Evolutionary biology articles within Nature Communications

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  • 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

    The effect of temperature fluctuations on the evolution of new phenotypes is largely unknown. Using experimental evolution of fluorescent protein in E. coli, this study shows that a cooling environment can accelerate, and a warming environment decelerate, the evolution of a new protein phenotype.

    • Jia Zheng
    • , Ning Guo
    •  & Andreas Wagner

  • 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

    Endogenous retroviruses constitute 5–10% of mammalian genome space. This study characterize the bovine ERVK[2-1- LTR] clade showing that its activity varies between individuals as a function of the number of inherited autonomous elements, yet that most de novo insertions are non-autonomous elements lacking functional genes.

    • Lijing Tang
    • , Benjamin Swedlund
    •  & Carole Charlier

  • 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

    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

    The origins of alpine plant diversity are unclear. Here, the authors provide a time-calibrated molecular phylogenetic tree for Saxifraga, a diverse alpine plant clade, and show that upslope biome shifts into the alpine zone occurred more often than dispersal between alpine regions.

    • Tom Carruthers
    • , Michelangelo S. Moerland
    •  & Wolf L. Eiserhardt

  • Article
    | Open Access

    It is unclear whether naturally evolved de novo proteins have stable, folded structures. Here, through 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.

    • Junhui Peng
    •  & Li Zhao

  • 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

    A species’ response to anthropogenic climate change may depend on its adaptations to past climate changes. Here, the authors use whole-genome resequencing and genetic-environment association to identify genes important for local adaptation and project adaptation under future climate scenarios across bank vole populations in Britain.

    • Silvia Marková
    • , Hayley C. Lanier
    •  & Petr Kotlík

  • 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

    Single reference genomes and short-read sequencing data are not enough to harness the full genetic variation of a species. Here, the authors report pan-genome of Arabidopsis thaliana based on chromosomal-level genomes of 32 accessions and identify variations associated with local adaptation.

    • Minghui Kang
    • , Haolin Wu
    •  & Jianquan Liu

  • Article
    | Open Access

    Industrial whaling drove several species to near extinction. From an analysis of 50 whole-genomes from fin whale populations, this study shows that the fin whale population in the Eastern North Pacific was reduced 99% during whaling but has maintained genomic diversity, whereas the Gulf of California population remained small and isolated, resulting in increased genetic load.

    • Sergio F. Nigenda-Morales
    • , Meixi Lin
    •  & Robert K. Wayne

  • Article
    | Open Access

    Ongoing retroviral invasion into vertebrates has been rarely documented. Here the authors have identified 412 endogenous retroviruses that are invading the genomes of over a hundred vertebrate species. This may be relevant to conservation of threatened species, zoonoses in the wild, and emerging infectious diseases in humans.

    • Jianhua Wang
    •  & Guan-Zhu Han

  • Article
    | Open Access

    3-finger toxins are unique to the venoms of caenophidian snakes. This study traces the evolution of these toxins in snakes, highlighting a key shift from membrane-bound to secretory proteins. This transformation, involving the loss of a membrane-anchoring domain and changes in gene expression, paved the way for their venomous function.

    • Ivan Koludarov
    • , Tobias Senoner
    •  & Burkhard Rost

  • Article
    | Open Access

    Camouflage is a widespread phenomenon in nature, and the orchid mantis is a particularly striking example. Here the authors use evolutionary genomics to uncover the genetic mechanisms behind the colour and morphology that produce innovative camouflage in the orchid mantis and dead leaf mantis.

    • Guangping Huang
    • , Lingyun Song
    •  & Fuwen Wei

  • 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

    CRISPR-Cas immunity systems safeguard prokaryotic genomes by inhibiting the invasion of mobile genetic elements. Here, the authors show that insertion sequences can efficiently insert into cas genes, thus inactivating CRISPR defenses and increasing bacterial susceptibility to foreign DNA invasion.

    • Yong Sheng
    • , Hengyu Wang
    •  & Qianjin Kang

  • 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

    The centromere is required for the segregation of chromosomes. Here, the authors report the organization and dynamic of holocentric chromosomes, each containing 7 to 11 evenly spaced megabase-sized centromere-specific histone H3-positive units.

    • Yi-Tzu Kuo
    • , Amanda Souza Câmara
    •  & Andreas Houben

  • 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

    Annelid worms have colonised extreme ecological niches, such as hydrothermal vents and whale falls thanks to symbiotic bacteria. This study finds that Osedax worms and the related Vestimentifera have evolved different genomic adaptations to sustain their bacterial symbioses and exploit different resources, such as decaying bone.

    • Giacomo Moggioli
    • , Balig Panossian
    •  & José M. Martín-Durán

  • Article
    | Open Access

    Stem cell niches regulate proliferation of stem cells, but variation in this control across natural populations has not been explored. Here they combine quantitative genetics and gene editing to show that natural variation in C. elegans germ stem cell niche activity is shaped by complex gene-gene interactions.

    • Sarah R. Fausett
    • , Asma Sandjak
    •  & Christian Braendle

  • Article
    | Open Access

    The role of DNA methylation in insects is poorly understood. Here, the authors knock out the DNA methyltransferase DNMT1 in an ant and find no obvious effects on development, rather showing that this enzyme seems to play a crucial role during early oogenesis.

    • Iryna Ivasyk
    • , Leonora Olivos-Cisneros
    •  & Daniel J. C. Kronauer

  • Article
    | Open Access

    Implementing high-throughput single-cell DNA sequencing for the study of solid tumours has been challenging. Here, the authors present an optimised approach for snap-frozen tissue single nuclei extraction and DNA sequencing, which can be applied to study pancreatic ductal adenocarcinoma evolution and heterogeneity.

    • Haochen Zhang
    • , Elias-Ramzey Karnoub
    •  & Christine A. Iacobuzio-Donahue

  • Article
    | Open Access

    Venom is a complex trait with unresolved underlying toxin expression dynamics. Here, the authors compare expression across sea anemone species, revealing variation in dominant toxin diploid copy number across populations which generates distinct haplotypes.

    • Edward G. Smith
    • , Joachim M. Surm
    •  & Yehu Moran

  • Article
    | Open Access

    Seahorses may have required adaptations to avoid immunological rejection of allogenic embryos by males. The authors show that a single substitution in tlx1 is associated with loss of the spleen in seahorses, and that across the clade, degree of male pregnancy is negatively correlated with immune gene repertoire complexity.

    • Yali Liu
    • , Meng Qu
    •  & Qiang Lin

  • Article
    | Open Access

    Evolution of the SARS-CoV-2 spike protein is likely driven by many factors, including immune escape and receptor binding. Here, by measuring the binding affinity of more than 30,000 variants of the SARS-CoV-2 RBD to its receptor ACE2, Moulana et al. show that the evolution of the Omicron BA.1 variant was driven by interactions between mutations.

    • Alief Moulana
    • , Thomas Dupic
    •  & Michael M. Desai

  • Article
    | Open Access

    Here, the authors study adaptation to altitude in 518 whole genomes from two species of tropical butterflies. They find repeated genetic differentiation within species, little molecular parallelism between these species, and introgression from closely related species, concluding that standing genetic variation promotes parallel local adaptation.

    • Gabriela Montejo-Kovacevich
    • , Joana I. Meier
    •  & Chris D. Jiggins

  • Article
    | Open Access

    Carpinus fangiana exhibits intermediate morphology between C. viminea and Ostrya rehderiana. Here, the authors report that Carpinus sect. Distegocarpus likely originate through homoploid hybrid speciation (HHS) during the early divergence between Carpinus and Ostrya through genomic analyses.

    • Zefu Wang
    • , Minghui Kang
    •  & Jianquan Liu

  • Article
    | Open Access

    Anopheles mosquitoes are vectors of human malaria, and better understanding of them has implications for public health. Here, the authors apply Hi-C, FISH, RNA-seq, and ChIP-seq techniques to comprehensively characterize chromatin architecture and its evolutionary dynamics in five Anopheles species.

    • Varvara Lukyanchikova
    • , Miroslav Nuriddinov
    •  & Veniamin Fishman

  • Article
    | Open Access

    Even in well-studied species, there is still substantial natural genetic variation that has not been characterized. Here, the authors use long read sequencing to discover transposable elements in the Drosophila genome not detected by short read sequencing, and link them to gene expression.

    • Gabriel E. Rech
    • , Santiago Radío
    •  & Josefa González

  • Article
    | Open Access

    The genus Drosophila originate in subSaharan Africa and spread North up to the polar circle where they experience long days in the summer or even constant light. Here, the authors show that a form of the TIMELESS protein enables flies to synchronise their behavioural activity to long summer days

    • Angelique Lamaze
    • , Chenghao Chen
    •  & Ralf Stanewsky

  • Article
    | Open Access

    Detailing how populations adapted to environmental change is needed to predict future responses, but identifying adaptive variants and detailing their fitness effects is rare. Here, the authors show that parallel loss of FRI and FLC function reduces time to flowering and drives adaptation in a drought prone environment.

    • Andrea Fulgione
    • , Célia Neto
    •  & Angela M. Hancock

  • Article
    | Open Access

    ‘A supergene that underlies variation in male mating phenotypes has consequences for female reproduction. Here, the authors use evolutionary models to show that the rarest variant of this supergene is maintained by disproportionally high male reproductive success.’

    • Lina M. Giraldo-Deck
    • , Jasmine L. Loveland
    •  & Clemens Küpper

  • Article
    | Open Access

    The small size (≤15-nt) of micorexons poses difficulties for genome annotation and identification using standard RNA sequence mapping approaches. Here, the authors develop computational pipelines to discover and predict microexons in plants and reveal diverse evolutionary trajectories via genomewide microexon modeling.

    • Huihui Yu
    • , Mu Li
    •  & Chi Zhang

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