Molecular evolution

  • 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
  • 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

    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

    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

    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

    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

    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

    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

    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 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

    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

    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

    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

    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

    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

    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

    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

    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

    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

    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

    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

    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

    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

    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

    Cyclohexadienyl dehydratase (CDT) evolved from a cationic amino acid binding protein ancestor without enzymatic activity (AncCDT-1) via a series of intermediates. Here, the authors combine EPR, X-ray crystallography and MD simulations to study the structural dynamics of these evolutionary intermediates and observe that they predominantly populate catalytically unproductive conformations, while CDT exclusively samples catalytically relevant compact states, and which reveals how the conformational landscape changes along the evolutionary trajectory.

    • Joe A. Kaczmarski
    • , Mithun C. Mahawaththa
    •  & Colin J. Jackson
  • Article
    | Open Access

    Highly pathogenic avian influenza viruses (HPAIV) can evolve via acquisition of polybasic cleavage sites, but the contribution of other mutations remains unclear. Here, the authors combine phylogenetic, statistical and structural approaches, and identify parallel mutations that are associated with HPAIV phenotype.

    • Marina Escalera-Zamudio
    • , Michael Golden
    •  & Oliver G. Pybus
  • Article
    | Open Access

    Contrary to most eukaryotes that lack sequence-specific origins of replication, S. cerevisiae origins are defined by specific DNA sequence motifs. Here the authors reveal that multiple subunits of ORC, including Orc2 and Orc4, contribute to the sequence-specificity of origins in S. cerevisiae.

    • Y. Hu
    • , A. Tareen
    •  & B. Stillman
  • Article
    | Open Access

    Urease is a nickel enzyme responsible for catalyzing the conversion of urea into ammonia and carbon dioxide. Here the authors report a high resolution cryo-EM structure of urease from the bacterial pathogen Yersinia enterocolitica, providing a detailed visualization of the urease bimetal active site and a basis for drug development.

    • Ricardo D. Righetto
    • , Leonie Anton
    •  & Henning Stahlberg
  • Article
    | Open Access

    The evolutionary progression from primary to metastatic prostate cancer is largely uncharted, and the implications for liquid biopsy are unexplored. Here, the authors use deep genomic sequencing and histopathological information to trace tumor evolution both within the prostate and during metastasis in ten men.

    • D. J. Woodcock
    • , E. Riabchenko
    •  & D. C. Wedge
  • Article
    | Open Access

    An E. coli and K. pneumoniae phenotype resistant to piperacillin/tazobactam has recently emerged. Here, the authors show that hyperproduction of the β-lactamase driving this resistance occurs due to excision and reinsertion of a translocatable unit containing blaTEM-1B, creating a tandem array.

    • Alasdair T. M. Hubbard
    • , Jenifer Mason
    •  & Thomas Edwards
  • Article
    | Open Access

    Emergence of tigecycline-resistance tet(X) genes is of concern. Here, the authors determine tet(X) prevalence in more than 6,000 clinical Gram-negative bacterial isolates collected between 1994 to 2019 in hospitals in China and suggest that Flavobacteriaceae could be the potential ancestral source of the tigecycline resistance genes.

    • Rong Zhang
    • , Ning Dong
    •  & Sheng Chen
  • Article
    | Open Access

    Amino acid propensities at sites change over evolutionary time, due to epistatically interacting sites or environmental changes. Here, the authors develop an approach to distinguish between these, and model the fitness dynamics of each, then annotate indicative sites in vertebrate and insect genomes.

    • A. V. Stolyarova
    • , E. Nabieva
    •  & G. A. Bazykin
  • Article
    | Open Access

    Lancelet expresses an ancestral RAG transposon, ProtoRAG, which predates human RAGgenes that are responsible for V(D)J recombination and adaptive immunity repertoire generation. Here the authors show that ProtoRAG is functionally regulated by a trans-acting factor, bbYY1, for tuning transposon activity and maintaining genome stability.

    • Song Liu
    • , Shaochun Yuan
    •  & Anlong Xu
  • Article
    | Open Access

    Reconstructing the early molecular evolution of animals requires genomic resources for non-bilaterian animals. Here, the authors present the chromosome-level genome of a freshwater sponge together with analyses of its genome architecture, methylation, developmental gene expression, and microbiome.

    • Nathan J. Kenny
    • , Warren R. Francis
    •  & Sally P. Leys
  • Article
    | Open Access

    Archaeal type IV pili (T4P) mediate adhesion to surfaces and are receptors for hyperthermophilic archaeal viruses. Here, the authors present the cryo-EM structures of two archaeal T4P from Pyrobaculum arsenaticum and Saccharolobus solfataricus and discuss evolutionary relationships between bacterial T4P, archaeal T4P and archaeal flagellar filaments.

    • Fengbin Wang
    • , Diana P. Baquero
    •  & Edward H. Egelman