Phylogenetics

  • Article
    | Open Access

    Snakes are one of the most successful groups of living vertebrates, but the timing of their diversification is unclear. Combining molecular clocks, fossils, and biogeography, Klein et al. show that snakes experienced a diversification, and underwent dispersal, around the time of the end-Cretaceous mass extinction.

    • Catherine G. Klein
    • , Davide Pisani
    •  & Nicholas R. Longrich
  • Article
    | Open Access

    Mycobacterium abscessus is an emerging infection that usually affects patients with structural lung diseases such as cystic fibrosis (CF). Here, the authors use phylogenetic analyses to demonstrate close relationships between isolates from CF and non-CF patients and identify antibiotic resistance markers.

    • Ryan A. Bronson
    • , Chhavi Gupta
    •  & Keira A. Cohen
  • Article
    | Open Access

    Salmonella enterica serovar 4,[5],12:i:- (Salmonella 4,[5],12:i:-) is a major pathogen of humans and animals with a reported incidence in Australia three times higher than the UK and USA. Here, the authors report the circulation, antimicrobial resistance signatures, and effects on host cells, of three Salmonella4,[5],12:i:- lineages within Australia.

    • Danielle J. Ingle
    • , Rebecca L. Ambrose
    •  & Deborah A. Williamson
  • Article
    | Open Access

    How early photosynthesizers managed oxidative stress remains relatively unresolved. Analyses of enzymes dealing with reactive oxygen species traces the evolutionary history of superoxide dismutases and finds evidence of CuZnSOD in the ancestor of all cyanobacteria, dating back to the Archaean.

    • Joanne S. Boden
    • , Kurt O. Konhauser
    •  & Patricia Sánchez-Baracaldo
  • Article
    | Open Access

    Plasmodium vivax generally accounts for a low proportion of malaria cases in Africa, but population-level data on the distribution of infections is limited. Here, the authors use data from the Democratic Republic of the Congo and show that the prevalence is low (~3%) and diffusely spread.

    • Nicholas F. Brazeau
    • , Cedar L. Mitchell
    •  & Jonathan J. Juliano
  • Article
    | Open Access

    Resistance of Neisseria gonorrhoeae to extended spectrum cephalosporins is an increasing concern. Here, the authors conduct whole genome sequencing of isolates from the United States and find that most resistant isolates were associated with a persistent circulating lineage.

    • Jesse C. Thomas IV
    • , Sandeep J. Joseph
    •  & Zach Perry
  • Article
    | Open Access

    There are relatively few known extant adaptive radiations in Europe that predate the Pleistocene. Here, Borko et al. characterize the diversity and diversification of the subterranean amphipod genus Niphargus, showing evidence for a large adaptive radiation associated with massif uplift 15 million years ago.

    • Špela Borko
    • , Peter Trontelj
    •  & Cene Fišer
  • Article
    | Open Access

    Molecular phylogenies are traditionally based on sequence variation, but genome rearrangements also contain phylogenetic information. Here, Zhao et al. develop an approach to reconstruct phylogenies based on microsynteny and illustrate it with a reconstruction of the angiosperm phylogeny.

    • Tao Zhao
    • , Arthur Zwaenepoel
    •  & Yves Van de Peer
  • Article
    | Open Access

    Dating early bacterial evolution is challenging due to the limited bacterial fossil record. Here Wang and Luo use the close evolutionary relationship between Alphaproteobacteria and mitochondria to leverage the eukaryotic fossil record in dating Alphaproteobacteria origin and diversification.

    • Sishuo Wang
    •  & Haiwei Luo
  • Article
    | Open Access

    Islands can provide insights into the evolution of diverse adaptations. The genomes of 34 major lineages of Mediterranean wall lizards reveal a highly reticulated pattern of evolution across the group, characterised by mosaic genomes and showing that hybrid lineages gave rise to several extant endemics.

    • Weizhao Yang
    • , Nathalie Feiner
    •  & Tobias Uller
  • Article
    | Open Access

    Whole genome sequencing is increasingly being adopted for Shigella sonnei outbreak investigation and surveillance, but there is no global classification standard. Here, the authors develop and validate a genomic framework implemented using open-source software, and demonstrate its application using surveillance data.

    • Jane Hawkey
    • , Kalani Paranagama
    •  & Kathryn E. Holt
  • Article
    | Open Access

    The evolution of metamorphic species may be constrained by different ecologies of the larval and adult stages. Here, Bardua et al. show that in frogs, adult ecology is more important than larval ecology for skull evolution, but species that don’t feed as tadpoles evolve faster than those that do.

    • Carla Bardua
    • , Anne-Claire Fabre
    •  & Anjali Goswami
  • Article
    | Open Access

    Here, the authors present results of the ZiBRA-2 project (https://www.zibra2project.org) which is an arbovirus surveillance project, across the Midwest of Brazil using a mobile genomics laboratory, combined with a genomic surveillance training program that targeted post-graduate students, laboratory technicians, and health practitioners in universities and laboratories.

    • Talita Émile Ribeiro Adelino
    • , Marta Giovanetti
    •  & Luiz Carlos Junior Alcantara
  • Article
    | Open Access

    Likelihood optimization in phylogenetic tree reconstruction is computationally intensive, especially as the number of sequences and taxa included increase. Here, Azouri et al. show how an artificial intelligence approach can reduce computational time without losing accuracy of tree inference.

    • Dana Azouri
    • , Shiran Abadi
    •  & Tal Pupko
  • Article
    | Open Access

    The trajectory of the emergence of Zika virus (ZIKV) into the Americas remains unclear. Here, the authors find that four mutations originated before ZIKV introduction to the Americas are direct reversions of previous mutations that accompanied spread many decades ago from ZIKV’s native Africa to Asia, and show in experimental infections of mosquitoes, human cells, and mice that the original mutations reduced fitness for urban transmission, while the reversions restored fitness, likely increasing epidemic risk.

    • Jianying Liu
    • , Yang Liu
    •  & Scott C. Weaver
  • Article
    | Open Access

    Arms races between herbivores and plants have likely affected their evolutionary histories, which could have led to their high diversity. Allio et al. find that butterflies shifting to new host plants have more adaptive molecular signatures across their genomes and show repeated bursts of speciation rates.

    • Rémi Allio
    • , Benoit Nabholz
    •  & Fabien L. Condamine
  • 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

    In this study, the authors present a genomic surveillance of avian influenza genomes sampled from live poultry markets in China. They report that a number of variants have emerged since 2016 that pose an increased risk to humans. They highlight the importance of continuous genome surveillance of circulating influenza strains.

    • Yuhai Bi
    • , Juan Li
    •  & Weifeng Shi
  • Article
    | Open Access

    Cichlids are a model for adaptive radiation, but the timing of their diversification is debated. Here the authors assemble 14 cichlid genomes, introduce a Bayesian approach to account for fossil-assignment uncertainty, and present a dated phylogenomic hypothesis of cichlid and teleost evolution.

    • Michael Matschiner
    • , Astrid Böhne
    •  & Walter Salzburger
  • Article
    | Open Access

    Cooperative interactions among tumor cells may have important implications for metastasis. Here, the authors examined the spatio-temporal nature of interactions among clonal populations of ovarian carcinoma cells and found that transient interactions cells can promote metastases via commensal interactions.

    • Suha Naffar-Abu Amara
    • , Hendrik J. Kuiken
    •  & Joan S. Brugge
  • Article
    | Open Access

    Classical epidemiological approaches have been limited in their ability to formally test hypotheses. Here, Dellicour et al. illustrate how phylodynamic and phylogeographic analyses can be leveraged for hypothesis testing in molecular epidemiology using West Nile virus in North America as an example.

    • Simon Dellicour
    • , Sebastian Lequime
    •  & Philippe Lemey
  • Article
    | Open Access

    In this study, the authors present an analysis of 247 full-genome SARS-CoV-2 sequences obtained from two communities in Wisconsin, USA, and report distinct patterns of viral spread. Their results suggest that patterns of SARS-CoV-2 transmission and spread may vary substantially, even between neighbouring communities.

    • Gage K. Moreno
    • , Katarina M. Braun
    •  & Thomas C. Friedrich
  • Article
    | Open Access

    The HIV reservoir is a major hurdle for a cure of HIV, but the factors determining its size and dynamics remain unclear. Here the authors show in a large cohort of 610 HIV-1 infected individuals, who are on suppressive ART for a median of 5.4 years, that viral genetic factors contribute substantially to the HIV-1 reservoir size.

    • Chenjie Wan
    • , Nadine Bachmann
    •  & Sabine Yerly
  • Article
    | Open Access

    In this study, Adi Stern and colleagues use full genome sequences of SARS-CoV-2 to look at the rate of infections in Israel. They report that social distancing had a significant effect on minimising the rate of transmission, and find evidence for transmission heterogeneity (superspreading events).

    • Danielle Miller
    • , Michael A. Martin
    •  & Adi Stern
  • Article
    | Open Access

    Highly pathogenic avian influenza viruses (HPAIV) can evolve via acquisition of polybasic cleavage sites, but the contribution of other mutations remains unclear. Here, the authors combine phylogenetic, statistical and structural approaches, and identify parallel mutations that are associated with HPAIV phenotype.

    • Marina Escalera-Zamudio
    • , Michael Golden
    •  & Oliver G. Pybus
  • Article
    | Open Access

    Ammonia-oxidising archaea of the phylum Thaumarchaeota are important organisms in the nitrogen cycle. Using 12 new genomes, this study finds evidence that Nitrososphaerales evolution was marked by lateral gene transfer followed by gene duplication.

    • Paul O. Sheridan
    • , Sebastien Raguideau
    •  & Cécile Gubry-Rangin
  • Article
    | Open Access

    In this study, Chen and colleagues present genomic sequences of 102 SARS-CoV-2 isolates collected in Beijing. They look closely at genomic variation between isolates that arose as a result of domestic and global transmission. Their data suggest that SARS-CoV-2 genomes have a high mutational tolerance, which may have potential implications for the development of vaccines.

    • Pengcheng Du
    • , Nan Ding
    •  & Chen Chen
  • Article
    | Open Access

    By greatly expanding the number of assembled genomes for Wolbachia (a group of intracellular bacteria) and constructing robust phylogenies, this study finds strong rate heterogeneity among Wolbachiapopulations and no support for synchronous divergence between Wolbachia and host mitochondria.

    • Matthias Scholz
    • , Davide Albanese
    •  & Omar Rota-Stabelli
  • Article
    | Open Access

    Spatiotemporal sampling gaps in existing pathogen genomic data limits their use in understanding epidemiological patterns. Here, the authors apply a phylogeographic approach with SARS-CoV-2 genomes to accurately reproduce pathogen spread by accounting for spatial biases and travel history of the individual.

    • Philippe Lemey
    • , Samuel L. Hong
    •  & Marc A. Suchard
  • Article
    | Open Access

    Song et al. inferred that stridulatory wings and tibial ears co-evolved in a sexual context among crickets, katydids, and their allies, while abdominal ears evolved first in a non-sexual context in grasshoppers, and were later co-opted for courtship. They found little evidence that the evolution of these organs increased lineage diversification.

    • Hojun Song
    • , Olivier Béthoux
    •  & Sabrina Simon
  • Article
    | Open Access

    Metagenomics allows virus genome discovery, but the viral hosts are often not identified. Here, Kinsella et al. use recombination events between virus genomes, statistical association of viruses to hosts in clinical samples, and analysis of endogenous viral elements in host genomes to identify probable hosts of three CRESS virus families.

    • Cormac M. Kinsella
    • , Aldert Bart
    •  & Lia van der Hoek
  • Article
    | Open Access

    Tea is an important beverage crop with a large and heterozygous genome. Here, the authors assemble the genome of the cultivar Longjing 43 and conduct a population genetics study to reveal divergent selection for disease resistance and flavor between the two variety groups.

    • Xinchao Wang
    • , Hu Feng
    •  & Yajun Yang
  • Article
    | Open Access

    Bats are a likely reservoir of zoonotic coronaviruses (CoVs). Here, analyzing bat CoV sequences in China, the authors find that alpha-CoVs have switched hosts more frequently than betaCoVs, identify a bat family and genus that are highly involved in host-switching, and define hotspots of CoV evolutionary diversity.

    • Alice Latinne
    • , Ben Hu
    •  & Peter Daszak
  • Article
    | Open Access

    The evolutionary relationships within Archaea remain unresolved. Here, the authors used genomic approaches to study the Undinarchaeota, a previously uncharacterized clade of DPANN, shed light on their position in an updated archaeal phylogeny and illuminate the history of archaeal genome evolution.

    • Nina Dombrowski
    • , Tom A. Williams
    •  & Anja Spang
  • Article
    | Open Access

    There is mixed evidence for how temperature affects diversification rates. Here, authors use a supermatrix of nearly 20,000 rosid species, comprising almost a quarter of flowering plants, to show that tropical groups are older and speciated twice as slowly as their counterparts from cooler climates.

    • Miao Sun
    • , Ryan A. Folk
    •  & Robert P. Guralnick
  • Article
    | Open Access

    The dynamics of how major clades and body plans arise and evolve in deep time remain poorly understood. Here, Simões et al. report major time lags between phases of rapid phenotypic change at the origin of major reptile lineages and periods of fast molecular change and adaptive radiation.

    • Tiago R. Simões
    • , Oksana Vernygora
    •  & Stephanie E. Pierce
  • Article
    | Open Access

    Both geography and ecology can drive the origins of new species. Siqueira et al. show how geological changes in the structure of Miocene reefs and the concurrent evolution of new feeding strategies combine to explain why coral reefs contain such a diversity of fish species.

    • Alexandre C. Siqueira
    • , Renato A. Morais
    •  & Peter F. Cowman
  • Article
    | Open Access

    In contrast to bird plumage, little is known about the evolution of bird skin color. Here, Nicolaï et al. find that black skin has evolved over 100 times in birds and is associated with baldness and/or white feathers as well as with high irradiation habitats, suggesting a role in UV protection.

    • Michaël P. J. Nicolaï
    • , Matthew D. Shawkey
    •  & Liliana D’Alba
  • Article
    | Open Access

    Developmental duration is a key life-history trait. Cooney et al. compile data on 3096 bird species to quantify the degree to which phylogenetic history, body size and ecological variables like predation risk or breeding phenology influence variation in developmental duration.

    • Christopher R. Cooney
    • , Catherine Sheard
    •  & Alison E. Wright