Phylogenetics articles within Nature Communications

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  • Article
    | Open Access

    Non-pharmaceutical interventions for COVID-19 also impacted the transmission of other viruses including respiratory syncytial virus (RSV). Here the authors describe the changing epidemiology, clinical severity, and genetic diversity of RSV in Chicago, Illinois, from July 2010 to April 2023.

    • Estefany Rios-Guzman
    • , Lacy M. Simons
    •  & Judd F. Hultquist

  • Article
    | Open Access

    Hepatocellular carcinomas (HCC) present spatial intratumour heterogeneity (sITH). Here, the authors perform a genomic and phylogenetic analysis of spatially-sampled HCC tumour sections, observe block-shaped sITH, and find ongoing natural selection where ancestral and derived clones spatially compete in the same tumor.

    • Xiaodong Liu
    • , Ke Zhang
    •  & Weiwei Zhai

  • Article
    | Open Access

    This study on respiratory syncytial virus (RSV) reveals global genomic gaps. Using INFORM-RSV data, it uncovers selection’s impact on RSVA and RSVB diversity. Analysing full genomes, it highlights non-neutral epidemic processes. The research emphasises air travel’s influence on global spread, underscoring the need for comprehensive RSV genomic surveillance.

    • Annefleur C. Langedijk
    • , Bram Vrancken
    •  & Shabir A. Madhi

  • Article
    | Open Access

    Bergmann’s Rule predicts larger body sizes in colder climates. Here, the authors examine extinct and extant dinosaurs (birds) and mammaliaforms, finding no evidence of body size variation with latitude in any group, but a small variation with temperature in extant birds.

    • Lauren N. Wilson
    • , Jacob D. Gardner
    •  & Chris L. Organ

  • Article
    | Open Access

    Hepatitis B virus is an ancient human pathogen that dates back more than 10,000 years. Here, the authors investigate the evolutionary history of the virus in Eastern Eurasia by sequencing 34 genomes dating from approximately 400–5,000 years ago and comparing them with other contemporary sequences.

    • Bing Sun
    • , Aida Andrades Valtueña
    •  & Yinqiu Cui

  • Article
    | Open Access

    Pliobates cataloniae is a small-bodied Miocene catarrhine primate with unclear systematic status. Here, the authors present additional dental remains from this species, conducting cladistic analyses that indicate it is a pliopithecoid convergent with apes in elbow and wrist morphology.

    • Florian Bouchet
    • , Clément Zanolli
    •  & David M. Alba

  • Article
    | Open Access

    Extinction threatens to erode the Tree of Life. Here, the authors calculate extinction risk for jawed vertebrates, predicting a loss of 86–150 billion years (11–19%) of evolutionary history through the next 50–500 years and indicating that cartilaginous fish, ray-finned fish, and turtles are most at risk from a phylogenetic perspective.

    • Rikki Gumbs
    • , Oenone Scott
    •  & James Rosindell

  • Article
    | Open Access

    The evolutionary origin of the domestic dog is uncertain. Here, the authors sequence the whole genomes of 9 extinct Japanese wolves and 11 modern Japanese dogs, applying a phylogenetic analysis to show that dogs may have originated in East Asia from a common ancestor with the Japanese wolf.

    • Jun Gojobori
    • , Nami Arakawa
    •  & Yohey Terai

  • Article
    | Open Access

    Cytochrome c maturation (CCM) is the process of covalent attachment of a heme group to the conserved cysteines to form the holocytochrome. Here, the authors report that the non-adaptive convergent evolution at the pathway level leads to mosaic distribution of CCM systems I and III among Archaeplastida species.

    • Huang Li
    • , Soujanya Akella
    •  & Jeffrey P. Mower

  • Article
    | Open Access

    Chemoreception - the ability to smell and taste - relies on diverse receptor genes. Examining 1,527 vertebrate genomes, this study explores the dynamic evolution, lineage-specific expansions and losses of chemoreceptor genes as well as ecological and morphological factors associated with these.

    • Maxime Policarpo
    • , Maude W. Baldwin
    •  & Walter Salzburger

  • Article
    | Open Access

    Escherichia coli ST131 is a globally dominant multidrug resistant clone associated with high rates of recurring urinary tract infections. In this genomic epidemiology study, the authors describe the evolution, population structure, and antimicrobial resistance in 142 E. coli ST131 samples from Wales, UK.

    • Rhys T. White
    • , Matthew J. Bull
    •  & Scott A. Beatson

  • Article
    | Open Access

    Heterostylous plants have floral morphs bearing female and male sex organs at reciprocal heights. Here the authors show that, across angiosperms, heterostyly is associated with tubed flowers pollinated by long-tongued insects, supporting the Darwinian hypothesis about precise pollen transfer between heterostylous morphs.

    • Violeta Simón-Porcar
    • , Marcial Escudero
    •  & Juan Arroyo

  • Article
    | Open Access

    The origins of alpine plant diversity are unclear. Here, the authors provide a time-calibrated molecular phylogenetic tree for Saxifraga, a diverse alpine plant clade, and show that upslope biome shifts into the alpine zone occurred more often than dispersal between alpine regions.

    • Tom Carruthers
    • , Michelangelo S. Moerland
    •  & Wolf L. Eiserhardt

  • Article
    | Open Access

    Using a dataset that included 341,846 species in 391 angiosperm floras worldwide, this study finds that the global phylogenetic structure of angiosperms shows clear and meaningful relationships with environmental factors and that current climatic variables have the highest predictive power for phylogenetic metrics reflecting recent evolutionary relationships.

    • Hong Qian
    • , Shenhua Qian
    •  & Michael Kessler

  • Article
    | Open Access

    The evolution of cicadas is unclear due to a lack of understanding of transitional features. Here, the authors assess adult and nymph mid-Cretaceous cicadas, to elucidate their morphological evolution and identify evidence of the origins of cicada sound-generation and subterranean lifestyle.

    • Hui Jiang
    • , Jacek Szwedo
    •  & Bo Wang

  • Article
    | Open Access

    Here, Rühlemann et al. analyze the gut microbiome of wild-living African great apes (Gorillas, Bonobos, Chimpanzees) in comparison to that of humans, identifying host specific patterns and shared evolutionary conserved traits disrupted in humans.

    • M. C. Rühlemann
    • , C. Bang
    •  & A. Franke

  • Article
    | Open Access

    The Omicron BA.2.86 subvariant differs from previous variants by over 30 spike mutations. Here, the authors report that BA.2.86 likely evolved in Southern Africa and that its immune escape is not larger than recently circulating SARS-CoV-2 strains. Neither its replication nor its pathogenicity are enhanced in vitro.

    • Khadija Khan
    • , Gila Lustig
    •  & Alex Sigal

  • Article
    | Open Access

    Hyaluronic acid is believed to plays a critical role in cancer resistance and longevity of the naked mole rat. Here, Zhao and colleagues show that accumulation of high levels of hyaluronic acid has co-evolved repeatedly in mammalian clades with adaptation to subterranean habitats.

    • Yang Zhao
    • , Zhizhong Zheng
    •  & Vera Gorbunova

  • Article
    | Open Access

    E. coli maintains membrane lipid asymmetry by transferring glycerophospholipids from the outer membrane to the inner membrane; this requires outer membrane protein MlaA, periplasmic chaperone MlaC, and inner-membrane complex MlaBDEF. Here, the authors show that in some bacteria that lack MlaA and MlaC, MlaD forms a transenvelope bridge comprising a typical inner-membrane domain and, in addition, an outer-membrane domain.

    • Kyrie P. Grasekamp
    • , Basile Beaud Benyahia
    •  & Christophe Beloin

  • Article
    | Open Access

    The timing of cellular evolution is poorly constrained. Here, the authors used improved molecular dating approaches to study the evolution of the ATP synthase in light of a dated tree of life thereby providing an absolute timescale for cellular evolution including eukaryotic origins.

    • Tara A. Mahendrarajah
    • , Edmund R. R. Moody
    •  & Anja Spang

  • Article
    | Open Access

    The contribution of adaptive radiation to species and phenotypic diversity within major clades is not clear. Here, the authors use morphological and phylogenetic data for 1226 species of frogs, finding that less than half of families resemble adaptive radiation, but that adaptive radiation contributed to 75% of diversity.

    • Gen Morinaga
    • , John J. Wiens
    •  & Daniel S. Moen

  • Article
    | Open Access

    The Marine Alveolates (MALVs) include important parasites of other protists/animals. Here, using new data from MALV-I, the psammosids, and a new group called the eleftherids, the authors show MALVs, and therefore parasitism in early dinoflagellates, evolved from two distinct free-living ancestors.

    • Corey C. Holt
    • , Elisabeth Hehenberger
    •  & Patrick J. Keeling

  • Article
    | Open Access

    Here, the authors report two fossil lampreys, jawless vertebrates, from the Middle-Late Jurassic fossil Lagerstätte Yanliao Biota of North China. These large lampreys have an extensively toothed feeding apparatus resembling the Southern Hemisphere pouched lamprey, suggesting an ancestral predatory habit and southern origin of living lampreys.

    • Feixiang Wu
    • , Philippe Janvier
    •  & Chi Zhang

  • Article
    | Open Access

    Kra-Dai language family exhibits great linguistic diversity and tremendous socio-cultural importance in East Asia. In this study, the authors found that Kra-Dai languages initially diverged ~4,000 years ago in Southern China coinciding with prehistoric demic and agricultural diffusions likely driven by climate change.

    • Yuxin Tao
    • , Yuancheng Wei
    •  & Menghan Zhang

  • Article
    | Open Access

    Photosynthesis is thought to be restricted to a few bacterial and eukaryotic phyla. Here, Li et al. provide evidence of photosynthetic abilities in uncultivated bacteria within the phylum Myxococcota, suggesting that some of these organisms may combine predatory and photosynthetic abilities.

    • Liuyang Li
    • , Danyue Huang
    •  & Yinzhao Wang

  • Article
    | Open Access

    Despite the significance of mosquitos for human health, little research has focused on their phylogeny. Here, the authors present a resolved phylogenetic history of mosquitoes based on phylogenomics showing that these major disease vectors radiated coincidentally with geologic events and the diversification of their hosts.

    • John Soghigian
    • , Charles Sither
    •  & Brian M. Wiegmann

  • Article
    | Open Access

    There is still no consensus on the factors favouring the evolution of same-sex sexual behaviour in mammals. This study presents evidence that it is a widespread behaviour that has evolved repeatedly in mammals, and that may play an adaptive role in bonding and conflict resolution.

    • José M. Gómez
    • , A. Gónzalez-Megías
    •  & M. Verdú

  • Article
    | Open Access

    Biodiversity is unevenly distributed across the tree of life, and theoretical work suggests that biological complexity may be influential in forming these patterns. Here, Brinkworth et al. have shown that bird clades with more complex appendicular skeletons tend to have lower extant species richness.

    • Andrew Brinkworth
    • , Emily Green
    •  & Matthew A. Wills

  • Article
    | Open Access

    The diverse Heliconius butterflies have evolved key innovations, including pollen feeding, and are a quintessential example of adaptive radiation. Using comparative genomics, Cicconardi et al. identify targets of selection at coding and non-coding loci during major ecological transitions in Heliconius.

    • Francesco Cicconardi
    • , Edoardo Milanetti
    •  & Stephen H. Montgomery

  • Article
    | Open Access

    Evolutionary relationships among green plants are unresolved and, in particular, the phylogenetic position of Prasinodermophyta remains controversial. Here, the authors conduct phylogenomic analyses to resolve relationships within Viridiplantae, suggesting that this group diverged between the Great Oxidation Event and the Neoproterozoic Oxygenation Event.

    • Zhiping Yang
    • , Xiaoya Ma
    •  & Bojian Zhong

  • Article
    | Open Access

    White-tailed deer are an important reservoir of SARS-CoV-2 in the USA and continued monitoring of the virus in deer populations is needed. In this genomic epidemiology study from Ohio, the authors show that the virus has been introduced multiple times to deer from humans, and that it has evolved faster in deer.

    • Dillon S. McBride
    • , Sofya K. Garushyants
    •  & Andrew S. Bowman

  • Article
    | Open Access

    Chikungunya virus is endemic in Brazil and cases have been rapidly increasing in recent years. Here, the authors describe the expansion of a genomic surveillance program across the country allowing them to characterise the emergence and dispersal of two distinct subclades mainly seeded from the north eastern region.

    • Joilson Xavier
    • , Luiz Carlos Junior Alcantara
    •  & Marta Giovanetti

  • Article
    | Open Access

    The maxilloturbinal, an area of the mammalian nasal cavity, has been proposed to play a pivotal role in body temperature maintenance. Here, the authors use computed tomographic data to show that neither corrected basal metabolic rate nor body temperature significantly correlate with the relative surface area of the maxilloturbinal.

    • Quentin Martinez
    • , Jan Okrouhlík
    •  & Pierre-Henri Fabre

  • Article
    | Open Access

    Herbarium collections are an important source of historical DNA, whose analysis can shed light on the evolutionary history of plant pathogens. Here, Campos et al. reconstruct historical genomes of the bacterial crop pathogen Xanthomonas citri pv. citri from citrus herbarium specimens, estimating that the pathogen originated in Southern Asia ~11,500 years ago and diversified during the beginning of the 13th century.

    • Paola E. Campos
    • , Olivier Pruvost
    •  & Lionel Gagnevin

  • Article
    | Open Access

    The chronology and mode of parallel evolution remain unclear. Here, the authors compare mid-Holocene and contemporary bottlenose dolphin adaptations between pelagic and coastal ecosystems with paleogenomics, finding rapid adaptation to newly emerged habitat from standing genetic variation.

    • Marie Louis
    • , Petra Korlević
    •  & Andrew D. Foote

  • Article
    | Open Access

    Acorales is sister to all other monocots and contains only one family with just one genus, Acorus. Here, the authors assemble the genome of the diploid Ac. gramineus and the tetraploid Ac. calamus, reconstruct an ancestral monocot karyotype and gene toolkit, and discuss the origin and evolution of the two species and other monocots.

    • Liang Ma
    • , Ke-Wei Liu
    •  & Zhong-Jian Liu

  • Article
    | Open Access

    Monocots are one of the most diverse and dominant clades of flowering plants. Here, the authors assemble the genome of Acorus gramineus, confirm its phylogenetic position as sister to the rest of monocots and reveal the absence of tau (τ) whole-genome duplication observed in the majority of monocot clades.

    • Xing Guo
    • , Fang Wang
    •  & Huan Liu

  • Article
    | Open Access

    The second SARS-CoV-2 wave in Peru had a high case fatality rate with Lambda and Gamma causing most cases. Using phylodynamics, the authors here show that Lambda most likely originated in Peru from where it spread to other South American countries and that the center of Peru played a key role in transmission to other regions.

    • Santiago Justo Arevalo
    • , Carmen Sofia Uribe Calampa
    •  & Joao Renato Rebello Pinho

  • Article
    | Open Access

    Monoamines act as neuromodulators in the nervous system, but their evolutionary origins are unclear. Here, the authors examine the evolution of genes involved in monoamine production, and processing suggesting that the monoaminergic system evolved in the bilaterian stem-group.

    • Matthew Goulty
    • , Gaelle Botton-Amiot
    •  & Roberto Feuda

  • Article
    | Open Access

    Hong Kong experienced a large wave of COVID-19 in early 2022 driven by Omicron BA.2. Here, the authors describe the epidemiological dynamics of this wave and show discordant inferences based on genomic and epidemiological data that underscore the need to improve near real-time epidemic growth estimates.

    • Ruopeng Xie
    • , Kimberly M. Edwards
    •  & Vijaykrishna Dhanasekaran

  • Article
    | Open Access

    Escherichia albertii is an emerging gastrointestinal pathogen that causes disease in humans and animals, notably birds. In this genomic epidemiology study, the authors investigate characteristics of isolates sampled from humans and birds in Great Britain and find that they tend to cluster separately.

    • Rebecca J. Bengtsson
    • , Kate S. Baker
    •  & Becki Lawson

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