Phylogenomics articles within Nature Communications

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  • Article
    | Open Access

    Highly pathogenic avian influenza virus subtype H5 is an important pathogen of wild birds and poultry that has also caused infection in humans and other mammals. Here the authors use wild bird movement tracking data and virus genome sequences to quantify how seasonal bird migration facilitates global dispersal of the virus.

    • Qiqi Yang
    • , Ben Wang
    •  & Bryan Grenfell

  • Article
    | Open Access

    Heeren et al study the evolutionary genomics of leishmaniasis in Peru and Bolivia to show that parasite hybridization increases the prevalence, diversity and spread of viruses that have been previously associated with disease severity and treatment failure.

    • Senne Heeren
    • , Ilse Maes
    •  & Frederik Van den Broeck

  • 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

    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

    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

    While the organelle genome is commonly considered to be a single circular DNA molecule, extensive variation exists. Here, the authors report multipartite minicircular genomes in red algae and indicate an origin driven by recombination due to loss of DNA replication, recombination, and repair genes.

    • Yongsung Lee
    • , Chung Hyun Cho
    •  & Hwan Su Yoon

  • Article
    | Open Access

    An increase in shigellosis cases among men who have sex with men in the United Kingdom has been linked to an extensively drug-resistant strain of Shigella sonnei. In this genomic epidemiology study, the authors investigate the genetic basis, evolutionary history, and international dissemination of the outbreak strain.

    • Lewis C. E. Mason
    • , David R. Greig
    •  & Kate S. Baker

  • Article
    | Open Access

    Hymenoptera is an incredibly diverse order, with numerous behavioral and morphological innovations. Here, the authors compile a time-calibrated Hymenoptera phylogeny and find that secondary transitions to phytophagy, plant feeding, are associated with significant increases in diversification rate in this group.

    • Bonnie B. Blaimer
    • , Bernardo F. Santos
    •  & Matthew L. Buffington

  • Article
    | Open Access

    In March 2022, Aotearoa New Zealand re-opened its border allowing quarantine-free travel for many travellers. Here, the authors describe circulating Omicron sub-variants before and after the reopening of the border and show that the rate of viral introductions grew roughly linearly with the increase in daily international travel.

    • Jordan Douglas
    • , David Winter
    •  & Jemma L. Geoghegan

  • Article
    | Open Access

    The relative importance of the mechanisms underlying species radiation remains unclear. Here, the authors combine reference genome assembly and population genetics analyses to show that neutral forces have contributed to the radiation of the most species-rich tree genus Syzygium.

    • Yee Wen Low
    • , Sitaram Rajaraman
    •  & Victor A. Albert

  • Article
    | Open Access

    Mycobacterium abscessus is an emerging infection of increasing public health concern due to outbreaks and intrinsic multidrug-resistance. Here, the authors develop and evaluate a core-genome multilocus sequence typing scheme for this pathogen to facilitate standardised molecular surveillance.

    • Margo Diricks
    • , Matthias Merker
    •  & Florian P. Maurer

  • Article
    | Open Access

    The O139 Vibrio cholerae serogroup emerged in the 1990s and spread rapidly but did not become globally dominant. Here, the authors describe the genomic epidemiology of this strain and identify changes in virulence and antimicrobial resistance characteristics that they hypothesise may have contributed to its decline.

    • Thandavarayan Ramamurthy
    • , Agila Kumari Pragasam
    •  & Ankur Mutreja

  • Article
    | Open Access

    While a large amount of genomic resources is available, the phylogeny of wild and cultivated beets remains unclear. Here, the authors use the k-mer-based Mash method to analyze resequenced genomes of 606 accessions of the genus Beta and reveal Greece as the domestication site of sugar beet.

    • Felix L. Sandell
    • , Nancy Stralis-Pavese
    •  & Juliane C. Dohm

  • Article
    | Open Access

    SARS-CoV-2 genomic surveillance has been important for informing pandemic responses but many regions remain under-sampled, limiting knowledge of circulating strains. Here, the authors sequence 378 isolates from Nigeria and identify two strains that appear to be important locally though globally uncommon.

    • Egon A. Ozer
    • , Lacy M. Simons
    •  & Ramon Lorenzo-Redondo

  • Article
    | Open Access

    Lab-based surveillance of Shigella has traditionally been based on serotyping but increasing availability of whole genome sequencing could enable higher resolution typing. Here, the authors apply a core genome multilocus sequence typing scheme to Shigella sequence data and describe its population structure.

    • Iman Yassine
    • , Sophie Lefèvre
    •  & François-Xavier Weill

  • 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

    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

    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

    The evolutionary and domestication history of apricots is poorly understood. Here, the authors provide four apricot high-quality genome assemblies, the genomes of 578 accessions from natural and cultivated populations, and show that Chinese and European apricots constitute two different gene pools, resulting from independent domestication events.

    • Alexis Groppi
    • , Shuo Liu
    •  & Véronique Decroocq

  • Article
    | Open Access

    Mycobacterium kansasii can cause serious pulmonary disease. Here, the authors present a population genomics analysis of 358 environmental and clinical isolates from around the world, supporting the idea that municipal water is a main source of infection, and shedding light into the pathogen’s diversity and adaptation to the human host.

    • Tao Luo
    • , Peng Xu
    •  & Qian Gao

  • 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

    Mechanism of high altitude adaptation of wheat remains unknown. Here, the authors assemble the draft genome of a Tibetan semi-wild wheat accession and resequence 245 wheat accessions to reveal that Tibetan semi-wild wheat has been de-domesticated from local landraces to adapt to high altitude.

    • Weilong Guo
    • , Mingming Xin
    •  & Qixin Sun

  • Article
    | Open Access

    Although SARS-CoV-2 has spread rapidly, the contribution of super-spreading events to transmission is unclear. Here, the authors show that the number of secondary infections arising from an individual infection in the early phase of the outbreak was highly skewed, indicating that super-spreading events occurred.

    • Liang Wang
    • , Xavier Didelot
    •  & Yuhai Bi

  • 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

    Exceptional alpine plant diversity exists in the Hengduan Mountains. Here, through genome assembly and population genomics studies, the authors find notable intraspecific divergence among Cushion willow populations isolated by the sky island-like habitats and consider it contributes to speciation and biodiversity.

    • Jia-hui Chen
    • , Yuan Huang
    •  & Hang Sun

  • Article
    | Open Access

    The pygmy hog (Porcula salvania), now highly endangered and restricted in a small region at the southern foothills of the Himalaya, is the only suid species in mainland Eurasia that outlived the expansion of wild boar (Sus scrofa). Here, the authors analyze genomes of pygmy hog and related suid species, and identify signals of introgression among these species.

    • Langqing Liu
    • , Mirte Bosse
    •  & Ole Madsen

  • Article
    | Open Access

    Gene synthesis has expanded the ability to modify and create DNA sequences, with implications for biosurveillance. The authors use machine learning and codon theory to identify synthetic genes in Addgene data, and show that synthesis accelerates human-directed gene transfer across the tree of life.

    • Aditya M. Kunjapur
    • , Philipp Pfingstag
    •  & Neil C. Thompson

  • Article
    | Open Access

    Detecting the targets of positive selection in the human genome is challenging. Here, the authors combine modern and ancient genomes to show that alleles strongly differentiated between Africans and Europeans mediated local adaptation in European populations, and were mostly contributed by ancient hunter-gatherers.

    • Felix M. Key
    • , Qiaomei Fu
    •  & Aida M. Andrés

  • Article
    | Open Access

    The common bedbug is a pest for humans, yet its molecular biology is poorly understood. Here, the authors sequence the common bedbug genome and profile gene expression across all life stages to show major changes in gene expression after feeding on human blood.

    • Jeffrey A. Rosenfeld
    • , Darryl Reeves
    •  & Christopher E. Mason

  • Article
    | Open Access

    Trichinellosis is a globally important food-borne disease caused by roundworms of the Trichinella complex. Here the authors present genomic sequences representing all 12 recognized Trichinellaspecies and genotypes, and reconstruct their phylogeny and biogeography.

    • Pasi K. Korhonen
    • , Edoardo Pozio
    •  & Robin B. Gasser

  • Article
    | Open Access

    The evolution of non-recombining chromosomes is poorly understood. Here, the authors sequence the collared flycatcher female-specific W chromosome and show nonrandom survival of genes during W chromosome degeneration which is due to selection for maintaining gene dose and expression levels of essential genes.

    • Linnéa Smeds
    • , Vera Warmuth
    •  & Hans Ellegren

  • Article |

    Chloroplasts originate from endosymbiosis between a cyanobacterium and a eukaryotic mitochondriate ancestor. Here, the authors show that the plastid ancestor is related to a cyanobacterial lineage that include N2-fixing filamentous cyanobacteria and species with specialized nitrogen-fixing cells.

    • Jesús A. G. Ochoa de Alda
    • , Rocío Esteban
    •  & Jean Houmard

  • Article
    | Open Access

    Genetic variation in Mycobacterium tuberculosiscomplex (MTBC) bacteria is responsible for differences in factors such as virulence and transmissibility. Here, the authors analyse the genomes of 1,601 MTBC isolates from diverse geographic locations and identify 62 SNPs that may be used to resolve lineages and sublineages of these strains.

    • Francesc Coll
    • , Ruth McNerney
    •  & Taane G. Clark

  • Article
    | Open Access

    Turnover of sediment organic matter contributes to global carbon cycling, yet the microorganisms involved are largely unknown. Castelleet al.reveal that an aquifer sediment core hosts a ‘zoo’ of organisms, including representatives of a previously undescribed phylum (Zixibacteria).

    • Cindy J. Castelle
    • , Laura A. Hug
    •  & Jillian F. Banfield

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