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Computationally efficient demographic history inference from allele frequencies with supervised machine learning Mol. Biol. Evol. (IF 10.7) Pub Date : 2024-04-18 Linh N Tran, Connie K Sun, Travis J Struck, Mathews Sajan, Ryan N Gutenkunst
Inferring past demographic history of natural populations from genomic data is of central concern in many studies across research fields. Previously, our group had developed dadi, a widely used demographic history inference method based on the allele frequency spectrum (AFS) and maximum composite likelihood optimization. However, dadi’s optimization procedure can be computationally expensive. Here
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Comparison of Bayesian Coalescent Skyline Plot Models for Inferring Demographic Histories Mol. Biol. Evol. (IF 10.7) Pub Date : 2024-04-17 Ronja J Billenstein, Sebastian Höhna
Bayesian coalescent skyline plot models are widely used to infer demographic histories. The first (non-Bayesian) coalescent skyline plot model assumed a known genealogy as data, while subsequent models and implementations jointly inferred the genealogy and demographic history from sequence data, including heterochronous samples. Overall, there exist multiple different Bayesian coalescent skyline plot
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Terrestrial birth and body size tune UCP1 functionality in seals Mol. Biol. Evol. (IF 10.7) Pub Date : 2024-04-10 Michael J Gaudry, Jane Khudyakov, Laura Pirard, Cathy Debier, Daniel Crocker, Paul G Crichton, Martin Jastroch
The molecular evolution of the mammalian heater protein UCP1 is a powerful biomarker to understand thermoregulatory strategies during species radiation into extreme climates, such as aquatic life with high thermal conductivity. While fully aquatic mammals lost UCP1, most semi-aquatic seals display intact UCP1 genes, apart from large elephant seals. Here, we show that UCP1 thermogenic activity of the
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Phased assembly of neo-sex chromosomes reveals extensive Y degeneration and rapid genome evolution in Rumex hastatulus Mol. Biol. Evol. (IF 10.7) Pub Date : 2024-04-10 Bianca Sacchi, Zoë Humphries, Jana Kružlicová, Markéta Bodláková, Cassandre Pyne, Baharul Choudhury, Yunchen Gong, Václav Bačovský, Roman Hobza, Spencer C H Barrett, Stephen I Wright
Y chromosomes are thought to undergo progressive degeneration due to stepwise loss of recombination and subsequent reduction in selection efficiency. However, the timescales and evolutionary forces driving degeneration remain unclear. To investigate the evolution of sex chromosomes on multiple timescales, we generated a high-quality phased genome assembly of the massive older (<10MYA) and neo (<200
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Viral Receptor-Binding Protein Evolves New Function through Mutations That Cause Trimer Instability and Functional Heterogeneity Mol. Biol. Evol. (IF 10.7) Pub Date : 2024-04-08 Hannah M Strobel, Sweetzel D Labador, Dwaipayan Basu, Mrudula Sane, Kevin D Corbett, Justin R Meyer
When proteins evolve new activity, a concomitant decrease in stability is often observed because the mutations that confer new activity can destabilize the native fold. In the conventional model of protein evolution, reduced stability is considered a purely deleterious cost of molecular innovation because unstable proteins are prone to aggregation and are sensitive to environmental stressors. However
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Earl Grey: A Fully Automated User-Friendly Transposable Element Annotation and Analysis Pipeline Mol. Biol. Evol. (IF 10.7) Pub Date : 2024-04-05 Tobias Baril, James Galbraith, Alex Hayward
Transposable elements (TEs) are major components of eukaryotic genomes and are implicated in a range of evolutionary processes. Yet, TE annotation and characterization remain challenging, particularly for nonspecialists, since existing pipelines are typically complicated to install, run, and extract data from. Current methods of automated TE annotation are also subject to issues that reduce overall
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fastDFE: fast and flexible inference of the distribution of fitness effects Mol. Biol. Evol. (IF 10.7) Pub Date : 2024-04-04 Janek Sendrowski, Thomas Bataillon
Estimating the distribution of fitness effects (DFE) of new mutations is of fundamental importance in evolutionary biology, ecology, and conservation. However, existing methods for DFE estimation suffer from limitations, such as slow computation speed and limited scalability. To address these issues, we introduce fastDFE, a Python-based software package, offering fast and flexible DFE inference from
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Inter-species transcriptomic analysis reveals a constitutive adaptation against oxidative stress for the highly virulent Leptospira species Mol. Biol. Evol. (IF 10.7) Pub Date : 2024-04-04 Alexandre Giraud-Gatineau, Garima Ayachit, Cecilia Nieves, Kouessi C Dagbo, Konogan Bourhy, Francisco Pulido, Samuel G Huete, Nadia Benaroudj, Mathieu Picardeau, Frédéric J Veyrier
Transcriptomic analyses across large scales of evolutionary distance have great potential to shed light on regulatory evolution but are complicated by difficulties in establishing orthology and limited availability of accessible software. We introduce here a method and a graphical user interface (GUI) wrapper, called Annotator-RNAtor, for performing interspecies transcriptomic analysis and studying
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Ancient Genomes From Bronze Age Remains Reveal Deep Diversity and Recent Adaptive Episodes for Human Oral Pathobionts Mol. Biol. Evol. (IF 10.7) Pub Date : 2024-03-27 Iseult Jackson, Peter Woodman, Marion Dowd, Linda Fibiger, Lara M Cassidy
Ancient microbial genomes can illuminate pathobiont evolution across millenia, with teeth providing a rich substrate. However, the characterization of prehistoric oral pathobiont diversity is limited. In Europe, only preagricultural genomes have been subject to phylogenetic analysis, with none compared to more recent archaeological periods. Here, we report well-preserved microbiomes from two 4,000-year-old
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Emergence of an orphan nitrogenase protein following atmospheric oxygenation Mol. Biol. Evol. (IF 10.7) Pub Date : 2024-03-25 Bruno Cuevas Zuviría, Amanda K Garcia, Alex J Rivier, Holly R Rucker, Brooke M Carruthers, Betül Kaçar
Molecular innovations within key metabolisms can have profound impacts on element cycling and ecological distribution. Yet, much of the molecular foundations of early evolved enzymes and metabolisms are unknown. Here, we bring one such mystery to relief by probing the birth and evolution of the G-subunit protein, an integral component of certain members of the nitrogenase family, the only enzymes capable
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The Origin and Evolution of Sex Peptide and Sex Peptide Receptor Interactions Mol. Biol. Evol. (IF 10.7) Pub Date : 2024-03-22 Junhui Peng, Nicolas Svetec, Henrik Molina, Li Zhao
Post-mating responses play a vital role in successful reproduction across diverse species. In fruit flies, sex peptide (SP) binds to the sex peptide receptor (SPR), triggering a series of post-mating responses. However, the origin of SPR predates the emergence of SP. The evolutionary origins of the interactions between SP and SPR and the mechanisms by which they interact remain enigmatic. In this study
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Genomic diversity in the endosymbiotic bacteria of human head lice Mol. Biol. Evol. (IF 10.7) Pub Date : 2024-03-21 Bret M Boyd, Niyomi House, Christopher W Carduck, David L Reed
Insects have repeatedly forged symbioses with heritable microbes, gaining novel traits. For the microbe, the transition to symbioses can lead to the degeneration of the symbiont’s genome through transmission bottlenecks, isolation, and the loss of DNA repair enzymes. However, some insect-microbial symbioses have persisted for millions of years, suggesting natural selection slows genetic drift and maintains
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Multiple genomic landscapes of recombination and genomic divergence in wild populations of house mice - the role of chromosomal fusions and Prdm9 Mol. Biol. Evol. (IF 10.7) Pub Date : 2024-03-21 Cristina Marín-García, Lucía Álvarez-González, Laia Marín-Gual, Sònia Casillas, Judith Picón, Keren Yam, María Magdalena Garcias-Ramis, Covadonga Vara, Jacint Ventura, Aurora Ruiz-Herrera
Chromosomal fusions represent one of the most common types of chromosomal rearrangements found in nature. Yet, their role in shaping the genomic landscape of recombination and hence genome evolution remains largely unexplored. Here, we take advantage of wild mice populations with chromosomal fusions to evaluate the effect of this type of structural variant on genomic landscapes of recombination and
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Scalepopgen: bioinformatics workflow resources implemented in Nextflow for comprehensive population genomic analyses Mol. Biol. Evol. (IF 10.7) Pub Date : 2024-03-20 Maulik Upadhyay, Neza Pogorevc, Ivica Medugorac
Population genomic analyses such as inference of population structure and identifying signatures of selection usually involve the application of a plethora of tools. The installation of tools and their dependencies, data transformation, or series of data preprocessing in a particular order, sometimes makes the analyses challenging. While the usage of container-based technologies has significantly resolved
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Ancient mitogenomes reveal the maternal genetic history of East Asian dogs Mol. Biol. Evol. (IF 10.7) Pub Date : 2024-03-20 Ming Zhang, Yanbo Song, Caihui Wang, Guoping Sun, Lina Zhuang, Mingjian Guo, Lele Ren, Shargan Wangdue, Guanghui Dong, Qingyan Dai, Peng Cao, Ruowei Yang, Feng Liu, Xiaotian Feng, E Andrew Bennett, Xiaoling Zhang, Xi Chen, Fen Wang, Fengshi Luan, Wenbin Dong, Guoquan Lu, Daohua Hao, Hongwei Hou, Hui Wang, Hong Qiao, Zhongxin Wang, Xiaojun Hu, Wei He, Lin Xi, Weilin Wang, Jing Shao, Zhouyong Sun, Lianjian
Recent studies have suggested that dogs were domesticated during the Last Glacial Maximum (LGM) in Siberia, which contrasts with previous proposed domestication centers (e.g., Europe, the Middle East, and East Asia). Ancient DNA provides a powerful resource for the study of mammalian evolution and has been widely used to understand the genetic history of domestic animals. To understand the maternal
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Correlated allele frequency changes reveal clonal structure and selection in temporal genetic data Mol. Biol. Evol. (IF 10.7) Pub Date : 2024-03-20 Yunxiao Li, John P Barton
In evolving populations where the rate of beneficial mutations is large, subpopulations of individuals with competing beneficial mutations can be maintained over long times. Evolution with this kind of clonal structure is commonly observed in a wide range of microbial and viral populations. However, it can be difficult to completely resolve clonal dynamics in data. This is due to limited read lengths
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The diverse evolutionary histories of domesticated metaviral capsid genes in mammals Mol. Biol. Evol. (IF 10.7) Pub Date : 2024-03-20 William S Henriques, Janet M Young, Artem Nemudryi, Anna Nemudraia, Blake Wiedenheft, Harmit S Malik
Selfish genetic elements comprise significant fractions of mammalian genomes. In rare instances, host genomes domesticate segments of these elements for function. Using a complete human genome assembly and 25 additional vertebrate genomes, we re-analyzed the evolutionary trajectories and functional potential of capsid genes domesticated from Metaviridae, a lineage of retrovirus-like retrotransposons
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Adaptation in unstable environments and global gene losses - Small but stable gene networks by the May-Wigner theory Mol. Biol. Evol. (IF 10.7) Pub Date : 2024-03-19 Shaohua Xu, Shao Shao, Xiao Feng, Sen Li, Lingjie Zhang, Weihong Wu, Min Liu, Miles E Tracy, Cairong Zhong, Zixiao Guo, Chung-I Wu, Suhua Shi, Ziwen He
Although gene loss is common in evolution, it remains unclear whether it is an adaptive process. In a survey of seven major mangrove clades that are woody plants in the intertidal zones of daily environmental perturbations, we noticed that they generally evolved reduced gene numbers. We then focused on the largest clade of Rhizophoreae and observed the continual gene set reduction in each of the eight
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Fermentation practices select for thermostable endolysins in phages Mol. Biol. Evol. (IF 10.7) Pub Date : 2024-03-15 Frank Oechslin, Xiaojun Zhu, Carlee Morency, Vincent Somerville, Rong Shi, Sylvain Moineau
Endolysins are produced by (bacterio)phages and play a crucial role in degrading the bacterial cell wall and the subsequent release of new phage progeny. These lytic enzymes exhibit a remarkable diversity, often occurring in a multimodular form that combines different catalytic and cell wall-binding domains, even in phages infecting the same species. Yet, our current understanding lacks insight into
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Genetic basis and evolutionary forces of sexually dimorphic colour variation in a toad-headed agamid lizard Mol. Biol. Evol. (IF 10.7) Pub Date : 2024-03-11 Bin Lu, Xia Qiu, Weizhao Yang, Zhongyi Yao, Xiaofeng Ma, Shunyan Deng, Qi Zhang, Jinzhong Fu, Yin Qi
In the animal kingdom, sexually dimorphic colour variation is a widespread phenomenon that significantly influences survival and reproductive success. However, the genetic underpinnings of this variation remain inadequately understood. Our investigation into sexually dimorphic colour variation in the desert-dwelling Guinan population (GN) of the toad-headed agamid lizard (Phrynocephalus putjatai) utilized
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Predicting functional consequences of recent natural selection in Britain Mol. Biol. Evol. (IF 10.7) Pub Date : 2024-03-11 Lin Poyraz, Laura L Colbran, Iain Mathieson
Ancient DNA can directly reveal the contribution of natural selection to human genomic variation. However, while the analysis of ancient DNA has been successful at identifying genomic signals of selection, inferring the phenotypic consequences of that selection has been more difficult. Most trait-associated variants are non-coding, so we expect that a large proportion of the phenotypic effects of selection
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The Expected Behaviors of Posterior Predictive Tests and Their Unexpected Interpretation Mol. Biol. Evol. (IF 10.7) Pub Date : 2024-03-04 Luiza Guimarães Fabreti, Lyndon M. Coghill, Robert C. Thomson, Sebastian Höhna, Jeremy M. Brown
Poor fit between models of sequence or trait evolution and empirical data is known to cause biases and lead to spurious conclusions about evolutionary patterns and processes. Bayesian posterior prediction is a flexible and intuitive approach for detecting such cases of poor fit. However, the expected behavior of posterior predictive tests has never been characterized for evolutionary models, which
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Evolution of a restriction factor by domestication of a yeast retrotransposon Mol. Biol. Evol. (IF 10.7) Pub Date : 2024-03-03 J Adam Hannon-Hatfield, Jingxuan Chen, Casey M Bergman, David J Garfinkel
Transposable elements (TEs) drive genome evolution in all branches of life. TE insertions are often deleterious to their hosts and necessitate evolution of control mechanisms to limit their spread. The long terminal repeat retrotransposon Ty1 prime (Ty1’), a subfamily of the Ty1 family, is present in many Saccharomyces cerevisiae strains but little is known about what controls its copy number. Here
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PAPipe: a pipeline for comprehensive population genetic analysis Mol. Biol. Evol. (IF 10.7) Pub Date : 2024-03-01 Nayoung Park, Hyeonji Kim, Jeongmin Oh, Jinseok Kim, Charyeong Heo, Jaebum Kim
Advancements in next-generation sequencing (NGS) technologies have led to a substantial increase in the availability of population genetic variant data, thus prompting the development of various population analysis tools to enhance our understanding of population structure and evolution. The tools that are currently used to analyze population genetic variant data generally require different environments
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Aneuploidy can be an evolutionary diversion on the path to adaptation Mol. Biol. Evol. (IF 10.7) Pub Date : 2024-03-01 Ilia Kohanovski, Martin Pontz, Pétra Vande Zande, Anna Selmecki, Orna Dahan, Yitzhak Pilpel, Avihu H Yona, Yoav Ram
Aneuploidy is common in eukaryotes, often leading to decreased fitness. However, evidence from fungi and human tumur cells suggests that specific aneuploidies can be beneficial under stressful conditions and facilitate adaptation. In a previous evolutionary experiment with yeast, populations evolving under heat stress became aneuploid, only to later revert to euploidy after beneficial mutations accumulated
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Formation of different polyploids through disrupting meiotic crossover frequencies based on cntd1 knockout in zebrafish Mol. Biol. Evol. (IF 10.7) Pub Date : 2024-02-29 Yuan Ou, Huilin Li, Juan Li, Xiangyan Dai, Jiaxin He, Shi Wang, Qingfeng Liu, Conghui Yang, Jing Wang, Rurong Zhao, Zhan Yin, Yuqin Shu, Shaojun Liu
Polyploidy, a significant catalyst for speciation and evolutionary processes in both plant and animal kingdoms, has been recognized for a long time. However, the exact molecular mechanism that leads to polyploid formation, especially in vertebrates, is not fully understood. Our study aimed to elucidate this phenomenon using the zebrafish model. We successfully achieved an effective knockout of the
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Genetic basis and evolution of structural color polymorphism in an Australian songbird Mol. Biol. Evol. (IF 10.7) Pub Date : 2024-02-28 Simon Yung Wa Sin, Fushi Ke, Guoling Chen, Pei-Yu Huang, Erik Enbody, Jordan Karubian, Michael S Webster, Scott V Edwards
Island organisms often evolve phenotypes divergent from their mainland counterparts, providing a useful system for studying adaptation under differential selection. In the white-winged fairywren (Malurus leucopterus), subspecies on two islands have a black nuptial plumage whereas the subspecies on the Australian mainland has a blue nuptial plumage. The black subspecies have a feather nanostructure
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Functional and evolutionary integration of a fungal gene with a bacterial operon Mol. Biol. Evol. (IF 10.7) Pub Date : 2024-02-28 Liang Sun, Kyle T David, John F Wolters, Steven D Karlen, Carla Gonçalves, Dana A Opulente, Abigail Leavitt LaBella, Marizeth Groenewald, Xiaofan Zhou, Xing-Xing Shen, Antonis Rokas, Chris Todd Hittinger
Siderophores are crucial for iron-scavenging in microorganisms. While many yeasts can uptake siderophores produced by other organisms, they are typically unable to synthesize siderophores themselves. In contrast, Wickerhamiella/Starmerella (W/S) clade yeasts gained the capacity to make the siderophore enterobactin following the remarkable horizontal acquisition of a bacterial operon enabling enterobactin
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Gene and Allele-Specific Expression Underlying the Electric Signal Divergence in African Weakly Electric Fish Mol. Biol. Evol. (IF 10.7) Pub Date : 2024-02-27 Feng Cheng, Alice B Dennis, Otto Baumann, Frank Kirschbaum, Salim Abdelilah-Seyfried, Ralph Tiedemann
In the African weakly electric fish genus Campylomormyrus, electric organ discharge signals are strikingly different in shape and duration among closely related species, contribute to prezygotic isolation, and may have triggered an adaptive radiation. We performed mRNA sequencing on electric organs and skeletal muscles (from which the electric organs derive) from 3 species with short (0.4 ms), medium
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Fitness effects of phenotypic mutations at proteome-scale reveal optimality of translation machinery Mol. Biol. Evol. (IF 10.7) Pub Date : 2024-02-27 Cedric Landerer, Jonas Pöhls, Agnes Toth-Petroczy
Errors in protein translation can lead to non-genetic, phenotypic mutations, including amino acid misincorporations. While phenotypic mutations can increase protein diversity, the systematic characterization of their proteome-wide frequencies and their evolutionary impact has been lacking. Here, we developed a mechanistic model of translation errors to investigate how selection acts on protein populations
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PlantFUNCO: Integrative functional genomics database reveals clues into duplicates divergence evolution Mol. Biol. Evol. (IF 10.7) Pub Date : 2024-02-27 Víctor Roces, Sara Guerrero, Ana Álvarez, Jesús Pascual, Mónica Meijón
Evolutionary epigenomics and, more generally, evolutionary functional-genomics, are emerging fields that study how non-DNA-encoded alterations in gene expression regulation are an important form of plasticity and adaptation. Previous evidence analysing plants’ comparative functional genomics has mostly focused on comparing same assay-matched experiments, missing the power of heterogeneous datasets
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Rapid and repeated climate adaptation involving chromosome inversions following invasion of an insect Mol. Biol. Evol. (IF 10.7) Pub Date : 2024-02-24 Li-Jun Ma, Li-Jun Cao, Jin-Cui Chen, Meng-Qing Tang, Wei Song, Fang-Yuan Yang, Xiu-Jing Shen, Ya-Jing Ren, Qiong Yang, Hu Li, Ary Anthony Hoffmann, Shu-Jun Wei
Following invasion, insects can become adapted to conditions experienced in their invasive range, but there are few studies on the speed of adaptation and its genomic basis. Here, we examine a small insect pest, Thrips palmi, following its contemporary range expansion across a sharp climate gradient from the subtropics to temperate areas. We first found a geographically associated population genetic
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Transposable element insertions are associated with Batesian mimicry in the pantropical butterfly Hypolimnas misippus Mol. Biol. Evol. (IF 10.7) Pub Date : 2024-02-23 Anna Orteu, Marek Kucka, Ian J Gordon, Ivy Ng’iru, Eva S M van der Heijden, Gerard Talavera, Ian A Warren, Steve Collins, Richard H ffrench-Constant, Dino J Martins, Yingguang Frank Chan, Chris D Jiggins, Simon H Martin
Hypolimnas misippus is a Batesian mimic of the toxic African Queen butterfly (Danaus chrysippus). Female H. misippus butterflies use two major wing patterning loci (M and A) to imitate three colour morphs of D. chrysippus found in different regions of Africa. In this study, we examine the evolution of the M locus and identify it as an example of adaptive atavism. This phenomenon involves a morphological
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Cytonuclear interactions and subgenome dominance shape the evolution of organelle-targeted genes in the Brassica triangle of U Mol. Biol. Evol. (IF 10.7) Pub Date : 2024-02-23 Shenglong Kan, Xuezhu Liao, Lan Lan, Jiali Kong, Jie Wang, Liyun Nie, Jun Zou, Hong An, Zhiqiang Wu
The interaction and co-evolution between nuclear and cytoplasmic genomes are one of the fundamental hallmarks of eukaryotic genome evolution and, two billion years later, are still major contributors to the formation of new species. Although many studies have investigated the role of cytonuclear interactions following allopolyploidization, the relative magnitude of the effect of subgenome dominance
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Adaptive Selection of Cis-regulatory Elements in the Han Chinese Mol. Biol. Evol. (IF 10.7) Pub Date : 2024-02-20 Shuai Liu, Huaxia Luo, Peng Zhang, Yanyan Li, Di Hao, Sijia Zhang, Tingrui Song, Tao Xu, Shunmin He
Cis-regulatory elements (CREs) have an important role in human adaptation to the living environment. However, the lag in population genomic cohort studies and epigenomic studies, hinders the research in the adaptive analysis of CREs in human populations. In this study, we collected 4,013 unrelated individuals and performed a comprehensive analysis of adaptive selection of genome-wide CREs in the Han
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Investigating the Evolution of Drosophila STING-dependent Antiviral Innate Immunity by Multispecies Comparison of 2′3′-cGAMP Responses Mol. Biol. Evol. (IF 10.7) Pub Date : 2024-02-20 Léna Hédelin, Antonin Thiébaut, Jingxian Huang, Xiaoyan Li, Aurélie Lemoine, Gabrielle Haas, Carine Meignin, Hua Cai, Robert M Waterhouse, Nelson Martins, Jean-Luc Imler
Viruses represent a major threat for all animals, which defend themselves through induction of a large set of virus-stimulated genes that collectively control the infection. In vertebrates, these genes include interferons that play a critical role in the amplification of the response to infection. Virus- and interferon-stimulated genes include restriction factors targeting the different steps of the
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Degeneration of the Olfactory System in a Murid Rodent that Evolved Diurnalism Mol. Biol. Evol. (IF 10.7) Pub Date : 2024-02-20 Ben-Yang Liao, Meng-Pin Weng, Ting-Yan Chang, Andrew Ying-Fei Chang, Yung-Hao Ching, Chia-Hwa Wu
In mammalian research, it has been debated what can initiate an evolutionary trade-off between different senses, and the phenomenon of sensory trade-off in rodents, the most abundant mammalian clade, is not evident. The Nile rat (Arvicanthis niloticus), a murid rodent, recently adapted to a diurnal niche through an evolutionary acquisition of daylight vision with enhanced visual acuity. As such, this
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A high-quality blue whale genome, segmental duplications, and historical demography Mol. Biol. Evol. (IF 10.7) Pub Date : 2024-02-20 Yury V Bukhman, Phillip A Morin, Susanne Meyer, Li-Fang Chu, Jeff K Jacobsen, Jessica Antosiewicz-Bourget, Daniel Mamott, Maylie Gonzales, Cara Argus, Jennifer Bolin, Mark E Berres, Olivier Fedrigo, John Steill, Scott A Swanson, Peng Jiang, Arang Rhie, Giulio Formenti, Adam M Phillippy, Robert S Harris, Jonathan M D Wood, Kerstin Howe, Bogdan M Kirilenko, Chetan Munegowda, Michael Hiller, Aashish Jain
The blue whale, Balaenoptera musculus, is the largest animal known to have ever existed, making it an important case study in longevity and resistance to cancer. To further this and other blue whale-related research, we report a reference-quality, long-read-based genome assembly of this fascinating species. We assembled the genome from PacBio long reads and utilized Illumina/10X, optical maps, and
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Genomic analyses capture the human-induced demographic collapse and recovery in a wide-ranging cervid Mol. Biol. Evol. (IF 10.7) Pub Date : 2024-02-19 Camille Kessler, Aaron B A Shafer
The glacial cycles of the Quaternary heavily impacted species through successions of population contractions and expansions. Similarly, populations have been intensely shaped by human pressures such as unregulated hunting and land use changes. White-tailed and mule deer survived in different refugia through the Last Glacial Maximum, and their populations were severely reduced after the European colonisation
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The effects of de novo mutation on gene expression and the consequences for fitness in Chlamydomonas reinhardtii Mol. Biol. Evol. (IF 10.7) Pub Date : 2024-02-17 Eniolaye J Balogun, Rob W Ness
Mutation is the ultimate source of genetic variation, the bedrock of evolution. Yet, predicting the consequences of new mutations remains a challenge in biology. Gene expression provides a potential link between a genotype and its phenotype. But the variation in gene expression created by de novo mutation and the fitness consequences of mutational changes to expression remain relatively unexplored
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Secondary contact, introgressive hybridization and genome stabilization in sticklebacks Mol. Biol. Evol. (IF 10.7) Pub Date : 2024-02-17 Xueyun Feng, Juha Merilä, Ari Löytynoja
Advances in genomic studies have revealed that hybridization in nature is pervasive and raised questions about the dynamics of different genetic and evolutionary factors following the initial hybridization event. While recent research has proposed that the genomic outcomes of hybridization might be predictable to some extent, many uncertainties remain. With comprehensive whole-genome sequence data
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A critical appraisal of DNA transfer from plants to parasitic cyst nematodes Mol. Biol. Evol. (IF 10.7) Pub Date : 2024-02-17 Itsuhiro Ko, Olaf Prosper Kranse, Beatrice Senatori, Sebastian Eves-van den Akker
Plant-parasitic nematodes are one of the most economically important pests of crops. It is widely accepted that Horizontal Gene Transfer (HGT) - the natural acquisition of foreign genes in parasitic nematodes - contributes to parasitism. However, an apparent paradox has emerged from HGT analyses: On one hand, distantly related organisms with very dissimilar genetic structures (i.e. bacteria), and only
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The Density of Regulatory Information Is a Major Determinant of Evolutionary Constraint on Noncoding DNA in Drosophila Mol. Biol. Evol. (IF 10.7) Pub Date : 2024-02-16 Gonzalo Sabarís, Daniela M Ortíz, Ian Laiker, Ignacio Mayansky, Sujay Naik, Giacomo Cavalli, David L Stern, Ella Preger-Ben Noon, Nicolás Frankel
Evolutionary analyses have estimated that ∼60% of nucleotides in intergenic regions of the Drosophila melanogaster genome are functionally relevant, suggesting that regulatory information may be encoded more densely in intergenic regions than has been revealed by most functional dissections of regulatory DNA. Here, we approached this issue through a functional dissection of the regulatory region of
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Adaptive evolution of Pseudomonas aeruginosa in human airways shows phenotypic convergence despite diverse patterns of genomic changes Mol. Biol. Evol. (IF 10.7) Pub Date : 2024-02-16 Akbar Espaillat, Claudia Antonella Colque, Daniela Rago, Ruggero La Rosa, Søren Molin, Helle Krogh Johansen
Selective forces in the environment drive bacterial adaptation to novel niches, choosing the fitter variants in the population. However, in dynamic and changing environments, the evolutionary processes controlling bacterial adaptation are difficult to monitor. Here, we follow 9 people with cystic fibrosis chronically infected with Pseudomonas aeruginosa, as a proxy for bacterial adaptation. We identify
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The predictable network topology of evolutionary genomic constraint Mol. Biol. Evol. (IF 10.7) Pub Date : 2024-02-15 Katharina C Wollenberg Valero
Large-scale comparative genomics studies offer valuable resources for understanding both functional and evolutionary rate constraints. It is suggested that constraint aligns with the topology of genomic networks, increasing towards the center, with intermediate nodes combining relaxed constraint with higher contributions to the phenotype due to pleiotropy. However, this pattern has yet to be demonstrated
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Biogeographic Perspectives on Our Species’ Genetic Diversification Mol. Biol. Evol. (IF 10.7) Pub Date : 2024-02-13 Tábita Hünemeier
Modern humans originated in Africa 300,000 years ago, and before leaving their continent of origin, they underwent a process of intense diversification involving complex demographic dynamics. Upon exiting Africa, different populations emerged on the four other existing continents, shaped by the interplay of various evolutionary processes, such as migrations, founder effects, and natural selection.
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Association analysis provides insights into plant mitonuclear interactions Mol. Biol. Evol. (IF 10.7) Pub Date : 2024-02-07 Qun Lian, Shuai Li, Shenglong Kan, Xuezhu Liao, Sanwen Huang, Daniel B Sloan, Zhiqiang Wu
Cytonuclear interaction refers to the complex and ongoing process of coevolution between nuclear and organelle genomes, which are responsible for cellular respiration, photosynthesis, lipid metabolism, etc. and play a significant role in adaptation and speciation. There have been a large number of studies to detect signatures of cytonuclear interactions. However, identification of the specific nuclear
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Landscape heterogeneity explains the genetic differentiation of a forest bird across the Sino-Himalayan Mountains Mol. Biol. Evol. (IF 10.7) Pub Date : 2024-02-06 Xiaolu Jiao, Lei Wu, Dezhi Zhang, Huan Wang, Feng Dong, Le Yang, Shangyu Wang, Hitoha E Amano, Weiwei Zhang, Chenxi Jia, Frank E Rheindt, Fumin Lei, Gang Song
Mountains are the world’s most important centers of biodiversity. The Sino-Himalayan Mountains (SHM) are global biodiversity hotspot due to their extremely high species richness and endemicity. Ample research investigated the impact of the Qinghai-Tibet Plateau uplift and Quaternary glaciations in driving species diversification in plants and animals across the SHM. However, little is known about the
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Substitution models of protein evolution with selection on enzymatic activity Mol. Biol. Evol. (IF 10.7) Pub Date : 2024-02-05 David Ferreiro, Ruqaiya Khalil, Sergio F Sousa, Miguel Arenas
Substitution models of evolution are necessary for diverse evolutionary analyses including phylogenetic tree and ancestral sequence reconstructions. At the protein level, empirical substitution models are traditionally used due to their simplicity, but they ignore the variability of substitution patterns among protein sites. Next, in order to improve the realism of the modeling of protein evolution
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Mapping geological events and nitrogen fixation evolution onto the timetree of the evolution of nitrogen-fixation genes Mol. Biol. Evol. (IF 10.7) Pub Date : 2024-02-03 Hong-Wei Pi, Yin-Ru Chiang, Wen-Hsiung Li
Nitrogen is essential for all organisms, but biological nitrogen fixation (BNF) occurs only in a small fraction of prokaryotes. Previous studies divided nitrogenase-gene-carrying prokaryotes into Groups I to IV and provided evidence that BNF first evolved in bacteria. This study constructed a timetree of the evolution of nitrogen-fixation genes and estimated that archaea evolved BNF much later than
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Adaptive evolution of Nearctic deepwater fish vision: Implications for assessing functional variation for conservation Mol. Biol. Evol. (IF 10.7) Pub Date : 2024-02-02 Alexander Van Nynatten, Alexander T Duncan, Ryan Lauzon, Tom A Sheldon, Steven K Chen, Nathan R Lovejoy, Nicholas E Mandrak, Belinda S W Chang
Intraspecific functional variation is critical for adaptation to rapidly changing environments. For visual opsins, functional variation can be characterized in vitro and often reflects a species’ ecological niche but is rarely considered in the context of intraspecific variation or the impact of recent environmental changes on species of cultural or commercial significance. Investigation of adaptation
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The Dynamic Interplay between Ribosomal DNA and Transposable Elements: A Perspective from Genomics and Cytogenetics Mol. Biol. Evol. (IF 10.7) Pub Date : 2024-02-02 Sònia Garcia, Ales Kovarik, Sophie Maiwald, Ludwig Mann, Nicola Schmidt, Joan Pere Pascual-Díaz, Daniel Vitales, Beatrice Weber, Tony Heitkam
Although both are salient features of genomes, at first glance ribosomal DNAs (rDNAs) and transposable elements (TEs) are genetic elements with not much in common: whereas rDNAs are mainly viewed as housekeeping genes that uphold all prime genome functions, TEs are generally portrayed as selfish and disruptive. These opposing characteristics are also mirrored in other attributes: organization in tandem
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Bridge: A New Algorithm for Rooting Orthologous Genes in Large-Scale Evolutionary Analysis Mol. Biol. Evol. (IF 10.7) Pub Date : 2024-02-02 Leonardo RS Campos, Sheyla Trefflich, Diego AA Morais, Danilo O Imparato, Vinicius S Chagas, Ricardo D’Oliveira Albanus, Rodrigo JS Dalmolin, Mauro AA Castro
Orthology information has been used for searching patterns in high-dimensional data, allowing transferring functional information between species. The key concept behind this strategy is that orthologous genes share ancestry to some extent. While reconstructing the history of a single gene is feasible with the existing computational resources, the reconstruction of entire biological systems remains
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Positive selection drives cis-regulatory evolution across the threespine stickleback Y chromosome Mol. Biol. Evol. (IF 10.7) Pub Date : 2024-02-02 Daniel E Shaw, Alice Shanfelter Naftaly, Michael A White
Allele-specific gene expression evolves rapidly on heteromorphic sex chromosomes. Over time, the accumulation of mutations on the Y chromosome leads to widespread loss of gametolog expression, relative to the X chromosome. It remains unclear if expression evolution on degrading Y chromosomes is primarily driven by mutations that accumulate through processes of selective interference, or if positive
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Conservation of affinity rather than sequence underlies a dynamic evolution of the motif-mediated p53/MDM2 interaction in ray-finned fishes Mol. Biol. Evol. (IF 10.7) Pub Date : 2024-02-01 Filip Mihalič, Dahiana Arcila, Mats E Pettersson, Pouria Farkhondehkish, Eva Andersson, Leif Andersson, Ricardo Betancur-R, Per Jemth
The transcription factor and cell cycle regulator p53 is marked for degradation by the ubiquitin ligase MDM2. The interaction between these two proteins is mediated by a conserved binding motif in the disordered p53 transactivation domain (p53TAD) and the folded SWIB domain in MDM2. The conserved motif in p53TAD from zebrafish displays a 20-fold weaker interaction with MDM2, compared to the interaction
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Adaptive capacity of a DNA polymerase clamp-loader ATPase complex Mol. Biol. Evol. (IF 10.7) Pub Date : 2024-01-30 Subu Subramanian, Weilin Zhang, Siddharth Nimkar, Mazzin Kamel, Michael O’Donnell, John Kuriyan
The ability of mutations to facilitate adaptation is central to evolution. To understand how mutations can lead to functional adaptation in a complex molecular machine, we created a defective version of the T4 clamp-loader complex, which is essential for DNA replication. This variant, which is ∼5000-fold less active than the wildtype, was made by replacing the catalytic domains with those from another
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Exploring adaptive phenotypes for the human calcium-sensing receptor polymorphism R990G Mol. Biol. Evol. (IF 10.7) Pub Date : 2024-01-29 Barbara Sinigaglia, Jorge Escudero, Simone A Biagini, Jorge Garcia-Calleja, Josep Moreno, Begoña Dobon, Sandra Acosta, Mayukh Mondal, Sandra Walsh, Gabriela Aguileta, Mònica Vallès, Stephen Forrow, Juan Martin-Caballero, Andrea Bamberg Migliano, Jaume Bertranpetit, Francisco J Muñoz, Elena Bosch
Rainforest hunter-gatherers from South-East Asia are characterized by specific morphological features including a particularly dark skin color (D), short stature (S), woolly hair (W), and the presence of steatopygia (S) – fat accumulation localized in the hips (DSWS phenotype). Based on previous evidence in the Andamanese population, we first characterized signatures of adaptive natural selection around
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Encyclopaedia of family A DNA polymerases localized in organelles: Evolutionary contribution of bacteria including the proto-mitochondrion Mol. Biol. Evol. (IF 10.7) Pub Date : 2024-01-25 Ryo Harada, Yoshihisa Hirakawa, Akinori Yabuki, Eunsoo Kim, Euki Yazaki, Ryoma Kamikawa, Kentaro Nakano, Marek Eliáš, Yuji Inagaki
DNA polymerases (DNAPs) synthesize DNA from deoxyribonucleotides in a semi-conservative manner and serve as the core of DNA replication and repair machineries. In eukaryotic cells, there are two genome-containing organelles, mitochondria and plastids, that were derived from an alphaproteobacterium and a cyanobacterium, respectively. Except for rare cases of genome-lacking mitochondria and plastids
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Diurnal rhythms in the red seaweed Gracilariopsis chorda are characterized by unique regulatory networks of carbon metabolism Mol. Biol. Evol. (IF 10.7) Pub Date : 2024-01-25 JunMo Lee, Ji Hyun Yang, Andreas P M Weber, Debashish Bhattacharya, Woe-Yeon Kim, Hwan Su Yoon
Cellular and physiological cycles are driven by endogenous pacemakers, the diurnal and circadian rhythms. Key functions such as cell cycle progression and cellular metabolism are under rhythmic regulation, thereby maintaining physiological homeostasis. The photoreceptors phytochrome and cryptochrome, in response to light cues, are central input pathways for physiological cycles in most photosynthetic
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Cross-species comparative DNA methylation reveals novel insights into complex traits genetics among cattle, sheep and goats Mol. Biol. Evol. (IF 10.7) Pub Date : 2024-01-24 Siqian Chen, Shuli Liu, Shaolei Shi, Hongwei Yin, Yongjie Tang, Jinning Zhang, Wenlong Li, Gang Liu, Kaixing Qu, Xiangdong Ding, Yachun Wang, Jianfeng Liu, Shengli Zhang, Lingzhao Fang, Ying Yu
The cross-species characterization of evolutionary changes in the functional genome can facilitate the translation of genetic findings across species and the interpretation of the evolutionary basis underlying complex phenotypes. Yet, this has not been fully explored between cattle, sheep, goats, and other mammals. Here, we systematically characterized the evolutionary dynamics of DNA methylation and