Article
Multidisciplinary Sciences
Sergio Nolazco, Kaspar Delhey, Shinichi Nakagawa, Anne Peters
Summary: This article examines the ornament traits and adaptive signals in birds. The study finds that although female ornaments are often less elaborate than male ornaments, both sexes show similar associations between ornaments and indicators of health and reproductive success.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Alejandro V. Cano, Hana Rozhonova, Arlin Stoltzfus, David M. McCandlish, Joshua L. Payne
Summary: This study investigates the influence of mutation spectrum on the spectrum of adaptive substitutions, demonstrating that the mutation spectrum has a proportional influence on the spectrum of adaptive substitutions in all three species, but the predictive power of the model differs substantially between the species.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Psychology, Biological
Weichen Song, Yueqi Shi, Weidi Wang, Weihao Pan, Wei Qian, Shunying Yu, Min Zhao, Guan Ning Lin
Summary: The study reveals that 88% of complex traits in European populations have shown signals of natural selection in the past 3,000 years, with traits related to pigmentation, body shape, and food intake showing strong selection signals.
NATURE HUMAN BEHAVIOUR
(2021)
Article
Biochemistry & Molecular Biology
M. J. Shepherd, J. S. Horton, T. B. Taylor
Summary: This study reveals the importance of genomic features in facilitating the formation of mutational hotspots, including genomic location, local nucleotide sequence, gene strandedness, and the presence of mismatch repair proteins.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Ecology
Ashvitha Kannan, Robert J. Dugand, Nicholas C. Appleton, Stephen F. Chenoweth, Carla M. Sgro, Katrina Mcguigan
Summary: This study investigates how mild perturbations in diet and temperature affect mutational (co)variances of traits and contribute to individual fitness in Drosophila serrata. The results suggest that mutational effects are influenced by environmental heterogeneity and exhibit environment-dependent variations. These findings indicate the importance of environmental factors in maintaining genetic variance.
Article
Biochemistry & Molecular Biology
Thibault Latrille, Vincent Lanore, Nicolas Lartillot
Summary: Mutation-selection phylogenetic codon models are a principled approach for studying the interplay between mutation, selection, and drift, but their assumption of constant genetic drift is unrealistic. By introducing variation in effective population size and mutation rate between lineages, the model can better account for the joint evolutionary process of these lineage-specific variables. The model, tested on simulated and empirical data, suggests reasonable reconstructions of evolutionary trends, although potential issues with assumptions about epistatic interactions between sites remain.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Mathematics
Liming Zheng, Shiqi Luo
Summary: In this paper, a novel adaptive differential evolution algorithm based on fitness landscape (FL-ADE) is proposed, which utilizes the local fitness landscape characteristics to adaptively adjust the population size and generate mutation strategies. Experimental results show that the FL-ADE algorithm outperforms other state-of-the-art differential evolution variants and can effectively allocate computational resources for different fitness landscapes.
Article
Genetics & Heredity
Brent W. Bever, Zachary P. Dietz, Jennifer A. Sullins, Ariana M. Montoya, Ulfar Bergthorsson, Vaishali Katju, Suzanne Estes
Summary: This study provides a partial test of the mitonuclear sex hypothesis by examining the evolution of male frequencies in response to mitonuclear mismatch in C. elegans nematodes. The results show that male frequencies increase in certain mutant backgrounds, while declining in later generations in other backgrounds. The study also suggests that males and sexual outcrossing are most beneficial for populations evolving from a state of low ancestral fitness. Further research can explore the evolution of other traits and the role of compensatory mutations.
FRONTIERS IN GENETICS
(2022)
Article
Genetics & Heredity
Philip Ruelens, J. Arjan G. M. de Visser
Summary: Experimental evolution studies show that in very small populations, mutant clones with higher mutation rates can adapt faster by acquiring beneficial mutations, while wild-type populations have limited adaptive potential with inactivating mutations.
Article
Biology
Swantje Enge, Claire Merot, Raimondas Mozuraitis, Violeta Apsegaite, Louis Bernatchez, Gerrit A. Martens, Sandra Radziute, Henrik Pavia, Emma L. Berdan
Summary: In this study, researchers found that a overdominant supergene in seaweed flies strongly modulates male traits but only weakly affects female traits. Gas chromatography-electroantennographic detection revealed that females can sense male traits and there may be differential perception between genotypes. Gene expression analysis showed that candidate genes for trait biosynthesis primarily showed differential expression in males, while odorant detection genes were differentially expressed in both sexes but showed high levels of divergence between supergene haplotypes. The reduced recombination between supergene haplotypes may have led to rapid divergence in mate preferences and increasing linkage between male traits and overdominant loci, helping to maintain the polymorphism despite deleterious effects in homozygotes.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Article
Evolutionary Biology
Hongkai Zhang, Max Lundberg, Maja Tarka, Dennis Hasselquist, Bengt Hansson
Summary: Germline mutations are the ultimate source of genetic variation and the raw material for organismal evolution. This study examined the frequency and genomic locations of mutations, as well as the potential sex bias, in great reed warblers. The researchers identified 82 de novo mutations and observed a pronounced sex bias, with male warblers exhibiting three times more mutations than females. The mutation rate was determined to be 7.16 x 10-9 mutations per site per generation for autosomes and 5.10 x 10-9 mutations per site per generation for the Z chromosome.
GENOME BIOLOGY AND EVOLUTION
(2023)
Article
Entomology
Donato Romano, Giovanni Benelli, Cesare Stefanini
Summary: This study investigated the courtship and mating behavior of the neem bug, Halys dentatus, and found population-level lateralization in males approaching females. Furthermore, the male mating success was affected by lateralization, where right-biased males achieved higher mating success rates. The study highlights the importance of lateralized traits in determining male mating success in insects.
Article
Biochemical Research Methods
Dominik Deffner, Anne Kandler, Laurel Fogarty
Summary: The importance of population size for cultural diversity and complexity is examined in this study. The authors highlight the concept of effective population size for culturally evolving traits and show how it depends on various factors such as the way traits are learned, population connectedness, and social network structure. The results provide insights into understanding cultural evolution and emphasize the need for a careful definition of effective population size in cultural systems.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Engineering, Marine
Marc Krasovec, Dmitry A. Filatov
Summary: This study provides a comparative analysis of codon bias across multiple major phytoplankton groups. The results show that most groups have modest codon bias, with Haptophyta having the strongest bias and Chlorarachniophyta having the weakest bias. The optimal codons are typically GC-ending, but shifts to AT-ending codons were observed in Ochrophyta and Ciliophora. The study also highlights the modest codon bias in marine phytoplankton, which can be explained by the lower effective population sizes compared to the astronomically large census population sizes.
JOURNAL OF MARINE SCIENCE AND ENGINEERING
(2022)
Article
Ecology
Tejinder Singh Chechi, Aaditya Narasimhan, Broti Biswas, Nagaraj Guru Prasad
Summary: Male-biased operational sex ratios increase male-male competition and select for increased pre- and postcopulatory male success. In this study, we found that males evolved under male-biased sex ratios had higher mating success and courtship frequency compared to females evolved under female-biased sex ratios. Female mating status also influenced male mating success.
Article
Biochemistry & Molecular Biology
Ke Xu, Eric E. Schadt, Katherine S. Pollard, Panos Roussos, Joel T. Dudley
MOLECULAR BIOLOGY AND EVOLUTION
(2015)
Article
Biochemistry & Molecular Biology
Natalie M. Jameson Kiesling, Soojin V. Yi, Ke Xu, F. Gianluca Sperone, Derek E. Wildman
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2015)
Article
Psychiatry
A. Dincer, D. P. Gavin, K. Xu, B. Zhang, J. T. Dudley, E. E. Schadt, S. Akbarian
TRANSLATIONAL PSYCHIATRY
(2015)
Article
Biochemistry & Molecular Biology
John F. Fullard, Claudia Giambartolomei, Mads E. Hauberg, Ke Xu, Georgios Voloudakis, Zhiping Shao, Christopher Bare, Joel T. Dudley, Manuel Mattheisen, Nikolaos K. Robakis, Vahram Haroutunian, Panos Roussos
HUMAN MOLECULAR GENETICS
(2017)
Correction
Biochemistry & Molecular Biology
John F. Fullard, Claudia Giambartolomei, Mads E. Hauberg, Ke Xu, Georgios Voloudakis, Zhiping Shao, Christopher Bare, Joel T. Dudley, Manuel Mattheisen, Nikolaos K. Robakis, Vahram Haroutunian, Panos Roussos
HUMAN MOLECULAR GENETICS
(2020)
Article
Biochemistry & Molecular Biology
Ravi Patel, Laura B. Scheinfeldt, Maxwell D. Sanderford, Tamera R. Lanham, Koichiro Tamura, Alexander Platt, Benjamin S. Glicksberg, Ke Xu, Joel T. Dudley, Sudhir Kumar
MOLECULAR BIOLOGY AND EVOLUTION
(2018)
Article
Clinical Neurology
Ke Xu, Liang Ding, Ti-Cheng Chang, Ying Shao, Jason Chiang, Heather Mulder, Shuoguo Wang, Tim I. Shaw, Ji Wen, Laura Hover, Clay McLeod, Yong-Dong Wang, John Easton, Michael Rusch, James Dalton, James R. Downing, David W. Ellison, Jinghui Zhang, Suzanne J. Baker, Gang Wu
ACTA NEUROPATHOLOGICA
(2019)
Article
Biochemistry & Molecular Biology
Ke Xu, Jianrong Wang, Navin Elango, Soojin V. Yi
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2013)
Article
Genetics & Heredity
Ke Xu, Roman Kosoy, Khader Shameer, Sudhir Kumar, Li Liu, Ben Readhead, Gillian M. Belbin, Hao-Chih Lee, Rong Chen, Joel T. Dudley
Article
Hematology
Benshang Li, Samuel W. Brady, Xiaotu Ma, Shuhong Shen, Yingchi Zhang, Yongjin Li, Karol Szlachta, Li Dong, Yu Liu, Fan Yang, Ningling Wang, Diane A. Flasch, Matthew A. Myers, Heather L. Mulder, Lixia Ding, Yanling Liu, Liqing Tian, Kohei Hagiwara, Ke Xu, Xin Zhou, Edgar Sioson, Tianyi Wang, Liu Yang, Jie Zhao, Hui Zhang, Ying Shao, Hongye Sun, Lele Sun, Jiaoyang Cai, Hui-Ying Sun, Ting-Nien Lin, Lijuan Du, Hui Li, Michael Rusch, Michael N. Edmonson, John Easton, Xiaofan Zhu, Jingliao Zhang, Cheng Cheng, Benjamin J. Raphael, Jingyan Tang, James R. Downing, Ludmil B. Alexandrov, Bin-Bing S. Zhou, Ching-Hon Pui, Jun J. Yang, Jinghui Zhang
Article
Clinical Neurology
Kyle S. Smith, Ke Xu, Kimberly S. Mercer, Frederick Boop, Paul Klimo, Michael DeCupyere, Jose Grenet, Sarah Robinson, Paige Dunphy, Suzanne J. Baker, David W. Ellison, Thomas E. Merchant, Santhosh A. Upadayaya, Amar Gajjar, Gang Wu, Brent A. Orr, Giles W. Robinson, Paul A. Northcott, Martine F. Roussel
ACTA NEUROPATHOLOGICA
(2020)
Article
Multidisciplinary Sciences
John DeSisto, John T. Lucas, Ke Xu, Andrew Donson, Tong Lin, Bridget Sanford, Gang Wu, Quynh T. Tran, Dale Hedges, Chih-Yang Hsu, Gregory T. Armstrong, Michael Arnold, Smita Bhatia, Patrick Flannery, Rakeb Lemma, Lakotah Hardie, Ulrich Schueller, Sujatha Venkataraman, Lindsey M. Hoffman, Kathleen Dorris, Jean M. Mulcahy Levy, Todd C. Hankinson, Michael Handler, Arthur K. Liu, Nicholas Foreman, Rajeev Vibhakar, Kenneth Jones, Sariah Allen, Jinghui Zhang, Suzanne J. Baker, Thomas E. Merchant, Brent A. Orr, Adam L. Green
Summary: Radiation-induced high-grade gliomas (RIGs) are an incurable late complication of cranial radiation therapy. Genomic analysis revealed common copy-number alterations and different subgroups based on DNA methylation and transcriptome profiles, suggesting potential therapeutic targets such as microtubule inhibitors and MEK inhibitors. These findings provide insights into the molecular mechanisms of RIGs and potential treatment strategies.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Chen He, Ke Xu, Xiaoyan Zhu, Paige S. Dunphy, Brian Gudenas, Wenwei Lin, Nathaniel Twarog, Laura D. Hover, Chang-Hyuk Kwon, Lawryn H. Kasper, Junyuan Zhang, Xiaoyu Li, James Dalton, Barbara Jonchere, Kimberly S. Mercer, Duane G. Currier, William Caufield, Yingzhe Wang, Jia Xie, Alberto Broniscer, Cynthia Wetmore, Santhosh A. Upadhyaya, Ibrahim Qaddoumi, Paul Klimo, Frederick Boop, Amar Gajjar, Jinghui Zhang, Brent A. Orr, Giles W. Robinson, Michelle Monje, Burgess B. Freeman, Martine F. Roussel, Paul A. Northcott, Taosheng Chen, Zoran Rankovic, Gang Wu, Jason Chiang, Christopher L. Tinkle, Anang A. Shelat, Suzanne J. Baker
Summary: In this study, researchers established a series of models related to pediatric high-grade gliomas, replicating the histopathology, DNA methylation signatures, and gene expression patterns of patient tumors. High-throughput screening results showed variable responses to PI3K/mTOR and MEK pathway inhibitors. These models provide a rich resource for pediatric brain tumor research.
NATURE COMMUNICATIONS
(2021)
Article
Oncology
Allison Pribnow, Barbara Jonchere, Jingjing Liu, Kyle S. Smith, Olivia Campagne, Ke Xu, Sarah Robinson, Yogesh Patel, Arzu Onar-Thomas, Gang Wu, Clinton F. Stewart, Paul A. Northcott, Jiyang Yu, Giles W. Robinson, Martine F. Roussel
Summary: Combining ribociclib and gemcitabine can effectively slow down tumor progression and metastasis, and improve survival in patients with G3MB. Molecular analysis reveals significant changes in gene activity and expression, which may be related to cell cycle progression, DNA damage response, and neuronal differentiation. This study suggests that the combination therapy of ribociclib and gemcitabine is a promising treatment strategy for children with G3MB and deserves further investigation.
MOLECULAR CANCER THERAPEUTICS
(2022)
Article
Oncology
Rose B. McGee, Ninad Oak, Lynn Harrison, Ke Xu, Regina Nuccio, Alise K. Blake, Roya Mostafavi, Sara Lewis, Leslie M. Taylor, Manish Kubal, Annastasia Ouma, Stacy J. Hines-Dowell, Cheng Cheng, Larissa V. Furtado, Kim E. Nichols
Summary: This study retrospectively examined the prevalence and impact of pathogenic variants in adult-onset cancer predisposition genes (aoCPGs) in pediatric tumors. They found that a small percentage of patients had tumors with aoCPG variants, with some of these variants being of germline origin. These variants were associated with alterations in tumor molecular profiles, but were not commonly used to change treatment decisions in pediatric cancers.
CLINICAL CANCER RESEARCH
(2023)