Evolution

  • 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
  • Article
    | Open Access

    Microbial symbionts can help their hosts metabolise diverse diets. A study on herbivorous turtle ants identifies the cuticular components which are nitrogen-enriched by gut bacteria, highlighting the role of symbionts in insect evolution.

    • Christophe Duplais
    • , Vincent Sarou-Kanian
    •  & Corrie S. Moreau
  • Article
    | Open Access

    Fungi may have evolved up to 2.4 billion years ago, but it is unclear when they first colonized land. Here Gan and colleagues report filamentous Ediacaran microfossils from South China that may represent early terrestrial fungi.

    • Tian Gan
    • , Taiyi Luo
    •  & Shuhai Xiao
  • Article
    | Open Access

    Consuming the milk of other species is a unique adaptation of Homo sapiens. Here, the authors carry out proteomic analysis of dental calculus of 41 ancient individuals from Sudan and Kenya, indicating milk consumption occurred as soon as herding spread into eastern Africa.

    • Madeleine Bleasdale
    • , Kristine K. Richter
    •  & Nicole Boivin
  • Article
    | Open Access

    Mutualists benefit their partners by providing resources that would be difficult to obtain independently. Here, the authors show in a bacterial community and with mathematical modeling how a mutualist can promote coexistence between competitors by providing them with different limiting resources.

    • Sarah P. Hammarlund
    • , Tomáš Gedeon
    •  & William R. Harcombe
  • Article
    | Open Access

    Genome-wide studies of de novo genes have tended to focus on genomic open reading frames (ORFs). Here, Blevins et al. use deep transcriptomics and synteny information to identify de novo transcripts in the yeast Saccharomyces cerevisiae, many of which are expressed from the alternative DNA strand.

    • William R. Blevins
    • , Jorge Ruiz-Orera
    •  & M. Mar Albà
  • Article
    | Open Access

    The trajectory of the emergence of Zika virus (ZIKV) into the Americas remains unclear. Here, the authors find that four mutations originated before ZIKV introduction to the Americas are direct reversions of previous mutations that accompanied spread many decades ago from ZIKV’s native Africa to Asia, and show in experimental infections of mosquitoes, human cells, and mice that the original mutations reduced fitness for urban transmission, while the reversions restored fitness, likely increasing epidemic risk.

    • Jianying Liu
    • , Yang Liu
    •  & Scott C. Weaver
  • Article
    | Open Access

    Strong social bonds are known to affect pairwise cooperation in primates such chimpanzees. Here, Samuni et al. show that strong social bonds also influence participation in group-level cooperation (collective action in intergroup encounters) using a long-term dataset of wild chimpanzees.

    • Liran Samuni
    • , Catherine Crockford
    •  & Roman M. Wittig
  • Article
    | Open Access

    A global analysis of population-level variation in genetic diversity for 727 plant and animal species finds that biogeography, life history traits and climate are important for predicting the distribution of local genetic diversity, and should be considered together when assessing the local conservation status of species.

    • H. De Kort
    • , J. G. Prunier
    •  & S. Blanchet
  • Article
    | Open Access

    Global oxygen regulation over Earth history has largely depended on variations in organic carbon burial, which includes the suppression of land vegetation due to fires. Here, the authors show that major evolutionary changes in plant ecosystems could have influenced fire regimes and thus affected atmospheric O2.

    • Claire M. Belcher
    • , Benjamin J. W. Mills
    •  & Andrew J. Watson
  • Article
    | Open Access

    Family 1 glycosidases (GH1) are present in the three domains of life and share classical TIM-barrel fold. Structural and biochemical analyses of a resurrected ancestral GH1 enzyme reveal heme binding, not known in its modern descendants. Heme rigidifies the TIM-barrel and allosterically enhances catalysis.

    • Gloria Gamiz-Arco
    • , Luis I. Gutierrez-Rus
    •  & Jose M. Sanchez-Ruiz
  • Article
    | Open Access

    Arms races between herbivores and plants have likely affected their evolutionary histories, which could have led to their high diversity. Allio et al. find that butterflies shifting to new host plants have more adaptive molecular signatures across their genomes and show repeated bursts of speciation rates.

    • Rémi Allio
    • , Benoit Nabholz
    •  & Fabien L. Condamine
  • Article
    | Open Access

    The PAM specificity of SpCas9 can be altered with positive selection during directed evolution. Here the authors use simultaneous positive and negative selection to improve activity on NAG PAMs while reducing activity on NGG PAMs.

    • Gregory W. Goldberg
    • , Jeffrey M. Spencer
    •  & Marcus B. Noyes
  • Article
    | Open Access

    Category systems exhibit striking agreement across many cultures, yet paradoxically individuals exhibit large variation in the categorization of novel stimuli. Here the authors show that critical mass dynamics explain the convergence of independent populations on shared category systems.

    • Douglas Guilbeault
    • , Andrea Baronchelli
    •  & Damon Centola
  • Article
    | Open Access

    Patients with solid cancers have high rates of clonal haematopoiesis associated with increased risk of secondary leukemias. Here, by using peripheral blood sequencing data from patients with solid non-hematologic cancer, the authors profile the landscape of mosaic chromosomal alterations and gene mutations, defining patients at high risk of leukemia progression.

    • Teng Gao
    • , Ryan Ptashkin
    •  & Elli Papaemmanuil
  • Article
    | Open Access

    Virus speciation cannot be fully explained by the evolution of different host specificities. Here, Chaikeeratisak et al. identify ways viruses can remain genetically isolated despite co-infecting the same cell, providing insight into how new virus species evolve.

    • Vorrapon Chaikeeratisak
    • , Erica A. Birkholz
    •  & Joe Pogliano
  • Article
    | Open Access

    As spiteful behaviors harm both the actor and the target, it is challenging to understand how these behaviors could be adaptive. Here Fulker et al. show that spite can be favored by feedbacks with network structure that create correlated and anti-correlated behavioral interactions simultaneously.

    • Zachary Fulker
    • , Patrick Forber
    •  & Christoph Riedl
  • Article
    | Open Access

    The kinetochore is a multi-complex structure that helps attach chromosomes to spindle microtubules, ensuring accurate chromosome segregation during cell division. Kinetochores are thought to be evolutionarily conserved, but which components are conserved is unclear. Here, the authors report that some members of the fungal phylum of Basidomycota lack many conventional kinetochore linker proteins. Instead, they possess a human Ki67-like protein that bridges the outer part of the kinetochore to centromere DNA, which may compensate for the loss of a conventional linker.

    • Shreyas Sridhar
    • , Tetsuya Hori
    •  & Kaustuv Sanyal
  • Article
    | Open Access

    Oldupai Gorge, Tanzania is a key site for understanding early human evolution. Here, the authors report a multiproxy dataset from the Western basin of Oldupai Gorge dating to 2 million years ago, enabling the in situ comparison of lithic assemblages, paleoenvironments and hominin behavioral adaptability.

    • Julio Mercader
    • , Pam Akuku
    •  & Michael Petraglia
  • Article
    | Open Access

    Structural and functional analysis of mitochondria from the human parasite Toxoplasma gondii reveals that its ATP synthase assembles into cyclic hexamers, arranged together in a form of pentagonal pyramids required for maintenance of cristae morphology in Apicomplexa.

    • Alexander Mühleip
    • , Rasmus Kock Flygaard
    •  & Alexey Amunts
  • Article
    | Open Access

    Gene flow is classically thought to impede local adaptation via parallel evolution. However, a genomic study on Hawaiian crickets from different island populations finds evidence of parallel adaptation to the same lethal parasitoid in spite of strong ongoing gene flow.

    • Xiao Zhang
    • , Jack G. Rayner
    •  & Nathan W. Bailey
  • Article
    | Open Access

    The accumulation of recombination events in selfing species may lead to a rapid fixation of both beneficial and deleterious mutations. Here, the authors resequence 781 soybean accessions, show purging of deleterious mutation during domestication, and report genome-wide associations for seed protein and oil traits.

    • Myung-Shin Kim
    • , Roberto Lozano
    •  & Soon-Chun Jeong
  • Article
    | Open Access

    In most model yeast species the Origin Recognition Complex (ORC) binds defined and species-specific base sequences while in humans what determines the binding appears to be more complex. Here the authors reveal that the yeast’s ORC complex binding specificity is dependent on a 19-amino acid insertion helix in the Orc4 subunit which is lost in human.

    • Clare S. K. Lee
    • , Ming Fung Cheung
    •  & Bik-Kwoon Tye
  • Article
    | Open Access

    The causes and consequences of social intelligence are challenging to establish. A study on wild cleaner fish reports that large forebrains enable individuals to score higher in a social competence test, suggesting forebrain size is important for complex social decision-making.

    • Zegni Triki
    • , Yasmin Emery
    •  & Redouan Bshary
  • Article
    | Open Access

    Ancient, asexual lineages are rare as a lack of recombination is usually an evolutionary dead end. Here, authors compare complete genomes of 11 individual bdelloid rotifers that suggest evidence of regular genetic exchange between individuals in a species that was previously thought to be asexual.

    • Olga A. Vakhrusheva
    • , Elena A. Mnatsakanova
    •  & Alexey S. Kondrashov
  • Article
    | Open Access

    It is unclear how a gene regulatory network (GRN) incorporates novelty whilst still maintaining overall stability. Here, the authors provide a comprehensive GRN for endomesoderm specification in the sea star from zygote stage to gastrulation, showing conserved network kernels stabilize evolutionary changes in signaling modes.

    • Gregory A. Cary
    • , Brenna S. McCauley
    •  & Veronica F. Hinman
  • Article
    | Open Access

    The sea anemone Nematostella vectensis expresses miRNAs and two Argonaute (AGO) proteins. Here the authors show that NveAGO1 and NveAGO2 are loaded with overlapping but different sets of miRNAs and that NveAGO2 binds both miRNAs and endo-siRNAs. Both AGO proteins are essential for development.

    • Arie Fridrich
    • , Vengamanaidu Modepalli
    •  & Yehu Moran
  • Article
    | Open Access

    Photosynthetic formation of manganese (Mn) oxides from dissolved Mn ions was proposed to occur in ancestral photosystems before oxygenic photosynthesis evolved. Here, the authors provide evidence for this hypothesis by showing that photosystem II devoid of the Mn cluster oxidises Mn ions leading to formation of Mn-oxide nanoparticles.

    • Petko Chernev
    • , Sophie Fischer
    •  & Holger Dau
  • Article
    | Open Access

    Replicate runs of maximum likelihood phylogenetic analyses can generate different tree topologies due to differences in parameters, such as random seeds. Here, Shen et al. demonstrate that replicate runs can generate substantially different tree topologies even with identical data and parameters.

    • Xing-Xing Shen
    • , Yuanning Li
    •  & Antonis Rokas