Evolution

  • Article
    | Open Access

    The ‘invariant rate of ageing’ hypothesis suggests that the rate of ageing tends to be constant within species. Here, Colchero et al. find support for the hypothesis across primates, including humans, suggesting biological constraints on the rate of ageing.

    • Fernando Colchero
    • , José Manuel Aburto
    •  & Susan C. Alberts
  • Article
    | Open Access

    Here, the authors examine how altruism can emerge as people come to trust a public institution of moral assessment, which broadcasts whether individuals have good or bad reputations for reciprocity.

    • Arunas L. Radzvilavicius
    • , Taylor A. Kessinger
    •  & Joshua B. Plotkin
  • Article
    | Open Access

    Molecular phylogenies are traditionally based on sequence variation, but genome rearrangements also contain phylogenetic information. Here, Zhao et al. develop an approach to reconstruct phylogenies based on microsynteny and illustrate it with a reconstruction of the angiosperm phylogeny.

    • Tao Zhao
    • , Arthur Zwaenepoel
    •  & Yves Van de Peer
  • Article
    | Open Access

    Natural and sexual selection can be in opposition favouring different trait sizes, but disentangling these processes empirically is difficult. Here Okada et al. show that predation on males shifts the balance of selection in experimentally evolving beetle populations, disfavoring a sexually-selected male trait but increasing female fitness.

    • Kensuke Okada
    • , Masako Katsuki
    •  & David J. Hosken
  • Perspective
    | Open Access

    Effective biological engineering requires the acknowledgement of evolution and its consideration during the design process. In this perspective, the authors present the concept of the evotype to reason about and shape the evolutionary potential of natural and engineered biosystems.

    • Simeon D. Castle
    • , Claire S. Grierson
    •  & Thomas E. Gorochowski
  • Article
    | Open Access

    Dating early bacterial evolution is challenging due to the limited bacterial fossil record. Here Wang and Luo use the close evolutionary relationship between Alphaproteobacteria and mitochondria to leverage the eukaryotic fossil record in dating Alphaproteobacteria origin and diversification.

    • Sishuo Wang
    •  & Haiwei Luo
  • Article
    | Open Access

    Social interaction outcomes can depend on the type of information individuals possess and how it is used in decision-making. Here, Zhou et al. find that self-evaluation based decision-making rules lead to evolutionary outcomes that are robust to different population structures and ways of self-evaluation.

    • Lei Zhou
    • , Bin Wu
    •  & Long Wang
  • Article
    | Open Access

    Long-term infection of cystic fibrosis patients with Pseudomonas aeruginosa is often accompanied by a reduction in bacterial growth rate. Here, La Rosa et al. use adaptive laboratory evolution to increase the growth rate of clinical isolates, and identify mechanisms and evolutionary trajectories that, in reverse direction, may help the pathogen to adapt to the patients’ airways.

    • Ruggero La Rosa
    • , Elio Rossi
    •  & Søren Molin
  • Article
    | Open Access

    Natural selection may favor traits underlying aging-related diseases if they benefit the young. Wang et al. find that oxidative activation of CaMKII provides physiological benefits critical to the initial and continued success of vertebrates but at the cost of disease, frailty, and shortened lifespan.

    • Qinchuan Wang
    • , Erick O. Hernández-Ochoa
    •  & Mark E. Anderson
  • Article
    | Open Access

    Evolution selects for the fittest but must operate within the realm of the physically possible. Here, the authors present a theoretical framework that allows them to explore how ten abiotic constraints can shape the operation, regulation, and adaptation of metabolism in E. coli.

    • Amir Akbari
    • , James T. Yurkovich
    •  & Bernhard O. Palsson
  • Article
    | Open Access

    The interaction between hybridisation and polyploidisation is thought to play an important role in eukaryote speciation. Here the authors sequence yeast crosses and show associations between hybridisation, genome instability, and genome duplication, suggesting these may have roles in the establishment of new hybrids.

    • S. Marsit
    • , M. Hénault
    •  & C. R. Landry
  • Article
    | Open Access

    Comparative epigenomics has revealed principles underlying the evolution of gene expression regulation, and the integration of epigenomic data is important for a deeper understanding of this evolution. Here the authors report the evolutionary dynamics of the epigenomic regulatory landscape in primates and their impact in recent human evolution.

    • Raquel García-Pérez
    • , Paula Esteller-Cucala
    •  & Tomàs Marquès-Bonet
  • Article
    | Open Access

    Captive breeding could prevent species extinctions, but selection for captivity may decrease fitness. Here the authors analyse pedigree data on 15 long-running vertebrate breeding programs and find generational fitness changes that processes such as inbreeding depression cannot explain.

    • Katherine A. Farquharson
    • , Carolyn J. Hogg
    •  & Catherine E. Grueber
  • Article
    | Open Access

    Here, the authors report a large-scale comparative analysis of <30,000 Diversity-Generating Retroelements (DGRs) across ~9000 metagenomes (representing diverse taxa and biomes), to identify patterns in terms of prevalence and activity. Combined with examination of longitudinal data on <100 metagenomes part of time series, they demonstrate that DGRs are broadly and consistently active, implying an important role in microbiota ecology and evolution.

    • Simon Roux
    • , Blair G. Paul
    •  & Emiley A. Eloe-Fadrosh
  • Article
    | Open Access

    The genetic architecture underlying rapid adaptive responses to novel environments are poorly understood. A study of great tits from nine European cities finds that urban adaptation in a widespread songbird occurred through unique and shared selective sweeps in a core-set of behaviour-linked genes.

    • Pablo Salmón
    • , Arne Jacobs
    •  & Caroline Isaksson
  • Article
    | Open Access

    Without understanding the genetic architecture of inbreeding depression, its effects are hard to pinpoint. Long-term data from wild Soay sheep shows that inbreeding manifests in long runs of homozygosity, which made up nearly half of the genome in the most inbred individuals with severe fitness consequences.

    • M. A. Stoffel
    • , S. E. Johnston
    •  & J. M. Pemberton
  • Article
    | Open Access

    Age-richness rate (ARR) estimates of evolutionary diversification are widely used to study factors that influence species richness among clades. Here the authors show that ARR inference is based on problematic assumptions and recommend against its use in comparison of past diversity or diversification rates across clades.

    • Daniel L. Rabosky
    •  & Roger B. J. Benson
  • Article
    | Open Access

    The efficacy of the antibiotic trimethoprim, which inhibits bacterial dihydrofolate reductase (DHFR), is limited by the rapid emergence of resistant bacteria. Here, Manna et al. show that 4’-desmethyltrimethoprim inhibits DHFR and a common TMP-resistant variant, and impedes evolution of antibiotic resistance by selecting against the emergence of this variant.

    • Madhu Sudan Manna
    • , Yusuf Talha Tamer
    •  & Erdal Toprak
  • Article
    | Open Access

    Bacteria use the type 2 secretion system to secrete enzymes and toxins across the outer membrane to the environment. Here the authors analyse the T2SS pathway in three protist lineages and suggest that the early mitochondrion may have been capable of secreting proteins into the cytosol.

    • Lenka Horváthová
    • , Vojtěch Žárský
    •  & Pavel Doležal
  • Article
    | Open Access

    Many obligate symbionts, including parasites, have reduced genomes. A comparison of leaf-cutter ant genomes reveals parallel gene losses, particularly in olfactory receptors, in socially parasitic species compared to their closely-related hosts, consistent with relaxed selection for cooperative colony life in the parasites.

    • Lukas Schrader
    • , Hailin Pan
    •  & Christian Rabeling
  • Article
    | Open Access

    While there is strong evidence that many mutualisms evolved from antagonism, how or why remains unclear. A study combining theory and a data-based model sheds light on how mutualisms evolve without extremely tight host fidelity and how ecological context affects evolutionary outcomes and vice-versa.

    • Christopher A. Johnson
    • , Gordon P. Smith
    •  & Régis Ferrière
  • Article
    | Open Access

    Here, the authors show that the Hox genes Antennapedia (Antp) and Ultrabithorax (Ubx) control flight appendage morphology in Drosophila. This role is dependent on a particular spatial expression profile and dosage, which was also found in evolutionary distant four-winged insect species.

    • Rachel Paul
    • , Guillaume Giraud
    •  & Samir Merabet
  • Article
    | Open Access

    Many organisms, including moths, use pheromones to attract mates. A study using multiple genomic tools and gene editing identifies a new, neuronal gene underlying mate preference and shows that signal and response loci are in linkage disequilibrium despite being physically unlinked.

    • Melanie Unbehend
    • , Genevieve M. Kozak
    •  & Erik B. Dopman
  • Article
    | Open Access

    The evolution of multicellular life is hypothesized to have been promoted by rising oxygen levels. Through experimental evolution and modeling, Bozdag et al. demonstrate that our planet’s first oxygenation would have strongly constrained, not promoted, the evolution of multicellular life.

    • G. Ozan Bozdag
    • , Eric Libby
    •  & William C. Ratcliff
  • Article
    | Open Access

    Terrestrial ecosystems underwent major restructuring through the early Mesozoic, culminating in dinosaur-dominated faunas. Here Singh et al. use jaw morphology to classify tetrapod herbivores into distinct feeding groups and show that their success was shaped by environmental changes and competitive constraints.

    • Suresh A. Singh
    • , Armin Elsler
    •  & Michael J. Benton
  • Article
    | Open Access

    Higher vitamin D is associated with improved pregnancy and live birth rates, but its potential role in the human offspring sex ratio in unknown. Here, the authors show that the levels of vitamin D at preconception are positively associated with male live birth, particularly among women presenting inflammatory markers.

    • Alexandra C. Purdue-Smithe
    • , Keewan Kim
    •  & Sunni L. Mumford
  • Article
    | Open Access

    Islands can provide insights into the evolution of diverse adaptations. The genomes of 34 major lineages of Mediterranean wall lizards reveal a highly reticulated pattern of evolution across the group, characterised by mosaic genomes and showing that hybrid lineages gave rise to several extant endemics.

    • Weizhao Yang
    • , Nathalie Feiner
    •  & Tobias Uller
  • Article
    | Open Access

    A fundamental principle of evolutionary theory is that the force of natural selection is weaker on traits expressed late in life relative to traits expressed early. Here, the authors find strong and consistent patterns of molecular evolution reflecting this principle in four species of animals, including humans.

    • Changde Cheng
    •  & Mark Kirkpatrick
  • Article
    | Open Access

    The herbivorous horseradish flea beetle sequesters plant toxins to defend against predators. Here the authors identify glucosinolate transporters expressed in the beetle Malpighian tubules and provide evidence that these reabsorb glucosinolates from the tubule lumen to prevent their loss by excretion.

    • Zhi-Ling Yang
    • , Hussam Hassan Nour-Eldin
    •  & Franziska Beran
  • Article
    | Open Access

    The SARS-CoV-2 gene set remains unresolved, hindering dissection of COVID-19 biology. Comparing 44 Sarbecovirus genomes provides a high-confidence protein-coding gene set. The study characterizes protein-level and nucleotide-level evolutionary constraints, and prioritizes functional mutations from the ongoing COVID-19 pandemic.

    • Irwin Jungreis
    • , Rachel Sealfon
    •  & Manolis Kellis
  • Article
    | Open Access

    Whole genome sequencing is increasingly being adopted for Shigella sonnei outbreak investigation and surveillance, but there is no global classification standard. Here, the authors develop and validate a genomic framework implemented using open-source software, and demonstrate its application using surveillance data.

    • Jane Hawkey
    • , Kalani Paranagama
    •  & Kathryn E. Holt
  • Article
    | Open Access

    Selection on alleles contributing to human evolution is not well understood. Here, the authors investigate positive selection on skin barrier adaptation, identifying a selective sweep on involucrin alleles associated with migration out of Africa, and confirming enhancer regulatory effects with functional assays.

    • Mary Elizabeth Mathyer
    • , Erin A. Brettmann
    •  & Cristina de Guzman Strong
  • Article
    | Open Access

    Studying how songbirds learn songs can shed light on the development of human speech. An analysis of 160 tutor-pupil zebra finch pairs suggests that frequency dependent balanced imitation prevents the extinction of rare song elements and the overabundance of common ones, promoting song diversity within groups and species recognition across groups.

    • Ofer Tchernichovski
    • , Sophie Eisenberg-Edidin
    •  & Erich D. Jarvis
  • Article
    | Open Access

    The genomic organization and origin of the avenacin biosynthetic gene cluster remain unknown. Here, the authors assemble the genome of diploid oat Avena strigosa, reveal the structure and organization of the consecutive genes, characterize the last two missing pathway steps, and investigate the origin of the pathway in cereals.

    • Yan Li
    • , Aymeric Leveau
    •  & Anne Osbourn
  • Article
    | Open Access

    The evolution of metamorphic species may be constrained by different ecologies of the larval and adult stages. Here, Bardua et al. show that in frogs, adult ecology is more important than larval ecology for skull evolution, but species that don’t feed as tadpoles evolve faster than those that do.

    • Carla Bardua
    • , Anne-Claire Fabre
    •  & Anjali Goswami
  • Article
    | Open Access

    Mycobacterium kansasii can cause serious pulmonary disease. Here, the authors present a population genomics analysis of 358 environmental and clinical isolates from around the world, supporting the idea that municipal water is a main source of infection, and shedding light into the pathogen’s diversity and adaptation to the human host.

    • Tao Luo
    • , Peng Xu
    •  & Qian Gao
  • 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