Article
Agriculture, Dairy & Animal Science
Deyanira Figueroa, Flor-Anita Corredor, Ruben. H. H. Mamani-Cato, Roberto. F. F. Gallegos-Acero, Nicoll Condori-Rojas, Richard Estrada, Lizeth Heredia, Wilian Salazar, Carlos Quilcate, Carlos. I. I. Arbizu
Summary: This study aimed to estimate the genetic diversity and population structure of two Huacaya alpaca populations (Ajoyani and Quimsachata) in Southern Peru. DNA extraction and genotyping were conducted using fourteen and twelve microsatellite markers for each population, respectively. The results showed no structure in the population with K = 2. These findings provide useful indicators for the development of alpaca conservation programs.
Article
Biochemistry & Molecular Biology
William Hemstrom, Melissa Jones
Summary: Genomic data analysis can be intimidating, especially for researchers without programming experience. snpR is a user-friendly R package that automates data subsetting and analysis based on categorical metadata, integrating methods from multiple packages to streamline repeated analyses.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Multidisciplinary Sciences
Geofroy Kinhoegbe, Gustave Djedatin, Rachit Kumar Saxena, Anu Chitikineni, Prasad Bajaj, Johiruddin Molla, Clement Agbangla, Alexandre Dansi, Rajeev Kumar Varshney
Summary: The genetic diversity and population structure of pigeonpea in Benin were revealed using the GBS approach. This study found four clear subpopulations and a high gene exchange between them. The results suggest that the genetic diversity and population structure can be utilized for improving genetic gain in pigeonpea breeding programs in Benin through Genome Wide Association Studies and Marker-Assisted Selection.
Article
Plant Sciences
Daniel W. Heck, Frank Hay, Sarah J. Pethybridge
Summary: Stemphylium leaf blight (SLB) caused by Stemphylium vesicarium is a major foliar disease affecting onion production in New York. This study developed microsatellite markers to characterize the S. vesicarium populations, revealing high genotypic and allelic diversities within and between populations in different years. The lack of distinct clustering pattern and minor differences between populations suggest clonal populations. These markers will be valuable for further research on the population biology of S. vesicarium and disease management.
Editorial Material
Multidisciplinary Sciences
Luke M. M. Evans, Pamela N. Romero N. Villela
Summary: An analysis of rare genetic variants shows their impact on human traits is mediated through similar biological pathways as common variants, enhancing our understanding of their influence on complex traits.
Article
Clinical Neurology
Sumaiya Iqbal, Tobias Bruenger, Eduardo Perez-Palma, Marie Macnee, Andreas Brunklaus, Mark J. Daly, Arthur J. Campbell, David Hoksza, Patrick May, Dennis Lal
Summary: Neurodevelopmental disorders (NDDs) are heterogeneous conditions, and genetic testing can identify pathogenic variants. However, the significance of most identified variants is still uncertain. We developed a consensus approach to identify essential sites on NDD-associated proteins and found that missense variants at these sites are enriched in patients. Our findings provide valuable insights for variant interpretation and drug target development.
Article
Multidisciplinary Sciences
Baohua Duan, Tongxu Kang, Haifu Wan, Weibiao Liu, Fenghao Zhang, Shumei Mu, Yueqiang Guan, Zejian Li, Yang Tian, Xianjiang Kang
Summary: This study investigated the genetic diversity and population structure of 420 Portunus trituberculatus individuals collected from seven populations in the Bohai Sea using 40 SSR loci. The results showed a low genetic diversity in the cultured population compared to the wild populations. Population structure analysis revealed the subdivision of P. trituberculatus into four subpopulations, but there was no obvious correlation between genetic structure and geographical distribution.
SCIENTIFIC REPORTS
(2023)
Article
Multidisciplinary Sciences
Emmanuel Amponsah Adjei, Williams Esuma, Titus Alicai, Ranjana Bhattacharjee, Isaac Onziga Dramadri, Richard Edema, Emmanuel Boache Chamba, Thomas Lapaka Odong
Summary: Assessing the genetic diversity of yam germplasm from different geographical origins is crucial for crop genetic resource conservation and improvement. This study classified the population structure and assessed the genetic diversity of 207 Dioscorea rotundata genotypes from three geographical origins. Single nucleotide polymorphism markers were used and revealed informative genetic diversity across the genotypes. The analysis grouped the genotypes into three clusters and showed that within-population variation accounted for a significant portion of the observed variation.
Article
Ecology
Kelsey E. Johnson, Christopher J. Adams, Benjamin F. Voight
Summary: Researchers have discovered that the analysis of genetic variation in a population often assumes that rare variants are inherited from a single common ancestral event. However, this assumption may not hold true due to genetic and technical processes such as recurrent mutations, gene conversions, and genotyping errors. By using a Bayesian hierarchical model and Gibbs sampling, researchers can accurately distinguish rare variants consistent and inconsistent with a simple inheritance model. The findings suggest that inconsistent variants are correlated with higher local mutation rates and genomic features, providing insights into recent mutations in human populations.
METHODS IN ECOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Remi Matthey-Doret
Summary: SimBit is a high-performance population genetics simulator that can simulate various selection, demographic and mating scenarios, track QTLs and model ecological relationships among multiple species. It comes with a convenient R wrapper for project management and outperforms other simulators in most benchmarks.
MOLECULAR ECOLOGY RESOURCES
(2021)
Review
Biochemistry & Molecular Biology
Robin S. Waples
Summary: This article reviews and summarizes performance evaluations of the method to estimate contemporary effective population size (Ne) based on patterns of linkage disequilibrium (LD), with a focus on practical application to real populations in nature.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Genetics & Heredity
Tamara Soledad Frontanilla, Guilherme Valle-Silva, Jesus Ayala, Celso Teixeira Mendes-Junior
Summary: By conducting a comprehensive genotyping analysis of STRs obtained from the 1000 Genome populations, we established a reliable open-access STR database and identified limitations of HipSTR in detecting longer alleles.
Editorial Material
Multidisciplinary Sciences
Anthony J. Hannan
Summary: The study found a link between tandem repeats in DNA and autism spectrum disorder, which could provide insights into other human disorders. Bioinformatic analysis was used to study tandem repeat mutations in autism.
Article
Clinical Neurology
Matteo Zanovello, Kristina Ibanez, Anna-Leigh Brown, Prasanth Sivakumar, Alessandro Bombaci, Liana Santos, Joke J. F. A. van Vugt, Giuseppe Narzisi, Ramita Karra, Sonja W. Scholz, Jinhui Ding, J. Raphael Gibbs, Adriano Chio, Clifton Dalgard, Ben Weisburd, Michael G. Hanna, Linda Greensmith, Hemali Phatnani, Jan H. Veldink, Bryan J. Traynor, James Polke, Henry Houlden, Pietro Fratta, Arianna Tucci
Summary: The researchers established a method to detect AR CAG expansions and found a higher mutation frequency than previously reported, possibly due to underdiagnosis or pleomorphic manifestations. This mutation causes spinal and bulbar muscular atrophy, a male-specific progressive neuromuscular disorder.
Article
Biochemistry & Molecular Biology
Angel G. Rivera-Colon, Nicolas C. Rochette, Julian M. Catchen
Summary: RADseq has become a powerful tool in population genomics, with different protocol variants developed to suit specific experimental needs. However, choosing the optimal molecular and sequencing protocols remains a challenge for researchers, as strategic errors can lead to biased data generation and reduced power to answer biological questions.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Infectious Diseases
Eliseo Albert, Javier S. Burgos, Salvador Peiro, Dolores Salas, Hermelinda Vanaclocha, Estela Gimenez, Ramon Limon, Maria Jesus Alcaraz, Jose Sanchez-Paya, Javier Diez-Domingo, David Navarro
Summary: This study examined the immune responses of elderly people in nursing homes following the administration of the Comirnaty (R) COVID-19 vaccine. The results showed that the vaccine was highly immunogenic, with a high detection rate of antibodies in nursing home residents. The study also found that residents without detectable antibodies still had S-reactive T cells, indicating a potential cellular immune response.
CLINICAL MICROBIOLOGY AND INFECTION
(2022)
Article
Entomology
Margarita C. G. Correa, Ferran Palero, Vitor C. Pacheco da Silva, M. Bora Kaydan, Jean-Francois Germain, Shaaban Abd-Rabou, Kent M. Daane, Arturo Cocco, Elie Poulin, Thibaut Malausa
Summary: This study used molecular tools and morphological analysis to investigate the mealybug Planococcus ficus in the Eastern Mediterranean region, and found two distinct species: P. ficus and P. vitis. These results have direct implications for pest management and may explain the previous failures of biological control programs against this pest in several vineyard regions.
JOURNAL OF PEST SCIENCE
(2023)
Article
Zoology
Alberto Sendra, Ferran Palero, Alba Sanchez-Garcia, Jesus Selfa, Sadreddin Tusun, Ali Satar
Summary: A new genus of cave-dwelling dipluran, Anatoliacampa diclensis, is described from southeastern Anatolia, Turkey. This new taxon belongs to the well-established subfamily Plusiocampinae and has unique morphological characteristics, including a distinctive pretarsus and abundant urosternal macrosetae. The discovery of this new genus provides new evidence for the colonization of Euro-Mediterranean lands by cave-adapted Plusiocampinae and their soil-dwelling relatives, highlighting the importance of Anatolia as a land bridge.
ZOOLOGISCHER ANZEIGER
(2022)
Article
Environmental Sciences
Marta Gellert, Ferran Palero, Magdalena Blazewicz
Summary: Typhlotanaidae is one of the most diverse Tanaidacea families in deep-sea waters, but its diversity is underestimated and the evolutionary relationships within the family are mostly unknown. An integrative taxonomy approach combining morphology and genetic data was used to study deep-sea typhlotanaids from the NW Pacific, revealing new taxa and supporting the monophyly of known groups.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Microbiology
Neris Garcia-Gonzalez, Beatriz Beamud, Begona Fuster, Salvador Giner, Maria Victoria Dominguez, Antonia Sanchez, Jordi Sevilla, Teresa M. Coque, Concepcion Gimeno, Fernando Gonzalez-Candelas
Summary: At a time when antimicrobial resistance has become one of the biggest concerns worldwide, the emergence of novel alleles and extremely drug-resistant plasmids is a threat to public health worldwide, especially when they produce carbapenem resistance in one of the most problematic pathogens, such as Klebsiella pneumoniae. We used genomic epidemiology to describe the emergence of a novel NDM-23 allele and identify it in a MDR plasmid that has disseminated through a K. pneumoniae ST437 clone in several hospitals in Spain.
MICROBIOLOGY SPECTRUM
(2023)
Article
Biochemistry & Molecular Biology
Yiguan Wang, Paul McNeil, Rashidatu Abdulazeez, Marta Pascual, Susan E. Johnston, Peter D. Keightley, Darren J. Obbard
Summary: Mutation, recombination, and transposition rates are important parameters in models of evolution, but little is known about their variation between individuals, sexes, or populations. This study provides direct estimates of these rates in different populations of Drosophila melanogaster and Drosophila simulans. The results show variation in mutation, recombination, and transposition rates among populations and sexes, with paternal-derived mutations being more frequent. These findings will benefit future studies in population and evolutionary genetics.
Article
Ornithology
Ivan Alambiaga, Roberto Gonzalez, Pablo Vera, Juan S. Monros, Ferran Palero
Summary: This study reports the first complete mitogenome of the eastern Iberian reed bunting (E. s. witherbyi) and compares it with an unpublished mitogenome from northeast Asia (most likely E. s. pyrrhulina). Genetic distance analyses reveal two distinct lineages of E. schoeniclus. A fossil-calibrated phylogeny suggests that open forest buntings have undergone two rapid speciation events correlating with climatic changes and habitat shifts. The adaptation to wetlands may have facilitated the expansion of reed bunting across the Palearctic, resulting in high intraspecific variation and the establishment of resident populations within small areas.
JOURNAL OF AVIAN BIOLOGY
(2023)
Article
Virology
Vicente Arnau, Wladimiro Diaz-Villanueva, Jorge Mifsut Benet, Paula Villasante, Beatriz Beamud, Paula Mompo, Rafael Sanjuan, Fernando Gonzalez-Candelas, Pilar Domingo-Calap, Maria Dzunkova
Summary: The environmental impact of uncultured phages is influenced by their life cycle, which can be predicted by comparing their genomic signatures to those of their hosts. This study used oligonucleotide-based methods to successfully discriminate between lytic and lysogenic phages and predict their relationships with host bacteria.
Article
Genetics & Heredity
Neris Garcia-Gonzalez, Begona Fuster, Nuria Tormo, Carme Salvador, Concepcion Gimeno, Fernando Gonzalez-Candelas
Summary: This study investigated the emergence and spread of carbapenem-resistant Klebsiella pneumoniae in a Spanish hospital from 2015 to 2019. The results showed a complex situation with six different lineages, various resistance genes, and different plasmids involved.
MICROBIAL GENOMICS
(2023)
Article
Infectious Diseases
Andrea Sanchez-Serrano, Lorena Mejia, Maria Luisa Camaro, Susana Ortola-Malvar, Martin Llacer-Luna, Neris Garcia-Gonzalez, Fernando Gonzalez-Candelas
Summary: Salmonella enterica subspecies enterica is an important foodborne pathogen that causes salmonellosis, affecting both humans and animals. The study of its epidemiology is crucial for monitoring and controlling these bacteria. With the advancements in whole-genome sequencing, genomic surveillance is replacing traditional serotyping and phenotypic tests.
Article
Biochemistry & Molecular Biology
Ainhoa Lopez, Carlos Carreras, Marta Pascual, Cinta Pegueroles
Summary: Conservation genomic studies rely on reduced representation sequencing techniques based on restriction enzymes. This study evaluated the distribution and functional composition of loci obtained using Genotyping-by-Sequencing (GBS) in different species. The selection of restriction enzymes was found to affect the enrichment of loci in specific regions and emphasized the importance of high-quality annotated genomes.
MOLECULAR ECOLOGY RESOURCES
(2023)
Review
Genetics & Heredity
Kathrin Theissinger, Carlos Fernandes, Giulio Formenti, Iliana Bista, Paul R. Berg, Christoph Bleidorn, Aureliano Bombarely, Angelica Crottini, Guido R. Gallo, Jose A. Godoy, Sissel Jentoft, Joanna Malukiewicz, Alice Mouton, Rebekah A. Oomen, Sadye Paez, Per J. Palsboll, Christophe Pampoulie, Maria J. Ruiz-Lopez, Simona Secomandi, Hannes Svardal, Constantina Theofanopoulou, Jan de Vries, Ann-Marie Waldvogel, Guojie Zhang, Erich D. Jarvis, Miklos Balint, Claudio Ciofi, Robert M. Waterhouse, Camila J. Mazzoni, Jacob Hoglund
Summary: The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts. Reference genomes play a key role in facilitating biodiversity research and conservation. Integrating the use of reference genomes as a best practice in conservation genomics is essential.
TRENDS IN GENETICS
(2023)
Article
Virology
Franziska Hufsky, Ana B. Abecasis, Artem Babaian, Sebastian Beck, Liam Brierley, Simon Dellicour, Christian Eggeling, Santiago F. Elena, Udo Gieraths, Anh D. Ha, Will Harvey, Terry C. Jones, Kevin Lamkiewicz, Gabriel L. Lovate, Dominik Luecking, Martin Machyna, Luca Nishimura, Maximilian K. Nocke, Bernard Y. Renard, Shoichi Sakaguchi, Lygeri Sakellaridi, Jannes Spangenberg, Maria Tarradas-Alemany, Sandra Triebel, Yulia Vakulenko, Rajitha Yasas Wijesekara, Fernando Gonzalez-Candelas, Sarah Krautwurst, Alba Perez-Cataluna, Walter Randazzo, Gloria Sanchez, Manja Marz
Summary: The 2023 International Virus Bioinformatics Meeting held in Valencia, Spain was a significant event for researchers and scientists worldwide interested in virus bioinformatics. With the primary objective of fostering discussions and collaborations, it provided a platform for sharing insights, research findings, and novel ideas related to virus bioinformatics research.
Article
Cell Biology
Ferdinand Marletaz, Arnaud Couloux, Julie Poulain, Karine Labadie, Corinne Da Silva, Sophie Mangenot, Benjamin Noel, Albert J. Poustka, Philippe Dru, Cinta Pegueroles, Marco Borra, Elijah K. Lowe, Guy Lhomond, Lydia Besnardeau, Stephanie Le Gras, Tao Ye, Daria Gavriouchkina, Roberta Russo, Caterina Costa, Francesca Zito, Letizia Anello, Aldo Nicosia, Maria Antonietta Ragusa, Marta Pascual, M. Dolores Molina, Aline Chessel, Marta Di Carlo, Xavier Turon, Richard R. Copley, Jean-Yves Exposito, Pedro Martinez, Vincenzo Cavalieri, Smadar Ben Tabou de Leon, Jenifer Croce, Paola Oliveri, Valeria Matranga, Maria Di Bernardo, Julia Morales, Patrick Cormier, Anne-Marie Genevieve, Jean Marc Aury, Valerie Barbe, Patrick Wincker, Maria Ina Arnone, Christian Gache, Thierry Lepage
Summary: Through the analysis of genome assembly and gene expression in sea urchins, we have identified unique characteristics in their chromosomal structure and gene duplication. Additionally, we have discovered conserved gene-regulatory modules between sea urchins and chordates. These findings contribute to a better understanding of the evolutionary mechanisms behind development.
Review
Ecology
Emma L. Berdan, Nicholas H. Barton, Roger Butlin, Brian Charlesworth, Rui Faria, Ines Fragata, Kimberly J. Gilbert, Paul Jay, Martin Kapun, Katie E. Lotterhos, Claire Merot, Esra Durmaz Mitchell, Marta Pascual, Catherine L. Peichel, Marina Rafajlovic, Anja M. Westram, Stephen W. Schaeffer, Kerstin Johannesson, Thomas Flatt
Summary: Inversions are structural mutations that have a significant impact on adaptation and speciation. However, their study has been challenging due to reduced recombination and the effects of drift and hitchhiking. This review examines the different mechanisms of selection that affect the evolution of inversions, emphasizing the complexity of analyzing the causes underlying their evolution.
JOURNAL OF EVOLUTIONARY BIOLOGY
(2023)
