotype block structure, and runs of homozygosity in several cattle populations using SNP genotypes. The results showed a decrease in genetic diversity with increasing distance between SNP pairs. The Iranian Holstein population had the lowest level of genomic inbreeding, while the French Holstein population had the highest. The number of runs of homozygosity decreased with increasing distance due to the increased recombination rate. This is concerning as it leads to a reduction in the effective population size.
ANIMAL BIOTECHNOLOGY
(2023)
Article
Biochemical Research Methods
Shan-Shan Dong, Wei-Ming He, Jing-Jing Ji, Chi Zhang, Yan Guo, Tie-Lin Yang
Summary: LDBlockShow is an open source software that visualizes LD and haplotype blocks, providing faster speed and lower memory consumption compared to other tools.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Agriculture, Dairy & Animal Science
Njabulo M. Dlamini, Edgar F. Dzomba, Mpumelelo Magawana, Sphamandla Ngcamu, Farai C. Muchadeyi
Summary: This study investigated the genetic diversity and similarities and differences within and between two conservation herds of the South African Nguni Cattle. The results showed reduced genetic diversity in the two herds, calling for measures to protect the diversity of the South African Nguni cattle.
Review
Genetics & Heredity
Paolo Abondio, Elisabetta Cilli, Donata Luiselli
Summary: Signatures of positive selection in the genome can reveal how populations adapt to environmental changes. Statistical methods can help detect these selection marks and identify genetic variants that affect gene regulation, expression, and protein function.
Article
Biochemistry & Molecular Biology
Chen Cao, Jingni He, Lauren Mak, Deshan Perera, Devin Kwok, Jia Wang, Minghao Li, Tobias Mourier, Stefan Gavriliuc, Matthew Greenberg, A. Sorana Morrissy, Laura K. Sycuro, Guang Yang, Daniel C. Jeffares, Quan Long
Summary: DNA sequencing technologies offer unprecedented opportunities to study within-host evolution of microorganism populations, but current instruments struggle to directly distinguish long haplotypes. PoolHapX is a computational approach that integrates information from genetic sharing and genomic sequencing, outperforming other tools and capable of inferring whole-chromosome-scale haplotypes.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Martin Kapun, Joaquin C. B. Nunez, Maria Bogaerts-Marquez, Jesus Murga-Moreno, Margot Paris, Joseph Outten, Marta Coronado-Zamora, Courtney Tern, Omar Rota-Stabelli, Maria P. Garcia Guerreiro, Sonia Casillas, Dorcas J. Orengo, Eva Puerma, Maaria Kankare, Lino Ometto, Volker Loeschcke, Banu S. Onder, Jessica K. Abbott, Stephen W. Schaeffer, Subhash Rajpurohit, Emily L. Behrman, Mads F. Schou, Thomas J. S. Merritt, Brian P. Lazzaro, Amanda Glaser-Schmitt, Eliza Argyridou, Fabian Staubach, Yun Wang, Eran Tauber, Svitlana Serga, Daniel K. Fabian, Kelly A. Dyer, Christopher W. Wheat, John Parsch, Sonja Grath, Marija Savic Veselinovic, Marina Stamenkovic-Radak, Mihailo Jelic, Antonio J. Buendia-Ruiz, Maria Josefa Gomez-Julian, Maria Luisa Espinosa-Jimenez, Francisco D. Gallardo-Jimenez, Aleksandra Patenkovic, Katarina Eric, Marija Tanaskovic, Anna Ullastres, Lain Guio, Miriam Merenciano, Sara Guirao-Rico, Vivien Horvath, Darren J. Obbard, Elena Pasyukova, Vladimir E. Alatortsev, Cristina P. Vieira, Jorge Vieira, Jorge Roberto Torres, Iryna Kozeretska, Oleksandr M. Maistrenko, Catherine Montchamp-Moreau, Dmitry Mukha, Heather E. Machado, Keric Lamb, Tania Paulo, Leeban Yusuf, Antonio Barbadilla, Dmitri Petrov, Paul Schmidt, Josefa Gonzalez, Thomas Flatt, Alan O. Bergland
Summary: Utilizing a newly developed bioinformatics pipeline, Drosophila melanogaster's Pool-Seq data is mapped to a hologenome to create the largest genomic data repository to date, called DEST, including 271 population samples from over 100 locations worldwide. This dataset can be used to study spatiotemporal genetic patterns and evolutionary dynamics of D. melanogaster populations.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biology
Anusha Amanullah, Shabana Arzoo, Ayesha Aslam, Iffat Waqar Qureshi, Mushtaq Hussain
Summary: Inbreeding, the mating between closely related individuals, has been shown to negatively impact the biological fitness of plants, animals, and humans. While the effects of inbreeding on reproductive fitness and stress tolerance in D. melanogaster have been extensively studied, its influence on innate behavior has received less attention. This study found that inbreeding in D. melanogaster resulted in abnormalities in locomotor and phototactic behaviors, as well as changes in aggression and courtship behavior. Interestingly, inbred flies demonstrated improved learning ability in positive phototactic behavior compared to outbred flies. These findings highlight the influence of inbreeding on innate behavior and its potential implications in various fields.
Article
Genetics & Heredity
Zhong Xu, Shuqi Mei, Jiawei Zhou, Yu Zhang, Mu Qiao, Hua Sun, Zipeng Li, Lianghua Li, Binke Dong, Favour Oluwapelumi Oyelami, Junjing Wu, Xianwen Peng
Summary: The study assessed genetic diversity, runs of homozygosity (ROH) and ROH islands in a Chinese composite pig, identifying genes associated with fat deposition and muscular development in ROH islands. The findings shed light on the effects of environmental and artificial selection on genome structure of composite pigs, providing a basis for genomic selection (GS) and hybrid utilization of other pig breeds.
FRONTIERS IN GENETICS
(2021)
Article
Multidisciplinary Sciences
Jie Zheng, Yuan-yuan Wu, Wen-liang Fang, Xin-ying Cai, Zeng-yun-ou Zhang, Chong-xian Yu, Xiao-dong Zheng, Feng-li Xiao
Summary: This study confirmed the association between the TMEM232 gene and AD through haplotype analysis and targeted capture sequencing. The most strongly associated haplotype with AD was H15.
SCIENTIFIC REPORTS
(2021)
Article
Agriculture, Dairy & Animal Science
Haoqiang Ye, Zhenqiang Xu, Semiu Folaniyi Bello, Qianghui Zhu, Shaofen Kong, Ming Zheng, Xiang Fang, Xinzheng Jia, Haiping Xu, Xiquan Zhang, Qinghua Nie
Summary: In this study, the performance of haplotype models for genomic prediction in a Chinese yellow-feathered chicken population was comprehensively evaluated. It was found that haplotype methods were beneficial for genomic prediction, and the accuracy could be further increased by incorporating genomic annotation information. Moreover, using LD information would potentially improve the performance of genomic prediction.
Article
Evolutionary Biology
Hongwei Li, Zezhao Wang, Lei Xu, Qian Li, Han Gao, Haoran Ma, Wentao Cai, Yan Chen, Xue Gao, Lupei Zhang, Huijiang Gao, Bo Zhu, Lingyang Xu, Junya Li
Summary: In this study, haplotype blocks were constructed using LD-based and fixed-SNP methods in beef cattle. The predictive performance of different haplotype block partitioning methods was evaluated, and it was found that LD-based and fixed-SNP haplotype Bayesian methods outperform the Bayesian models. Filtering minor haplotype allele frequency can also improve the performance of genomic prediction.
EVOLUTIONARY APPLICATIONS
(2022)
Article
Genetics & Heredity
Lucas Lima Verardo, Fabyano Fonseca e Silva, Marco Antonio Machado, Joao Claudio do Carmo Panetto, Daniele Ribeiro de Lima Reis Faza, Pamela Itajara Otto, Luciana Correia de Almeida Regitano, Luiz Otavio Campos da Silva, Andrea Alves do Egito, Maria do Socorro Maues Albuquerque, Ricardo Zanella, Marcos Vinicius Gualberto Barbosa da Silva
Summary: The study evaluated the genotype of 19 cattle breeds raised in Brazil and provided an overview of the genomic architecture of cattle breeds currently raised in Brazil and other tropical countries. Different marker densities should be used among evaluated breeds to improve genomic prediction accuracy and power of genome-wide association studies. Breeds showing low Ne values indicate recent inbreeding, which require special attention in mating schemes to avoid extensive inbreeding.
FRONTIERS IN GENETICS
(2021)
Editorial Material
Biochemistry & Molecular Biology
Zachariah Gompert, Jeffrey L. Feder, Patrik Nosil
Summary: This paper quantifies the genome-wide consequences of natural selection and addresses the effects of indirect selection due to the correlation of genetic regions. The critiques on the paper do not substantially affect the findings of the study.
Article
Ecology
Shawna J. Zimmerman, Cameron L. Aldridge, Kathryn M. Langin, Gregory T. Wann, R. Scott Cornman, Sara J. Oyler-McCance
Summary: The warming climate may expose alpine species to novel environmental conditions, potentially challenging their adaptation. Using genomic approaches to study adaptive divergence in the white-tailed ptarmigan may provide insights into how species adapt to harsh environments.
Article
Biology
Grant Kinsler, Kerry Geiler-Samerotte, Dmitri Petrov
Article
Genetics & Heredity
Nandita R. Garud, Philipp W. Messer, Dmitri A. Petrov
Summary: The debate over whether hard sweeps or soft sweeps dominate adaptation has continued, with the authors proposing that soft sweeps are prevalent in North American Drosophila melanogaster. Another study by Harris et al. has raised doubts about the reliability of soft sweeps detected, instead suggesting that hard sweeps may be more likely. However, upon reanalysis, the authors confirm that soft sweeps are the dominant mode of adaptation in North American Drosophila melanogaster.
Article
Infectious Diseases
Emily R. Ebel, Fatima Reis, Dmitri A. Petrov, Sandra Beleza
Summary: Based on a study of antimalarial drug resistance in Angola, genetic markers of resistance to chloroquine are likely declining while markers of sulfadoxine-pyrimethamine (SP) resistance remain high, suggesting continued use of SP. Monitoring of multiple genetic markers will be important for understanding changing drug efficacy and supporting effective drug policy decisions in Angola.
Article
Biology
Carly Weiss, Lana Harshman, Fumitaka Inoue, Hunter B. Fraser, Dmitri A. Petrov, Nadav Ahituv, David Gokhman
Summary: The study utilized massively parallel reporter assays to investigate the regulatory effects of modern human-specific variants, revealing that a portion of these variants drove differential gene expression between human populations, particularly in genes related to vocal tract and brain anatomy and function.
Review
Biology
Joy Bergelson, Martin Kreitman, Dmitri A. Petrov, Alvaro Sanchez, Mikhail Tikhonov
Summary: The complexity present at every level of biological organization poses a challenge for understanding biological function. It is important to consider the risks of simplifying this complexity and pursue a path towards achieving emergent simplicity of understanding, while still embracing the ever-changing complexity of biotic interactions in nature.
Article
Biology
Emily R. Ebel, Frans A. Kuypers, Carrie Lin, Dmitri A. Petrov, Elizabeth S. Egan
Summary: The study on 121 healthy donors of African ancestry found that various genes and phenotypes related to red blood cell variation were closely associated with the adaptability of Plasmodium falciparum within red blood cells, indicating globally widespread variations play a role in modulating parasite fitness.
Editorial Material
Microbiology
Nandita Garud
Summary: Microbes can evolve rapidly to adapt to selection pressures, but our understanding of the adaptation in microbiomes is still incomplete. Advances in modeling complex populations and scenarios will help us better understand adaptation in microbiomes and other natural populations experiencing similar complexities.
Review
Parasitology
Emily R. Ebel, Lawrence H. Uricchio, Dmitri A. Petrov, Elizabeth S. Egan
Summary: The malaria hypothesis suggests local, balancing selection of deleterious alleles. Though protective variants are more common in African populations, the heritability of severe malaria is largely attributed to multiple genome-wide loci. Furthermore, most functional polygenic variation is pleiotropic for multiple traits, indicating that genetic variation impacting malaria risk does not show specific enrichment in African populations.
TRENDS IN PARASITOLOGY
(2022)
Article
Biochemical Research Methods
Leah Briscoe, Brunilda Balliu, Sriram Sankararaman, Eran Halperin, Nandita R. Garud
Summary: The ability to predict human phenotypes and identify disease biomarkers from metagenomic data is important for microbiome-associated disease therapeutics. However, technical variables unrelated to the phenotype can complicate prediction and biomarker discovery. Supervised methods may be limited in correcting for unmeasured variation, while unsupervised approaches can struggle with the unique characteristics of microbiome data. A comparative analysis of denoising transformations and correction methods reveals that unsupervised principal component correction has comparable effectiveness in reducing false discovery as supervised approaches, without requiring knowledge of the sources of variation. However, the unsupervised approach only improves prediction when technical variables contribute to the majority of data variance. Background noise correction will be crucial as more metagenomic datasets become available.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Daisy W. Chen, Nandita R. Garud
Summary: By analyzing longitudinal fecal metagenomic data from over 700 infants and their mothers, this study reveals distinct evolutionary dynamics in the infant gut microbiome compared to adults. The rate of evolution and strain turnover in the infant gut is significantly higher than in healthy adults, with gene loss dominating during the mother-infant transition at delivery. These dynamics stabilize within a few months after birth, with an increase in gene gains as the microbiome matures.
Article
Multidisciplinary Sciences
Seth M. Rudman, Sharon Greenblum, Subhash Rajpurohit, Nicolas J. Betancourt, Jinjoo Hanna, Susanne Tilk, Tuya Yokoyama, Dmitri A. Petrov, Paul Schmidt
Summary: Studying the evolution of fruit fly populations in response to natural environmental changes revealed rapid and dynamic adaptations over different generations, demonstrating the temporally dynamic nature of adaptation.
Article
Genetics & Heredity
Ellie E. Armstrong, Michael G. Campana, Katherine A. Solari, Simon R. Morgan, Oliver A. Ryder, Vincent N. Naude, Gustaf Samelius, Koustubh Sharma, Elizabeth A. Hadly, Dmitri A. Petrov
Summary: This study assembled the genomes of three species within the Panthera genus, providing important data for genomic research. This contributes to a better understanding and conservation of this iconic group of mammals.
G3-GENES GENOMES GENETICS
(2022)
Article
Biology
Susanne Tilk, Svyatoslav Tkachenko, Christina Curtis, Dmitri A. Petrov, Christopher D. McFarland
Summary: The lack of observed negative selection in most tumors is not due to relaxed selective pressures, but rather the inability of selection to remove deleterious mutations in the presence of genome-wide linkage.
Editorial Material
Genetics & Heredity
Nandita R. Garud
Summary: Nandita Garud discusses two influential papers by Hermisson and Pennings that offer a framework for determining whether adaptation should occur gradually or rapidly.
NATURE REVIEWS GENETICS
(2023)
Article
Microbiology
Richard Wolff, William Shoemaker, Nandita Garud
Summary: The human gut microbiome exhibits substantial ecological diversity at both the species and strain levels. The majority of species maintain stable genetic diversity over time, and strain abundances can be predicted by a stochastic logistic model, suggesting dynamic stability. Additionally, strain abundances follow macroecological laws known to hold at the species level. These findings highlight the importance of strains as an ecological unit in the human gut microbiome.
