Phylogenetics articles within Nature

Featured

  • Article
    | Open Access

    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

  • Article
    | Open Access

    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

  • Article
    | Open Access

    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

  • Article
    | Open Access

    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

  • Article
    | Open Access

    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

  • Article
    | Open Access

    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

  • Article |

    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

  • Article
    | Open Access

    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

  • Article
    | Open Access

    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

  • Article |

    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

  • Article |

    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

  • Article |

    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

  • Article |

    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

  • Article |

    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

  • Article |

    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

  • Article |

    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

  • Article
    | Open Access

    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

  • Article
    | Open Access

    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

  • Article |

    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

  • Article |

    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

  • Analysis
    | Open Access

    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

  • Article |

    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

  • Article |

    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

  • Article
    | Open Access

    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

  • Article
    | Open Access

    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

  • Article |

    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

  • Article |

    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

  • Article |

    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

  • Article |

    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

  • Article |

    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

  • Article |

    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

  • Letter |

    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

  • Letter |

    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

Browse broader subjects

Browse Phylogenetics across other nature.com journals