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Evolution of phenotypic variance provides insights into the genetic basis of adaptation Genome Biol. Evol. (IF 3.3) Pub Date : 2024-04-15 Wei-Yun Lai, Viola Nolte, Ana Marija Jakšić, Christian Schlötterer
Most traits are polygenic, and the contributing loci can be identified by GWAS. The genetic basis of adaptation is, however, difficult to characterize. Here, we propose to study the genetic basis of trait evolution by monitoring the evolution of their phenotypic variance during adaptation to a new environment in well-defined laboratory conditions. Extensive computer simulations show that the evolution
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Microbial Diversity and Open Questions about the Deep Tree of Life Genome Biol. Evol. (IF 3.3) Pub Date : 2024-04-15 Laura Eme, Daniel Tamarit
In this perspective, we explore the transformative impact and inherent limitations of metagenomics and single-cell genomics on our understanding of microbial diversity and their integration into the Tree of Life. We delve into the key challenges associated with incorporating new microbial lineages into the Tree of Life through advanced phylogenomic approaches. Additionally, we shed light on enduring
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Re-examining correlations between synonymous codon usage and protein bond angles in E. coli Genome Biol. Evol. (IF 3.3) Pub Date : 2024-04-15 Opetunde J Akeju, Alexander L Cope
Rosenberg et al. (2022) recently found a surprising correlation between synonymous codon usage and the dihedral bond angles of the resulting amino acid. However, their analysis did not account for the strongest known correlate of codon usage: gene expression. We re-examined the relationship between bond angles and codon usage by applying the approach of Rosenberg et al. to simulated protein-coding
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Patterns of change in nucleotide diversity over gene length Genome Biol. Evol. (IF 3.3) Pub Date : 2024-04-12 Farhan Ali
Nucleotide diversity at a site is influenced by the relative strengths of neutral and selective population genetic processes. Therefore, attempts to estimate Effective population size based on the diversity of synonymous sites demand a better understanding of their selective constraints. The nucleotide diversity of a gene was previously found to correlate with its length. In this work, I measure nucleotide
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High-quality, chromosome-level reference genomes of the viviparous Caribbean skinks Spondylurus nitidus and S. culebrae Genome Biol. Evol. (IF 3.3) Pub Date : 2024-04-11 Danielle Rivera, James B Henderson, Athena W Lam, Nathan J Hostetter, Jaime A Collazo, Rayna C Bell
New World mabuyine skinks are a diverse radiation of morphologically cryptic lizards with unique reproductive biologies. Recent studies examining population-level data (morphological, ecological, and genomic) have uncovered novel biodiversity and phenotypes, including the description of dozens of new species and insights into the evolution of their highly complex placental structures. Beyond the potential
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High-throughput selection of human de novo-emerged sORFs with high folding potential Genome Biol. Evol. (IF 3.3) Pub Date : 2024-04-09 Margaux Aubel, Filip Buchel, Brennen Heames, Alun Jones, Ondrej Honc, Erich Bornberg-Bauer, Klara Hlouchova
De novo genes emerge from previously non-coding stretches of the genome. Their encoded de novo proteins are generally expected to be similar to random sequences and, accordingly, with no stable tertiary fold and high predicted disorder. However, structural properties of de novo proteins and whether they differ during the stages of emergence and fixation have not been studied in depth and rely heavily
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Chromosome-scale genome assembly of the rough periwinkle Littorina saxatilis Genome Biol. Evol. (IF 3.3) Pub Date : 2024-04-08 Aurélien De Jode, Rui Faria, Giulio Formenti, Ying Sims, Timothy P Smith, Alan Tracey, Jonathan M D Wood, Zuzanna B Zagrodzka, Kerstin Johannesson, Roger K Butlin, Erica H Leder
The intertidal gastropod Littorina saxatilis is a model system to study speciation and local adaptation. The repeated occurrence of distinct ecotypes showing different levels of genetic divergence makes L. saxatilis particularly suited to study different stages of the speciation continuum in the same lineage. A major finding is the presence of several large chromosomal inversions associated with the
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Retention of an endosymbiont for the production of a single molecule Genome Biol. Evol. (IF 3.3) Pub Date : 2024-04-05 Arkadiy I Garber, Andrés Garcia de la Filia Molina, Isabelle Vea, Andrew J Mongue, Laura Ross, John P McCutcheon
Sap-feeding insects often maintain two or more nutritional endosymbionts which act in concert to produce compounds essential for insect survival. Many mealybugs have endosymbionts in a nested configuration: one or two bacterial species reside within the cytoplasm of another bacterium, and together these bacteria have genomes which encode interdependent sets of genes needed to produce key nutritional
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Parthenogenetic stick insects exhibit signatures of preservation in the molecular architecture of male reproduction Genome Biol. Evol. (IF 3.3) Pub Date : 2024-04-04 Giobbe Forni, Barbara Mantovani, Alexander S Mikheyev, Andrea Luchetti
After the loss of a trait, theory predicts that the molecular machinery underlying its phenotypic expression should decay. Yet, empirical evidence is contrasting. Here, we test the hypotheses that (1) the molecular ground plan of a lost trait could persist due to pleiotropic effects on other traits and (2) that gene co-expression network architecture could constrain individual gene expression. Our
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Remarkably high repeat content in the genomes of sparrows: the importance of genome assembly completeness for transposable element discovery Genome Biol. Evol. (IF 3.3) Pub Date : 2024-04-03 Phred M Benham, Carla Cicero, Merly Escalona, Eric Beraut, Colin Fairbairn, Mohan P A Marimuthu, Oanh Nguyen, Ruta Sahasrabudhe, Benjamin L King, W Kelley Thomas, Adrienne I Kovach, Michael W Nachman, Rauri C K Bowie
Transposable elements (TE) play critical roles in shaping genome evolution. Highly repetitive TE sequences are also a major source of assembly gaps making it difficult to fully understand the impact of these elements on host genomes. The increased capacity of long-read sequencing technologies to span highly repetitive regions promises to provide new insights into patterns of TE activity across diverse
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The genome of the rayed Mediterranean limpet Patella caerulea (Linnaeus, 1758) Genome Biol. Evol. (IF 3.3) Pub Date : 2024-03-28 Gwyneth Halstead-Nussloch, Silvia Giorgia Signorini, Marco Giulio, Fabio Crocetta, Marco Munari, Camilla Della Torre, Alexandra Anh-Thu Weber
Patella caerulea (Linnaeus, 1758) is a mollusc limpet species of the class Gastropoda. Endemic to the Mediterranean Sea, it is considered a keystone species due to its primary role in structuring and regulating the ecological balance of tidal and subtidal habitats. It is currently being used as a bioindicator to assess the environmental quality of coastal marine waters and as a model species to understand
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Phylogeny and Expansion of Serine/Threonine Kinases in Phagocytotic Bacteria in the Phylum Planctomycetota Genome Biol. Evol. (IF 3.3) Pub Date : 2024-03-28 Anna Odelgard, Emil Hägglund, Lionel Guy, Siv G E Andersson
The recently isolated bacterium “Candidatus Uabimicrobium amorphum” is the only known prokaryote that can engulf other bacterial cells. Its proteome contains a high fraction of proteins involved in signal transduction systems, which is a feature normally associated with multicellularity in eukaryotes. Here, we present a protein-based phylogeny which shows that “Ca. Uabimicrobium amorphum” represents
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Identification of parthenogenesis-inducing effector proteins in Wolbachia Genome Biol. Evol. (IF 3.3) Pub Date : 2024-03-26 Laura C Fricke, Amelia R I Lindsey
Bacteria in the genus Wolbachia have evolved numerous strategies to manipulate arthropod sex, including the conversion of would-be male offspring to asexually reproducing females. This so-called “parthenogenesis-induction” phenotype can be found in a number of Wolbachia strains that infect arthropods with haplodiploid sex determination systems, including parasitoid wasps. Despite the discovery of microbe-mediated
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Mutation rate and effective population size of the model cooperative bacterium Myxococcus xanthus Genome Biol. Evol. (IF 3.3) Pub Date : 2024-03-25 Sébastien Wielgoss, J David Van Dyken, Gregory J Velicer
Intrinsic rates of genetic mutation have diverged greatly across taxa and exhibit statistical associations with several other parameters and features. These include effective population size (Ne), genome size, and gametic multicellularity, with the latter being associated with both increased mutation rates and decreased effective population sizes. However, data sufficient to test for possible relationships
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Using a handful of transcriptomes to detect sex-linked markers and develop molecular sexing assays in a species with homomorphic sex chromosomes Genome Biol. Evol. (IF 3.3) Pub Date : 2024-03-25 Paul A Saunders, Carles Ferre-Ortega, Peta L Hill, Oleg Simakov, Tariq Ezaz, Christopher P Burridge, Erik Wapstra
To understand the biology of a species it is often crucial to be able to differentiate males and females. However, many species lack easily identifiable sexually dimorphic traits. In those that possess sex chromosomes, molecular sexing offers a good alternative, and molecular sexing assays can be developed through the comparison of male and female genomic sequences. However, in many non-model species
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ClockstaRX: Testing molecular clock hypotheses with genomic data Genome Biol. Evol. (IF 3.3) Pub Date : 2024-03-25 David A Duchêne, Sebastián Duchêne, Josefin Stiller, Rasmus Heller, Simon Y W Ho
Phylogenomic data provide valuable opportunities for studying evolutionary rates and timescales. These analyses require theoretical and statistical tools based on molecular clocks. We present ClockstaRX, a flexible platform for exploring and testing evolutionary rate signals in phylogenomic data. Here, information about evolutionary rates in branches across gene trees is placed in Euclidean space,
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Reconstructing the genetic relationship between ancient and present-day Siberian populations Genome Biol. Evol. (IF 3.3) Pub Date : 2024-03-25 Haechan Gill, Juhyeon Lee, Choongwon Jeong
Human populations across a vast area in northern Eurasia, from Fennoscandia to Chukotka, share a distinct genetic component often referred to as the Siberian ancestry. Most enriched in present-day Samoyedic-speaking populations such as Nganasans, its origins and history still remain elusive despite the growing list of ancient and present-day genomes from Siberia. Here we reanalyze published ancient
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Dollo parsimony overestimates ancestral gene content reconstructions Genome Biol. Evol. (IF 3.3) Pub Date : 2024-03-22 Alex Gàlvez-Morante, Laurent Guéguen, Paschalis Natsidis, Maximilian J Telford, Daniel J Richter
Ancestral reconstruction is a widely-used technique that has been applied to understand the evolutionary history of gain and loss of gene families. Ancestral gene content can be reconstructed via different phylogenetic methods, but many current and previous studies employ Dollo parsimony. We hypothesize that Dollo parsimony is not appropriate for ancestral gene content reconstruction inferences based
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scRNA-seq reveals novel genetic pathways and sex chromosome regulation in Tribolium spermatogenesis Genome Biol. Evol. (IF 3.3) Pub Date : 2024-03-21 Michael Robben, Balan Ramesh, Shana Pau, Demetra Meletis, Jacob Luber, Jeffery Demuth
Spermatogenesis is critical to sexual reproduction yet evolves rapidly in many organisms. High throughput single cell transcriptomics promises unparalleled insight into this important process but understanding can be impeded in non-model systems by a lack of known genes that can reliably demarcate biologically meaningful cell populations. Tribolium castaneum, the red flour beetle, lacks known markers
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Genome assembly and annotation of the Dark-branded Bushbrown butterfly Mycalesis mineus (Nymphalidae: Satyrinae) Genome Biol. Evol. (IF 3.3) Pub Date : 2024-03-20 Suriya Narayanan Murugesan, Shen Tian, Antónia Monteiro
We report a high-quality genome draft assembly of the Dark-branded Bushbrown, Mycalesis mineus, a member of the Satyrinae subfamily of nymphalid butterflies. This species is emerging as a promising model organism for investigating the evolution and development of phenotypic plasticity. Using 45.99 Gb of long-read data (N50=11.11 Kb), we assembled a genome size of 497.4 Mb for M. mineus. The assembly
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Conserved non-coding elements evolve around the same genes throughout Metazoan evolution Genome Biol. Evol. (IF 3.3) Pub Date : 2024-03-19 Paul Gonzalez, Quinn C Hauck, Andreas D Baxevanis
Conserved noncoding elements (CNEs) are DNA sequences located outside of protein-coding genes that can remain under purifying selection for up to hundreds of millions of years. Studies in vertebrate genomes have revealed that most CNEs carry out regulatory functions. Notably, many of them are enhancers that control the expression of homeodomain transcription factors and other genes that play crucial
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Giants among Cnidaria: large nuclear genomes and rearranged mitochondrial genomes in siphonophores Genome Biol. Evol. (IF 3.3) Pub Date : 2024-03-19 Namrata Ahuja, Xuwen Cao, Darrin T Schultz, Natasha Picciani, Arianna Lord, Shengyuan Shao, Kejue Jia, David R Burdick, Steven H D Haddock, Yuanning Li, Casey W Dunn
Siphonophores (Cnidaria:Hydrozoa) are abundant predators found throughout the ocean and are important constituents of the global zooplankton community. They range in length from a few centimeters to tens of meters. They are gelatinous, fragile, and difficult to collect, so many aspects of the biology of these roughly 200 species remain poorly understood. To survey siphonophore genome diversity, we
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A Small Genome Amidst the Giants: Evidence of Genome Reduction in a Small Tubulinid Free-Living Amoeba Genome Biol. Evol. (IF 3.3) Pub Date : 2024-03-19 Yonas I Tekle, Hanna Tefera
This study investigates the genomic characteristics of Echinamoeba silvestris, a small-sized amoeba within the Tubulinea clade of the Amoebozoa supergroup. Despite Tubulinea's significance in various fields, genomic data for this clade have been scarce. E. silvestris presents the smallest free-living amoeba genome within Tubulinea and Amoebozoa to date. Comparative analysis reveals intriguing parallels
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Chromosome-level assembly and annotation of the pearly heath Coenonympha arcania butterfly genome Genome Biol. Evol. (IF 3.3) Pub Date : 2024-03-15 Fabrice Legeai, Sandra Romain, Thibaut Capblancq, Paul Doniol-Valcroze, Mathieu Joron, Claire Lemaitre, Laurence Després
We present the first chromosome-level genome assembly and annotation of the pearly heath Coenonympha arcania, generated with a PacBio HiFi sequencing approach, and complemented with Hi-C data. We additionally compare synteny, gene and repeat content between C. arcania and other Lepidopteran genomes. This reference genome will enable future population genomics studies with Coenonympha butterflies, a
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Calling structural variants with confidence from short-read data in wild bird populations Genome Biol. Evol. (IF 3.3) Pub Date : 2024-03-15 Gabriel David, Alicia Bertolotti, Ryan Layer, Douglas Scofield, Alexander Hayward, Tobias Baril, Hamish A Burnett, Erik Gudmunds, Henrik Jensen, Arild Husby
Comprehensive characterisation of structural variation in natural populations has only become feasible in the last decade. To investigate the population genomic nature of structural variation (SV), reproducible and high-confidence SV callsets are first required. We created a population-scale reference of the genome-wide landscape of structural variation across 33 Nordic house sparrows (Passer domesticus)
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Evidence of Nonrandom Patterns of Functional Chromosome Organization in Danaus plexippus Genome Biol. Evol. (IF 3.3) Pub Date : 2024-03-15 Ashlyn Kimura, Alwyn C Go, Therese Markow, José M Ranz
Our understanding on the interplay between gene functionality and gene arrangement at different chromosome scales relies on a few Diptera and the honeybee, species with quality-reference genome assemblies, accurate gene annotations, and abundant transcriptome data. Using recently generated ‘omics resources in the monarch butterfly D. plexippus, a species with many more and smaller chromosomes relative
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The complex landscape of structural divergence between the Drosophila pseudoobscura and D. persimilis genomes Genome Biol. Evol. (IF 3.3) Pub Date : 2024-03-14 Javier Carpinteyro-Ponce, Carlos A Machado
Structural genomic variants are key drivers of phenotypic evolution. They can span hundreds to millions of base pairs and can thus affect large numbers of genetic elements. Although structural variation is quite common within and between species, its characterization depends upon the quality of genome assemblies and the proportion of repetitive elements. Using new high-quality genome assemblies, we
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Background selection from unlinked sites causes non-independent evolution of deleterious mutations Genome Biol. Evol. (IF 3.3) Pub Date : 2024-03-13 Joseph Matheson, Joanna Masel
Background selection describes the reduction in neutral diversity caused by selection against deleterious alleles at other loci. It is typically assumed that the purging of deleterious alleles affects linked neutral variants, and indeed simulations typically only treat a genomic window. However, background selection at unlinked loci also depresses neutral diversity. In agreement with previous analytical
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Where are the formerly Y-linked genes in the Ryukyu spiny rat that has lost its Y chromosome? Genome Biol. Evol. (IF 3.3) Pub Date : 2024-03-13 Jiachen Li, Siliang Song, Jianzhi Zhang
It has been predicted that the highly degenerate mammalian Y chromosome will be lost eventually. Indeed, Y was lost in the Ryukyu spiny rat Tokudaia osimensis, but the fate of the formerly Y-linked genes is not completely known. We looked for all 12 ancestrally Y-linked genes in a draft T. osimensis genome sequence. Zfy1, Zfy2, Kdm5d, Eif2s3y, Usp9y, Uty, and Ddx3y are putatively functional and are
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Highly resolved genomes of two closely related lineages of the rodent louse Polyplax serrata with different host specificities Genome Biol. Evol. (IF 3.3) Pub Date : 2024-03-13 Jana Martinů, Hassan Tarabai, Jan Štefka, Václav Hypša
Sucking lice of the parvorder Anoplura are permanent ectoparasites with specific lifestyle and highly derived features. Currently, genomic data are only available for a single species, the human louse Pediculus humanus. Here, we present genomes of two distinct lineages, with different host spectra, of a rodent louse Polyplax serrata. Genomes of these ecologically different lineages are closely similar
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Accurate Detection of Convergent Mutations in Large Protein Alignments with ConDor Genome Biol. Evol. (IF 3.3) Pub Date : 2024-03-06 Marie Morel, Anna Zhukova, Frédéric Lemoine, Olivier Gascuel
Evolutionary convergences are observed at all levels, from phenotype to DNA and protein sequences, and changes at these different levels tend to be correlated. Notably, convergent mutations can lead to convergent changes in phenotype, such as changes in metabolism, drug resistance, and other adaptations to changing environments. We propose a two-component approach to detect mutations subject to convergent
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Ancient loss of catalytic selenocysteine spurred convergent adaptation in a mammalian oxidoreductase Genome Biol. Evol. (IF 3.3) Pub Date : 2024-03-06 Jasmin Rees, Gaurab Sarangi, Qing Cheng, Martin Floor, Aida M Andrés, Baldomero Oliva Miguel, Jordi Villà-Freixa, Elias SJ Arnér, Sergi Castellano
Selenocysteine (Sec), the 21st amino acid specified by the genetic code, is a rare selenium-containing residue found in the catalytic site of selenoprotein oxidoreductases. Sec is analogous to the common cysteine (Cys) amino acid but its selenium atom offers physical-chemical properties not provided by the corresponding sulfur atom in Cys. Catalytic sites with Sec in selenoproteins of vertebrates are
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Chromosome-scale genome assembly for clubrush (Bolboschoenus planiculmis) indicates a karyotype with high chromosome number and heterogeneous centromere distribution Genome Biol. Evol. (IF 3.3) Pub Date : 2024-03-06 Yu Ning, Yang Li, Hai Yan Lin, En Ze Kang, Yu Xin Zhao, Shu Bin Dong, Yong Li, Xiao Fei Xia, Yi Fei Wang, Chun Yi Li
Bolboschoenus planiculmis (F.Schmidt) T.V.Egorova is a typical wetland plant in the species-rich Cyperaceae family. This species contributes prominently to carbon dynamics and trophic integration in wetland ecosystems.Previous studies have reported that the chromosomes of B. planiculmis are holocentric, i.e. they have kinetic activity along their entire length and carry multiple centromeres. This feature
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Distribution and functional analysis of isocitrate dehydrogenases across kinetoplastids Genome Biol. Evol. (IF 3.3) Pub Date : 2024-03-06 Ľubomíra Chmelová, Kristína Záhonová, Amanda T S Albanaz, Liudmyla Hrebenyk, Anton Horváth, Vyacheslav Yurchenko, Ingrid Škodová-Sveráková
Isocitrate dehydrogenase (IDH) is an enzyme converting isocitrate to α-ketoglutarate in the canonical tricarboxylic acid (TCA) cycle. There are three different types of IDH documented in eukaryotes. Our study points out the complex evolutionary history of IDHs across kinetoplastids, where the common ancestor of Trypanosomatidae and Bodonidae was equipped with two isoforms of the IDH enzyme: the NADP+-dependent
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Genomic resources and annotations for a colonial ascidian, the light-bulb sea squirt Clavelina lepadiformis Genome Biol. Evol. (IF 3.3) Pub Date : 2024-03-05 Vladimir Daric, Maxence Lanoizelet, Hélène Mayeur, Cécile Leblond, Sébastien Darras
Ascidian embryos have been studied since the birth of experimental embryology at the end of the 19th century. They represent textbook examples of mosaic development characterized by a fast development with very few cells and invariant cleavage patterns and lineages. Ascidians belong to tunicates, the vertebrate sister group, and their study is essential to shed light on the emergence of vertebrates
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Ancient and modern genomes reveal microsatellites maintain a dynamic equilibrium through deep time Genome Biol. Evol. (IF 3.3) Pub Date : 2024-02-27 Bennet J McComish, Michael A Charleston, Matthew Parks, Carlo Baroni, Maria Cristina Salvatore, Ruiqiang Li, Guojie Zhang, Craig D Millar, Barbara R Holland, David M Lambert
Microsatellites are widely used in population genetics, but their evolutionary dynamics remain poorly understood. It is unclear whether microsatellite loci drift in length over time. This is important because the mutation processes that underlie these important genetic markers are central to the evolutionary models that employ microsatellites. We identify more than 27 million microsatellites using
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Exploring FGFR3 Mutations in the Male Germline: Implications for Clonal Germline Expansions and Paternal Age-Related Dysplasias Genome Biol. Evol. (IF 3.3) Pub Date : 2024-02-27 Sofia Moura, Ingrid Hartl, Veronika Brumovska, Peter P Calabrese, Atena Yasari, Yasmin Striedner, Marina Bishara, Theresa Mair, Thomas Ebner, Gerhard J Schütz, Eva Sevcsik, Irene Tiemann-Boege
Delayed fatherhood results in a higher risk of inheriting a new germline mutation that might result in a congenital disorder in the offspring. In particular, some FGFR3 mutations increase in frequency with age, but there are still a large number of uncharacterized FGFR3 mutations that could be expanding in the male germline with potentially early- or late-onset effects in the offspring. Here, we used
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Turnovers of sex-determining mutation in the golden pompano and related species provide insights into microevolution of undifferentiated sex chromosome Genome Biol. Evol. (IF 3.3) Pub Date : 2024-02-25 Liang Guo, Danilo Malara, Pietro Battaglia, Khor Waiho, D Allen Davis, Yu Deng, Zhongyuan Shen, Ke Rao
The suppression of recombination is considered a hallmark of sex chromosome evolution. However, previous research has identified undifferentiated sex chromosomes and sex determination by single SNP in the greater amberjack (Seriola dumerili). We observed the same phenomena in the golden pompano (Trachinotus ovatus) of the same family Carangidae and discovered a different sex-determining SNP within
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Mutational signatures in wild type Escherichia coli strains reveal predominance of DNA polymerase errors Genome Biol. Evol. (IF 3.3) Pub Date : 2024-02-23 Sofya K Garushyants, Mrudula Sane, Maria V Selifanova, Deepa Agashe, Georgii A Bazykin, Mikhail S Gelfand
While mutational processes operating in the Escherichia coli genome have been revealed by multiple laboratory experiments, the contribution of these processes to accumulation of bacterial polymorphism and evolution in natural environments is unknown. To address this question, we reconstruct signatures of distinct mutational processes from experimental data on E. coli hypermutators, and ask how these
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Impact of homologous recombination on core genome evolution and host adaptation of Pectobacterium parmentieri Genome Biol. Evol. (IF 3.3) Pub Date : 2024-02-22 Dario Arizala, Mohammad Arif
Homologous recombination is a major force mechanism driving bacterial evolution, host adaptability and acquisition of novel virulence traits. Pectobacterium parmentieri is a plant bacterial pathogen distributed worldwide, primarily affecting potatoes, by causing soft rot and blackleg diseases. The goal of this investigation was to understand the impact of homologous recombination on the genomic evolution
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High-quality genome assemblies of four members of the Podospora anserina species complex Genome Biol. Evol. (IF 3.3) Pub Date : 2024-02-22 S Lorena Ament-Velásquez, Aaron A Vogan, Ola Wallerman, Fanny Hartmann, Valérie Gautier, Philippe Silar, Tatiana Giraud, Hanna Johannesson
The filamentous fungus Podospora anserina is a model organism used extensively in the study of molecular biology, senescence, prion biology, meiotic drive, mating-type chromosome evolution, and plant biomass degradation. It has recently been established that P. anserina is a member of a complex of seven, closely related species. In addition to P. anserina, high-quality genomic resources are available
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The genome of Plasmodium gonderi: Insights into the evolution of human malaria parasites Genome Biol. Evol. (IF 3.3) Pub Date : 2024-02-19 Axl S Cepeda, Beatriz Mello, M Andreína Pacheco, Zunping Luo, Steven A Sullivan, Jane M Carlton, Ananias A Escalante
Plasmodium species causing malaria in humans are not monophyletic, sharing common ancestors with nonhuman primate parasites. Plasmodium gonderi is one of the few known Plasmodium species infecting African old-world monkeys that is not found in apes. This study reports a de novo assembled P. gonderi genome with complete chromosomes. The P. gonderi genome shares codon usage, syntenic blocks, and other
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The Biofilm Lifestyle Shapes the Evolution of β-Lactamases Genome Biol. Evol. (IF 3.3) Pub Date : 2024-02-17 Øyvind M Lorentzen, Anne Sofie B Haukefer, Pål J Johnsen, Christopher Frøhlich
The evolutionary relationship between the biofilm lifestyle and antibiotic resistance enzymes remains a subject of limited understanding. Here, we investigate how β-lactamases affect biofilm formation in Vibrio cholerae and how selection for a biofilm lifestyle impacts the evolution of these enzymes. Genetically diverse β-lactamases expressed in V. cholerae displayed a strong inhibitory effect on biofilm
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Nucleosomes at the dawn of eukaryotes Genome Biol. Evol. (IF 3.3) Pub Date : 2024-02-16 Antoine Hocher, Tobias Warnecke
Genome regulation in eukaryotes revolves around the nucleosome, the fundamental building block of eukaryotic chromatin. Its constituent parts, the four core histones (H3, H4, H2A, H2B), are universal to eukaryotes. Yet despite its exceptional conservation and central role in orchestrating transcription, repair, and other DNA-templated processes, the origins and early evolution of the nucleosome remain
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A chromosome-level genome assembly and annotation for the clouded apollo butterfly (Parnassius mnemosyne), a species of global conservation concern Genome Biol. Evol. (IF 3.3) Pub Date : 2024-02-15 J Höglund, G Dias, R -A Olsen, A Soares, I Bunikis, V Talla, N Backström
The clouded apollo (Parnassius mnemosyne) is a palearctic butterfly distributed over a large part of western Eurasia, but population declines and fragmentation have been observed in many parts of the range. Development of genomic tools can help to shed light on the genetic consequences of the decline and to make informed decisions about direct conservation actions. Here, we present a high-contiguity
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Cytogenetic analysis of the fish genus Carassius indicates divergence, fission and segmental duplication as drivers of tandem repeat and microchromosome evolution Genome Biol. Evol. (IF 3.3) Pub Date : 2024-02-08 Nicola R Fornaini, Halina Černohorská, Lívia do Vale Martins, Martin Knytl
Fishes of the genus Carassius are useful experimental vertebrate models for study of evolutionary biology and cytogenetics. Carassius demonstrates diverse biological characteristics, such as variation in ploidy levels and chromosome numbers, and presence of microchromosomes. Carassius polyploids with ≥ 150 chromosomes have microchromosomes, but their origin, especially in European populations, is unknown
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Cryogenian origins of multicellularity in Archaeplastida Genome Biol. Evol. (IF 3.3) Pub Date : 2024-02-08 Alexander M C Bowles, Christopher J Williamson, Tom A Williams, Philip C J Donoghue
Earth was impacted by global glaciations during the Cryogenian (720-635 million years ago; Ma), events invoked to explain both the origins of multicellularity in Archaeplastida and radiation of the first land plants. However, the temporal relationship between these environmental and biological events is poorly established, due to a paucity of molecular and fossil data, precluding resolution of the
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Potential Role of DNA Methylation as a Driver of Plastic Responses to the Environment across Cells, Organisms, and Populations Genome Biol. Evol. (IF 3.3) Pub Date : 2024-02-07 Samuel N Bogan, Soojin V Yi
There is great interest in exploring epigenetic modifications as drivers of adaptive organismal responses to environmental change. Extending this hypothesis to populations, epigenetically driven plasticity could influence phenotypic changes across environments. The canonical model posits that epigenetic modifications alter gene regulation and, subsequently impact phenotypes. We first discuss origins
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Lack of dosage balance and incomplete dosage compensation in the ZZ/ZW Gila monster (Heloderma suspectum) revealed by de novo genome assembly Genome Biol. Evol. (IF 3.3) Pub Date : 2024-02-06 Timothy H Webster, Annika Vannan, Brendan J Pinto, Grant Denbrock, Matheo Morales, Greer A Dolby, Ian T Fiddes, Dale F DeNardo, Melissa A Wilson
Reptiles exhibit a variety of modes of sex determination, including both temperature-dependent and genetic mechanisms. Among those species with genetic sex determination, sex chromosomes of varying heterogamety (XX/XY and ZZ/ZW) have been observed with different degrees of differentiation. Karyotype studies have demonstrated that Gila monsters (Heloderma suspectum) have ZZ/ZW sex determination and
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Divergent evolutionary rates of primate brain regions as revealed by genomics and transcriptomics Genome Biol. Evol. (IF 3.3) Pub Date : 2024-02-05 Xiao-Lin Zhuang, Yong Shao, Chun-Yan Chen, Long Zhou, Yong-Gang Yao, David N Cooper, Guo-Jie Zhang, Wen Wang, Dong-Dong Wu
Although the primate brain contains numerous functionally distinct structures that have experienced diverse genetic changes during the course of evolution and development, these changes remain to be explored in detail. Here we utilize two classic metrics from evolutionary biology, the evolutionary rate index (ERI) and the transcriptome age index (TAI), to investigate the evolutionary alterations that
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The Addis Ababa Lions: whole-genome sequencing of a rare and precious population Genome Biol. Evol. (IF 3.3) Pub Date : 2024-02-01 Marjan Barazandeh, Divya Kriti, Jörns Fickel, Corey Nislow
Lions are widely known as charismatic predators that once roamed across the globe, but their populations have been greatly affected by environmental factors and human activities over the last 150 years. Of particular interest is the Addis Ababa lion population, which has been maintained in captivity at around 20 individuals for over 75 years, while many wild African lion populations have become extinct
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Patterns of genomic diversity in a fig-associated close relative of C. elegans Genome Biol. Evol. (IF 3.3) Pub Date : 2024-02-01 Gavin C Woodruff, John H Willis, Patrick C Phillips
The evolution of reproductive mode is expected to have profound impacts on the genetic composition of populations. At the same time, ecological interactions can generate close associations among species, which can in turn generate a high degree of overlap in their spatial distributions. Caenorhabditis elegans is a hermaphroditic nematode that has enabled extensive advances in developmental genetics
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Phylogenomics of the ecdysteroid kinase-like (EcKL) gene family in insects highlights roles in both steroid hormone metabolism and detoxification Genome Biol. Evol. (IF 3.3) Pub Date : 2024-01-31 Jack L Scanlan, Charles Robin
The evolutionary dynamics of large gene families can offer important insights into the functions of their individual members. While the ecdysteroid kinase-like (EcKL) gene family has previously been linked to the metabolism of both steroid moulting hormones and xenobiotic toxins, the functions of nearly all EcKL genes are unknown and there is little information on their evolution across all insects
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The mutational road not taken: using Ancestral Sequence Resurrection to evaluate the evolution of plant enzyme substrate preferences Genome Biol. Evol. (IF 3.3) Pub Date : 2024-01-30 Emily M Catania, Nicole M Dubs, Shejal Soumen, Todd J Barkman
We investigated the flowering plant Salicylic Acid Methyl Transferase (SAMT) enzyme lineage to understand the evolution of substrate preference change. Previous studies indicated that a single amino acid replacement to the SAMT active site (H150 M) was sufficient to change ancestral enzyme substrate preference from benzoic acid to the structurally similar substrate, salicylic acid. Yet, subsequent
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Epigenetic and genetic differentiation between Coregonus species pairs Genome Biol. Evol. (IF 3.3) Pub Date : 2024-01-25 Clare J Venney, Claire Mérot, Eric Normandeau, Clément Rougeux, Martin Laporte, Louis Bernatchez
Phenotypic diversification is classically associated with genetic differentiation and gene expression variation. However, increasing evidence suggests that DNA methylation is involved in evolutionary processes due to its phenotypic and transcriptional effects. Methylation can increase mutagenesis and could lead to increased genetic divergence between populations experiencing different environmental
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The Site/Group Extended Data format and tools Genome Biol. Evol. (IF 3.3) Pub Date : 2024-01-22 Julien Y Dutheil, Diyar Hamidi, Basile Pajot
Comparative sequence analysis permits unravelling the molecular processes underlying gene evolution. Many statistical methods generate candidate positions within genes, such as fast or slowly-evolving sites, coevolving groups of residues, sites undergoing positive selection or changes in evolutionary rates. Understanding the functional causes of these evolutionary patterns requires combining the results
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Transposon removal Reveals Their Adaptive Fitness Contribution Genome Biol. Evol. (IF 3.3) Pub Date : 2024-01-21 Susanne Cranz-Mileva, Eve Reilly, Noor Chalhoub, Rohan Patel, Tania Atanassova, Weihuan Cao, Christopher Ellison, Mikel Zaratiegui
Transposable Elements (TE) are molecular parasites that persist in their host genome by generating new copies to outpace natural selection. TE exert a large influence on host genome evolution, in some cases providing adaptive changes. Here we measure the fitness effect of the TE insertions in the fission yeast Schizosaccharomyces pombe type strain by removing all insertions of its only native TE family
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Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation Genome Biol. Evol. (IF 3.3) Pub Date : 2024-01-21 Vincent Kiplangat Bett, Ariana Macon, Beatriz Vicoso, Marwan Elkrewi
Since the commercialization of brine shrimp (genus Artemia) in the 1950s, this lineage, and in particular the model species Artemia franciscana, has been the subject of extensive research. However, our understanding of the genetic mechanisms underlying various aspects of their reproductive biology, including sex determination, are still lacking. This is partly due to the scarcity of genomic resources
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The Promise of Inferring the Past using the Ancestral Recombination Graph (ARG) Genome Biol. Evol. (IF 3.3) Pub Date : 2024-01-20 Débora Y C Brandt, Christian D Huber, Charleston W K Chiang, Diego Ortega-Del Vecchyo
The Ancestral Recombination Graph (ARG) is a structure that represents the history of coalescent and recombination events connecting a set of sequences (Hudson 1991). The full ARG can be represented as a set of genealogical trees at every locus in the genome, annotated with recombination events that change the topology of the trees between adjacent loci and the mutations that occurred along the branches
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Genomic architecture predicts tree topology, population structuring, and demographic history in Amazonian birds Genome Biol. Evol. (IF 3.3) Pub Date : 2024-01-18 Gregory Thom, Lucas Rocha Moreira, Romina Batista, Marcelo Gehara, Alexandre Aleixo, Brian Tilston Smith
Geographic barriers are frequently invoked to explain genetic structuring across the landscape. However, inferences on the spatial and temporal origins of population variation have been largely limited to evolutionary neutral models, ignoring the potential role of natural selection and intrinsic genomic processes known as genomic architecture in producing heterogeneity in differentiation across the