Article
Cell Biology
Zhen Xu, Jiajia Shi, Yu Zhang, Yuhan Liu, Junzheng Zhao, Qian Chen, Chenglin Song, Shuhui Geng, Wei Xie, Feizhen Wu, Yun Bai, Yang Yang, Xiajun Li
Summary: Zfp57 plays important roles in both maternal and zygotic functions in mouse, regulating the allelic expression and DNA methylation imprinting of imprinted genes. Loss of Zfp57 results in the loss of DNA methylation imprint at multiple imprinting control regions, with maternal Zfp57 being essential for maintaining DNA methylation at a subset of imprinted regions. Zfp57 also has sexually dimorphic effects on allelic expression switch and expression level changes of imprinted genes in mouse embryos.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Andres G. de la Filia, Andrew J. Mongue, Jennifer Dorrens, Hannah Lemon, Dominik R. Laetsch, Laura Ross
Summary: Genetic conflict drives evolution of reproductive systems with non-Mendelian inheritance, such as paternal genome elimination (PGE) in insects like mealybugs. This conflict leads to biased gene expression patterns and elevated rates of molecular evolution, providing insights into the origin and mechanisms of PGE.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Plant Sciences
Haixia Jiang, Dongliang Guo, Jiali Ye, Yanfang Gao, Huiqing Liu, Yue Wang, Min Xue, Qingcheng Yan, Jiaxun Chen, Lepeng Duan, Gongze Li, Xiao Li, Liqiong Xie
Summary: Genomic imprinting causes biased expression of maternally and paternally inherited alleles in the triploid endosperm of flax, with a total of 248 candidate imprinted genes identified. These imprinted genes are not well conserved among plant species and contribute to intraspecific variation in flax, with some undergoing positive selection during domestication. Imprinted genes related to flax functions, including seed size and weight, were found to have undergone positive selection and could provide insights into the function and genomic variation of imprinted genes in the flax population.
Review
Biology
Benjamin P. Oldroyd, Boris Yagound
Summary: Social insects, due to haplo-diploidy and relatedness asymmetries, are prime candidates for the evolution of genomic imprinting. Different mating systems may lead to different evolutionary pressures on genes, influencing their direction of evolution. Crosses between subspecies of honeybees have shown evidence of genomic imprinting affecting genes related to worker reproduction.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Forestry
Atsushi Ejima, Kentaro Uchiyama, Hideki Mori, Yoshihiko Tsumura
Summary: This study tested the use of genomic prediction (GP) to improve the efficiency of breeding long-lived trees, specifically Cryptomeria japonica. The results showed that GP was more accurate than traditional pedigree-based methods, but parent-offspring relationships reduced its accuracy for traits strongly affected by selection pressure.
Article
Evolutionary Biology
Lynn Ayache, Aiden Bushell, Jessica Lee, Iiro Salminen, Bernard Crespi
Summary: This study supports the kinship theory of imprinting and highlights the important role of imprinted genes and associated genomic conflicts in the development and activity of brown adipose tissue (BAT).
EVOLUTION MEDICINE AND PUBLIC HEALTH
(2023)
Article
Multidisciplinary Sciences
Chachrit Khunsriraksakul, Daniel McGuire, Renan Sauteraud, Fang Chen, Lina Yang, Lida Wang, Jordan Hughey, Scott Eckert, J. Dylan Weissenkampen, Ganesh Shenoy, Olivia Marx, Laura Carrel, Bibo Jiang, Dajiang J. Liu
Summary: Here, the authors propose an integrative method PUMICE to improve gene expression predictions by integrating 3D genomic and epigenomic data with expression quantitative trait loci (eQTL). The method outperforms other competing methods and identifies more novel genes. Additionally, an extension to the method, PUMICE +, shows improved performance in computational drug repurposing.
NATURE COMMUNICATIONS
(2022)
Article
Biotechnology & Applied Microbiology
Vincent P. Richards, Annette Nigsch, Paulina Pavinski Bitar, Qi Sun, Tod Stuber, Kristina Ceres, Rebecca L. Smith, Suelee Robbe Austerman, Ynte Schukken, Yrjo T. Grohn, Michael J. Stanhope
Summary: This study conducted a prolonged longitudinal analysis of MAP isolates and dairy cow Johne's disease phenotypes from three commercial dairy farms, identifying several genes associated with the disease. The results provide insights for improving strategies to control Johne's disease.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Ecology
Jonathan M. Parrett, Sebastian Chmielewski, Eylem Aydogdu, Aleksandra Lukasiewicz, Stephane Rombauts, Agnieszka Szubert-Kruszynska, Wieslaw Babik, Mateusz Konczal, Jacek Radwan
Summary: Populations of a bulb mite experimentally selected for a male weapon showed reduced diversity across the genome, indicating increased purifying selection due to strong sexual selection. The populations selected for the weapon exhibited lower genome-wide diversity, particularly in terms of non-synonymous positions, suggesting enhanced purifying selection.
NATURE ECOLOGY & EVOLUTION
(2022)
Article
Religion
Kerstin Stucky, Andy Gardner
Summary: Despite the widespread existence of religion, hypotheses about the selection pressures that have shaped its cognitive foundations remain controversial. This study develops a mathematical model inspired by previous research to explore the causes and consequences of selection pressures on religious beliefs. The findings suggest that an individual's propensity for religiosity and patterns of gene expression are influenced by genetic relatedness, age, and sex, and that religiosity can lead to conflicts of interest and associated clinical disorders. The study also presents a theoretical framework for making clear predictions about adaptive and maladaptive religious phenotypes.
RELIGION BRAIN & BEHAVIOR
(2022)
Article
Biochemistry & Molecular Biology
Jessica L. Soyer, Colin Clairet, Elise J. Gay, Nicolas Lapalu, Thierry Rouxel, Eva H. Stukenbrock, Isabelle Fudal
Summary: Leptosphaeria maculans 'brassicae' (Lmb) and Leptosphaeria maculans 'lepidii' (Lml) are closely related phytopathogenic species with contrasting genome structure. Chromatin organization influences the expression of effector genes in these fungi, with facultative heterochromatin containing many genes lacking functional annotation. Additionally, Lmb has distinctive heterochromatin landscapes compared to other fungal species, with large H3K9me3 domains associated with repeat-rich regions containing species-specific effector genes.
CHROMOSOME RESEARCH
(2021)
Article
Multidisciplinary Sciences
Hyejin Youn, Logan Sutton, Eric Smith, Cristopher Moore, Jon F. Wilkins, Ian Maddieson, William Croft, Tanmoy Bhattacharya
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2016)
Article
Multidisciplinary Sciences
Francisco Ubeda, Vincent A. A. Jansen
NATURE COMMUNICATIONS
(2016)
Article
Genetics & Heredity
Jon F. Wilkins, Peter T. McHale, Joshua Gervin, Arthur D. Lander
Article
Ecology
Andy Gardner, Francisco Ubeda
NATURE ECOLOGY & EVOLUTION
(2017)
Article
Genetics & Heredity
Claire L. Dent, Trevor Humby, Katie Lewis, Andrew Ward, Reiner Fischer-Colbrie, Lawrence S. Wilkinson, Jon F. Wilkins, Anthony R. Isles
Article
Genetics & Heredity
Claire L. Dent, Trevor Humby, Katie Lewis, Andrew Ward, Reiner Fischer-Colbrie, Lawrence S. Wilkinson, Jon F. Wilkins, Anthony R. Isles
Article
Ecology
Francisco Ubeda, Timothy W. Russell, Vincent A. A. Jansen
THEORETICAL POPULATION BIOLOGY
(2019)
Article
Biology
Jon F. Wilkins, Tanmoy Bhattacharya
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2019)
Article
Biology
Timothy W. Russell, Matthew J. Russell, Francisco Ubeda, Vincent A. A. Jansen
JOURNAL OF THEORETICAL BIOLOGY
(2019)
Article
Multidisciplinary Sciences
David V. McLeod, Geoff Wild, Francisco Ubeda
Summary: The study shows that the virulence of infectious diseases may be influenced by the sex of the host the infection originated from, as well as the current host. Furthermore, the retention of epigenetic memories by pathogens plays a crucial role in the evolution of virulence. The findings suggest that pathogens can be selected to carry memories of past environments other than sex, leading to potential new directions in personalized medicine.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Evan Mitchell, Andrea L. Graham, Francisco Ubeda, Geoff Wild
Summary: Women generally exhibit stronger immune responses and pathogens tend to be more virulent in men, which current explanations cannot account for. This study proposes an alternative explanation based on the transmission of pathogens from mother to child, using a mathematical model of the co-evolution of host immunocompetence and pathogen virulence.
NATURE COMMUNICATIONS
(2022)
Article
Ecology
Frederic Fyon, Waldir Miron Berbel-Filho, Ingo Schlupp, Geoff Wild, Francisco Ubeda
Summary: This study presents a mathematical model proposing an alternative, adaptive route for the evolution of asexuality from previously sexual hybrids. The results show that when incompatibilities only affect the fusion of sperm and egg's genomes, the two traits that characterize asexuality can evolve separately, greatly facilitating the overall evolutionary route.
Article
Ecology
Francisco Ubeda, Frederic Fyon, Reinhard Buerger
Summary: The gene PRDM9 determines the location of recombination hotspots in many vertebrates, including humans. Contrary to expectations, these hotspots do not go extinct but are maintained through the interaction of gene conversion and mutation.
THEORETICAL POPULATION BIOLOGY
(2023)