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The Landscape of Recombination Events That Create Nonribosomal Peptide Diversity Mol. Biol. Evol. (IF 11.062) Pub Date : 2021-01-22 Martin Baunach; Somak Chowdhury; Pierre Stallforth; Elke Dittmann
Nonribosomal peptides (NRP) are crucial molecular mediators in microbial ecology and provide indispensable drugs. Nevertheless, the evolution of the flexible biosynthetic machineries that correlates with the stunning structural diversity of NRPs is poorly understood. Here, we show, that recombination is a key driver in the evolution of bacterial NRP synthetase (NRPS) genes across distant bacterial
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Transcription factors drive opposite relationships between gene age and tissue specificity in male and female Drosophila gonads Mol. Biol. Evol. (IF 11.062) Pub Date : 2021-01-22 Evan Witt; Nicolas Svetec; Sigi Benjamin; Li Zhao
Evolutionarily young genes are usually preferentially expressed in the testis across species. While it is known that older genes are generally more broadly expressed than younger genes, the properties that shaped this pattern are unknown. Older genes may gain expression across other tissues uniformly, or faster in certain tissues than others. Using Drosophila gene expression data, we confirmed previous
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The hunt for ancient prions: Archaeal prion-like domains form amyloid-based epigenetic elements Mol. Biol. Evol. (IF 11.062) Pub Date : 2021-01-22 Tomasz Zajkowski; Michael D Lee; Shamba S Mondal; Amanda Carbajal; Robert Dec; Patrick D Brennock; Radoslaw W Piast; Jessica E Snyder; Nicholas B Bense; Wojciech Dzwolak; Daniel F Jarosz; Lynn J Rothschild
Prions, proteins that can convert between structurally and functionally distinct states and serve as non-Mendelian mechanisms of inheritance, were initially discovered and only known in eukaryotes, and consequently considered to likely be a relatively late evolutionary acquisition. However, the recent discovery of prions in bacteria and viruses has intimated a potentially more ancient evolutionary
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Recreated ancestral opsin associated with marine to freshwater croaker invasion reveals kinetic and spectral adaptation Mol. Biol. Evol. (IF 11.062) Pub Date : 2021-01-22 Alexander Van Nynatten; Gianni M Castiglione; Eduardo de A Gutierrez; Nathan R Lovejoy; Belinda S W Chang
Rhodopsin, the light-sensitive visual pigment expressed in rod photoreceptors, is specialized for vision in dim light environments. Aquatic environments are particularly challenging for vision due to the spectrally-dependent attenuation of light, which can differ greatly in marine and freshwater systems. Among fish lineages that have successfully colonized freshwater habitats from ancestrally marine
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Compatibility of evolutionary responses to constituent antibiotics drive resistance evolution to drug pairs Mol. Biol. Evol. (IF 11.062) Pub Date : 2021-01-22 Leonie Johanna Jahn; Daniel Simon; Mia Jensen; Charles Bradshaw; Mostafa Mostafa Hashim Ellabaan; Morten Otto Alexander Sommer
Antibiotic combinations are considered a relevant strategy to tackle the global antibiotic resistance crisis since they are believed to increase treatment efficacy and reduce resistance evolution (World Health Organization and Global Tuberculosis Programme, 2016). However, studies of the evolution of bacterial resistance to combination therapy have focused on a limited number of drugs and have provided
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Maintenance of adaptive dynamics and no detectable load in a range-edge out-crossing plant population Mol. Biol. Evol. (IF 11.062) Pub Date : 2021-01-22 Margarita Takou; Tuomas Hämälä; Evan M Koch; Kim A Steige; Hannes Dittberner; Levi Yant; Mathieu Genete; Shamil Sunyaev; Vincent Castric; Xavier Vekemans; Outi Savolainen; Juliette de Meaux
During range expansion, edge populations are expected to face increased genetic drift, which in turn can alter and potentially compromise adaptive dynamics, preventing the removal of deleterious mutations and slowing down adaptation. Here, we contrast populations of the European sub-species Arabidopsis lyrata ssp petraea, which expanded its Northern range after the last glaciation. We document a sharp
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Integrating Linguistics, Social Structure, and Geography to Model Genetic Diversity within India Mol. Biol. Evol. (IF 11.062) Pub Date : 2021-01-22 Aritra Bose; Daniel E Platt; Laxmi Parida; Petros Drineas; Peristera Paschou
India represents an intricate tapestry of population substructure shaped by geography, language, culture and social stratification. While geography closely correlates with genetic structure in other parts of the world, the strict endogamy imposed by the Indian caste system and the large number of spoken languages add further levels of complexity to understand Indian population structure. To date, no
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dadi.CUDA: Accelerating Population Genetics Inference with Graphics Processing Units Mol. Biol. Evol. (IF 11.062) Pub Date : 2021-01-22 Ryan N Gutenkunst
dadi is a popular but computationally intensive program for inferring models of demographic history and natural selection from population genetic data. I show that running dadi on a Graphics Processing Unit can dramatically speed computation compared to the CPU implementation, with minimal user burden. Motivated by this speed increase, I also extended dadi to four- and five-population models. This
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Phylogenomics of the Maverick Virus-like Mobile Genetic Elements of Vertebrates Mol. Biol. Evol. (IF 11.062) Pub Date : 2021-01-22 Jose Gabriel Nino Barreat; Aris Katzourakis
Mavericks are virus-like mobile genetic elements found in the genomes of eukaryotes. Although Mavericks encode capsid morphogenesis homologues, their viral particles have not been observed. Here, we provide new evidence supporting the viral nature of Mavericks and the potential existence of virions. To this end, we conducted a phylogenomic analysis of Mavericks in hundreds of vertebrate genomes, discovering
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Corrigendum to: Phylogenetics Identifies Two Eumetazoan TRPM Clades and an Eighth TRP Family, TRP Soromelastatin (TRPS) Mol. Biol. Evol. (IF 11.062) Pub Date : 2020-12-24 Himmel N, Gray T, Cox D.
Mol. Biol. Evol. 37(7):2034–2044; doi:10.1093/molbev/msaa065
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MBE Emerging Classics 2021 Mol. Biol. Evol. (IF 11.062) Pub Date : 2020-12-23 Rowe H, Kumar S.
Molecular Biology and Evolution provides yearly recognition of recently published manuscripts that have made strong impressions on our research community since their publication. Below, we highlight ten discoveries, five methods, and five resources as “Emerging Classics” based on citations accrued per fractional year since print publication. Articles are listed alphabetically by the first author’s
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An unbiased molecular approach using 3'UTRs resolves the avian family-level tree of life. Mol. Biol. Evol. (IF 11.062) Pub Date : 2020-11-08 H Kuhl,C Frankl-Vilches,A Bakker,G Mayr,G Nikolaus,S T Boerno,S Klages,B Timmermann,M Gahr
AbstractPresumably, due to a rapid early diversification, major parts of the higher-level phylogeny of birds are still resolved controversially in different analyses or are considered unresolvable. To address this problem, we produced an avian tree of life, which includes molecular sequences of one or several species of ∼90% of the currently recognized family-level taxa (429 species, 379 genera) including
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Population dynamics and structural effects at short and long range support the hypothesis of the selective advantage of the G614 SARS-Cov2 spike variant Mol. Biol. Evol. (IF 11.062) Pub Date : 2021-01-02 Emiliano Trucchi; Paolo Gratton; Fabrizio Mafessoni; Stefano Motta; Francesco Cicconardi; Filippo Mancia; Giorgio Bertorelle; Ilda D’Annessa; Daniele Di Marino
SARS-CoV-2 epidemics quickly propagated worldwide, sorting virus genomic variants in newly established propagules of infections. Stochasticity in transmission within and between countries or an actual selective advantage could explain the global high frequency reached by some genomic variants. Using statistical analyses, demographic reconstructions, and molecular dynamics simulations, we show that
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MBE Transitions to the Open Access Publication Model in 2021 Mol. Biol. Evol. (IF 11.062) Pub Date : 2020-12-10 Kumar S, Rowe H.
AbstractFrom the first day of 2021, all manuscripts published in the journal Molecular Biology and Evolution (MBE) will be freely accessible online without a subscription. This exciting change will make all the MBE content available to all readers immediately upon publication.
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HAPHPIPE: Haplotype Reconstruction and Phylodynamics for Deep Sequencing of Intra-Host Viral Populations Mol. Biol. Evol. (IF 11.062) Pub Date : 2020-12-26 Matthew L Bendall; Keylie M Gibson; Margaret C Steiner; Uzma Rentia; Marcos Pérez-Losada; Keith A Crandall
Deep sequencing of viral populations using next generation sequencing (NGS) offers opportunities to understand and investigate evolution, transmission dynamics, and population genetics. Currently, the standard practice for processing NGS data to study viral populations is to summarize all the observed sequences from a sample as a single consensus sequence, thus discarding valuable information about
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Bidirectional genetic control of phenotypic heterogeneity and its implication for cancer drug resistance Mol. Biol. Evol. (IF 11.062) Pub Date : 2020-12-23 Ning Mo; Xiaoyu Zhang; Wenjun Shi; Gongwang Yu; Xiaoshu Chen; Jian-Rong Yang
Negative genetic regulators of phenotypic heterogeneity, or phenotypic capacitors/stabilizers, elevate population-average fitness by limiting deviation from the optimal phenotype and increase the efficacy of natural selection by enhancing the phenotypic differences among genotypes. Stabilizers can presumably be switched off to release phenotypic heterogeneity in the face of extreme or fluctuating environments
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Acoel single-cell transcriptomics: cell type analysis of a deep branching bilaterian Mol. Biol. Evol. (IF 11.062) Pub Date : 2020-12-23 Jules Duruz; Cyrielle Kaltenrieder; Peter Ladurner; Rémy Bruggmann; Pedro Martìnez; Simon G Sprecher
Bilaterian animals display a wide variety of cell types, organized into defined anatomical structures and organ systems, which are mostly absent in pre-bilaterian animals. Xenacoelomorpha are an early-branching bilaterian phylum displaying an apparently relatively simple anatomical organization that have greatly diverged from other bilaterian clades. In this study, we use whole-body single-cell transcriptomics
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Fast and robust identity-by-descent inference with the templated positional Burrows-Wheeler transform Mol. Biol. Evol. (IF 11.062) Pub Date : 2020-12-23 William A Freyman; Kimberly F McManus; Suyash S Shringarpure; Ethan M Jewett; Katarzyna Bryc; the 23andMe Research Team; Adam Auton
Estimating the genomic location and length of identical-by-descent (IBD) segments among individuals is a crucial step in many genetic analyses. However, the exponential growth in the size of biobank and direct-to-consumer (DTC) genetic data sets makes accurate IBD inference a significant computational challenge. Here we present the templated positional Burrows-Wheeler transform (TPBWT) to make fast
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A Report by the Editor-in-Chief for Molecular Biology and Evolution (MBE), Volume 36. Mol. Biol. Evol. (IF 11.062) Pub Date : 2020-09-15 Sudhir Kumar
Molecular Biology and Evolution is a prominent and highly respected journal, owned exclusively by the Society for Molecular Biology and Evolution and published by the Oxford University Press. MBE provides society members an opportunity for active participation in the creation of a journal supporting our community’s needs and interests.
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Using GC content to compare recombination patterns on the sex chromosomes and autosomes of the guppy, Poecilia reticulata, and its close outgroup species. Mol. Biol. Evol. (IF 11.062) Pub Date : 2020-07-22 Deborah Charlesworth,Yexin Zhang,Roberta Bergero,Chay Graham,Jim Gardner,Lengxob Yong
AbstractGenetic and physical mapping of the guppy (Poecilia reticulata) have shown that recombination patterns differ greatly between males and females. Crossover events occur evenly across the chromosomes in females, but in male meiosis they are restricted to the tip furthest from the centromere of each chromosome, creating very high recombination rates per megabase, as in pseudoautosomal regions
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The Molecular Machinery of Gametogenesis in Geodia Demosponges (Porifera): Evolutionary Origins of a Conserved Toolkit across Animals. Mol. Biol. Evol. (IF 11.062) Pub Date : 2020-07-16 Vasiliki Koutsouveli,Paco Cárdenas,Nadiezhda Santodomingo,Anabel Marina,Esperanza Morato,Hans Tore Rapp,Ana Riesgo
AbstractAll animals are capable of undergoing gametogenesis. The ability of forming haploid cells from diploid cells through meiosis and recombination appeared early in eukaryotes, whereas further gamete differentiation is mostly a metazoan signature. Morphologically, the gametogenic process presents many similarities across animal taxa, but little is known about its conservation at the molecular level
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Genome-wide association analysis identifies a genetic basis of infectivity in a model bacterial pathogen. Mol. Biol. Evol. (IF 11.062) Pub Date : 2020-07-13 Jason P Andras,Peter D Fields,Louis Du Pasquier,Maridel Fredericksen,Dieter Ebert
AbstractKnowledge of the genetic architecture of pathogen infectivity and host resistance is essential for a mechanistic understanding of coevolutionary processes, yet the genetic basis of these interacting traits remains unknown for most host–pathogen systems. We used a comparative genomic approach to explore the genetic basis of infectivity in Pasteuria ramosa, a Gram-positive bacterial pathogen
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The theory and applications of measuring broad-range and chromosome-wide recombination rate from allele frequency decay around a selected locus. Mol. Biol. Evol. (IF 11.062) Pub Date : 2020-07-13 Kevin H-C Wei,Aditya Mantha,Doris Bachtrog
AbstractRecombination is the exchange of genetic material between homologous chromosomes via physical crossovers. High-throughput sequencing approaches detect crossovers genome wide to produce recombination rate maps but are difficult to scale as they require large numbers of recombinants individually sequenced. We present a simple and scalable pooled-sequencing approach to experimentally infer near
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Prdm9 inter-subspecific interactions in hybrid male sterility of house mouse. Mol. Biol. Evol. (IF 11.062) Pub Date : 2020-07-08 Amisa Mukaj,Jaroslav Piálek,Vladana Fotopulosova,Andrew Parker Morgan,Linda Odenthal-Hesse,Emil D Parvanov,Jiri Forejt
AbstractThe classical definition posits hybrid sterility as a phenomenon when two parental taxa each of which is fertile produce a hybrid that is sterile. The first hybrid sterility gene in vertebrates, Prdm9, coding for a histone methyltransferase, was identified in crosses between two laboratory mouse strains derived from Mus mus musculus and M. m. domesticus subspecies. The unique function of PRDM9
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Distinguishing Felsenstein zone from Farris zone using neural networks. Mol. Biol. Evol. (IF 11.062) Pub Date : 2020-07-08 Alina F Leuchtenberger,Stephen M Crotty,Tamara Drucks,Heiko A Schmidt,Sebastian Burgstaller-Muehlbacher,Arndt von Haeseler
AbstractMaximum likelihood and maximum parsimony are two key methods for phylogenetic tree reconstruction. Under certain conditions, each of these two methods can perform more or less efficiently, resulting in unresolved or disputed phylogenies. We show that a neural network can distinguish between four-taxon alignments that were evolved under conditions susceptible to either long-branch attraction
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Co-evolution in hybrid genomes: nuclear-encoded rubisco small subunits and their plastid-targeting translocons accompanying sequential allopolyploidy events in Triticum. Mol. Biol. Evol. (IF 11.062) Pub Date : 2020-06-30 Changping Li,Xiaofei Wang,Yaxian Xiao,Xuhan Sun,Jinbin Wang,Xuan Yang,Yuchen Sun,Yan Sha,Ruili Lv,Yanan Yu,Baoxu Ding,Zhibin Zhang,Ning Li,Tianya Wang,Jonathan F Wendel,Bao Liu,Lei Gong
AbstractThe Triticum/Aegilops complex includes hybrid species resulting from homoploid hybrid speciation and allopolyploid speciation. Sequential allotetra- and allohexaploidy events presumably result in two challenges for the hybrids, which involve 1) cytonuclear stoichiometric disruptions caused by combining two diverged nuclear genomes with the maternal inheritance of the cytoplasmic organellar
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Flexible mixture model approaches that accommodate footprint size variability for robust detection of balancing selection. Mol. Biol. Evol. (IF 11.062) Pub Date : 2020-05-27 Xiaoheng Cheng,Michael DeGiorgio
AbstractLong-term balancing selection typically leaves narrow footprints of increased genetic diversity, and therefore most detection approaches only achieve optimal performances when sufficiently small genomic regions (i.e., windows) are examined. Such methods are sensitive to window sizes and suffer substantial losses in power when windows are large. Here, we employ mixture models to construct a
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Intragenic conflict in phylogenomic datasets. Mol. Biol. Evol. (IF 11.062) Pub Date : 2020-07-13 Stephen A Smith,Nathanael Walker-Hale,Joseph F Walker
AbstractMost phylogenetic analyses assume that a single evolutionary history underlies one gene. However, both biological processes and errors can cause intragenic conflict. The extent to which this conflict is present in empirical data sets is not well documented, but if common, could have far-reaching implications for phylogenetic analyses. We examined several large phylogenomic data sets from diverse
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How a Scorpion Toxin Selectively Captures a Prey Sodium Channel: the Molecular and Evolutionary Basis Uncovered. Mol. Biol. Evol. (IF 11.062) Pub Date : 2020-09-08 Shunyi Zhu,Bin Gao,Steve Peigneur,Jan Tytgat
AbstractThe growing resistance of insects to chemical pesticides is reducing the effectiveness of conventional methods for pest control and thus, the development of novel insecticidal agents is imperative. Scorpion toxins specific for insect voltage-gated sodium channels (Navs) have been considered as one of the most promising insecticide alternatives due to their host specificity, rapidly evoked toxicity
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Consequences of Stability-Induced Epistasis for Substitution Rates. Mol. Biol. Evol. (IF 11.062) Pub Date : 2020-06-17 Noor Youssef,Edward Susko,Joseph P Bielawski
AbstractDo interactions between residues in a protein (i.e., epistasis) significantly alter evolutionary dynamics? If so, what consequences might they have on inference from traditional codon substitution models which assume site-independence for the sake of computational tractability? To investigate the effects of epistasis on substitution rates, we employed a mechanistic mutation-selection model
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Frequent retroviral gene co-option during the evolution of vertebrates. Mol. Biol. Evol. (IF 11.062) Pub Date : 2020-07-15 Jianhua Wang,Guan-Zhu Han
AbstractEndogenous retroviruses are ubiquitous in the vertebrate genomes. On occasion, hosts recruited retroviral genes to mediate their own biological functions, a process formally known as co-option or exaptation. Much remains unknown about the extent of retroviral gene co-option in vertebrates, although more than ten retroviral gene co-option events have been documented. Here, we use a phylogenomic
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Asterid phylogenomics/phylotranscriptomics uncover morphological evolutionary histories and support phylogenetic placement for numerous whole genome duplications. Mol. Biol. Evol. (IF 11.062) Pub Date : 2020-07-11 Caifei Zhang,Taikui Zhang,Federico Luebert,Yezi Xiang,Chien-Hsun Huang,Yi Hu,Mathew Rees,Michael W Frohlich,Ji Qi,Maximilian Weigend,Hong Ma
AbstractAsterids are one of the most successful angiosperm lineages, exhibiting extensive morphological diversity and including a number of important crops. Despite their biological prominence and value to humans, the deep asterid phylogeny has not been fully resolved, and the evolutionary landscape underlying their radiation remains unknown. To resolve the asterid phylogeny, we sequenced 213 transcriptomes/genomes
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Higher germline mutagenesis of genes with stronger testis expressions refutes the transcriptional scanning hypothesis. Mol. Biol. Evol. (IF 11.062) Pub Date : 2020-07-08 Haoxuan Liu,Jianzhi Zhang
AbstractWhy are more genes expressed in the testis than in any other organ in mammals? The recently proposed transcriptional scanning hypothesis posits that transcription alleviates mutagenesis through transcription-coupled repair so has been selected in the testis to modulate the germline mutation rate in a gene-specific manner. Here, we show that this hypothesis is theoretically untenable because
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A simulation study to examine the information content in phylogenomic datasets under the multispecies coalescent model. Mol. Biol. Evol. (IF 11.062) Pub Date : 2020-07-08 Jun Huang,Tomáš Flouri,Ziheng Yang
AbstractWe use computer simulation to examine the information content in multilocus data sets for inference under the multispecies coalescent model. Inference problems considered include estimation of evolutionary parameters (such as species divergence times, population sizes, and cross-species introgression probabilities), species tree estimation, and species delimitation based on Bayesian comparison
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Bayesian Evaluation of Temporal Signal in Measurably Evolving Populations. Mol. Biol. Evol. (IF 11.062) Pub Date : 2020-07-06 Sebastian Duchene,Philippe Lemey,Tanja Stadler,Simon Y W Ho,David A Duchene,Vijaykrishna Dhanasekaran,Guy Baele
AbstractPhylogenetic methods can use the sampling times of molecular sequence data to calibrate the molecular clock, enabling the estimation of evolutionary rates and timescales for rapidly evolving pathogens and data sets containing ancient DNA samples. A key aspect of such calibrations is whether a sufficient amount of molecular evolution has occurred over the sampling time window, that is, whether
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Broccoli: combining phylogenetic and network analyses for orthology assignment. Mol. Biol. Evol. (IF 11.062) Pub Date : 2020-06-30 Romain Derelle,Hervé Philippe,John K Colbourne
AbstractOrthology assignment is a key step of comparative genomic studies, for which many bioinformatic tools have been developed. However, all gene clustering pipelines are based on the analysis of protein distances, which are subject to many artifacts. In this article, we introduce Broccoli, a user-friendly pipeline designed to infer, with high precision, orthologous groups, and pairs of proteins
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Recent common origin, reduced population size, and marked admixture have shaped European Roma genomes. Mol. Biol. Evol. (IF 11.062) Pub Date : 2020-06-26 Erica Bianco,Guillaume Laval,Neus Font-Porterias,Carla García-Fernandez,Begoña Dobon,Rubén Sabido-Vera,Emilija Sukarova Stefanovska,Vaidutis Kučinskas,Halyna Makukh,Horolma Pamjav,Lluis Quintana-Murci,Mihai G Netea,Jaume Bertranpetit,Francesc Calafell,David Comas
AbstractThe Roma Diaspora—traditionally known as Gypsies—remains among the least explored population migratory events in historical times. It involved the migration of Roma ancestors out-of-India through the plateaus of Western Asia ultimately reaching Europe. The demographic effects of the Diaspora—bottlenecks, endogamy, and gene flow—might have left marked molecular traces in the Roma genomes. Here
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ModelTeller: model selection for optimal phylogenetic reconstruction using machine learning. Mol. Biol. Evol. (IF 11.062) Pub Date : 2020-06-25 Shiran Abadi,Oren Avram,Saharon Rosset,Tal Pupko,Itay Mayrose
AbstractStatistical criteria have long been the standard for selecting the best model for phylogenetic reconstruction and downstream statistical inference. Although model selection is regarded as a fundamental step in phylogenetics, existing methods for this task consume computational resources for long processing time, they are not always feasible, and sometimes depend on preliminary assumptions which
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Synteny-guided resolution of gene trees clarifies the functional impact of whole genome duplications. Mol. Biol. Evol. (IF 11.062) Pub Date : 2020-06-18 Elise Parey,Alexandra Louis,Cédric Cabau,Yann Guiguen,Hugues Roest Crollius,Camille Berthelot
AbstractWhole-genome duplications (WGDs) have major impacts on the evolution of species, as they produce new gene copies contributing substantially to adaptation, isolation, phenotypic robustness, and evolvability. They result in large, complex gene families with recurrent gene losses in descendant species that sequence-based phylogenetic methods fail to reconstruct accurately. As a result, orthologs
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Lateral gene transfer acts as an evolutionary shortcut to efficient C4 biochemistry. Mol. Biol. Evol. (IF 11.062) Pub Date : 2020-06-10 Chatchawal Phansopa,Luke T Dunning,James D Reid,Pascal-Antoine Christin
AbstractThe adaptation of proteins for novel functions often requires changes in their kinetics via amino acid replacement. This process can require multiple mutations, and therefore extended periods of selection. The transfer of genes among distinct species might speed up the process, by providing proteins already adapted for the novel function. However, this hypothesis remains untested in multicellular
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Peptide-oleate complexes create novel membrane-bound compartments. Mol. Biol. Evol. (IF 11.062) Pub Date : 2020-06-10 Jesper S Hansen,Tuan Hiep Tran,Michele Cavalera,Sanchari Paul,Arunima Chaudhuri,Karin Lindkvist-Petersson,C S Ho James,Catharina Svanborg
AbstractA challenging question in evolutionary theory is the origin of cell division and plausible molecular mechanisms involved. Here, we made the surprising observation that complexes formed by short alpha-helical peptides and oleic acid can create multiple membrane-enclosed spaces from a single lipid vesicle. The findings suggest that such complexes may contain the molecular information necessary
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High and highly variable spontaneous mutation rates in Daphnia. Mol. Biol. Evol. (IF 11.062) Pub Date : 2020-06-10 Eddie K H Ho,Fenner Macrae,Leigh C Latta,Peter McIlroy,Dieter Ebert,Peter D Fields,Maia J Benner,Sarah Schaack
AbstractThe rate and spectrum of spontaneous mutations are critical parameters in basic and applied biology because they dictate the pace and character of genetic variation introduced into populations, which is a prerequisite for evolution. We use a mutation–accumulation approach to estimate mutation parameters from whole-genome sequence data from multiple genotypes from multiple populations of Daphnia
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Ancient DNA Suggests Single Colonization and Within-Archipelago Diversification of Caribbean Caviomorph Rodents Mol. Biol. Evol. (IF 11.062) Pub Date : 2020-10-09 Woods R, Barnes I, Brace S, et al.
AbstractReconstructing the evolutionary history of island biotas is complicated by unusual morphological evolution in insular environments. However, past human-caused extinctions limit the use of molecular analyses to determine origins and affinities of enigmatic island taxa. The Caribbean formerly contained a morphologically diverse assemblage of caviomorph rodents (33 species in 19 genera), ranging
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Corrigendum to: Bacterial Group II Intron Genomic Neighborhoods Reflect Survival Strategies: Hiding and Hijacking. Mol. Biol. Evol. (IF 11.062) Pub Date : 2020-09-04 Justin Waldern,Nicholas J Schiraldi,Marlene Belfort,Olga Novikova
Mol. Biol. Evol., doi:
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Ionotropic receptors as a driving force behind human synapse establishment Mol. Biol. Evol. (IF 11.062) Pub Date : 2020-09-28 Lucas Henriques Viscardi; Danilo Oliveira Imparato; Maria Cátira Bortolini; Rodrigo Juliani Siqueira Dalmolin
The origin of nervous systems is a main theme in biology and its mechanisms are largely underlied by synaptic neurotransmission. One problem to explain synapse establishment is that synaptic orthologs are present in multiple aneural organisms. We questioned how the interactions among these elements evolved and to what extent it relates to our understanding of the nervous systems complexity. We identified
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Interrogating genomic-scale data to resolve recalcitrant nodes in the Spider Tree of Life Mol. Biol. Evol. (IF 11.062) Pub Date : 2020-09-28 Siddharth Kulkarni; Robert J Kallal; Hannah Wood; Dimitar Dimitrov; Gonzalo Giribet; Gustavo Hormiga
Genome-scale data sets are converging on robust, stable phylogenetic hypotheses for many lineages; however, some nodes have shown disagreement across classes of data. We use spiders (Araneae) as a system to identify the causes of incongruence in phylogenetic signal between three classes of data: exons (as in phylotranscriptomics), non-coding regions (included in ultraconserved elements [UCE] analyses)
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Microchromosomes exhibit distinct features of vertebrate chromosome structure and function with underappreciated ramifications for genome evolution Mol. Biol. Evol. (IF 11.062) Pub Date : 2020-09-28 Blair W Perry; Drew R Schield; Richard H Adams; Todd A Castoe
Microchromosomes are common yet poorly understood components of many vertebrate genomes. Recent studies have revealed that microchromosomes contain a high density of genes and possess other distinct characteristics compared to macrochromosomes. Whether distinctive characteristics of microchromosomes extend to features of genome structure and organization, however, remains an open question. Here we
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Gene-level, but not chromosome-wide, divergence between a very young house fly proto-Y chromosome and its homologous proto-X chromosome Mol. Biol. Evol. (IF 11.062) Pub Date : 2020-09-28 Jae Hak Son; Richard P Meisel
X and Y chromosomes are usually derived from a pair of homologous autosomes, which then diverge from each other over time. Although Y-specific features have been characterized in sex chromosomes of various ages, the earliest stages of Y chromosome evolution remain elusive. In particular, we do not know whether early stages of Y chromosome evolution consist of changes to individual genes or happen via
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Population Genomics Reveals Incipient Speciation, Introgression, and Adaptation in the African Mona Monkey (Cercopithecus mona) Mol. Biol. Evol. (IF 11.062) Pub Date : 2020-09-28 Adeola Oluwakemi Ayoola; Bao-Lin Zhang; Richard P Meisel; Lotanna M Nneji; Yong Shao; Olanrewaju B Morenikeji; Adeniyi C Adeola; Said I Ng’ang’a; Babafemi G Ogunjemite; Agboola O Okeyoyin; Christian Roos; Dong-Dong Wu
Guenons (tribe Cercopithecini) are the most widely distributed non-human primate in the tropical forest belt of Africa and show considerable phenotypic, taxonomic, and ecological diversity. However, genomic information for most species within this group is still lacking. Here, we present a high-quality de novo genome (total 2.90 Gb, contig N50 equal to 22.7 Mb) of the mona monkey (Cercopithecus mona)
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Contrasting gene decay in subterranean vertebrates: insights from cavefishes and fossorial mammals Mol. Biol. Evol. (IF 11.062) Pub Date : 2020-09-28 Maxime Policarpo; Julien Fumey; Philippe Lafargeas; Delphine Naquin; Claude Thermes; Magali Naville; Corentin Dechaud; Jean-Nicolas Volff; Cedric Cabau; Christophe Klopp; Peter Rask Møller; Louis Bernatchez; Erik García-Machado; Sylvie Rétaux; Didier Casane
Evolution sometimes proceeds by loss, especially when structures and genes become dispensable after an environmental shift relaxes functional constraints. Subterranean vertebrates are outstanding models to analyze this process, and gene decay can serve as a readout. We sought to understand some general principles on the extent and tempo of the decay of genes involved in vision, circadian clock and
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Biased mutation and selection in RNA viruses Mol. Biol. Evol. (IF 11.062) Pub Date : 2020-09-28 Talia Kustin; Adi Stern
RNA viruses are responsible for some of the worst pandemics known to mankind, including outbreaks of Influenza, Ebola, and the recent COVID-19. One major challenge in tackling RNA viruses is the fact they are extremely genetically diverse. Nevertheless, they share common features that include their dependence on host cells for replication, and high mutation rates. We set out to search for shared evolutionary
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Sex-specific selection drives the evolution of alternative splicing in birds. Mol. Biol. Evol. (IF 11.062) Pub Date : 2020-09-25 Thea F Rogers,Daniela H Palmer,Alison E Wright
Males and females of the same species share the majority of their genomes, yet they are frequently exposed to conflicting selection pressures. Gene regulation is widely assumed to resolve these conflicting sex-specific selection pressures, and although there has been considerable focus on elucidating the role of gene expression level in sex-specific adaptation, other regulatory mechanisms have been
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A truncated singleton NLR causes hybrid necrosis in Arabidopsis thaliana. Mol. Biol. Evol. (IF 11.062) Pub Date : 2020-09-23 A Cristina Barragan,Maximilian Collenberg,Jinge Wang,Rachelle R Q Lee,Wei Yuan Cher,Fernando A Rabanal,Haim Ashkenazy,Detlef Weigel,Eunyoung Chae
Hybrid necrosis in plants arises from conflict between divergent alleles of immunity genes contributed by different parents, resulting in autoimmunity. We investigate a severe hybrid necrosis case in Arabidopsis thaliana, where the hybrid does not develop past the cotyledon stage and dies three weeks after sowing. Massive transcriptional changes take place in the hybrid, including the upregulation
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Chromosome-scale genome assemblies of aphids reveal extensively rearranged autosomes and long-term conservation of the X chromosome. Mol. Biol. Evol. (IF 11.062) Pub Date : 2020-09-23 Thomas C Mathers,Roland H M Wouters,Sam T Mugford,David Swarbreck,Cock Van Oosterhout,Saskia A Hogenhout
Chromosome rearrangements are arguably the most dramatic type of mutations, often leading to rapid evolution and speciation. However, chromosome dynamics have only been studied at the sequence level in a small number of model systems. In insects, Diptera and Lepidoptera have conserved genome structure at the scale of whole chromosomes or chromosome arms. Whether this reflects the diversity of insect
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Origin and evolution of the gene family of proteinaceous pheromones, the exocrine gland-secreting peptides, in rodents. Mol. Biol. Evol. (IF 11.062) Pub Date : 2020-09-22 Yoshihito Niimura,Mai Tsunoda,Sari Kato,Ken Murata,Taichi Yanagawa,Shunta Suzuki,Kazushige Touhara
The exocrine-gland secreting peptide (ESP) gene family encodes proteinaceous pheromones that are recognized by the vomeronasal organ in mice. For example, ESP1 is a male pheromone secreted in tear fluid that regulates socio-sexual behavior, and ESP22 is a juvenile pheromone that suppresses adult sexual behavior. The family consists of multiple genes and has been identified only in mouse and rat genomes
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Genomic signatures of coevolution between non-model mammals and parasitic roundworms. Mol. Biol. Evol. (IF 11.062) Pub Date : 2020-09-22 Yibo Hu,Lijun Yu,Huizhong Fan,Guangping Huang,Qi Wu,Yonggang Nie,Shuai Liu,Li Yan,Fuwen Wei
Antagonistic coevolution between host and parasite drives species evolution. However, most of the studies only focus on parasitism adaptation and do not explore the coevolution mechanisms from the perspective of both host and parasite. Here, through the de novo sequencing and assembly of the genomes of giant panda roundworm, red panda roundworm, and lion roundworm parasitic on tiger, we investigated
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Host-Endosymbiont Genome Integration in a Deep-Sea Chemosymbiotic Clam. Mol. Biol. Evol. (IF 11.062) Pub Date : 2020-09-21 Jack Chi-Ho Ip,Ting Xu,Jin Sun,Runsheng Li,Chong Chen,Yi Lan,Zhuang Han,Haibin Zhang,Jiangong Wei,Hongbin Wang,Jun Tao,Zongwei Cai,Pei-Yuan Qian,Jian-Wen Qiu
Endosymbiosis with chemosynthetic bacteria has enabled many deep-sea invertebrates to thrive at hydrothermal vents and cold seeps, but most previous studies on this mutualism have focused on the bacteria only. Vesicomyid clams dominate global deep-sea chemosynthesis-based ecosystems. They differ from most deep-sea symbiotic animals in passing their symbionts from parent to offspring, enabling intricate
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Human SIRT1 multi-specificity is modulated by active-site vicinity substitutions during natural evolution. Mol. Biol. Evol. (IF 11.062) Pub Date : 2020-09-21 Adi Hendler,Eyal Akiva,Mahakaran Sandhu,Dana Goldberg,Eyal Arbely,Colin J Jackson,Amir Aharoni
Many enzymes that catalyze protein post-translational modifications (PTM) can specifically modify multiple target proteins. However, little is known regarding the molecular basis and evolution of multi-specificity in these enzymes. Here, we used a combined bioinformatics and experimental approaches to investigate the evolution of multi-specificity in the sirtuin-1 (SIRT1) deacetylase. Guided by bioinformatics
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Genus-wide characterization of bumblebee genomes provides insights into their evolution and variation in ecological and behavioral traits. Mol. Biol. Evol. (IF 11.062) Pub Date : 2020-09-18 Cheng Sun,Jiaxing Huang,Yun Wang,Xiaomeng Zhao,Long Su,Gregg W C Thomas,Mengya Zhao,Xingtan Zhang,Irwin Jungreis,Manolis Kellis,Saverio Vicario,Igor V Sharakhov,Semen M Bondarenko,Martin Hasselmann,Chang N Kim,Benedict Paten,Luca Penso-Dolfin,Li Wang,Yuxiao Chang,Qiang Gao,Ling Ma,Lina Ma,Yuxiao Zhang,Hongbo Zhang,Huahao Zhang,Livio Ruzzante,Hugh M Robertson,Yihui Zhu,Yanjie Liu,Huipeng Yang,Lele Ding
Bumblebees are a diverse group of globally important pollinators in natural ecosystems and for agricultural food production. With both eusocial and solitary life-cycle phases, and some social parasite species, they are especially interesting models to understand social evolution, behavior, and ecology. Reports of many species in decline point to pathogen transmission, habitat loss, pesticide usage
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Signatures of introgression across the allele frequency spectrum. Mol. Biol. Evol. (IF 11.062) Pub Date : 2020-09-17 Simon H Martin,William Amos