Article
Ecology
Dengcheng Yang, Fan Li, Jing Wang, Ang Dong, Rongling Wu
Summary: LD in tetraploids is studied with a specific model for different loci disequilibrium, using EM algorithm for parameter estimation and experimental verification in populations. Analysis of switchgrass genomic data reveals the importance of LD in inferring evolutionary history.
METHODS IN ECOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Ben A. Flanagan, Stacy A. Krueger-Hadfield, Courtney J. Murren, Chris C. Nice, Allan E. Strand, Erik E. Sotka
Summary: The genomic variation of an invasive species is influenced by complex demographic histories, with founder effects playing a key role. Bottlenecks, clonality, and population expansion all impact the genomic variability of the red macroalga Agarophyton vermiculophyllum. The study suggests that a severe population bottleneck, shift towards clonal reproduction, and genetic source diversity contribute to the observed patterns of genomic variability in invasive populations.
Article
Endocrinology & Metabolism
Claes Lindh, Hemamali Samaratunga, Brett Delahunt, Rebecka Bergstrom, Venkatesh Chellappa, John Yaxley, Johan Lindberg, Lars Egevad
Summary: Most ductal and acinar prostate adenocarcinoma components of mixed tumors share the same clonal origin. Ductal adenocarcinoma components often exhibit genome doubling events leading to aneuploidy, consistent with the aggressive nature of high grade prostate cancer.
Article
Genetics & Heredity
Burak Yelmen, Aurelien Decelle, Linda Ongaro, Davide Marnetto, Corentin Tallec, Francesco Montinaro, Cyril Furtlehner, Luca Pagani, Flora Jay
Summary: Generative models have the potential to create high-quality synthetic genomic data, improving the imputation quality for low-frequency alleles while protecting individual privacy. This could provide valuable assets in genetic studies by offering an easy-access and anonymous alternative for private genetic databases.
Article
Microbiology
Michel Tibayrenc, Francisco J. Ayala
Summary: Recent data based on high-resolution markers and genomic polymorphisms fully confirm the predominant clonal evolution (PCE) model down to a microevolutionary level, indicating that genetic exchange may not be sufficient to erase the persistent phylogenetic signal and the existence of bifurcating trees in natural Leishmania populations.
Article
Multidisciplinary Sciences
Vivian Link, Yuomi Jhony A. Zavaleta, Rochelle-Jan Reyes, Linda Ding, Judy Wang, Rori V. Rohlfs, Michael D. Edge
Summary: The 20 short tandem repeat (STR) loci of the combined DNA index system (CODIS) are widely used in forensic genetics in the United States. Although CODIS loci were previously believed to contain limited information about ancestry or traits, recent research has shown that the regions surrounding CODIS loci are enriched with trait-related variants.
Article
Genetics & Heredity
Laurence J. Howe, Thomas Battram, Tim T. Morris, Fernando P. Hartwig, Gibran Hemani, Neil M. Davies, George Davey Smith
Summary: The study suggests that genome-wide association studies capture associations related to environmental factors and that within-spouse pair models can be used to disentangle different sources of these associations. While within-spouse pair models can detect genuine confounding, they may also be susceptible to collider bias induced by comparing assorted pairs. These models could be useful for combining evidence from different study designs, but caution should be taken due to potential collider bias.
Article
Genetics & Heredity
Arjun Biddanda, Matthias Steinrucken, John Novembre
Summary: This study derives several results for summary statistics of haplotypic variation, including the correlation between pair-wise differences observed between time-staggered samples, the measure of haplotypic similarity between ancient and modern samples, and the expected switch rate in the haplotype copying model. These results are important for interpreting and analyzing haplotype data from ancient and modern samples.
Article
Biochemistry & Molecular Biology
Enrique Santiago, Armando Caballero, Carlos Kopke, Irene Novo
Summary: A new method is developed to estimate the contemporary effective population size (Ne) based on linkage disequilibrium (LD) in non-model species. It can be applied to different mating systems and variations in family size distribution. The method uses an artificial neural network to predict confidence intervals, providing more consistent estimates.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Microbiology
Luiza Chaves de Miranda Leonhardt Losada, Ruan Campos Monteiro, Jamile Ambrosio de Carvalho, Ferry Hagen, Matthew C. Fisher, Bram Spruijtenburg, Jacques F. Meis, Theun de Groot, Sarah Santos Goncalves, Ricardo Negroni, Rui Kano, Alexandro Bonifaz, Zoilo Pires de Camargo, Anderson Messias Rodrigues
Summary: This study developed a panel of highly polymorphic SSR markers suitable for genotyping Sporothrix species. PCR amplification revealed 240 alleles in 180 Sporothrix isolates, supporting the effectiveness of SSR markers in uncovering cryptic genetic diversity. The analysis of SSR diversity provided insights into the origins and transmission dynamics of cat-transmitted sporotrichosis.
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
Agronomy
Lucas Fernandes Rocha, Eneas Ricardo Konzen, Dulcineia de Carvalho
Summary: Habitat fragmentation and management of natural populations of tree species can interfere with their reproduction dynamics. The management practices for Eremanthus erythropappus can increase clonality rates and negatively impact the genetic diversity and long-term conservation of the species in their natural environment.
GENETIC RESOURCES AND CROP EVOLUTION
(2023)
Article
Biology
Isabel Gamache, Marc-Andre Legault, Jean-Christophe Grenier, Rocio Sanchez, Eric Rheaume, Samira Asgari, Amina Barhdadi, Yassamin Feroz Zada, Holly Trochet, Yang Luo, Leonid Lecca, Megan Murray, Soumya Raychaudhuri, Jean-Claude Tardif, Marie-Pierre Dube, Julie Hussin
Summary: Pharmacogenomic studies have identified associations between ADCY9 and CETP genes in recent human evolution, potentially due to sex-specific selection, pointing towards a biological link between dalcetrapib's pharmacogene ADCY9 and its therapeutic target CETP.
Article
Ecology
Lisa Mazumder, Rick Kesseli
Summary: Dandelions have a worldwide distribution in urban environments despite the lack of sexual reproduction in most areas. The impact of this unusual natural history on population structure and diversity is investigated using genetic markers, showing high levels of genetic diversity within populations and seasonal genotypic differentiation.
ECOLOGY AND EVOLUTION
(2021)
Article
Genetics & Heredity
Keisuke Ejima, Nianjun Liu, Luis Miguel Mestre, Gustavo de los Campos, David B. Allison
Summary: Mendelian randomization (MR) is often used in epidemiological studies, but it can be biased when confounding variables are correlated with the instrumental variable. In this study, a new approach is proposed to condition on parental mating types in MR, which can reduce bias and the need for assumptions. Simulation results show that this approach eliminates type I error inflation and bias caused by assortative mating or population stratification.
FRONTIERS IN GENETICS
(2023)