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Cell-type-resolved mosaicism reveals clonal dynamics of the human forebrain
Using mosaic variant barcode analysis, clonal dynamics of specific cell types are deconvolved in the human forebrain.
- Changuk Chung
- , Xiaoxu Yang
- & Joseph G. Gleeson
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Article
| Open AccessComplexity of avian evolution revealed by family-level genomes
Using intergenic regions and coalescent methods to analyse the genomes of 363 bird species, the authors present a well-supported tree confirming that Neoaves experienced rapid radiation at or near the Cretaceous–Palaeogene boundary.
- Josefin Stiller
- , Shaohong Feng
- & Guojie Zhang
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Article
| Open AccessRevealing uncertainty in the status of biodiversity change
This study presents an approach to deal with spatial, temporal and phylogenetic non-independence in large-scale analyses of biodiversity change, improving trend estimation and inference across scales.
- T. F. Johnson
- , A. P. Beckerman
- & R. P. Freckleton
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Article
| Open AccessThe hagfish genome and the evolution of vertebrates
A chromosome-scale genome assembly for the hagfish Eptatretus atami, combined with a series of phylogenetic analyses, sheds light on ancient polyploidization events that had a key role in the early evolution of vertebrates.
- Ferdinand Marlétaz
- , Nataliya Timoshevskaya
- & Daniel S. Rokhsar
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Article
| Open AccessFossil evidence for a pharyngeal origin of the vertebrate pectoral girdle
Computed tomography analysis of the braincase of the Early Devonian placoderm fish Kolymaspis sibirica suggests a skeletal gill support was involved in the origin of the shoulder girdle and provides new evidence reconciling historic theories about the evolution of paired fins.
- Martin D. Brazeau
- , Marco Castiello
- & Matt Friedman
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Article
| Open AccessBridging two insect flight modes in evolution, physiology and robophysics
Asynchronous flight in all major groups of insects likely arose from a single common ancestor with reversions to a synchronous flight mode enabled by shifts back and forth between different regimes in the same set of dynamic parameters.
- Jeff Gau
- , James Lynch
- & Simon Sponberg
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| Open AccessThe oldest three-dimensionally preserved vertebrate neurocranium
Computed tomography reveals that the cranial anatomy of Ordovician stem-group gnathostome Eriptychius americanus from the Harding Sandstone of Colorado, USA, is distinct among vertebrates.
- Richard P. Dearden
- , Agnese Lanzetti
- & Ivan J. Sansom
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| Open AccessInference and reconstruction of the heimdallarchaeial ancestry of eukaryotes
Analyses of multiple phylogenetic marker datasets of Asgard archaea provide insight into the transition from prokaryotes to eukaryotes, specifically placing eukaryotes within Asgard archaea and as a sister lineage to Hodarchaeales.
- Laura Eme
- , Daniel Tamarit
- & Thijs J. G. Ettema
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The evolution of fast-growing coral reef fishes
The high global temperatures of the Eocene and subsequent habitat reconfigurations might have been critical for the rise and retention of the highly productive, high-turnover fish faunas that characterize modern coral reef ecosystems.
- Alexandre C. Siqueira
- , Helen F. Yan
- & David R. Bellwood
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Article
| Open AccessAncient gene linkages support ctenophores as sister to other animals
Deeply conserved syntenic characters unite sponges with bilaterians, cnidarians, and placozoans in a monophyletic clade to the exclusion of the comb jellies (ctenophores)—placing ctenophores as the sister group to all other animals.
- Darrin T. Schultz
- , Steven H. D. Haddock
- & Daniel S. Rokhsar
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| Open AccessMirusviruses link herpesviruses to giant viruses
A phylogeny-guided genome-resolved metagenomic analysis of DNA viruses in the ocean reveals atypical plankton-infecting relatives of herpesviruses that form a putative new phylum dubbed Mirusviricota.
- Morgan Gaïa
- , Lingjie Meng
- & Tom O. Delmont
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Adeno-associated virus type 2 in US children with acute severe hepatitis
A retrospective analysis using PCR testing, viral enrichment-based sequencing and agnostic metagenomic sequencing finds an association between adeno-associated virus type 2 and paediatric hepatitis of unknown cause.
- Venice Servellita
- , Alicia Sotomayor Gonzalez
- & Charles Y. Chiu
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Matters Arising
| Open AccessReply to: The case for standardizing gene nomenclature in vertebrates
- Constantina Theofanopoulou
- & Erich D. Jarvis
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Article
| Open AccessTriassic stem caecilian supports dissorophoid origin of living amphibians
Analysis of fossils of the oldest known caecilian provide insights into the origin and morphological and functional evolution of caecilians.
- Ben T. Kligman
- , Bryan M. Gee
- & Michelle R. Stocker
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Synchrotron tomography of a stem lizard elucidates early squamate anatomy
A study using high-resolution synchrotron phase-contrast tomography documents the near-complete skeleton of a stem squamate, Bellairsia gracilis, from the Middle Jurassic epoch of Scotland, providing insights into early squamate anatomy.
- Mateusz Tałanda
- , Vincent Fernandez
- & Roger J. Benson
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Saccorhytus is an early ecdysozoan and not the earliest deuterostome
Analyses of newly discovered specimens of the early Cambrian microscopic animal Saccorhytus coronarius support its taxonomic classification in total-group Ecdysozoa.
- Yunhuan Liu
- , Emily Carlisle
- & Philip C. J. Donoghue
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Article
| Open AccessSpatially resolved clonal copy number alterations in benign and malignant tissue
Copy number variations inferred from spatial transcriptomics data in benign and malignant tissue reveal clonal architecture at the organ-wide level.
- Andrew Erickson
- , Mengxiao He
- & Joakim Lundeberg
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| Open AccessWastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission
Emerging SARS-CoV-2 variants of concern were detected early and multiple cases of virus spread not captured by clinical genomic surveillance were identified using high-resolution wastewater and clinical sequencing.
- Smruthi Karthikeyan
- , Joshua I. Levy
- & Rob Knight
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| Open AccessA time-resolved, multi-symbol molecular recorder via sequential genome editing
A DNA memory device, DNA Typewriter, uses sequential prime editing to record the order of multiple cellular events.
- Junhong Choi
- , Wei Chen
- & Jay Shendure
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Morphology of Palaeospondylus shows affinity to tetrapod ancestors
Detailed structural analysis of Palaeospondylus gunni from the Middle Devonian period shows strong resemblance to Eusthenopteron and Panderichthys, indicating that it was a sarcopterygian and most probably a stem-tetrapod.
- Tatsuya Hirasawa
- , Yuzhi Hu
- & Shigeru Kuratani
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Evolution of inner ear neuroanatomy of bats and implications for echolocation
The presence of a variety of highly derived spiral ganglion structures of the inner ear is associated with diverse echolocation strategies in yangochiropteran bats and distinguishes them from Yinpterochiroptera.
- R. Benjamin Sulser
- , Bruce D. Patterson
- & Zhe-Xi Luo
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SARS-CoV-2 infection in free-ranging white-tailed deer
More than one-third of wild deer tested in northeast Ohio showed evidence of SARS-CoV-2 infection of human origin.
- Vanessa L. Hale
- , Patricia M. Dennis
- & Andrew S. Bowman
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A species-level timeline of mammal evolution integrating phylogenomic data
Bayesian analysis of datasets comprising genomes from multiple mammalian species can efficiently and precisely decipher their evolutionary timeline.
- Sandra Álvarez-Carretero
- , Asif U. Tamuri
- & Mario dos Reis
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A body map of somatic mutagenesis in morphologically normal human tissues
Laser-capture microdissection and mini-bulk exome sequencing are combined to analyse somatic mutations in morphologically normal tissues from nine organs from five donors, revealing variation in mutation burdens, mutational signatures and clonal expansions.
- Ruoyan Li
- , Lin Di
- & Chen Wu
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A Triassic stem lepidosaur illuminates the origin of lizard-like reptiles
Taytalura alcoberi, represented by a three-dimensionally preserved skull from the Late Triassic epoch of Argentina, is phylogenetically inferred as the earliest known lepidosauromorph, and reveals that sphenodontian skull architecture is plesiomorphic for lepidosaurs.
- Ricardo N. Martínez
- , Tiago R. Simões
- & Sebastián Apesteguía
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The mutational landscape of human somatic and germline cells
The authors report the mutational landscape of 29 cell types from microdissected biopsies from 19 organs and explore the mechanisms underlying mutation rates in normal tissues.
- Luiza Moore
- , Alex Cagan
- & Raheleh Rahbari
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Untangling introductions and persistence in COVID-19 resurgence in Europe
In many European countries, more than half of the SARS-CoV-2 lineages circulating in late summer 2020 resulted from new introductions, highlighting the threat of viral dissemination when restrictions are lifted.
- Philippe Lemey
- , Nick Ruktanonchai
- & Simon Dellicour
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Spread of a SARS-CoV-2 variant through Europe in the summer of 2020
Analysis of the spread of the 20E (EU1) variant of SARS-CoV-2 through Europe suggests that international travel and insufficient containment, rather than increased transmissibility, led to a resurgence of infections.
- Emma B. Hodcroft
- , Moira Zuber
- & Richard A. Neher
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Article
| Open AccessUniversal nomenclature for oxytocin–vasotocin ligand and receptor families
A revised, universal nomenclature for the vertebrate genes that encode the oxytocin and vasopressin–vasotocin ligands and receptors will improve our understanding of gene evolution and facilitate the translation of findings across species.
- Constantina Theofanopoulou
- , Gregory Gedman
- & Erich D. Jarvis
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Expanded diversity of Asgard archaea and their relationships with eukaryotes
Comparative analysis of 162 genomes of Asgard archaea results in six newly proposed phyla, including a deep branch that is provisionally named Wukongarchaeota, and sheds light on the evolutionary history of this clade.
- Yang Liu
- , Kira S. Makarova
- & Meng Li
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Article
| Open AccessGiant lungfish genome elucidates the conquest of land by vertebrates
A chromosome-quality genome of the lungfish Neoceratodus fosteri sheds light on the development of obligate air-breathing and the gain of limb-like gene expression in lobed fins, providing insights into the water-to-land transition in vertebrate evolution.
- Axel Meyer
- , Siegfried Schloissnig
- & Manfred Schartl
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Dire wolves were the last of an ancient New World canid lineage
Dire wolves split from living canids around 5.7 million years ago and originated in the New World isolated from the ancestors of grey wolves and coyotes, which evolved in Eurasia and colonized North America only relatively recently.
- Angela R. Perri
- , Kieren J. Mitchell
- & Laurent A. F. Frantz
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Enigmatic dinosaur precursors bridge the gap to the origin of Pterosauria
Lagerpetids, bipedal archosaurs that are thought to be related to dinosaurs, are instead a sister group to pterosaurs, and although they have no obvious flight adaptations they share numerous synapomorphies with pterosaurs across the entire skeleton.
- Martín D. Ezcurra
- , Sterling J. Nesbitt
- & Max C. Langer
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Analysis
| Open AccessA comparative genomics multitool for scientific discovery and conservation
A whole-genome alignment of 240 phylogenetically diverse species of eutherian mammal—including 131 previously uncharacterized species—from the Zoonomia Project provides data that support biological discovery, medical research and conservation.
- Diane P. Genereux
- , Aitor Serres
- & Elinor K. Karlsson
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An early Cambrian euarthropod with radiodont-like raptorial appendages
Kylinxia zhangi is a transitional fossil that is an evolutionary ‘missing link’ between radiodonts (also known as anomalocaridids) and true arthropods, providing insights into the origin and early evolution of Arthropoda.
- Han Zeng
- , Fangchen Zhao
- & Diying Huang
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150 million years of sustained increase in pterosaur flight efficiency
Phylogenetic statistical analyses, biophysical models and information from the fossil record show that an evolutionary signal of natural selection acted to increase the flight efficiency of pterosaurs over millions of years.
- Chris Venditti
- , Joanna Baker
- & Stuart Humphries
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Article
| Open AccessThe tuatara genome reveals ancient features of amniote evolution
The approximately 5-Gb tuatara (Sphenodon punctatus) genome assembly provides a resource for analysing amniote evolution, and highlights the imperative for meaningful cultural engagement with Indigenous communities in genome-sequencing endeavours.
- Neil J. Gemmell
- , Kim Rutherford
- & Haydn Edmonds
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| Open AccessSix reference-quality genomes reveal evolution of bat adaptations
Reference-quality genomes for six bat species shed light on the phylogenetic position of Chiroptera, and provide insight into the genetic underpinnings of the unique adaptations of this clade.
- David Jebb
- , Zixia Huang
- & Emma C. Teeling
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A Cambrian crown annelid reconciles phylogenomics and the fossil record
Dannychaeta tucolus, a bristle worm from the early Cambrian period, belongs to crown annelids, and has characters that provide evidence of ecological and morphological diversity in ancient annelids, thus reconciling the fossil record with molecular phylogenetic analyses.
- Hong Chen
- , Luke A. Parry
- & Xiaoya Ma
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Extant timetrees are consistent with a myriad of diversification histories
An infinite number of alternative diversification scenarios—which may have markedly different, but equally plausible, dynamics—can underpin a given time-calibrated phylogeny of extant species, suggesting many previous studies have over-interpreted phylogenetic evidence.
- Stilianos Louca
- & Matthew W. Pennell
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Elpistostege and the origin of the vertebrate hand
The pectoral fin of an Elpistostege watsoni specimen from the Upper Devonian period of Canada combines digits and fin rays, blurring the line between the appendages of fish and land vertebrates.
- Richard Cloutier
- , Alice M. Clement
- & John A. Long
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Late Cretaceous neornithine from Europe illuminates the origins of crown birds
A newly discovered fossil from the Cretaceous of Belgium is the oldest modern bird ever found, showing a unique combination of features and suggesting attributes shared by avian survivors of the end-Cretaceous extinction.
- Daniel J. Field
- , Juan Benito
- & Daniel T. Ksepka
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A simple dynamic model explains the diversity of island birds worldwide
Using a global molecular phylogenetic dataset of birds on islands, the sensitivity of island-specific rates of colonization, speciation and extinction to island features (area and isolation) is estimated.
- Luis Valente
- , Albert B. Phillimore
- & Rampal S. Etienne
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Cretaceous fossil reveals a new pattern in mammalian middle ear evolution
The mammalian middle ear is thought to have evolved independently several times, and a specimen of the new species Jeholbaatar kielanae provides support for the idea, with evolution of the chewing apparatus perhaps driving migration of the auditory bones.
- Haibing Wang
- , Jin Meng
- & Yuanqing Wang
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Enamel proteome shows that Gigantopithecus was an early diverging pongine
The enamel proteome from a 1.9-million-year-old Gigantopithecus tooth shows that the Gigantopithecus and Pongo (orangutan) lineages diverged 12–10 million years ago.
- Frido Welker
- , Jazmín Ramos-Madrigal
- & Enrico Cappellini
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Morphology of the earliest reconstructable tetrapod Parmastega aelidae
Three-dimensionally preserved fossils of Parmastega aelidae, a newly described tetrapod from the earliest Famennian (Late Devonian) of Russia, provide detailed insights into the morphology and palaeobiology of the earliest tetrapods.
- Pavel A. Beznosov
- , Jennifer A. Clack
- & Per Erik Ahlberg
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Letter |
A middle Cambrian arthropod with chelicerae and proto-book gills
Mollisonia plenovenatrix, a small predatory arthropod from the Burgess Shale dated to about 508 million years ago, is morphologically close to horseshoe crabs, which suggests chelicerates arose as micropredators early during the Cambrian explosion.
- Cédric Aria
- & Jean-Bernard Caron
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Letter |
Non-photosynthetic predators are sister to red algae
Species of the eukaryotic phylum Rhodelphidia are non-photosynthetic, flagellate predators with gene-rich genomes, in contrast to their closely related sister lineage—the red algae—which are immotile, typically photoautotrophic and have relatively small intron-poor genomes and reduced metabolism.
- Ryan M. R. Gawryluk
- , Denis V. Tikhonenkov
- & Patrick J. Keeling