Editorial Material
Biochemistry & Molecular Biology
Brian Charlesworth, Thomas Flatt
Summary: Recent publications suggest that epistatic fitness interactions lead to the fixation of inversions that suppress recombination. However, under this type of selection, the suppression of recombination in an inversion heterozygote can create a heterozygote advantage, preventing the inversion from being fixed by selection. This process has been explicitly modeled by previous researchers.
Article
Biology
Anastasia Stolyarova, Tatiana Neretina, Elena A. Zvyagina, Anna Fedotova, Alexey S. Kondrashov, Georgii A. Bazykin
Summary: Studying patterns of genetic variation in hyperpolymorphic species, such as the fungus Schizophyllum commune, can reveal large-scale properties of the fitness landscape that are difficult to detect in species with ordinary levels of genetic variation. In S. commune, short-range linkage disequilibrium tends to be higher between pairs of nonsynonymous variants, especially those located within the same gene and covered by haploblocks, which are segments of the genome consisting of two highly divergent haplotypes and a signature of balancing selection. LD is also higher for pairs of nonsynonymous variants encoding interacting amino acids within the protein. Additionally, there is a correlation between LDs at the same pairs of nonsynonymous mutations in different populations.
Article
Biotechnology & Applied Microbiology
Jose Marcelo Soriano Viana, Antonio Augusto Franco Garcia
Summary: Additive variance is generally the most important component of genotypic variance. LD and inbreeding have a significant effect on the magnitude of the genetic variances and covariances. In general, the additive x additive variance is the most important component of epistatic variance.
Article
Genetics & Heredity
Aaron P. Ragsdale
Summary: This study explores patterns of linkage disequilibrium between mutations and finds that positive linkage disequilibrium between missense mutations within protein-coding genes is driven by strong positive allele-frequency correlations between mutations within the same conserved domain. Linkage disequilibrium is reduced outside of conserved domains, consistent with Hill-Robertson interference.
Article
Biochemistry & Molecular Biology
George Sandler, Stephen Wright, Aneil F. Agrawal
Summary: Most types of mutations exhibit positive linkage disequilibrium, especially if they are predicted to be less deleterious. Through simulations, it has been shown that this pattern arises easily in a model of admixture or distance-biased mating. Additionally, loss of function mutations exhibit particularly positive LD across short distances.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Plant Sciences
Jose Marcelo Soriano Viana
Summary: This study assessed the influence of gene interaction on heterosis and combining ability analysis. It found that only linkage disequilibrium and additive x dominance interaction affected the analysis, and the impact depended on the type, percentage, and effect size of the interaction.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Maria-Agustina Rossi, Timothy Palzkill, Fabio C. L. Almeida, Alejandro J. Vila
Summary: Protein evolution involves the adaptation of molecules to different functional challenges through the accumulation of mutations. This study focuses on CTX-M beta-lactamases and demonstrates the optimization of protein dynamics through two mutations outside the active site, which enhance the enzyme's activity against a specific substrate. NMR analysis reveals that these mutations increase backbone dynamics and the exposure to solvent of a buried beta-sheet. The conformational changes induced by the mutations in this beta-sheet trigger further changes in loops at the opposite side of the active site. These findings highlight the importance of alternative conformations in protein evolution.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Multidisciplinary Sciences
Shai Torgeman, Dani Zamir
Summary: Controlled population development and genome-wide association studies are powerful methods for identifying genes and alleles that contribute to complex traits. However, the contribution of nonadditive interactions between quantitative trait loci (QTLs) has been understudied. In this study, the researchers used a population of backcross inbred lines (BILs) to examine epistasis. They found that nonadditive interactions can improve crop productivity by increasing fruit yield in hybrids.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
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)
Review
Biology
Masato Yamamichi
Summary: Recent studies have highlighted the significance of feedbacks between contemporary rapid evolution and ecological dynamics. However, most studies in this area have been focused on ecological aspects and adaptation at the phenotypic level, neglecting the genetic architecture of evolutionary processes. Empirical studies have often compared ecological dynamics when a species has single or multiple genotypes. Theoretical studies tend to use models of quantitative traits or Mendelian traits to investigate evolutionary dynamics. Nevertheless, it is well recognized that genetic architecture can influence short-term evolutionary dynamics in population genetics. Theoretical approaches integrating population genetics, ecology, and nonlinear time-series analyses can facilitate the synthesis of functional genomics and eco-evolutionary dynamics, particularly with emerging big data.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Multidisciplinary Sciences
Fei He, Wei Wang, William B. Rutter, Katherine W. Jordan, Jie Ren, Ellie Taagen, Noah DeWitt, Deepmala Sehgal, Sivakumar Sukumaran, Susanne Dreisigacker, Matthew Reynolds, Jyotirmoy Halder, Sunish Kumar Sehgal, Shuyu Liu, Jianli Chen, Allan Fritz, Jason Cook, Gina Brown-Guedira, Mike Pumphrey, Arron Carter, Mark Sorrells, Jorge Dubcovsky, Matthew J. Hayden, Alina Akhunova, Peter L. Morrell, Les Szabo, Matthew Rouse, Eduard Akhunov
Summary: This study reveals the impact of genetic variants leading to biased expression of homoeologous genes in hexaploid wheat on agronomic traits. It shows that the variation in homoeolog expression dosage is largely influenced by cis-acting variants, which have predictive value for yield-related traits and may have been impacted by breeding for increased productivity.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Matteo Bisardi, Juan Rodriguez-Rivas, Francesco Zamponi, Martin Weigt
Summary: The study proposes stochastic models of experimental protein evolution based on reconstructed data-driven fitness landscapes, predicting important features of experimentally evolved sequence libraries. It showcases the potential of the approach in determining protein structure from epistasis signals in experimental sequence libraries, offering a quantitative explanation for outcomes of recent experiments and enabling forecasts for future evolution experiments.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biology
Alex N. Nguyen Ba, Katherine R. Lawrence, Artur Rego-Costa, Shreyas Gopalakrishnan, Daniel Temko, Franziska Michor, Michael M. Desai
Summary: Mapping the genetic basis of complex traits is crucial to understanding the biology behind diseases and other phenotypes. The use of barcoded bulk quantitative trait locus (BB-QTL) mapping helps overcome limitations in sample size and statistical confounders. This study reveals that the genetic architecture of complex traits involves hundreds of small-effect loci throughout the genome, many of which have pleiotropic effects across multiple traits. Epistasis also plays a central role in understanding genetic networks.
Article
Genetics & Heredity
Cong Liu, Casey N. Ta, Jim M. Havrilla, Jordan G. Nestor, Matthew E. Spotnitz, Andrew S. Geneslaw, Yu Hu, Wendy K. Chung, Kai Wang, Chunhua Weng
Summary: This study presents an open annotation resource, derived from real-world data, for annotating phenotypic traits related to rare genetic diseases. By leveraging ontology mapping and natural language processing methods, this resource can automatically extract concepts for rare diseases and their phenotypic traits. Compared to manual annotation, it can identify more disease-phenotype associations and can be shared across different institutions.
AMERICAN JOURNAL OF HUMAN GENETICS
(2022)
Article
Infectious Diseases
Dillon Muzondiwa, Hleliwe Hlanze, Oleg N. Reva
Summary: The study reveals that different lineages of Mycobacterium tuberculosis employ different evolutionary trajectories to achieve multidrug resistance and reduce the fitness cost associated with drug resistance.
