Phylogeny

  • Article
    | Open Access

    SARS-CoV-2 was first detected in Kenya in March 2020 and there was evidence of local transmission in the following months. Here, the authors characterise the early stages of the epidemic in coastal Kenya using phylogenetics and find evidence of multiple strain importations from international points of entry.

    • George Githinji
    • , Zaydah R. de Laurent
    •  & Charles N. Agoti
  • Article
    | Open Access

    Estimating the effects of non-pharmaceutical interventions for COVID-19 is challenging, partly due to variations in testing. Here, the authors use viral sequence data as an alternative means of inferring intervention effects, and show that delays in implementation resulted in more severe epidemics.

    • Manon Ragonnet-Cronin
    • , Olivia Boyd
    •  & Erik Volz
  • Article
    | Open Access

    Trans-acyltransferase polyketide synthases are multimodular enzymes that synthesise diverse polyketides. Here, the authors present an algorithm for the global study of their diversity, showing exchange of conserved consecutive modules as a driver of diversification, and guiding the discovery of polyketides.

    • Eric J. N. Helfrich
    • , Reiko Ueoka
    •  & Marnix H. Medema
  • Article
    | Open Access

    Replicate runs of maximum likelihood phylogenetic analyses can generate different tree topologies due to differences in parameters, such as random seeds. Here, Shen et al. demonstrate that replicate runs can generate substantially different tree topologies even with identical data and parameters.

    • Xing-Xing Shen
    • , Yuanning Li
    •  & Antonis Rokas
  • Article
    | Open Access

    Plasmids can mediate gene transfer across bacterial populations. Here, the authors describe a global map of the prokaryotic plasmidome, where plasmids organize into discrete ‘plasmid taxonomic units’ based on their genomic composition and pairwise sequence identity.

    • Santiago Redondo-Salvo
    • , Raúl Fernández-López
    •  & Fernando de la Cruz
  • Article
    | Open Access

    Lineage tracing studies combining CRISPR-Cas9 editing and scRNA-seq face several challenges and cannot integrate lineages from multiple individuals. Here the authors show that integration of mutation and expression leads to accurate lineage tree inference and enables the learning of a species-invariant lineage tree.

    • Hamim Zafar
    • , Chieh Lin
    •  & Ziv Bar-Joseph
  • Article
    | Open Access

    Tracking tumour evolution in a patient via circulating tumour DNA (ctDNA) is complicated due to the unknown mix of fragmented alleles from different cancer lesions. Here, the authors make use of a rapid autopsy program to demonstrate how representative ctDNA profiling is of metastasis, as well as presenting methylation profiling method to track evolutionary change.

    • George D. Cresswell
    • , Daniel Nichol
    •  & Andrea Sottoriva
  • Article
    | Open Access

    Multiple sequence alignments of proteins carry information about evolution, the protein’s fitness landscape and its stability in the face of mutations. Here, the authors demonstrate the utility of latent space models learned using variational autoencoders to infer these properties from sequences.

    • Xinqiang Ding
    • , Zhengting Zou
    •  & Charles L. Brooks III
  • Article
    | Open Access

    The clonal origins of metastases and the timing of dissemination remains an open question for most cancer types. Using primary and metastatic samples taken from one colorectal cancer patient, Alves et al. use Bayesian phylogenetics to reconstruct the history of metastasis.

    • Joao M. Alves
    • , Sonia Prado-López
    •  & David Posada
  • Article
    | Open Access

    Invasive non-typhoidal Salmonella (iNTS) infections are dominated by antibiotic resistant isolates of the sequence type (ST) 313. Here, the authors identify the ST313 sublineage II.1 in the Democratic Republic of the Congo exhibiting extensive drug resistance and genetic signatures potentially associated with host adaptation.

    • Sandra Van Puyvelde
    • , Derek Pickard
    •  & Stijn Deborggraeve
  • Article
    | Open Access

    Model selection is a time-intensive step of molecular phylogenetic analysis. Here, Abadi, Azouri and colleagues show that all model selection criteria lead to similar inferences, and that for topology and ancestral sequence reconstruction, using the GTR+I+G model is as accurate.

    • Shiran Abadi
    • , Dana Azouri
    •  & Itay Mayrose
  • Article
    | Open Access

    Cross-cell heterogeneity of genotypes can be revealed by analyzing single-cell sequencing data. Here the authors develop a tool for single-cell variant calling via phylogenetic inference, and use it to analyze cancer genomics datasets.

    • Jochen Singer
    • , Jack Kuipers
    •  & Niko Beerenwinkel
  • Article
    | Open Access

    Cation/proton antiporters (CPAs) play a major role in maintaining living cells’ homeostasis and are divided in two main groups: CPA1 and CPA2. Here authors use a comprehensive evolutionary analysis of 6537 representative CPAs and reveal a sequence motif that determines central phenotypic characteristics.

    • Gal Masrati
    • , Manish Dwivedi
    •  & Nir Ben-Tal
  • Article
    | Open Access

    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
    | Open Access

    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 |

    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
    | Open Access

    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 |

    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 |

    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
    | Open Access

    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