Phylogenetics articles within Nature Communications

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  • Article
    | Open Access

    The evolution and systematics of Madagascar’s extinct elephant birds remains unclear. Here, the authors recover genetic, stable isotope, morphological, and geographic data from fossil eggshell to describe variation among clades, identifying cryptic diversity and potential drivers of speciation.

    • Alicia Grealy
    • , Gifford H. Miller
    •  & Michael Bunce

  • Article
    | Open Access

    Asgard archaea include the closest known archaeal relatives of eukaryotes. Here, the authors provide evidence that eukaryotic and Asgard thymidylate synthases (required for DNA synthesis) may have a bacterial origin, and additional lateral transfer of bacterial genes may have shaped the metabolism of Asgard archaea.

    • Jonathan Filée
    • , Hubert F. Becker
    •  & Hannu Myllykallio

  • Article
    | Open Access

    This study finds that high-latitude fish clades with the fastest speciation rates also exhibit elevated rates of depth evolution, creating a prevailing latitudinal gradient of deep-sea invasions concentrated in poleward regions. These results advance our understanding of how niche lability and climate shape global patterns of species distributions.

    • Sarah T. Friedman
    •  & Martha M. Muñoz

  • Article
    | Open Access

    Here, the authors describe the geographies, hosts, substrates, and phylogenetic relationships for 1,794 Saccharomyces strains. They provide insight into the genetic and phenotypic diversity in the genus, not seen through prior work focused on the model species Saccharomyces cerevisiae.

    • David Peris
    • , Emily J. Ubbelohde
    •  & Chris Todd Hittinger

  • Article
    | Open Access

    Madagascar is a threatened biodiversity hotspot. Here, using a newly assembled dataset and island biogeography models, the authors estimate how many millions of years of evolutionary history have been lost since human colonisation and may be further lost in the future for Malagasy mammals.

    • Nathan M. Michielsen
    • , Steven M. Goodman
    •  & Luis Valente

  • Article
    | Open Access

    External ecological interactions and intrinsic biological parameters affect evolutionary pathways and animal diversity. Here, the authors use ruminant inner ear morphology to investigate patterns of diversity through 33 million years, finding clade-dependent climate and paleogeographic trends.

    • Bastien Mennecart
    • , Laura Dziomber
    •  & Loïc Costeur

  • Article
    | Open Access

    Here, the authors present two well preserved fossil lizard skulls from the Late Jurassic of North America. These fossils, placed at the base of the clade Pan-Scincoidea, suggest that squamates had a wide geographic distribution and preserve characteristics that show the complex early evolutionary history of squamate anatomy.

    • Chase D. Brownstein
    • , Dalton L. Meyer
    •  & Jacques A. Gauthier

  • Article
    | Open Access

    Here, the authors use reproductive mode data with matching phylogenetic data to explore the evolution of reproductive mode, transitions between reproductive modes, and diversification rates in amphibians.

    • H. Christoph Liedtke
    • , John J. Wiens
    •  & Ivan Gomez-Mestre

  • Article
    | Open Access

    The location where fertilization takes place can be highly variable across species, and especially between internal and external fertilizers. Kahrl et al. find that fertilization environment plays a significant role in the evolution and diversification of sperm morphology across vertebrate species.

    • Ariel F. Kahrl
    • , Rhonda R. Snook
    •  & John L. Fitzpatrick

  • Article
    | Open Access

    Although giant viruses are abundant in aquatic environments, less is known about giant viruses in soil. Here, the authors use permafrost metagenomics to reveal giant virus diversity and heterogeneity, as well as gene transfers between viruses from different families.

    • Sofia Rigou
    • , Sébastien Santini
    •  & Matthieu Legendre

  • Article
    | Open Access

    It is currently unknown how climate and land use changes could affect the endemic area of Lassa virus, a zoonotic pathogen responsible for Lassa fever. Here, the authors show that by 2070, new regions in Africa will likely become ecologically suitable for Lassa virus, drastically increasing the population living in conditions favourable for virus circulation.

    • Raphaëlle Klitting
    • , Liana E. Kafetzopoulou
    •  & Simon Dellicour

  • Article
    | Open Access

    SARS-CoV-2 genome sequencing data can be used to infer epidemiological parameters, but the impact of the strategy used to select samples on these estimates is rarely considered. Here, the authors produce estimates using different sampling strategies and compare results to those based on case reporting data.

    • Rhys P. D. Inward
    • , Kris V. Parag
    •  & Nuno R. Faria

  • Article
    | Open Access

    The dynamics of SARS-CoV-2 transmission in the Middle East have been relatively under-studied. Here, the authors integrate genomic and travel data and show that introductions to the region were initially driven by intercontinental air travel, after which regional land travel became a more important driver.

    • Edyth Parker
    • , Catelyn Anderson
    •  & Issa Abu-Dayyeh

  • Article
    | Open Access

    This study presents data from the REACT-1 SARS-CoV-2 community sampling study in England from November 2021 to March 2022. They show that the Omicron variant peaked in January with a prevalence of ~7% and that the BA.2 sublineage had a 1.5x higher reproduction number compared to other Omicron sublineages.

    • Oliver Eales
    • , Leonardo de Oliveira Martins
    •  & Marc Chadeau-Hyam

  • Article
    | Open Access

    Genetic recombination can confound standard phylogenetic approaches. Here, the authors present a method to reconstruct virus recombination networks, and show the importance of recombination in shaping the ongoing evolution of SARS-like, MERS and 3 human seasonal coronaviruses.

    • Nicola F. Müller
    • , Kathryn E. Kistler
    •  & Trevor Bedford

  • Article
    | Open Access

    Here, the authors characterize a case of SARS-CoV-2 superinfection with Alpha and Epsilon variants, in which, via full genome sequencing analyses, they identify recombinant haplotypes in the spike, nucleocapsid, and ORF 8 coding regions, suggesting recombination could play a role in SARS-CoV-2 genetic diversity.

    • Joel O. Wertheim
    • , Jade C. Wang
    •  & Scott Hughes

  • Article
    | Open Access

    Here, the authors use full-plastome phylogenomics and multiclade comparative models to reconstruct the tempo and drivers of six European Alpine angiosperm lineages before and during the Pleistocene. They find that geographic divergence and bedrock shifts drive speciation events, while diversification rates remained steady.

    • Jan Smyčka
    • , Cristina Roquet
    •  & Sébastien Lavergne

  • Article
    | Open Access

    The bacterial genus Rickettsia includes vector-borne pathogens and arthropod symbionts that are close relatives of symbionts of microeukaryotes classified under the genus ‘Candidatus Megaira’. Here, Davison et al. clarify the evolutionary relationships between these organisms by assembling 28 genomes of understudied species, and propose that a distinct clade known as Torix Rickettsia should be considered a separate genus.

    • Helen R. Davison
    • , Jack Pilgrim
    •  & Stefanos Siozios

  • Article
    | Open Access

    In this genomic epidemiology study from Ghana, the authors sequence ~1,000 SARS-CoV-2 whole genomes from March 2020 to September 2021. They describe changes in the predominant circulating lineages over time and infer how variants of concern were likely introduced into the country.

    • Collins M. Morang’a
    • , Joyce M. Ngoi
    •  & Gordon A. Awandare

  • Article
    | Open Access

    “Ulvophyceae is a remarkably morphologically and ecologically diverse clade of green algae. Here, the authors reconstruct the Ulvophyceae phylogeny, showing that these algae originated earlier than expected and may have influenced biogeochemical cycles at the Mesoproterozoic-Neoproterozoic transition.”

    • Zheng Hou
    • , Xiaoya Ma
    •  & Bojian Zhong

  • Article
    | Open Access

    The A.27 SARS-CoV-2 lineage spread globally in 2021 but did not become dominant. Here, the authors show that A.27 shares some mutations in the spike gene that are present in variants of concern, but lacks the D614G mutation, indicating independent evolution of immune escape properties.

    • Tamara Kaleta
    • , Lisa Kern
    •  & Jonas Fuchs

  • Article
    | Open Access

    ‘Macroevolution posed difficulties for Darwin and later theorists because species frequently change abruptly, or experience long periods of stasis, both counter to the theory of incremental change or gradualism. Here, the authors propose a macroevolutionary statistical model that accommodates this uneven evolutionary landscape, and shows how even abrupt macroevolutionary changes are compatible with gradualist microevolutionary processes.’

    • Mark Pagel
    • , Ciara O’Donovan
    •  & Andrew Meade

  • Article
    | Open Access

    Hong Kong has used an elimination strategy to control SARS-CoV-2 with stringent measures including traveller quarantine. Here, the authors show that the majority of community-acquired cases until January 2021 resulted from three importations, and that increased transmission followed prolonged periods of restrictions, likely due to adherence fatigue.

    • Haogao Gu
    • , Ruopeng Xie
    •  & Leo L. M. Poon

  • Article
    | Open Access

    Gamma triplication arises via two whole-genome duplications early in eudicot history, but the relative timing of these is unclear. Here, the authors report the genomes of Buxales and Trochodendrales and reject the hypothesis of gamma arising via inter-lineage hybridization between ancestral eudicot lineages.

    • Andre S. Chanderbali
    • , Lingling Jin
    •  & Pamela S. Soltis

  • Article
    | Open Access

    Signals of antimicrobial resistance in pathogen genomes may be detectable before the organism evolves an antimicrobial resistance phenotype. Here, the authors investigate this hypothesis using Mycobacterium tuberculosis data from Peru and identify candidate “pre-resistance” markers.

    • Arturo Torres Ortiz
    • , Jorge Coronel
    •  & Louis Grandjean

  • Article
    | Open Access

    Chloranthales remain the last lineage of core angiosperms that lacks a nuclear genome assembly. Here, the authors report the genome assembly of Chloranthus sesilifolius and show that both hybridization and incomplete lineage sorting may have contributed to the phylogenetic incongruities in the literature.

    • Jianxiang Ma
    • , Pengchuan Sun
    •  & Yongzhi Yang

  • Article
    | Open Access

    Chloranthales remain the last lineage of core angiosperms that lacks a nuclear genome assembly. Here, the authors report the genome assembly of Chloranthus spicatus and show its contribution to deepen our understanding on diversification, phylogeny, and genome evolution in angiosperms.

    • Xing Guo
    • , Dongming Fang
    •  & Huan Liu

  • Article
    | Open Access

    With the rise in number of eukaryotic species being fully sequenced, large scale phylogenetic profiling can give insights on gene function, Here, the authors describe a machine-learning approach that integrates co-evolution across eukaryotic clades to predict gene function and functional interactions among human genes.

    • Doron Stupp
    • , Elad Sharon
    •  & Yuval Tabach

  • Article
    | Open Access

    Mycobacterium tuberculosis is a clonal pathogen that has co-evolved with humans for millennia. Here, Freschi et al. reevaluate the population structure of M. tuberculosis, providing an in-depth analysis of the ancient Indo-Oceanic Lineage 1 and the modern Central Asian Lineage 3, and expanding our understanding of Lineages 2 and 4.

    • Luca Freschi
    • , Roger Vargas Jr.
    •  & Maha Reda Farhat

  • Article
    | Open Access

    Tooth morphology has provided many insights into the tempo and mode of dietary evolution in mammals. A study of fossil and extant squamates shows that this group also repeatedly evolved increasingly complex teeth with more flexibility than mammals, and that higher tooth complexity and herbivory likely led to higher speciation rates.

    • Fabien Lafuma
    • , Ian J. Corfe
    •  & Nicolas Di-Poï

  • Article
    | Open Access

    A phylogeny of Nymphalidae butterflies unveils the origin of the latitudinal diversity gradient. This study showed that the modern pattern of species richness emerged from dynamics of dispersal and diversification that varied through time and across regions, and that global climate change throughout the Cenozoic probably played a major role in generating the biodiversity pattern.

    • Nicolas Chazot
    • , Fabien L. Condamine
    •  & Niklas Wahlberg

  • 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

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