Phylogenetics articles within Nature

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  • Letter |

    Phylogenetic analyses based on single-cell transcriptomic data from two hemimastigotes, a Spironema species and the newly described Hemimastix kukwesjijk, indicate that Hemimastigophora is a supra-kingdom-level lineage of eukaryotes.

    • Gordon Lax
    • , Yana Eglit
    •  & Alastair G. B. Simpson

  • Letter |

    Contrary to previous hypotheses, high-latitude fish lineages form new species at much faster rates than their tropical counterparts especially in geographical regions that are characterized by low surface temperatures and high endemism.

    • Daniel L. Rabosky
    • , Jonathan Chang
    •  & Michael E. Alfaro

  • Article |

    Sequences of 137 ancient and 502 modern human genomes illuminate the population history of the Eurasian steppes after the Bronze Age and document the replacement of Indo-European speakers of West Eurasian ancestry by Turkic-speaking groups of East Asian ancestry.

    • Peter de Barros Damgaard
    • , Nina Marchi
    •  & Eske Willerslev

  • Letter |

    High-resolution computed tomography of three-dimensionally preserved specimens of Ichthyornis dispar clarifies the mosaic evolution of the avian head, revealing a kinetic feeding apparatus reminiscent of modern birds, a transitional beak and a dinosaurian temporal region.

    • Daniel J. Field
    • , Michael Hanson
    •  & Bhart-Anjan S. Bhullar

  • Letter |

    Genome data for thirteen alphaproteobacteria-related clades expand the coverage of alphaproteobacterial diversity and suggest that mitochondria diverged from Alphaproteobacteria before the diversification of all currently known alphaproteobacterial lineages.

    • Joran Martijn
    • , Julian Vosseberg
    •  & Thijs J. G. Ettema

  • Letter |

    A dated phylogeny and spatial distribution data for Chinese angiosperms show that eastern China has tended to act as a refugium for older taxa whereas western China has acted as a centre for their evolutionary diversification.

    • Li-Min Lu
    • , Ling-Feng Mao
    •  & Zhi-Duan Chen

  • Article |

    Maiopatagium, a haramiyid from the Jurassic Tiaojishan Formation (around 160 million years ago) of China was specialised for gliding with a patagium (wing membrane) and a fused wishbone, reminiscent of that of birds.

    • Qing-Jin Meng
    • , David M. Grossnickle
    •  & Zhe-Xi Luo

  • Letter |

    Detailed micro-computed tomography analysis of the skull of Lethiscus stocki places it much earlier in the tetrapod lineage that was previously thought, showing that early tetrapods were more morphologically diverse than has been believed.

    • Jason D. Pardo
    • , Matt Szostakiwskyj
    •  & Jason S. Anderson

  • Letter |

    Analysis of a comprehensive database of mammalian host–virus relationships reveals that both the total number of viruses that infect a given species and the proportion likely to be zoonotic are predictable and that this enables identification of mammalian species and geographic locations where novel zoonoses are likely to be found.

    • Kevin J. Olival
    • , Parviez R. Hosseini
    •  & Peter Daszak

  • Letter |

    Tokummia katalepsis from the Burgess Shale had a pair of mandibles and maxilliped claws, showing that large bivalved arthropods from the Cambrian period are forerunners of myriapods and pancrustaceans, thereby providing a basis for the origin of the hyperdiverse mandibulate body plan.

    • Cédric Aria
    •  & Jean-Bernard Caron

  • Article |

    Analysis of a wide range of dinosaurs and dinosauromorphs recovers a sister-taxon relationship between Ornithischia and Theropoda, calling for the redefinition of all the major clades within Dinosauria and the revival of the clade Ornithoscelida.

    • Matthew G. Baron
    • , David B. Norman
    •  & Paul M. Barrett

  • Letter |

    Analysis of exceptionally preserved fossils of the Cambrian hyolith Haplophrentis leads to a proposed evolutionary relationship with Lophophorata, the group containing brachiopods and phoronids, on the basis of a newly described tentacular feeding apparatus.

    • Joseph Moysiuk
    • , Martin R. Smith
    •  & Jean-Bernard Caron

  • Article |

    This work describes the Asgard superphylum, an assemblage of diverse archaea that comprises Odinarchaeota, Heimdallarchaeota, Lokiarchaeota and Thorarchaeota, offering insights into the earliest days of eukaryotic cells and their complex features.

    • Katarzyna Zaremba-Niedzwiedzka
    • , Eva F. Caceres
    •  & Thijs J. G. Ettema

  • Letter |

    The chimaeroids are one of the four principal divisions of the living jawed vertebrates and their evolutionary origins have been hard to discern; here, the study of a skull of the extinct shark Dwykaselachus shows that the chimaeroids nest among the once fairly common and widespread symmoriiforms.

    • Michael I. Coates
    • , Robert W. Gess
    •  & Kristen Tietjen

  • Article |

    Profiling the total RNA of 220 invertebrate species leads to the discovery of almost 1,500 new species of RNA virus, revealing that the RNA virosphere is much more diverse than was previously thought.

    • Mang Shi
    • , Xian-Dan Lin
    •  & Yong-Zhen Zhang

  • Letter |

    The percentage of human deaths caused by interpersonal violence reflects our membership of a particularly violent clade of mammals, although changes in socio-political organization have led to marked variations in this proportion.

    • José María Gómez
    • , Miguel Verdú
    •  & Marcos Méndez

  • Letter |

    Phylogenetic methods were applied to a cross-cultural database of traditional Austronesian societies to test the link between ritual human sacrifice and the origins of social hierarchy—the presence of sacrifice in a society stabilized social stratification and promoted inherited class systems.

    • Joseph Watts
    • , Oliver Sheehan
    •  & Russell D. Gray

  • Letter |

    Robust phylogenetic analysis based on transcriptomes of Xenoturbella and acoelomorph worms shows that Xenacoelomorpha is an early bilaterian lineage forming the sister group to Nephrozoa.

    • Johanna Taylor Cannon
    • , Bruno Cossermelli Vellutini
    •  & Andreas Hejnol

  • Article |

    By examining viral sequences in lymphoid tissue from three HIV-1-infected individuals receiving drug therapy, the authors find phylogenetic evidence for ongoing virus replication, suggesting that the antiretroviral drug concentration in the lymphoid tissue is insufficient to fully suppress the virus; using a mathematical model, they further explain why drug resistance does not necessarily arise as a result.

    • Ramon Lorenzo-Redondo
    • , Helen R. Fryer
    •  & Steven M. Wolinsky

  • Letter
    | Open Access

    An analysis of 85 Ebola virus sequences collected in Guinea from July to November 2014 provides insight into the evolution of the Ebola virus responsible for the epidemic in West Africa; the results show sustained transmission of three co-circulating lineages, each defined by multiple mutations.

    • Etienne Simon-Loriere
    • , Ousmane Faye
    •  & Amadou A. Sall

  • Letter |

    A re-analysis of the 508-million-year-old stem-group onychophoran Hallucigenia sparsa from the Burgess Shale shows that its anterior gut has structures that indicate evolutionary links with more disparate phyla such as nematodes and kinorhynchs; Hallucigenia now provides concrete evidence of structures that might have existed in the last common ancestor of the Ecdysozoa, previously a matter of conjecture.

    • Martin R. Smith
    •  & Jean-Bernard Caron

  • Letter |

    More than 15% of the bacterial domain consists of a radiation of phyla about which very little is known; here, metagenomics is used to reconstruct 8 complete and 789 draft genomes from more than 35 of these phyla, revealing a shared evolutionary history, metabolic limitations, and unusual ribosome compositions.

    • Christopher T. Brown
    • , Laura A. Hug
    •  & Jillian F. Banfield

  • Letter |

    The analysis of more than 9,000 haemagglutinin sequences of human seasonal influenza viruses over a 12-year time period shows that the global circulation patterns of A/H1N1 and B viruses are different from those of the well characterised A/H3N2 viruses; in particular the A/H1N1 and B viruses are shown to persist locally across several seasons and do not display the same degree of global movement as the H3N2 viruses.

    • Trevor Bedford
    • , Steven Riley
    •  & Colin A. Russell

  • Article |

    Trajectory-dependent firing of neurons within the nucleus reuniens of the thalamus–hippocampus circuit predicted subsequent running direction, and disruption of this circuit reduced predictive firing in the hippocampus, suggesting that the thalamus is a key node in the integration of signals during goal-oriented navigation.

    • Hiroshi T. Ito
    • , Sheng-Jia Zhang
    •  & May-Britt Moser

  • Brief Communications Arising |

    • Amy E. Zanne
    • , David C. Tank
    •  & Jeremy M. Beaulieu

  • Letter |

    The claws of the Cambrian lobopodian Hallucigenia resemble the claws and jaws of extant onychophorans, establishing a close relationship between hallucigeniid lobopodians and onychophorans, resolving tardigrades as the closest extant relatives of true arthropods, and showing that the earliest ancestor of the arthropods and their kin would have looked like a lobopodian.

    • Martin R. Smith
    •  & Javier Ortega-Hernández

  • Article
    | Open Access

    The draft genome of the ctenophore Pleurobrachia bachei (Pacific sea gooseberry) is presented, together with ten other ctenophore transcriptomes — these genomes have a very different neurogenic, immune and developmental gene content when compared with other animal genomes, and it is proposed that ctenophore neural systems, and possibly muscle specification, evolved independently from those in other animals.

    • Leonid L. Moroz
    • , Kevin M. Kocot
    •  & Andrea B. Kohn

  • Letter |

    A local molecular clock approach shows that most genetic diversity in avian influenza virus (AIV) arose in a recent global sweep and that avian strains are the sister group to equine H7N7; most of the 1918 pandemic virus’s genes originated from the resulting western hemispheric AIV lineage.

    • Michael Worobey
    • , Guan-Zhu Han
    •  & Andrew Rambaut

  • Letter |

    This large comparative phylogenetic study across angiosperms shows that species that are herbaceous or have small conduits evolved these traits before colonizing environments with freezing conditions, whereas deciduous species changed their climate niche before becoming deciduous.

    • Amy E. Zanne
    • , David C. Tank
    •  & Jeremy M. Beaulieu

  • Letter
    | Open Access

    By analysing genomic sequences in echolocating mammals it is shown that convergence is not a rare process restricted to a handful of loci but is instead widespread, continuously distributed and commonly driven by natural selection acting on a small number of sites per locus; analyses involved sequence comparisons across 22 mammals, including 4 new bat genomes, and found signatures consistent with convergence in genes linked to hearing or deafness, but surprisingly also to vision.

    • Joe Parker
    • , Georgia Tsagkogeorga
    •  & Stephen J. Rossiter

  • Letter |

    Evolutionary analyses show that H7 influenza viruses probably transferred from ducks to chickens in China on at least two independent occasions, and that reassortment with H9N2 viruses generated the H7N9 outbreak lineage that recently emerged in humans in China, and a related previously unrecognized H7N7 lineage; these H7N7 viruses are shown to have the ability to infect ferrets, and the current pandemic threat could extend beyond H7N9 viruses.

    • Tommy Tsan-Yuk Lam
    • , Jia Wang
    •  & Yi Guan

  • Article |

    Determining major branches in the tree of life generally relies on concatenating as much genetic information as possible, but, as shown here, phylogenomic analysis often produces results that are incongruent with the results of concatenation; a method that gives credence to genes or internodes with high average internode support reduces the incongruence.

    • Leonidas Salichos
    •  & Antonis Rokas

  • Letter |

    To identify comprehensively factors involved in RNAi and microRNA-mediated gene expression regulation, this study performed a phylogenetic analysis of 86 eukaryotic species; the candidates this approach highlighted were subjected to Bayesian analysis with transcriptional and proteomic interaction data, identifying protein orthologues of already known RNAi silencing factors, as well as other hits involved in splicing, suggesting a connection between the two processes.

    • Yuval Tabach
    • , Allison C. Billi
    •  & Gary Ruvkun

  • Article |

    An analysis of staged hagfish embryos shows that the hagfish adenohypophysis is ectodermal in origin, revealing it to be a developmental quirk unique to hagfishes that was hitherto misleading; from this and other observations a ‘pan-cyclostome’ developmental pattern is derived, indicating that it was primitive for all vertebrates.

    • Yasuhiro Oisi
    • , Kinya G. Ota
    •  & Shigeru Kuratani

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