Evolutionary genetics articles within Nature Communications

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  • Article
    | Open Access

    Here the authors report that enhancers appear more often in late-replicating DNA regions and are enriched for mutations affecting TF binding. This relationship with DNA replication time is seen in species evolution and cancer, suggesting a fundamental principle of genome evolution.

    • Paola Cornejo-Páramo
    • , Veronika Petrova
    •  & Emily S. Wong

  • Article
    | Open Access

    Little is known about the genetic basis of the rhythmic component of bird song, an important trait in sexual selection and species recognition. By studying a system with innate vocalizations, the Pogoniulus tinkerbirds, this study finds candidate genes that underlie differences in speed in vocal rhythm in this system.

    • Matteo Sebastianelli
    • , Sifiso M. Lukhele
    •  & Alexander N. G. Kirschel

  • Article
    | Open Access

    Naked mole-rats are long-lived rodents with remarkable resistance to cancer. Here authors show that their T-cell compartment is different from that of mice in that they have a large population of circulating cytotoxic γδ T cells harboring a dominant clonotype, and the clonotypic diversity of their conventional cytotoxic αβ T cells is more modest than that of mice.

    • Tzuhua D. Lin
    • , Nimrod D. Rubinstein
    •  & Rochelle Buffenstein

  • Article
    | Open Access

    Endogenous retroviruses (ERVs) are remnants of ancient viruses embedded in animal DNA. This study found that the solitary long terminal repeats of ERVs in birds, particularly Passeriformes, have evolved to influence gene expression, potentially contributing to adaptive diversification of species.

    • Guangji Chen
    • , Dan Yu
    •  & Shaohong Feng

  • Article
    | Open Access

    Modern sugarcane cultivars have complicated genome due to interspecific crosses and multiple backcrossing. Here, the authors report the haplotype-resolved, chromosome-level genome assembly of a modern hybrid sugarcane cultivar and reveal the expansion of genes related to sugar accumulation and smut resistance.

    • Yixue Bao
    • , Qing Zhang
    •  & Muqing Zhang

  • Article
    | Open Access

    The naked mole-rat exhibits extreme longevity, resistance to hypoxia and absence of cardiovascular disease. Here, Faulkes et al. identify mechanisms behind these traits by comparing cardiac metabolomes and transcriptomes of naked more-rats to other African mole-rat genera and evolutionary divergent mammals.

    • Chris G. Faulkes
    • , Thomas R. Eykyn
    •  & Dunja Aksentijevic

  • Article
    | Open Access

    Correspondence between genome and organismal complexity over macroevolutionary time is poorly understood. Here the authors show that multicellular eukaryotes increasingly simplify their genomes and suggest that the concept of functional outsourcing, via ecological interactions, could explain this paradoxical complexity decoupling.

    • Mirjana Domazet-Lošo
    • , Tin Široki
    •  & Tomislav Domazet-Lošo

  • Article
    | Open Access

    The timing and chronology of the movement of Homo sapiens after migration out of Africa remains unclear. Here, the authors combine a genetic approach with a palaeoecological model to estimate that the Persian Plateau could have been a hub for migration out of Africa, suggesting the environment may have been suitable for population maintenance.

    • Leonardo Vallini
    • , Carlo Zampieri
    •  & Luca Pagani

  • Article
    | Open Access

    Subgenome dominance is widely observed in allopolyploid species, but the molecular mechanisms remain unclear. Here, the authors generate genome-wide map of accessible chromatin regions (ACRs) in allo-octoploid cultivated strawberry and reveal that dynamics of the ACRs play an important role in its subgenome dominance.

    • Chao Fang
    • , Ning Jiang
    •  & Jiming Jiang

  • Article
    | Open Access

    There is limited data on immune factors contributing to SARS-CoV-2 viral clearance in people living with HIV. Here, the authors show that re-emergence of the neutralizing antibody response may be key to clearing persistent SARS-CoV-2 infection in ART-mediated recovery from immunosuppression in advanced HIV disease.

    • Farina Karim
    • , Catherine Riou
    •  & Alex Sigal

  • Article
    | Open Access

    Pathogenic germline variants associated with childhood cancer risk could be subject to evolutionary constraints. Here, the authors analyse publicly available germline data in large cohorts and observe that paediatric cancer predisposition syndrome genes are highly constrained in the general population.

    • Ulrik Kristoffer Stoltze
    • , Jon Foss-Skiftesvik
    •  & Kjeld Schmiegelow

  • Article
    | Open Access

    Dipterocarp trees are iconic but severely threatened species in Asian rainforests. This study assembles high-quality genomes of seven dipterocarp species to reveal the molecular basis of key adaptations and identifies a recent sharp population decline coinciding with local human activity.

    • Rong Wang
    • , Chao-Nan Liu
    •  & Xiao-Yong Chen

  • Article
    | Open Access

    The evolutionary trajectory of avian sex chromosomes may be more intricate than previously understood. In this study, sequencing and analysis of the neo-sex chromosomes and genome of the Crested Ibis suggests a multidirectional evolution of sex chromosomes in core waterbirds.

    • Lulu Xu
    • , Yandong Ren
    •  & Gang Li

  • Article
    | Open Access

    Polyploidization-rediploidization process plays an important role in plant adaptive evolution. Here, the authors assemble the genomes of mangrove species Sonneratia alba and its inland relative Lagerstroemia speciosa, and reveal genomic evidence for rediploidization and adaptive evolution after the whole-genome triplication.

    • Xiao Feng
    • , Qipian Chen
    •  & Ziwen He

  • Article
    | Open Access

    Genome-wide evidence to support that wild rice can contribute to weedy rice evolution by hybridization and adaptive introgression is very limited. Here, the authors sequence the weedy rice genomes and show reproductively compatible wild rice can contribute to weedy rice evolution.

    • Lin-Feng Li
    • , Tonapha Pusadee
    •  & Kenneth M. Olsen

  • Article
    | Open Access

    Cytochrome c maturation (CCM) is the process of covalent attachment of a heme group to the conserved cysteines to form the holocytochrome. Here, the authors report that the non-adaptive convergent evolution at the pathway level leads to mosaic distribution of CCM systems I and III among Archaeplastida species.

    • Huang Li
    • , Soujanya Akella
    •  & Jeffrey P. Mower

  • Article
    | Open Access

    Bats have been suggested to be resistant to cancer due to mechanisms related to their evolved longevity, but the associated molecular drivers are still understudied. Here, the authors examine cancer resistance mechanisms across seven bat species using in vitro and in vivo models, and identify HIF1A, COPS5, and RPS3 as related genes.

    • Rong Hua
    • , Yuan-Shuo Ma
    •  & Zhen Liu

  • Article
    | Open Access

    Chemoreception - the ability to smell and taste - relies on diverse receptor genes. Examining 1,527 vertebrate genomes, this study explores the dynamic evolution, lineage-specific expansions and losses of chemoreceptor genes as well as ecological and morphological factors associated with these.

    • Maxime Policarpo
    • , Maude W. Baldwin
    •  & Walter Salzburger

  • Article
    | Open Access

    Here the authors show that genetic changes between species often alter gene expression in a cell type-specific manner. Most of this variability is driven by locally functioning cis-acting variation, and this contributes to the speed at which cell types accumulate expression changes.

    • Jasper Panten
    • , Tobias Heinen
    •  & Duncan T. Odom

  • Article
    | Open Access

    Rickettsiales encompass diverse host-associated bacteria, including pathogens, parasites, and mutualists. This study shows that obligate associations with their hosts likely evolved multiple times independently, thus providing an alternative, generalisable view, on evolution of intracellularity.

    • Michele Castelli
    • , Tiago Nardi
    •  & Davide Sassera

  • Article
    | Open Access

    Chemosensory tissues are remarkably variable between species but the cause of this diversity is unclear. Here, the authors conduct transcriptomic analyses of chemosensory tissues from diverse Drosophila species, revealing evidence of stabilizing selection and recent species- and sex-specific changes.

    • Gwénaëlle Bontonou
    • , Bastien Saint-Leandre
    •  & J. Roman Arguello

  • Article
    | Open Access

    Telomeres protect the extremities of linear chromosomes and are involved in ageing, senescence and genome stability. Here, the authors have identified peculiar and specific telomeric DNA repeats in the genomes of devastating plant-parasitic nematodes, opening new perspectives for their control.

    • Ana Paula Zotta Mota
    • , Georgios D. Koutsovoulos
    •  & Etienne G. J. Danchin

  • Article
    | Open Access

    It is unclear whether naturally evolved de novo proteins have stable, folded structures. Here, systematic identification and structural modeling of de novo genes, this study reveals that a small subset of these proteins may have well-folded structures, and were likely born with these structures.

    • Balázs Bálint
    • , Zsolt Merényi
    •  & László G. Nagy

  • Article
    | Open Access

    Frogs are an ancient and ecologically diverse group of amphibians that include important model systems. This paper reports genome sequences of multiple frog species, revealing remarkable stability of frog chromosomes and centromeres, along with highly recombinogenic extended subtelomeres.

    • Jessen V. Bredeson
    • , Austin B. Mudd
    •  & Daniel S. Rokhsar

  • Article
    | Open Access

    Little is known about the genetic basis of many natural behaviours and how they contribute to speciation. Here the authors address this by identifying genes linked to migration of a songbird, investigating how these gene are regulated, and connecting them to potential barriers between species.

    • Matthew I. M. Louder
    • , Hannah Justen
    •  & Kira E. Delmore

  • Article
    | Open Access

    Hyoscyamine and scopolamine (HS) are two tropane alkaloids with medicinal significance produced by distantly related lineages in the Solanaceae family. Here, the authors assemble the genome of three HS-producing and one non-HS-producing species within Solanaceae, and reveal the evolution of the biosynthetic pathway.

    • Jiao Yang
    • , Ying Wu
    •  & Jianquan Liu

  • Article
    | Open Access

    Heeren et al study the evolutionary genomics of leishmaniasis in Peru and Bolivia to show that parasite hybridization increases the prevalence, diversity and spread of viruses that have been previously associated with disease severity and treatment failure.

    • Senne Heeren
    • , Ilse Maes
    •  & Frederik Van den Broeck

  • Article
    | Open Access

    Slowly evolving cnidarians are useful models to study genome architecture. This study shows that sea anemones have a high degree of chromosomal macrosynteny, but poor microsynteny conservation. This is correlated with a small genome size and short distances of cis-regulatory elements to genes.

    • Bob Zimmermann
    • , Juan D. Montenegro
    •  & Ulrich Technau

  • Article
    | Open Access

    The butterfly Parnassius glacialis experienced vast environmental transition when it dispersed out of the Qinghai-Tibet plateau. Here, the authors find that P. glacialis has an unusually large genome with rapid accumulation of transposable elements possibly facilitating its evolutionary adaptation.

    • Youjie Zhao
    • , Chengyong Su
    •  & Jiasheng Hao

  • Article
    | Open Access

    Hyaluronic acid is believed to plays a critical role in cancer resistance and longevity of the naked mole rat. Here, Zhao and colleagues show that accumulation of high levels of hyaluronic acid has co-evolved repeatedly in mammalian clades with adaptation to subterranean habitats.

    • Yang Zhao
    • , Zhizhong Zheng
    •  & Vera Gorbunova

  • Article
    | Open Access

    Self-incompatibility in diploid Arabidopsis relatives is determined by a dominance relationship that is epigenetically regulated. Using transgenic methods, this study demonstrates that the dominance relationship between subgenomes of the allopolyploid species Arabidopsis kamchatica underlies it’s self-compatibility.

    • Chow-Lih Yew
    • , Takashi Tsuchimatsu
    •  & Kentaro K. Shimizu

  • Article
    | Open Access

    Host-parasite interactions can lead to negative frequency-dependent selection. Here, the authors sequence the genomes of H. bakeri and H. polygyrus, parasites of house and wood mice, respectively, and find that proteins that interact with the host immune response are often highly diverse.

    • Lewis Stevens
    • , Isaac Martínez-Ugalde
    •  & Mark Blaxter

  • Article
    | Open Access

    Bdelloid rotifers can withstand a wide range of genotoxic stresses. Here the authors reveal that a DNA ligase of bacterial origin was acquired by horizontal gene transfer to confer high resistance to ionizing radiation in bdelloid rotifers and other organisms known for their extreme tolerance to stress.

    • Emilien Nicolas
    • , Paul Simion
    •  & Karine Van Doninck

  • Article
    | Open Access

    The Mycobacterium tuberculosis complex (MTBC) includes several pathogens thought to have originated in East Africa from an ancestor closely related to Mycobacterium canettii. Here, the authors describe a clinical tuberculosis strain isolated in Ethiopia that has typical M. canettii features but is phylogenetically much closer to the MTBC clade, supporting that the emergence of MTBC pathogens is a recent evolutionary event.

    • Bazezew Yenew
    • , Arash Ghodousi
    •  & Daniela Maria Cirillo

  • Article
    | Open Access

    Investigation of heterogametic transitions in sex chromosomes is challenging but fascinating from an evolutionary perspective. Here, Hu et al. have identified a transition from an XY to a ZW system in the genus Salix (willows) where both the Z and W chromosomes have originated from the ancestral Y.

    • Nan Hu
    • , Brian J. Sanderson
    •  & Matthew S. Olson

  • Article
    | Open Access

    Mutations provide the genetic variability required for evolutionary change. Here, using pedigree-based whole genome sequencing, the authors determine that the Epaulette shark appears to have the lowest mutation rate identified in a vertebrate, providing a potential explanation for slow evolution in the shark lineage.

    • Ashley T. Sendell-Price
    • , Frank J. Tulenko
    •  & Manfred Schartl

  • Article
    | Open Access

    Despite the significance of mosquitos for human health, little research has focused on their phylogeny. Here, the authors present a resolved phylogenetic history of mosquitoes based on phylogenomics showing that these major disease vectors radiated coincidentally with geologic events and the diversification of their hosts.

    • John Soghigian
    • , Charles Sither
    •  & Brian M. Wiegmann

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