Phylogeny articles within Nature Communications

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• Article
  08 June 2018 | Open Access

  Phylodynamic assessment of intervention strategies for the West African Ebola virus outbreak

  During the last Ebola virus outbreak in West Africa, a large amount of viral genomic data was obtained. Here, Dellicour et al. use phylodynamic approaches to assess effect of intervention strategies such as border closures.

  • Simon Dellicour
  • , Guy Baele
  •  & Philippe Lemey

• Article
  22 February 2018 | Open Access

  An ancient family of lytic polysaccharide monooxygenases with roles in arthropod development and biomass digestion

  LPMOs catalyze the oxidative breakdown of polysaccharides, thereby facilitating biomass degradation. By analyzing the digestive proteome of firebrats, the authors here identify a yet uncharacterized LPMO family and provide phylogenetic, structural and biochemical insights into its origin and functions.

  • Federico Sabbadin
  • , Glyn R. Hemsworth
  •  & Simon J. McQueen-Mason

• Article
  12 May 2015 | Open Access

  Planctomycetes do possess a peptidoglycan cell wall

  Planctomycetes appear to differ from all other bacteria in their cellular organization and their apparent lack of a peptidoglycan (PG) cell wall. Here Jeske et al. show that Planctomycetes do possess a typical PG cell wall and that their cellular architecture resembles that of Gram-negative bacteria.

  • Olga Jeske
  • , Margarete Schüler
  •  & Christian Jogler

• Article | 24 February 2015

  Hippos stem from the longest sequence of terrestrial cetartiodactyl evolution in Africa

  The evolutionary origin of Hippopotamidae, the family of hippos, is poorly understood. Here, the authors describe a new fossil from Kenya that unambiguously roots Hippopotamidae into the group that includes the first large terrestrial mammals to invade Africa, more than 30 million years ago.

  • Fabrice Lihoreau
  • , Jean-Renaud Boisserie
  •  & Stéphane Ducrocq

• Article
  08 July 2014 | Open Access

  Tipping elements in the human intestinal ecosystem

  Intestinal microbes can have important effects on our health. Here, the authors analyse the gut microbiota composition in 1,000 western adults and find that certain bacteria are either abundant or nearly absent, and that these alternative states are associated with ageing and overweight.

  • Leo Lahti
  • , Jarkko Salojärvi
  •  & Willem M. de Vos

• Article | 14 August 2013

  PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes

  Sequencing whole microbial genomes has become standard practice and methods to examine their phylogenetic relationships need to match the increasing demand. Segata et al. present a new computational pipeline that allows fast and accurate taxonomic assignment of microbial species.

  • Nicola Segata
  • , Daniela Börnigen
  •  & Curtis Huttenhower

• Article | 24 May 2011

  A novel methodology for large-scale phylogeny partition

  Phylogenetic analysis is used to identify transmission chains, but no software is available for the automated partition of large phylogenies. Prosperiet al. apply a new search algorithm to identify transmission clusters within the phylogeny of HIV-1gene sequences linking molecular and epidemiological data.

  • Mattia C.F. Prosperi
  • , Massimo Ciccozzi
  •  & Andrea De Luca

• Article
  15 February 2011 | Open Access

  Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations

  Leptosphaeria maculans is a plant pathogen that causes stem canker of oilseed rape. Rouxel et al. sequence and describe the key features of the L. maculansgenome, including partitioning into AT-rich blocks that are enriched in effector genes and transposable elements affected by repeat-induced point mutation.

  • Thierry Rouxel
  • , Jonathan Grandaubert
  •  & Barbara J. Howlett