Evolution

  • Article
    | Open Access

    Harmful algal and bacterial blooms are increasingly frequent in lakes and rivers. From the Sydney Basin, Australia, this study uses fossil, sedimentary and geochemical data to reveal bloom events following forest ecosystem collapse during the end-Permian event and that blooms have consistently followed warming-related extinction events, inhibiting the recovery of freshwater ecosystems for millennia.

    • Chris Mays
    • , Stephen McLoughlin
    •  & Vivi Vajda
  • Article
    | Open Access

    Modular, rather than integrated systems are classically thought to allow functional diversity to evolve rapidly. A study of cichlid fish shows integration between divergent jaw systems at the phylogenetic, population, and genetic scales, suggesting integration can and does facilitate rapid, coordinated trait evolution.

    • Andrew J. Conith
    •  & R. Craig Albertson
  • Article
    | Open Access

    Evolutionary arms races can drive adaptations in hosts and parasites as well as among competing parasites. A combination of multi-omics and functional tests identifies a set of genes that allow a parasitic wasp to minimize intraspecific competition by inducing hosts to escape before more wasps can parasitize them.

    • Jiani Chen
    • , Gangqi Fang
    •  & Jianhua Huang
  • Article
    | Open Access

    Snakes are one of the most successful groups of living vertebrates, but the timing of their diversification is unclear. Combining molecular clocks, fossils, and biogeography, Klein et al. show that snakes experienced a diversification, and underwent dispersal, around the time of the end-Cretaceous mass extinction.

    • Catherine G. Klein
    • , Davide Pisani
    •  & Nicholas R. Longrich
  • Article
    | Open Access

    How soybean, a temperate origin crop, adapted to a tropical environment remains unclear. Here, the authors report Tof16, an ortholog of LHY, and the previously identified J locus, control soybean yield under short-day condition and loss of function of these two genes contributes to the adaptation to tropics.

    • Lidong Dong
    • , Chao Fang
    •  & Baohui Liu
  • Article
    | Open Access

    Historical interbreeding between Neanderthals and humans should leave signatures of historical demographics in modern human genomes. Analysing the size distribution of Neanderthal fragments in non-African genomes suggests consistent differences in the generation interval across Eurasia, and that this could explain mutational spectrum variation.

    • Moisès Coll Macià
    • , Laurits Skov
    •  & Mikkel Heide Schierup
  • Article
    | Open Access

    Analyses of both natural and experimental evolution suggest that adaptation depends on the evolutionary past and adaptive potential decreases over time. Here, by tracking yeast adaptation with DNA barcoding, the authors show that such evolutionary phenomena can be observed even after a single adaptive step.

    • Dimitra Aggeli
    • , Yuping Li
    •  & Gavin Sherlock
  • Perspective
    | Open Access

    The microbiome is becoming recognized as a key determinant of host phenotype. Here, Henry et al. present a framework for building our understanding of how the microbiome also influences host evolution, review empirical examples and research approaches, and highlight emerging questions.

    • Lucas P. Henry
    • , Marjolein Bruijning
    •  & Julien F. Ayroles
  • Article
    | Open Access

    Mycobacterium abscessus is an emerging infection that usually affects patients with structural lung diseases such as cystic fibrosis (CF). Here, the authors use phylogenetic analyses to demonstrate close relationships between isolates from CF and non-CF patients and identify antibiotic resistance markers.

    • Ryan A. Bronson
    • , Chhavi Gupta
    •  & Keira A. Cohen
  • Article
    | Open Access

    Unicellular fungi with free-living flagellated stages (zoospores) remain poorly known. Here, Galindo et al. sequence single-cell genomes for two atypical parasitic fungi with amoeboid zoospores, and re-evaluate the branching order of early-diverging fungi and the evolution of fungal multicellularity and flagellum-mediated motility.

    • Luis Javier Galindo
    • , Purificación López-García
    •  & David Moreira
  • Article
    | Open Access

    Age-related clonal hematopoiesis is associated with risk for diseases like acute myeloid leukemia (AML), yet it is unclear why some individuals do not progress despite having AML driver mutations. Here, the authors use deep learning and population genetics models to investigate how the interplay of positive and negative selection influences AML progression.

    • Kimberly Skead
    • , Armande Ang Houle
    •  & Philip Awadalla
  • Article
    | Open Access

    How ecological divergence causes reproductive isolation between populations in close contact remains poorly understood at the genomic level. This study presents a clinal investigation based on whole-genome sequencing to characterize reproductive isolation between threespine stickleback adapted to contiguous but ecologically different lake and stream habitats.

    • Quiterie Haenel
    • , Krista B. Oke
    •  & Daniel Berner
  • Review Article
    | Open Access

    Seed banks are generated when individuals enter a dormant state, a phenomenon that has evolved among diverse taxa, but that is also found in stem cells, brains, and tumors. Here, Lennon et al. synthesize the fundamentals of seed-bank theory and the emergence of complex patterns and dynamics in mathematics and the life sciences.

    • Jay T. Lennon
    • , Frank den Hollander
    •  & Jochen Blath
  • Article
    | Open Access

    Salmonella enterica serovar 4,[5],12:i:- (Salmonella 4,[5],12:i:-) is a major pathogen of humans and animals with a reported incidence in Australia three times higher than the UK and USA. Here, the authors report the circulation, antimicrobial resistance signatures, and effects on host cells, of three Salmonella4,[5],12:i:- lineages within Australia.

    • Danielle J. Ingle
    • , Rebecca L. Ambrose
    •  & Deborah A. Williamson
  • Article
    | Open Access

    How early photosynthesizers managed oxidative stress remains relatively unresolved. Analyses of enzymes dealing with reactive oxygen species traces the evolutionary history of superoxide dismutases and finds evidence of CuZnSOD in the ancestor of all cyanobacteria, dating back to the Archaean.

    • Joanne S. Boden
    • , Kurt O. Konhauser
    •  & Patricia Sánchez-Baracaldo
  • Article
    | Open Access

    Schistosomiasis control strategies rely on mass drug administration (MDA) using praziquantel. Here, Berger et al. perform whole-genome sequencing of larvae from infected children across Ugandan regions with differing MDA histories. They find extensive gene flow with limited positive selection suggesting minimal change post MDA.

    • Duncan J. Berger
    • , Thomas Crellen
    •  & James A. Cotton
  • Article
    | Open Access

    The linkage between temperature change and extinction rates in the fossil record is well-known qualitatively but little explored quantitatively. Here the authors investigate the relationship of marine animal extinctions with rate and magnitude of temperature change across the last 450 million years, and identify thresholds in climate change linked to mass extinctions.

    • Haijun Song
    • , David B. Kemp
    •  & Xu Dai
  • Article
    | Open Access

    The common ancestor of all living arthropods had biramous postantennal appendages, with an endopodite and exopodite branching off the limb base. This study uses microtomographic imaging of the Cambrian arthropod Leanchoilia to reveal a previously undetected exite at the base of most appendages, suggesting a deeper origin for exites in arthropod phylogeny.

    • Yu Liu
    • , Gregory D. Edgecombe
    •  & Xianguang Hou
  • Article
    | Open Access

    To explore the nature of wild and cultivated mandarins, the authors carry out genomic analysis of diverse east Asian citrus. The discovery of a wild species Citrus ryukyuensis native to the Ryukyu islands and a new population of wild mainland Asian mandarin explains the origin and diversity of mandarins and their ability to reproduce apomictically.

    • Guohong Albert Wu
    • , Chikatoshi Sugimoto
    •  & Daniel S. Rokhsar
  • Article
    | Open Access

    Bordetella hinzii is an emerging pathogen with zoonotic risk to humans, known to be able to cause respiratory tract infection, bacteremia and endocarditis. Here, applying whole genome sequencing to bacterial isolates, the authors characterize the mechanisms driving adaptive evolution in B. hinzii in a patient with interleukin-12 receptor β1 deficiency, suggesting a role for host immune phenotype in shaping within-host pathogen evolution following zoonotic infection.

    • A. Launay
    • , C.-J. Wu
    •  & J. P. Dekker
  • Article
    | Open Access

    Early vertebrate genomes were shaped by multiple whole-genome duplication (WGD) events of debated timings. Here the authors’ reconstruction of ancestral genomes using the probabilistic macrosynteny model supports a WGD shared by all vertebrates and a gnathostome-specific WGD, and reveals evidence of a cyclostome-specific genome triplication.

    • Yoichiro Nakatani
    • , Prashant Shingate
    •  & Byrappa Venkatesh
  • Article
    | Open Access

    We lack a comprehensive understanding of how Neanderthal ancestry influences human traits. This study finds that regions with Neanderthal ancestry are broadly depleted of trait-associated variation; yet, introgressed variants likely contributed to human adaptation in a few traits, like skin color and immune response modulation.

    • Evonne McArthur
    • , David C. Rinker
    •  & John A. Capra
  • Article
    | Open Access

    Theory predicts that organisms in varied environments should evolve to be more phenotypically flexible. Evidence combining genetic and physiological variation with thermal acclimation experiments shows that the thermogenic flexibility of wild juncos is greatest in populations where temperatures are most variable.

    • Maria Stager
    • , Nathan R. Senner
    •  & Zachary A. Cheviron
  • Article
    | Open Access

    Standing genetic variation allows natural populations to evolve rapidly. Genome sequences of a resurrected Daphnia population show that genetic variation carried by only five founding individuals from the regional genotype pool is enough to fuel rapid evolution in response to strong selection pressures with no evidence of genetic erosion.

    • Anurag Chaturvedi
    • , Jiarui Zhou
    •  & Luc De Meester
  • Article
    | Open Access

    Little is known on how mitonuclear interactions influence genomic divergence among hybrid and parental lineages. A study of hybridizing wood warbler species complex finds a nuclear gene block with mitochondrial functions coevolves with mitochondrial genome, driven by climate-associated divergent selection underlying hybrid-parental population divergence.

    • Silu Wang
    • , Madelyn J. Ore
    •  & Darren Irwin
  • Article
    | Open Access

    The virulence of some infectious diseases seems to depend on the sex of the host the infection came from, as well as that of the current host. Here, McLeod et al. develop an epidemiological model to investigate the evolution of virulence when pathogens can retain epigenetic memories of their previous host.

    • David V. McLeod
    • , Geoff Wild
    •  & Francisco Úbeda
  • Article
    | Open Access

    Welwitschia mirabilis is a unique plant that only has two leaves, but it can survive in hostile conditions of the African desert. Here, the authors report its chromosome-level genome assembly and discuss how gene function and regulation have given rise to its unique morphology and environmental adaptions.

    • Tao Wan
    • , Zhiming Liu
    •  & Qingfeng Wang
  • Article
    | Open Access

    Multicellularity is a major evolutionary transition that remains poorly characterized at the ecological and genetic level. Exposing unicellular green algae to a rotifer predator showed that just 500 generations of predator selection were sufficient to lead to a convex trade-off and incorporate evolved changes into the prey genome.

    • Joana P. Bernardes
    • , Uwe John
    •  & Lutz Becks
  • Article
    | Open Access

    Increasing body and brain size constitutes a key pattern in human evolution, but the mechanisms driving these changes remain debated. Using a large fossil dataset combined with global paleoclimatic reconstructions, the authors show that different environmental variables influenced the evolution of brain and body size in Homo.

    • Manuel Will
    • , Mario Krapp
    •  & Andrea Manica
  • Article
    | Open Access

    Plasmodium vivax generally accounts for a low proportion of malaria cases in Africa, but population-level data on the distribution of infections is limited. Here, the authors use data from the Democratic Republic of the Congo and show that the prevalence is low (~3%) and diffusely spread.

    • Nicholas F. Brazeau
    • , Cedar L. Mitchell
    •  & Jonathan J. Juliano
  • Article
    | Open Access

    Despite the profound knowledge of sex pheromones, little is known about the coevolutionary mechanisms and constraints on their production and detection. Whole-genome sequences from 99 drosophilids, with chemical and behavioural data, show that sex pheromones and their cognate olfactory channels evolve rapidly and independently.

    • Mohammed A. Khallaf
    • , Rongfeng Cui
    •  & Markus Knaden
  • Article
    | Open Access

    Pecan is an important specialty crop that has experienced extensive interspecific hybridization and nearly-obligate outcrossing. Here, the authors assemble diploid genomes of four outbred genotypes, identify interspecific introgressions through comparative genomics analyses, and map QTLs associated with pest resistance.

    • John T. Lovell
    • , Nolan B. Bentley
    •  & Jennifer J. Randall
  • Article
    | Open Access

    How natural selection shapes the rate and molecular spectrum of mutations is debated. Yeast mutation accumulation experiments identify a gene promoting mutagenesis and show stabilizing selection maintaining the mutation rate above the drift barrier. Selection also preserves the mutation spectrum.

    • Haoxuan Liu
    •  & Jianzhi Zhang
  • Article
    | Open Access

    The authors show in Nematostella that the more orally expressed β-catenin targets repress the more aborally expressed β-catenin targets, thus patterning the oral-aboral axis. This likely represents the common mechanism of β-catenin-dependent axial patterning shared by Cnidaria and Bilateria.

    • Tatiana Lebedeva
    • , Andrew J. Aman
    •  & Grigory Genikhovich
  • Article
    | Open Access

    Population structure can influence the probability of and time to fixation of new mutants. Here, Tkadlec et al. demonstrate mathematically that structures that increase fixation probability necessarily slow fixation, but also identify amplifying structures with minimal reductions in fixation time.

    • Josef Tkadlec
    • , Andreas Pavlogiannis
    •  & Martin A. Nowak
  • Article
    | Open Access

    Many species learn through social transmission, which can alter co-evolutionary selection pressures. Experiments involving artificial prey and social networks show that wild birds can learn about unpalatable food by watching others, which helps explain the persistence of costly prey defences despite influxes of naïve juvenile predators.

    • Liisa Hämäläinen
    • , William Hoppitt
    •  & Rose Thorogood
  • Article
    | Open Access

    Pyrrolysine (Pyl) exists in nature as the 22nd proteinogenic amino acid, but studies of Pyl have been hindered by the difficulty and inefficiency of both its chemical and biological syntheses. Here, the authors developed an improved PANCE approach to evolve the pylBCD pathway for increased production of Pyl proteins in E. coli.

    • Joanne M. L. Ho
    • , Corwin A. Miller
    •  & Matthew R. Bennett
  • Article
    | Open Access

    In addition to major innovations in their locomotor system, early birds evolved highly derived skulls. Here, Wang et al. three dimensionally reconstruct the skull of a new enantiornithine bird from the Early Cretaceous that illustrates the early avialan transitions in skull morphology and function.

    • Min Wang
    • , Thomas A. Stidham
    •  & Zhonghe Zhou
  • Article
    | Open Access

    Obscuring knowledge of personal gains from individuals can theoretically maintain fairness in a cooperative group. Experiments show that wild, cooperatively breeding banded mongooses uncertain of kinship allocate postnatal care in a way that reduces inequality among offspring, suggesting a classic idea of moral philosophy can apply in biological systems.

    • H. H. Marshall
    • , R. A. Johnstone
    •  & M. A. Cant
  • Article
    | Open Access

    The metaphor of an adaptive landscape is presented quantitatively by looking at molecular adaptations and their catalytic consequences in a recently evolved bacterial enzyme. The study identifies both genotype-by-environment interactions and environment-dependent epistasis as factors that can alter the fitness of functional mutations.

    • Dave W. Anderson
    • , Florian Baier
    •  & Nobuhiko Tokuriki
  • Article
    | Open Access

    The parasite causing toxoplasmosis can manipulate prey to behave in ways that promote transmission to the parasite’s definitive feline hosts. The first study consistent with this extended phenotype in the wild finds that infected hyena cubs approach lions more closely than uninfected peers and have higher rates of lion mortality.

    • Eben Gering
    • , Zachary M. Laubach
    •  & Thomas Getty
  • Article
    | Open Access

    Beneficial plant-microbe interactions are common in nature, but direct evidence for the evolution of mutualism is scarce. Here, Li et al. experimentally evolve a rhizospheric bacterium and find that it can evolve into a mutualist on a relatively short timescale.

    • Erqin Li
    • , Ronnie de Jonge
    •  & Alexandre Jousset
  • Article
    | Open Access

    Resistance of Neisseria gonorrhoeae to extended spectrum cephalosporins is an increasing concern. Here, the authors conduct whole genome sequencing of isolates from the United States and find that most resistant isolates were associated with a persistent circulating lineage.

    • Jesse C. Thomas IV
    • , Sandeep J. Joseph
    •  & Zach Perry
  • Article
    | Open Access

    There are relatively few known extant adaptive radiations in Europe that predate the Pleistocene. Here, Borko et al. characterize the diversity and diversification of the subterranean amphipod genus Niphargus, showing evidence for a large adaptive radiation associated with massif uplift 15 million years ago.

    • Špela Borko
    • , Peter Trontelj
    •  & Cene Fišer