Evolution

  • Article
    | Open Access

    Parasitoids exploit host bodies for reproduction, selecting for host defences. A new host defence is reported, in which adult Drosophila accelerate mating behaviour at the sight of certain parasitoid wasps, mediated by the upregulation of a nervous system gene that encodes a 41-amino acid micropeptide.

    • Shimaa A. M. Ebrahim
    • , Gaëlle J. S. Talross
    •  & John R. Carlson
  • Article
    | Open Access

    Highly endangered species like the Sumatran rhinoceros are at risk from inbreeding. Five historical and 16 modern genomes from across the species range show mutational load, but little evidence for local adaptation, suggesting that future inbreeding depression could be mitigated by assisted gene flow among populations.

    • Johanna von Seth
    • , Nicolas Dussex
    •  & Love Dalén
  • Article
    | Open Access

    Geothermal environments are hotspots for carbon cycling. Here, De Anda et al. reconstruct archaeal genomes from terrestrial and deep-sea geothermal sediments, and propose the classification of these microbes as a new phylum, ‘Brockarchaeota’, with unique metabolic capabilities including non-methanogenic anaerobic methylotrophy.

    • Valerie De Anda
    • , Lin-Xing Chen
    •  & Brett J. Baker
  • Article
    | Open Access

    Social animals have sophisticated ways of classifying relationships with conspecifics. Data from 30 years of observations and playback experiments on dolphins with a multi-level alliance system show that individuals form social concepts that categorize conspecifics according to their shared cooperative history.

    • Stephanie L. King
    • , Richard C. Connor
    •  & Simon J. Allen
  • Article
    | Open Access

    Here, the authors present results of the ZiBRA-2 project (https://www.zibra2project.org) which is an arbovirus surveillance project, across the Midwest of Brazil using a mobile genomics laboratory, combined with a genomic surveillance training program that targeted post-graduate students, laboratory technicians, and health practitioners in universities and laboratories.

    • Talita Émile Ribeiro Adelino
    • , Marta Giovanetti
    •  & Luiz Carlos Junior Alcantara
  • Article
    | Open Access

    Though there is a long archaeological record of the use of honey, beeswax and other bee products, there are few known records from Africa. Here Dunne et al. analyse lipid residues from pottery from the Nok culture, Nigeria, dating to ~3500 years ago and find evidence of the collection and processing of bee products, likely honey.

    • Julie Dunne
    • , Alexa Höhn
    •  & Richard P. Evershed
  • Article
    | Open Access

    Trait-based approaches assume upper critical thermal limits (CTLs) are good predictors of climate change vulnerability. Here, the authors show that male fertility thermal limits, which are lower than CTLs, are better at predicting Drosophila extinction in the lab, suggesting species may be living close to their thermal limits.

    • Belinda van Heerwaarden
    •  & Carla M. Sgrò
  • Article
    | Open Access

    Despite linguistic and geographic diversity in South Eastern Bantu-speaking (SEB) groups of South Africa, genetic variation in these groups has not been investigated in depth. Here, the authors analyse genome-wide data from 5056 individuals, providing insights into demographic history across SEB groups.

    • Dhriti Sengupta
    • , Ananyo Choudhury
    •  & Michèle Ramsay
  • Article
    | Open Access

    DNA methylation plays an important role in brain development and function. Here, the authors compare whole-genome methylation in neurons and oligodendrocytes in humans, chimpanzees and macaques to reconstruct evolution of DNA methylation at cell-type level, including in regions associated with schizophrenia heritability.

    • Hyeonsoo Jeong
    • , Isabel Mendizabal
    •  & Soojin V. Yi
  • Article
    | Open Access

    Likelihood optimization in phylogenetic tree reconstruction is computationally intensive, especially as the number of sequences and taxa included increase. Here, Azouri et al. show how an artificial intelligence approach can reduce computational time without losing accuracy of tree inference.

    • Dana Azouri
    • , Shiran Abadi
    •  & Tal Pupko
  • Article
    | Open Access

    Anthropogenic changes, such as eutrophication from lake pollution, can lead to rapid evolution. Comparing Daphnia resurrected from generations adapted to historical pollution to contemporary, post-cleanup populations finds that Daphnia rapidly reversed their evolved resistance to harmful cyanobacteria.

    • Jana Isanta-Navarro
    • , Nelson G. Hairston Jr
    •  & Dominik Martin-Creuzburg
  • Article
    | Open Access

    Cryptophytes acquired plastids from red algae but replaced the light-harvesting phycobilisome with a unique cryptophyte antenna. Here via analysis of phycobilisome cryo-EM structures, Rathbone et al. propose that the α subunit of the cryptophyte antenna originated from phycobilisome linker proteins

    • Harry W. Rathbone
    • , Katharine A. Michie
    •  & Paul M. G. Curmi
  • Article
    | Open Access

    Most mammals are nocturnal, but a new analysis suggests that although most groups of species active at a particular time of day or night occupy different ecological niches, a surprisingly large proportion of species are more flexible in the timing of their activity than previously thought.

    • D. T. C. Cox
    • , A. S. Gardner
    •  & K. J. Gaston
  • Article
    | Open Access

    Previous work identified goddard as a putative de novo evolved gene in Drosophila melanogaster. Here, the authors characterize the structure and function of the Goddard protein in D. melanogaster, and they infer its ancestral and extant structures across the Drosophila genus.

    • Andreas Lange
    • , Prajal H. Patel
    •  & Erich Bornberg-Bauer
  • Article
    | Open Access

    Connecting conformational dynamics and epistasis has so far been limited to a few proteins and a single fitness trait. Here, the authors provide evidence of positive epistasis on multiple catalytic traits in the evolution and dynamics of engineered cytochrome P450 monooxygenase, offering insights for in silico protein design.

    • Carlos G. Acevedo-Rocha
    • , Aitao Li
    •  & Manfred T. Reetz
  • Article
    | Open Access

    Both ecological opportunity and phenotypic modularity have been suggested to facilitate adaptive radiations. Feiner et al. show that Anolis lizards evolved a new modularity structure in their island adaptive radiation, but that this modularity did not produce the same extreme diversification when Anolis returned to the mainland.

    • Nathalie Feiner
    • , Illiam S. C. Jackson
    •  & Tobias Uller
  • Article
    | Open Access

    Enterococcus faecalis is a commensal microorganism of animals, insects and humans, but also a nosocomial pathogen. Here, the authors analyse genomic sequences from E. faecalis isolates from animals and humans, and find that the last common ancestors of multiple hospital-associated lineages date to the pre-antibiotic era.

    • Anna K. Pöntinen
    • , Janetta Top
    •  & Jukka Corander
  • Article
    | Open Access

    Mexican Tetra cavefish have long been of interest in understanding adaptation to severe environmental change. Here the authors present a chromosome-level genome for the proxy-ancestral surface fish, and use CRISPR gene-editing to show the role of the rx3 gene in eye size.

    • Wesley C. Warren
    • , Tyler E. Boggs
    •  & Nicolas Rohner
  • Article
    | Open Access

    The mutations underlying sexually selected traits like the red fins on a male medaka fish can be hard to pinpoint. Using a new genome, transcriptomics and gene editing, Ansai et al. find that the gene csf1 causes male fins to be red, which attracts females and, surprisingly, is less attractive to predators.

    • Satoshi Ansai
    • , Koji Mochida
    •  & Jun Kitano
  • Article
    | Open Access

    Upstream open reading frames (uORFs) have widespread regulatory functions in eukaryotes, their genomic distribution and evolution is understudied. Here, the authors characterise ~17 million putative uORFs across 478 eukaryotic species, showing how evolution has shaped uORF contents and distribution.

    • Hong Zhang
    • , Yirong Wang
    •  & Jian Lu
  • Article
    | Open Access

    There are a number of competing explanations for the late Pleistocene extinction of many North American megafauna species. Here, the authors apply a Bayesian regression approach that finds greater concordance between megafaunal declines and climate change than with human population growth.

    • Mathew Stewart
    • , W. Christopher Carleton
    •  & Huw S. Groucutt
  • Article
    | Open Access

    Here, the authors analyze 4907 Circular Metagenome Assembled Genomes from human microbiomes and identify and characterize nearly 600 diverse genomes of crAss-like phages, finding two putative families with unusual genomic features, including high density of self-splicing introns and inteins.

    • Natalya Yutin
    • , Sean Benler
    •  & Eugene V. Koonin
  • Article
    | Open Access

    The Cambrian is known as a period of rapid animal diversification, but the development of these animals is not well characterized. Here, Steiner et al. describe a new assemblage of Cambrian eggs, embryos and early postembryonic stages from Mongolia that provides insight into ancient bilaterian development and evolution.

    • Michael Steiner
    • , Ben Yang
    •  & Philip Donoghue
  • Article
    | Open Access

    Hybrid zones are windows into the evolutionary process. Semenov et al. find that the head plumage differences between white wagtail subspecies have a simple genetic basis involving two small genetic regions, in which partially dominant and epistatic interactions help to explain how this sexual signal has become decoupled from other plumage traits.

    • Georgy A. Semenov
    • , Ethan Linck
    •  & Scott A. Taylor
  • Article
    | Open Access

    The genomic details of adaptation to extreme environments remain challenging to characterize. Using new methods to analyze flies experimentally evolved to survive extreme O2 conditions, the authors find a surprising level of synchronicity in selective sweeps, de novo mutations and adaptive recombination events.

    • Arya Iranmehr
    • , Tsering Stobdan
    •  & Gabriel G. Haddad
  • Article
    | Open Access

    While size exaggeration is common in the animal kingdom, Pisanski & Reby show that human listeners can detect deceptive vocal signals of people trying to sound bigger or smaller, and recalibrate their estimates accordingly, especially men judging the heights of other men, with implications for the evolution of vocal communication.

    • Katarzyna Pisanski
    •  & David Reby
  • Article
    | Open Access

    The deglaciation of Marinoan snowball Earth (~635 Myr ago) has been associated with potentially extensive CH4 emissions in relation to transient marine euxinia. Here, the authors find that active methanogenesis occurred during the termination of Marinoan snowball Earth, fueled by methyl sulfide production in sulfidic seawater.

    • Zhouqiao Zhao
    • , Bing Shen
    •  & Haoran Ma
  • Article
    | Open Access

    Sex chromosome gene content and expression is unusual. Here the authors use single cell RNA-Seq on Drosophila larvae to demonstrate that the single X and pair of 4th chromosomes are specifically inactivated in primary spermatocytes, while genes on the single Y chromosome become maximally active in primary spermatocytes.

    • Sharvani Mahadevaraju
    • , Justin M. Fear
    •  & Brian Oliver
  • Article
    | Open Access

    Autocatalytic networks may have started evolution during the origin of life. Here, the authors establish a landscape of thousands of RNA networks by barcoded sequencing and microfluidics, and derive relationships between topology and Darwinian properties such as variation and differential reproduction.

    • Sandeep Ameta
    • , Simon Arsène
    •  & Philippe Nghe
  • Article
    | Open Access

    Mycelial fusion can favour fungal strains that exploit each other, but the mechanism is not well understood. Here, Grum-Grzhimaylo et al. show that different cheater lineages share similar deficiencies in initiating fusion that nevertheless enable them to preferentially obtain the benefits of fusion initiated by wild-type mycelia.

    • Alexey A. Grum-Grzhimaylo
    • , Eric Bastiaans
    •  & Duur K. Aanen
  • Article
    | Open Access

    It is unclear how gut-dwelling E. coli bacteria often emerge to cause systemic infection in chickens. Here, Mageiros et al. use population genomics and pangenome-wide association studies to identify genetic elements associated with pathogenicity in avian E. coli.

    • Leonardos Mageiros
    • , Guillaume Méric
    •  & Samuel K. Sheppard
  • Article
    | Open Access

    Climate change may pose a challenge not only for survival of animals but also for their reproduction. Here, Schou et al. analyse how male and female ostrich fertility relates to fluctuating temperature across 20 years, finding reduced fertility away from the thermal optimum, but also individual variation in thermal tolerance.

    • Mads F. Schou
    • , Maud Bonato
    •  & Charlie K. Cornwallis