Evolution articles within Nature Communications

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  • Article
    | Open Access

    common assumption of evolution is that of an ecological limit to species diversity. This study tests whether sympatry with closely-related species leads to decreasing speciation rates. They find that, for terrestrial vertebrates, the probability of speciation seems to be unaffected by the number of other species of that lineage already present

    • Marcio R. Pie
    • , Raquel Divieso
    •  & Fernanda S. Caron
  • Article
    | Open Access

    Triple artemisinin-based combination therapies have shown high efficacy for treatment of malaria in preliminary studies. Here, the authors use mathematical modelling to assess whether these therapies could also delay the emergence and spread of antimalarial drug resistance when compared against frontline therapies.

    • Tran Dang Nguyen
    • , Bo Gao
    •  & Ricardo Aguas
  • Article
    | Open Access

    Songbirds have an extra chromosome with unknown function found only in their germline. This study assembles and compares this chromosome in two closely related nightingale species, finding large differences in genetic content and only one conserved gene with probable essential function.

    • Stephen A. Schlebusch
    • , Jakub Rídl
    •  & Radka Reifová
  • Article
    | Open Access

    The maxilloturbinal, an area of the mammalian nasal cavity, has been proposed to play a pivotal role in body temperature maintenance. Here, the authors use computed tomographic data to show that neither corrected basal metabolic rate nor body temperature significantly correlate with the relative surface area of the maxilloturbinal.

    • Quentin Martinez
    • , Jan Okrouhlík
    •  & Pierre-Henri Fabre
  • Article
    | Open Access

    Chikungunya virus is endemic in Brazil and cases have been rapidly increasing in recent years. Here, the authors describe the expansion of a genomic surveillance program across the country allowing them to characterise the emergence and dispersal of two distinct subclades mainly seeded from the north eastern region.

    • Joilson Xavier
    • , Luiz Carlos Junior Alcantara
    •  & Marta Giovanetti
  • Article
    | Open Access

    Asteraceae is the largest family of flowering plants. Here, the authors assemble the genomes of stem lettuce (within Asteraceae) and beach cabbage (within Goodeniaceae) for evolutionary genomics analyses and reveal the absence of the core regulatory gene of nitrogen and carbon assimilation in Asteraceae.

    • Fei Shen
    • , Yajuan Qin
    •  & Xiaozeng Yang
  • Article
    | Open Access

    Caenorhabditis elegans is used as a model species to investigate ageing, yet has a very high degree of plasticity in lifespan. This study argues that ageing in C. elegans is driven by suicidal reproductive effort, unlike many other organisms.

    • Carina C. Kern
    • , Shivangi Srivastava
    •  & David Gems
  • Article
    | Open Access

    Herbarium collections are an important source of historical DNA, whose analysis can shed light on the evolutionary history of plant pathogens. Here, Campos et al. reconstruct historical genomes of the bacterial crop pathogen Xanthomonas citri pv. citri from citrus herbarium specimens, estimating that the pathogen originated in Southern Asia ~11,500 years ago and diversified during the beginning of the 13th century.

    • Paola E. Campos
    • , Olivier Pruvost
    •  & Lionel Gagnevin
  • Article
    | Open Access

    The chronology and mode of parallel evolution remain unclear. Here, the authors compare mid-Holocene and contemporary bottlenose dolphin adaptations between pelagic and coastal ecosystems with paleogenomics, finding rapid adaptation to newly emerged habitat from standing genetic variation.

    • Marie Louis
    • , Petra Korlević
    •  & Andrew D. Foote
  • Article
    | Open Access

    Birds can adapt to temperature gradients by changing body size (Bergmann’s rule) or bill size (Allen’s rule), but many groups don’t conform to these patterns. Here the authors show that most bird families show subtle and complementary changes in bill and body size, while also being constrained by feeding ecology.

    • Justin W. Baldwin
    • , Joan Garcia-Porta
    •  & Carlos A. Botero
  • Article
    | Open Access

    In stochastic games, there is a feedback loop between a group’s social behaviors and its environment. Kleshnina et al. show that groups are often more cooperative when they know the exact state of their environment, although there are also intriguing cases when ignorance is beneficial.

    • Maria Kleshnina
    • , Christian Hilbe
    •  & Martin A. Nowak
  • Article
    | Open Access

    Detection of resistance to the antibiotic metronidazole in C. difficile often requires the presence of heme in the media, for unclear reasons. Here, the authors show that most metronidazole-resistant strains carry a mutation that promotes expression of a heme-dependent enzyme that degrades nitroimidazoles, and the mutation often co-occurs with an amino-acid substitution in DNA gyrase that confers resistance to another class of antibiotics, fluoroquinolones.

    • Abiola O. Olaitan
    • , Chetna Dureja
    •  & Julian G. Hurdle
  • Article
    | Open Access

    The SARS-CoV-2 virus has been documented to transmit between humans and animals, providing opportunities for viral reservoirs. Here, the authors show SARS-CoV-2 lineages in free-ranging white-tailed deer across the United States, long after the lineages had declined in human populations.

    • Aijing Feng
    • , Sarah Bevins
    •  & Xiu-Feng Wan
  • Article
    | Open Access

    Changes in the abundance and diversity of neural cell types provide the substrate for behavioral evolution. This study provides evidence of extensive, mosaic expansion of an integration brain center, among closely related Heliconiini butterflies, associated with increased neuron number, visual processing and long term memory.

    • Antoine Couto
    • , Fletcher J. Young
    •  & Stephen H. Montgomery
  • Article
    | Open Access

    Our understanding of the origins of tunicates, an important group of filter-feeding marine invertebrate chordates, is limited due to a poor fossil record. Here, the authors present a 500 million year old tunicate fossil, demonstrating that the modern tunicate body plan was established shortly after the Cambrian Explosion.

    • Karma Nanglu
    • , Rudy Lerosey-Aubril
    •  & Javier Ortega-Hernández
  • Article
    | Open Access

    A major part of the human Y chromosome consists of palindromes with multiple copies of genes primarily expressed in testis. Here, the authors investigate copy number variation in these palindromes based on whole genome sequence data from 11,527 Icelandic men.

    • Elise A. Lucotte
    • , Valdís Björt Guðmundsdóttir
    •  & Kari Stefansson
  • Article
    | Open Access

    ERK signalling is a core developmental pathway that is canonically activated by RTKs through activated RAS. Here they show that the process of ERK activation in skeletogenic precursors of the sea urchin embryo is growth factor and RAS-independent, uncovering a new mode of ERK signalling in non-chordate metazoa.

    • Aline Chessel
    • , Noémie De Crozé
    •  & Thierry Lepage
  • Article
    | Open Access

    Previous, a long-term evolution experiment in E.coli resulted in spontaneous emergence of ecotypes that coexisted for more than 14,000 generations. Here, the authors show that the emergence and persistence of this phenomenon results from two interacting trade-offs, rooted in biochemical constraints.

    • Avik Mukherjee
    • , Jade Ealy
    •  & Markus Basan
  • Article
    | Open Access

    Acorales is sister to all other monocots and contains only one family with just one genus, Acorus. Here, the authors assemble the genome of the diploid Ac. gramineus and the tetraploid Ac. calamus, reconstruct an ancestral monocot karyotype and gene toolkit, and discuss the origin and evolution of the two species and other monocots.

    • Liang Ma
    • , Ke-Wei Liu
    •  & Zhong-Jian Liu
  • Article
    | Open Access

    Monocots are one of the most diverse and dominant clades of flowering plants. Here, the authors assemble the genome of Acorus gramineus, confirm its phylogenetic position as sister to the rest of monocots and reveal the absence of tau (τ) whole-genome duplication observed in the majority of monocot clades.

    • Xing Guo
    • , Fang Wang
    •  & Huan Liu
  • Article
    | Open Access

    Most of the mutations accumulated in cancer cells are deleterious, and it is unclear how such alterations are tolerated. Here, the authors propose that copy number amplifications could increase the tolerance to deleterious mutations, and analyse the features that could determine the underlying selection process.

    • Fabio Alfieri
    • , Giulio Caravagna
    •  & Martin H. Schaefer
  • Article
    | Open Access

    Birdsong is simultaneously repetitive and highly diverse. Sierro et al. resolve this apparent paradox through experiments in blue tits showing that consistent repetition is a fitness indicator, while song diversity reduces habituation during singing displays.

    • Javier Sierro
    • , Selvino R. de Kort
    •  & Ian R. Hartley
  • Article
    | Open Access

    Diverse bacteria exhibit phenotypically plastic multicellular clustering. Here the authors show that a single mutation can genetically assimilate ancestrally inducible multicellularity by modulating plasticity at multiple levels of organization to make E. coli grow constitutively as macroscopic multicellular clusters.

    • Yashraj Chavhan
    • , Sutirth Dey
    •  & Peter A. Lind
  • Article
    | Open Access

    The second SARS-CoV-2 wave in Peru had a high case fatality rate with Lambda and Gamma causing most cases. Using phylodynamics, the authors here show that Lambda most likely originated in Peru from where it spread to other South American countries and that the center of Peru played a key role in transmission to other regions.

    • Santiago Justo Arevalo
    • , Carmen Sofia Uribe Calampa
    •  & Joao Renato Rebello Pinho
  • Article
    | Open Access

    The egg membrane protein Bouncer is an important mediator of gamete interaction and prevents cross-fertilisation between medaka and zebrafish. This study demonstrates unique functional and structural differences in Bouncer proteins of these and other distantly related fish species which may determine which species can hybridize.

    • Krista R. B. Gert
    • , Karin Panser
    •  & Andrea Pauli
  • Article
    | Open Access

    Here the authors report new human fossils from Tam Pà Ling cave, Laos, consisting of a cranial and a tibial fragment, dated to 68–86 thousand years ago. This find confirms that Homo sapiens were present in Southeast Asia by this time and the shape of the fossils indicates they may have descended from non-local populations.

    • Sarah E. Freidline
    • , Kira E. Westaway
    •  & Fabrice Demeter
  • Article
    | Open Access

    Challenges rearing juvenile cone snails have limited our understanding of their developmental biology. This study cultured Conus magus cone snails and revealed how complex morphological, behavioural and molecular changes facilitate the ontogenetic shift from juvenile worm-hunters to fish-hunting adults.

    • Aymeric Rogalski
    • , S. W. A. Himaya
    •  & Richard J. Lewis
  • Article
    | Open Access

    The notothenioid radiation is a remarkable group of fish adapted to life in the icy waters of the Southern Ocean. This study investigates the evolutionary history of this group and the basis of their adaption to cold environments through genomic analysis of 24 new genome assemblies.

    • Iliana Bista
    • , Jonathan M. D. Wood
    •  & Richard Durbin
  • Article
    | Open Access

    Bacteria release and respond to autoinducers in a process known as quorum sensing. While classically viewed as a strategy to coordinate cell behaviour, Moreno-Gámez et al. demonstrate using modelling that quorum sensing may also be used to sense the environment as a collective by pooling information at relevant scales and harnessing the wisdom of the crowds.

    • Stefany Moreno-Gámez
    • , Michael E. Hochberg
    •  & G. S. van Doorn
  • Article
    | Open Access

    Monoamines act as neuromodulators in the nervous system, but their evolutionary origins are unclear. Here, the authors examine the evolution of genes involved in monoamine production, and processing suggesting that the monoaminergic system evolved in the bilaterian stem-group.

    • Matthew Goulty
    • , Gaelle Botton-Amiot
    •  & Roberto Feuda
  • Article
    | Open Access

    Cooperative disease defense is part of group-level collective behavior. Here, the authors explore individual decisions, finding that garden ants increase grooming highly infectious individuals when they perceive a high pathogen load and suppress grooming after having been groomed by nestmates.

    • Barbara Casillas-Pérez
    • , Katarína Boďová
    •  & Sylvia Cremer
  • Article
    | Open Access

    There is limited understanding of SARS-CoV-2 intra-host evolution and subsequent transmission and adaptations in the context of persistent infection. Here, the authors describe sequential persistent SARS-CoV-2 infections that led to the emergence, transmission and further evolution of a novel Omicron BA.1.23 lineage.

    • Ana S. Gonzalez-Reiche
    • , Hala Alshammary
    •  & Harm van Bakel
  • Article
    | Open Access

    Protein secondary structures–α-helices and β-sheets–are generally assumed to be fixed over evolutionary history. By leveraging sequence information and sensitive statistical techniques, this work proposes that secondary structures in naturally occurring DNA-binding proteins switched in response to stepwise mutation.

    • Devlina Chakravarty
    • , Shwetha Sreenivasan
    •  & Lauren L. Porter
  • Article
    | Open Access

    Using data from the Tara Pacific expedition, this study shows that a key driver of variation in coral telomere DNA length across the Pacific Ocean is the history of water temperature. The telomere lengths of short-lived, stress-sensitive Pocillopora colonies are more sensitive to seasonal temperature variations than those of long-lived and stress-resistant Porites colonies.

    • Alice Rouan
    • , Melanie Pousse
    •  & Eric Gilson
  • Article
    | Open Access

    Assigning assembled chromosomes to subgenome in allopolypoid genome analysis is challenging. Here, the authors report a statistical formwork for identifying evolutionarily coherent subgneomes relying on transposable elements to group chromosomes into sets with shared ancestry and apply it in cyprinids, false flax and strawberry.

    • Adam M. Session
    •  & Daniel S. Rokhsar
  • Article
    | Open Access

    An extinct prehistoric plague lineage of Yersinia pestis has been documented from Central Europe to Asia during the Late Neolithic and Bronze Age. Here, Swali et al. show that this lineage spread to Europe’s northwestern periphery by sequencing three ~4000 year-old Yersinia pestis genomes from Britain.

    • Pooja Swali
    • , Rick Schulting
    •  & Pontus Skoglund
  • Article
    | Open Access

    Highly pathogenic avian influenza A(H5N1) viruses of clade 2.3.4.4b underwent an explosive geographic expansion in 2021 among wild birds and domestic poultry. Here, Kandeil et al. show that the Western movement of this clade was followed by reassortment with viruses circulating in wild birds in North America which resulted in different genotypes exhibiting a wide range of disease severity in mammal models (mice, ferrets, chicken) ranging from asymptomatic disease to severe neurological pathology.

    • Ahmed Kandeil
    • , Christopher Patton
    •  & Richard J. Webby