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.
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
Plant Sciences
Sonal Gupta, Alex Harkess, Anah Soble, Megan Van Etten, James Leebens-Mack, Regina S. Baucom
Summary: The adaptation of weeds to herbicide is a significant problem in agriculture and a model of rapid adaptation. However, there are still gaps in our understanding of resistance controlled by multiple loci and the evolutionary factors that maintain resistance. Using herbicide-resistant populations of Ipomoea purpurea, this study identified loci involved in nontarget-site herbicide resistance (NTSR) and explored the evolutionary forces underlying the maintenance of resistance. The findings suggest that NTSR glyphosate resistance in I. purpurea is conferred by multiple genes potentially maintained through generations via interchromosomal linkage disequilibrium (ILD), and the fitness cost associated with resistance is likely a by-product of genetic hitchhiking.
Article
Cell Biology
Simona Secomandi, Guido R. Gallo, Marcella Sozzoni, Alessio Iannucci, Elena Galati, Linelle Abueg, Jennifer Balacco, Manuela Caprioli, William Chow, Claudio Ciofi, Joanna Collins, Olivier Fedrigo, Luca Ferretti, Arkarachai Fungtammasan, Bettina Haase, Kerstin Howe, Woori Kwak, Gianluca Lombardo, Patrick Masterson, Graziella Messina, Anders P. Moller, Jacquelyn Mountcastle, Timothy A. Mousseau, Joan Ferrer Obiol, Anna Olivieri, Arang Rhie, Diego Rubolini, Marielle Saclier, Roscoe Stanyon, David Stucki, Francoise Thibaud-Alquati, James Torrance, Antonio Torroni, Kristina Weber, Roberto Ambrosini, Andrea Bonisoli-Alquati, Erich D. Jarvis, Luca Gianfranceschi, Giulio Formenti
Summary: This study provides a chromosome-level reference genome and pangenome for the barn swallow, allowing for the identification of potentially conserved and accelerated genes and the inference of core and accessory genes. These resources will facilitate population genomics studies, aid in detecting candidate genes in comparative genomics studies, and reduce bias towards a single reference genome.
Article
Biochemistry & Molecular Biology
Parul Johri, Charles F. Aquadro, Mark Beaumont, Brian Charlesworth, Laurent Excoffier, Adam Eyre-Walker, Peter D. Keightley, Michael Lynch, Gil McVean, Bret A. Payseur, Susanne P. Pfeifer, Wolfgang Stephan, Jeffrey D. Jensen
Summary: The field of population genomics has grown rapidly, but there is a tendency to focus on specific models at the expense of exploring underlying evolutionary processes. We need to pay more attention to statistical inference and theory and establish relevant baseline models for each analysis.
Article
Biochemistry & Molecular Biology
Zachariah Gompert, Jeffrey L. Feder, Patrik Nosil
Summary: Understanding the impact of selection on the genome is crucial in biology. Indirect selection can affect functionally neutral genetic regions through statistical associations with genes under direct selection, leading to widespread genetic loci being impacted across the genome. This process, including unknown causal variants and genetic associations, makes aspects of evolution more predictable and has implications for evolutionary principles in both basic and applied science.
Article
Nutrition & Dietetics
Jiawen Xu, Shuai Li, Yi Zeng, Haibo Si, Yuangang Wu, Shaoyun Zhang, Bin Shen
Summary: Osteoporosis (OP) is the most common bone disease. This study explored the relationship between OP and dietary habits using a large-scale genome-wide association study (GWAS). The analysis identified seven candidate dietary habits that showed genetic associations with OP, and found a causal relationship between OP and certain dietary habits such as butter consumption, decaffeinated coffee consumption, overall processed meat intake, monthly alcohol consumption, and daily servings of raw vegetables.
Article
Biochemistry & Molecular Biology
Michael A. Hardigan, Anne Lorant, Dominique D. A. Pincot, Mitchell J. Feldmann, Randi A. Famula, Charlotte B. Acharya, Seonghee Lee, Sujeet Verma, Vance M. Whitaker, Nahla Bassil, Jason Zurn, Glenn S. Cole, Kevin Bird, Patrick P. Edger, Steven J. Knapp
Summary: The cultivated strawberry, originating from early 18th-century Europe, has undergone significant genomic changes over 300 years of breeding history, leading to global expansion in production. Research shows increased heterozygosity in interspecific hybrids, selective sweeps across the genome, and substantial allelic diversity in octoploid species. Despite genetic gains in modern cultivars, nucleotide diversity and heterozygosity are lower, suggesting potential trade-offs in agricultural selection.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Ecology
Zachary L. Nikolakis, Drew R. Schield, Aundrea K. Westfall, Blair W. Perry, Kathleen N. Ivey, Richard W. Orton, Nicole R. Hales, Richard H. Adams, Jesse M. Meik, Joshua M. Parker, Cara F. Smith, Zachariah Gompert, Stephen P. Mackessy, Todd A. Castoe
Summary: Hybrid zones provide valuable insights into the genetic mechanisms of speciation. This study investigates introgression in a hybrid zone of two rattlesnake species, finding a large number of excess ancestry loci associated with higher recombination rates. The study also identifies correlated allele frequencies across physically unlinked genomic regions in hybrids. These findings highlight the impact of multilocus evolutionary processes on hybrid fitness in this system.
Article
Plant Sciences
Catja Selga, Alexander Koc, Aakash Chawade, Rodomiro Ortiz
Summary: The study introduces a pipeline to reduce genotyping costs by decreasing the number of SNPs and individuals, as well as pruning for linkage disequilibrium. Both GWAS and GS analyses can be performed without loss of information, making them applicable to large potato breeding populations.
Article
Biochemistry & Molecular Biology
Suo Qiu, Lengxob Yong, Alastair Wilson, Darren P. Croft, Chay Graham, Deborah Charlesworth
Summary: Research found that the guppy Y chromosome occasionally recombines with the X chromosome and showed recent demographic changes. Sequence variants are associated with the sex-determining locus, but any completely sex-linked region may be very small.
Article
Biochemical Research Methods
Dat Thanh Nguyen, Quan Hoang Nguyen, Nguyen Thuy Duong, Nam S. Vo
Summary: Despite the advancement of sequencing technology, SNP arrays remain the most cost-effective genotyping solution for large-scale genomic research. This study introduces a novel method called LmTag for tag SNP selection, which improves imputation performance and prioritizes highly functional SNP markers. It is particularly suitable for under-represented populations and non-model species in developing countries.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Fisheries
Afees Abiola Ajasa, Solomon Antwi Boison, Hans Magnus Gjoen, Marie Lillehammer
Summary: The Atlantic salmon industry in northern Europe is facing increasing losses due to amoebic gill disease (AGD). Genomic selection (GS) can potentially help reduce outbreaks and improve resistance to AGD. Linkage disequilibrium (LD) was evaluated in six Atlantic salmon breeding populations, and the use of genomic information for selection was investigated. The study found that LD decreased with increased physical distance between markers, and long-range LD was observed across all chromosomes. GS models had better performance than the pedigree-based best linear unbiased prediction (PBLUP) model. The use of genomic best linear unbiased prediction (GBLUP) model was recommended for the genetic evaluation of AGD resistance.
Article
Fisheries
Antoine Jourdan, Romain Morvezen, Florian Enez, Pierrick Haffray, Adeline Lange, Emilie Vetois, Francois Allal, Florence Phocas, Jerome Bugeon, Lionel Degremont, Pierre Boudry
Summary: Selective breeding programs have been initiated for the Pacific oyster Crassostrea gigas, using genomic tools to improve growth and disease resistance. The study evaluated the potential of genomic selection (GS) for growth-related and shell color traits in commercially selected populations. The results showed a high correlation between growth-related traits and low correlation with color traits. The accuracy of prediction was higher with the genomic model compared to the classical model, indicating the potential of GS in mixed-family breeding programs for C. gigas.
Article
Multidisciplinary Sciences
Philomin Juliana, Ravi Prakash Singh, Jesse Poland, Sandesh Shrestha, Julio Huerta-Espino, Velu Govindan, Suchismita Mondal, Leonardo Abdiel Crespo-Herrera, Uttam Kumar, Arun Kumar Joshi, Thomas Payne, Pradeep Kumar Bhati, Vipin Tomar, Franjel Consolacion, Jaime Amador Campos Serna
Summary: This study focused on improving wheat grain yield using genomic tools and identified GY-associated markers and LD-blocks, validating the feasibility of simultaneously improving yield potential and stress-resilience. The extensive resources presented in this study offer great opportunities to accelerate breeding for high-yielding and stress-resilient wheat varieties.
SCIENTIFIC REPORTS
(2021)
Article
Plant Sciences
Thibault Leroy, Quentin Rougemont, Jean-Luc Dupouey, Catherine Bodenes, Celine Lalanne, Caroline Belser, Karine Labadie, Gregoire Le Provost, Jean-Marc Aury, Antoine Kremer, Christophe Plomion
Article
Plant Sciences
Thibault Leroy, Jean-Marc Louvet, Celine Lalanne, Gregoire Le Provost, Karine Labadie, Jean-Marc Aury, Sylvain Delzon, Christophe Plomion, Antoine Kremer
Article
Biodiversity Conservation
Thibaut Frejaville, Natalia Vizcaino-Palomar, Bruno Fady, Antoine Kremer, Marta Benito Garzon
GLOBAL CHANGE BIOLOGY
(2020)
Article
Plant Sciences
Andrew L. Hipp, Paul S. Manos, Marlene Hahn, Michael Avishai, Catherine Bodenes, Jeannine Cavender-Bares, Andrew A. Crowl, Min Deng, Thomas Denk, Sorel Fitz-Gibbon, Oliver Gailing, M. Socorro Gonzalez-Elizondo, Antonio Gonzalez-Rodriguez, Guido W. Grimm, Xiao-Long Jiang, Antoine Kremer, Isabelle Lesur, John D. McVay, Christophe Plomion, Hernando Rodriguez-Correa, Ernst-Detlef Schulze, Marco C. Simeone, Victoria L. Sork, Susana Valencia-Avalos
Review
Plant Sciences
Antoine Kremer, Andrew L. Hipp
Article
Evolutionary Biology
Hermine Alexandre, Laura Truffaut, Etienne Klein, Alexis Ducousso, Emilie Chancerel, Isabelle Lesur, Benjamin Dencausse, Jean-Marc Louvet, Gerard Nepveu, Jose M. Torres-Ruiz, Frederic Lagane, Brigitte Musch, Sylvain Delzon, Antoine Kremer
EVOLUTIONARY APPLICATIONS
(2020)
Article
Plant Sciences
Unai Lopez de Heredia, Fernando Mora-Marquez, Pablo G. Goicoechea, Laura Guillardin-Calvo, Marco C. Simeone, Alvaro Soto
FRONTIERS IN PLANT SCIENCE
(2020)
Article
Plant Sciences
Clement Larue, Eva Austruy, Gaelle Basset, Remy J. Petit
Summary: The study found that chestnut trees primarily rely on insect pollination, specifically attracting a large number of beetles, bees, and flies. The characteristics of chestnut female flowers align with a beetle-pollination syndrome, and the uncertainty surrounding the pollination mode of chestnuts stems from the convergence with wind pollination.
Article
Ecology
Thomas Caignard, Antoine Kremer, Xavier P. Bouteiller, Julien Parmentier, Jean-Marc Louvet, Samuel Venner, Sylvain Delzon
Summary: The study found that reproductive effort decreases with increasing elevation and decreasing temperature. Significant genetic differentiation was observed between provenances, with trees from cold environments growing more slowly but producing larger acorns. Genetic and phenotypic variation for reproductive traits have opposite signs along the environmental gradient, unlike growth traits.
FUNCTIONAL ECOLOGY
(2021)
Article
Horticulture
Clement Larue, Teresa Barreneche, Remy J. Petit
Summary: This study adapted the international BBCH system to chestnuts and tested its suitability for high-throughput phenotyping studies, showing that the approach used can provide a particularly precise description of the complex flowering phenology of chestnut trees.
SCIENTIA HORTICULTURAE
(2021)
Article
Biodiversity Conservation
Clement Larue, Erwan Guichoux, Benoit Laurent, Teresa Barreneche, Cecile Robin, Marie Massot, Adline Delcamp, Remy J. Petit
Summary: Using restriction-associated DNA sequencing, we identified 68 SNP markers that meet stringent quality criteria for studying and managing chestnut trees and species, providing sufficient power for species, hybrids, and backcrosses. These markers can also be used for clonal identification and were compared with single sequenced repeat (SSR) loci to demonstrate their effectiveness.
CONSERVATION GENETICS RESOURCES
(2021)
Article
Plant Sciences
Fang K. Du, Min Qi, Yuan-Ye Zhang, Remy J. Petit
Summary: The study compared leaf traits in allopatric and sympatric populations of two East Asian deciduous oaks and found greater genetic divergence and resource-conservative traits in the later colonizing species growing in mixed stands. These results suggest that asymmetric trait divergence can occur where species coexist.
Article
Plant Sciences
Remy J. Petit, Clement Larue
Summary: New insect-exclusion experiments confirmed that chestnuts are mainly insect-pollinated, and they should be considered as one of the most important entomophilous tree genus in the northern temperate and subtropical regions.
Article
Biochemistry & Molecular Biology
Clement Larue, Etienne K. Klein, Remy J. Petit
Summary: Most seed plants face interferences between pollen export and import through self-pollination, leading to reduced fruit set. This study examined sexual interference in chestnut trees by analyzing mating system and fruit set. The results showed that fruit set was significantly lower in male-fertile trees compared to male-sterile trees. The main cause of reduced reproductive potential in chestnut was found to be sexual interference by self-pollen.
Article
Ecology
Jaroslav Klapste, Antoine Kremer, Kornel Burg, Pauline Garnier-Gere, Omnia Gamal El-Dien, Blaise Ratcliffe, Yousry A. El-Kassaby, Ilga Porth
Summary: Functional traits play a crucial role in organism adaptation and evolution. Leaf morphology in two European white oaks highlights modular features, with certain traits showing potential differences in evolutionary responses.