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| Open AccessGlobal conservation status of the jawed vertebrate Tree of Life
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
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| Open AccessGlobal evaluation of lineage-specific human papillomavirus capsid antigenicity using antibodies elicited by natural infection
Human Papillomaviruses (HPV) are classified in lineages based on their sequence. Here, the authors test neutralizing activity of sera from naturally infected women against vaccine-preventable HPV variants, delineating lineage-specific antibody responses.
- Gathoni Kamuyu
- , Filomeno Coelho da Silva
- & Simon Beddows
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Article
| Open AccessTowards estimating the number of strains that make up a natural bacterial population
What a microbial strain is and how many strains make up a natural bacterial population remain elusive concepts. Here, Viver et al. analyse Salinibacter ruber isolates and metagenomes from two solar salterns, revealing gaps within the species sequence space that they use to define and quantify sub-species categories, such as genomovars and strains, that co-exist in a saltern pond.
- Tomeu Viver
- , Roth E. Conrad
- & Ramon Rossello-Mora
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| Open AccessVESPA: an optimized protocol for accurate metabarcoding-based characterization of vertebrate eukaryotic endosymbiont and parasite assemblages
DNA sequencing methods for characterizing microbial communities are well developed for bacteria, archaea and fungi, but less so for eukaryotic parasites and commensals. Here, the authors present an optimized and validated metabarcoding protocol for host-associated eukaryotic communities.
- Leah A. Owens
- , Sagan Friant
- & Tony L. Goldberg
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| Open AccessDental morphology in Homo habilis and its implications for the evolution of early Homo
The origin of the genus Homo is debated. Here, the authors investigate the morphology of the H. habilis enamel-dentine junction using a sample of 911 hominin and extant ape teeth, finding that H. habilis has more in common with Australopithecus than later members of the genus Homo.
- Thomas W. Davies
- , Philipp Gunz
- & Matthew M. Skinner
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Matters Arising
| Open AccessReply to: Revisiting the identification of Syllipsimopodi bideni and timing of the decabrachian-octobrachian divergence
- Christopher D. Whalen
- & Neil H. Landman
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Matters Arising
| Open AccessRevisiting the identification of Syllipsimopodi bideni and timing of the decabrachian-octobrachian divergence
- Christian Klug
- , Kevin Stevens
- & Dirk Fuchs
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| Open AccessBony-fish-like scales in a Silurian maxillate placoderm
The origin and early evolution of large scales in bony fishes and small scales in cartilaginous fishes are unclear. Here, the authors report a 425-million-year-old fish, Entelognathus, with a mosaic of scale and fin spine characters.
- Xindong Cui
- , Matt Friedman
- & Min Zhu
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Article
| Open AccessFunctional divergence of CYP76AKs shapes the chemodiversity of abietane-type diterpenoids in genus Salvia
Functional divergence of CYP76AK subfamily, accompanied by oxidation variations at C-20, leads to diverse abietane-type diterpenoids in Salvia species. Enzyme activity loss contributes to this unique chemical diversity within the lineage.
- Jiadong Hu
- , Shi Qiu
- & Wansheng Chen
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Article
| Open AccessCellular differentiation into hyphae and spores in halophilic archaea
Bacteria of the genus Streptomyces have complex life cycles involving cellular differentiation and multicellular structures that have never been observed in archaea. Here, the authors show that several halophilic archaea display a life cycle resembling that of Streptomyces bacteria, undergoing cellular differentiation into mycelia and spores.
- Shu-Kun Tang
- , Xiao-Yang Zhi
- & Ping Xu
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Article
| Open AccessMolecular exploration of fossil eggshell uncovers hidden lineage of giant extinct bird
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
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| Open AccessEvolutionary origins of the prolonged extant squamate radiation
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
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| Open AccessOrdovician opabiniid-like animals and the role of the proboscis in euarthropod head evolution
Here, the authors describe two opabiniid-like euarthropods with anterior proboscises from the Middle Ordovician Castle Bank Biota, Wales, UK. Phylogenetic analysis suggests that these specimens may be sister to radiodonts and deuteropods.
- Stephen Pates
- , Joseph P. Botting
- & Joanna M. Wolfe
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| Open AccessRecovery of Lutacidiplasmatales archaeal order genomes suggests convergent evolution in Thermoplasmatota
Genome recovery of the order Lutacidiplasmatales reveals that key genes for environmental specialisation were acquired multiple times in the Thermoplasmatota phylum, suggesting a crucial role of convergent evolution in archaeal habitat adaptation.
- Paul O. Sheridan
- , Yiyu Meng
- & Cécile Gubry-Rangin
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| Open AccessGenomic diversity across the Rickettsia and ‘Candidatus Megaira’ genera and proposal of genus status for the Torix group
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
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| Open AccessFossil coleoid cephalopod from the Mississippian Bear Gulch Lagerstätte sheds light on early vampyropod evolution
The authors describe a new cephalopod from the Carboniferous (Mississippian) Bear Gulch Lagerstätte of Montana, USA. This specimen extends the fossil record of vampyropods back by ~82 million years and changes our understanding of their evolution.
- Christopher D. Whalen
- & Neil H. Landman
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Article
| Open AccessA supergene underlies linked variation in color and morphology in a Holarctic songbird
Trait genetic architecture influences how populations evolve and adapt. Genomic analysis finds that an inversion links genetic variation controlling redpoll finch color and bill shape, allowing the maintenance of latitudinal ecotypes despite a genome largely homogenized by gene flow.
- Erik R. Funk
- , Nicholas A. Mason
- & Scott A. Taylor
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| Open AccessCretaceous bird with dinosaur skull sheds light on avian cranial evolution
In addition to major innovations in their locomotor system, early birds evolved highly derived skulls. Here, Wang et al. three dimensionally reconstruct the skull of a new enantiornithine bird from the Early Cretaceous that illustrates the early avialan transitions in skull morphology and function.
- Min Wang
- , Thomas A. Stidham
- & Zhonghe Zhou
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Article
| Open AccessBrockarchaeota, a novel archaeal phylum with unique and versatile carbon cycling pathways
Geothermal environments are hotspots for carbon cycling. Here, De Anda et al. reconstruct archaeal genomes from terrestrial and deep-sea geothermal sediments, and propose the classification of these microbes as a new phylum, ‘Brockarchaeota’, with unique metabolic capabilities including non-methanogenic anaerobic methylotrophy.
- Valerie De Anda
- , Lin-Xing Chen
- & Brett J. Baker
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| Open AccessDiel niche variation in mammals associated with expanded trait space
Most mammals are nocturnal, but a new analysis suggests that although most groups of species active at a particular time of day or night occupy different ecological niches, a surprisingly large proportion of species are more flexible in the timing of their activity than previously thought.
- D. T. C. Cox
- , A. S. Gardner
- & K. J. Gaston
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| Open AccessNested whole-genome duplications coincide with diversification and high morphological disparity in Brassicaceae
As one of the most successful angiosperm clades with ~4000 species, the mustard family has been diversifying into many evolutionary lineages. Here, the authors construct plastid-based phylogeny and show nested whole-genome duplications coincide with diversification and high morphological disparity.
- Nora Walden
- , Dmitry A. German
- & Marcus A. Koch
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| Open AccessAn encrusting kleptoparasite-host interaction from the early Cambrian
Parasitic interactions are difficult to document in the fossil record. Here, Zhang et al. analyze a large population of a Cambrian brachiopod and show it was frequently encrusted by tubes aligned to its feeding currents and that encrustation was associated with reduced biomass, suggesting a fitness cost.
- Zhifei Zhang
- , Luke C. Strotz
- & Glenn A. Brock
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Matters Arising
| Open AccessRe-evaluating the phylogenetic position of the enigmatic early Cambrian deuterostome Yanjiahella
- Samuel Zamora
- , David F. Wright
- & Imran A. Rahman
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Matters Arising
| Open AccessReply to ‘Re-evaluating the phylogenetic position of the enigmatic early Cambrian deuterostome Yanjiahella’
- Timothy P. Topper
- , Junfeng Guo
- & Zhifei Zhang
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Article
| Open AccessNew insects feeding on dinosaur feathers in mid-Cretaceous amber
Numerous feathered dinosaurs and early birds have been discovered from the Jurassic and Cretaceous, but the early evolution of feather-feeding insects is not clear. Here, Gao et al. describe a new family of ectoparasitic insects from 10 specimens found associated with feathers in mid-Cretaceous amber.
- Taiping Gao
- , Xiangchu Yin
- & Dong Ren
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Article
| Open AccessUnexpected species diversity in electric eels with a description of the strongest living bioelectricity generator
A single species of electric eel, Electrophorus electricus, has been described. Here, de Santana et al. show that there are three major lineages of Electrophorus distributed across Greater Amazonia and describe two new species, one with a much stronger electric discharge than was previously known.
- C. David de Santana
- , William G. R. Crampton
- & Wolmar B. Wosiacki
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| Open AccessNew Eocene primate from Myanmar shares dental characters with African Eocene crown anthropoids
Recent fossil findings have suggested that anthropoid primates originated in Asia before dispersing into Africa. Here, Jaeger and colleagues describe a new fossil Asian primate, Aseanpithecus myanmarensis, that they interpret as a closer relative of African crown anthropoids.
- Jean-Jacques Jaeger
- , Olivier Chavasseau
- & Yaowalak Chaimanee
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| Open AccessTYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy
Information on type material is of fundamental importance in prokaryote taxonomy. Here, the authors develop TYGS, the Type (Strain) Genome Server, for genome-based prokaryote taxonomy and analysis using a comprehensive database of genomic and taxonomic data.
- Jan P. Meier-Kolthoff
- & Markus Göker
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| Open AccessResolution of the ordinal phylogeny of mosses using targeted exons from organellar and nuclear genomes
Mosses are a highly diverse lineage of land plants. Here, the authors provide a detailed phylogeny of 29 orders of moss, using nuclear and organelle data to provide robust hypotheses for most of the ordinal moss relationships.
- Yang Liu
- , Matthew G. Johnson
- & Bernard Goffinet
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| Open AccessA stem group echinoderm from the basal Cambrian of China and the origins of Ambulacraria
The early evolution of the deuterostomes is not well resolved. Here, Topper and colleagues investigate the early Cambrian metazoan Yanjiahella biscarpa, concluding that it is a stem echinoderm, is among the oldest known deuterstomes, and supports an ancestral enteropneust body plan in hemichordates.
- Timothy P. Topper
- , Junfeng Guo
- & Zhifei Zhang
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| Open AccessAn Early Cretaceous enantiornithine (Aves) preserving an unlaid egg and probable medullary bone
The fossil record of the reproductive traits of early birds is limited. Here, Bailleul and colleagues describe the Cretaceous enantiornithine bird Avimaia schweitzerae, which preserves an unlaid egg in the abdominal cavity and putative medullary bone.
- Alida M. Bailleul
- , Jingmai O’Connor
- & Zhonghe Zhou
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| Open AccessLife habits and evolutionary biology of new two-winged long-proboscid scorpionflies from mid-Cretaceous Myanmar amber
Long-proboscid scorpionflies were associated with mid-Mesozoic gymnosperm pollination. Here, Lin et al. establish a new family of long-proboscid scorpionflies from Myanmar amber, elucidate evolutionary mechanisms of hind-wing reduction, and detail feeding and reproductive habits of these insects.
- Xiaodan Lin
- , Conrad C. Labandeira
- & Dong Ren
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| Open AccessDiverse Cretaceous larvae reveal the evolutionary and behavioural history of antlions and lacewings
Larvae of the Myrmeleontiformia, which include antlions, are not well preserved in much of the fossil record. Here, Badano et al. describe a collection of predatory myrmeleontiform larvae from Cretaceous amber, resolving their evolutionary relationships and inferring their ecology.
- Davide Badano
- , Michael S. Engel
- & Pierfilippo Cerretti
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| Open AccessUnifying the global phylogeny and environmental distribution of ammonia-oxidising archaea based on amoA genes
Ammonia-oxidising archaea (AOA) were only discovered a little over a decade ago and remain poorly characterized despite their ubiquity and importance for nitrogen cycling. Here, the authors define a taxonomy of AOA based on a resolved amoA phylogeny and describe emergent global patterns in AOA diversity.
- Ricardo J. Eloy Alves
- , Bui Quang Minh
- & Christa Schleper
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| Open AccessEarly Cambrian fuxianhuiids from China reveal origin of the gnathobasic protopodite in euarthropods
The fuxianhuiids were a group of primitive true arthropods living in the Cambrian period. Here, Yang and colleagues describe a new species of fuxianhuiid, Alacaris mirabilis, from exceptionally-preserved specimens that illustrate the early evolution of specialized arthropod mouthparts.
- Jie Yang
- , Javier Ortega-Hernández
- & Xi-guang Zhang
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| Open AccessA bony-crested Jurassic dinosaur with evidence of iridescent plumage highlights complexity in early paravian evolution
A number of paravian dinosaurs have been described from the Jurassic Yanliao biota, but these have tended to be morphologically similar to Archaeopteryx. Here, Hu. describe the new paravian dinosaur, Caihong juji gen. et sp. nov., which possesses a suite of unusual skeletal and feather characteristics.
- Dongyu Hu
- , Julia A. Clarke
- & Xing Xu
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| Open AccessA Paleocene penguin from New Zealand substantiates multiple origins of gigantism in fossil Sphenisciformes
The oldest known penguin fossils date to approximately 62 million years ago. Here, Mayr et al. describe Kumimanu biceae, an extinct penguin from approximately 55–60 million years ago, which represents an independent origin of giant size soon after the evolutionary transition from flight to diving.
- Gerald Mayr
- , R. Paul Scofield
- & Alan J. D. Tennyson
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| Open AccessA mitogenomic timetree for Darwin’s enigmatic South American mammal Macrauchenia patachonica
Classification of the extinct South American native ungulates (SANUs) has posed a challenge given the absence of close, surviving relatives. Here, Westburyet al. sequence the mitochondrial genome of the extinct SANU Macrauchenia patachonicaand reconstruct the evolutionary history of the lineage.
- Michael Westbury
- , Sina Baleka
- & Michael Hofreiter
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| Open AccessA bizarre Early Cretaceous enantiornithine bird with unique crural feathers and an ornithuromorph plough-shaped pygostyle
Although now extinct, Enantiornithes was the most diverse group of birds in the Mesozoic. Here, Wang and colleagues describe a new species of enantiornithine bird from 131 million years ago with features that suggest extensive diversification had occurred in the enantiornithines by this time.
- Min Wang
- , Jingmai K O’Connor
- & Zhonghe Zhou
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| Open AccessBaleen whales host a unique gut microbiome with similarities to both carnivores and herbivores
Diet is a major factor determining the composition of gut microbiota in mammals, while host evolutionary history seems to play an unclear role. Here, Sanderset al. show that baleen whales, which prey on animals, harbour a unique gut microbiome with similarities to those of terrestrial herbivores.
- Jon G. Sanders
- , Annabel C. Beichman
- & Peter R. Girguis
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| Open AccessAnalysis of intestinal microbiota in hybrid house mice reveals evolutionary divergence in a vertebrate hologenome
Animal hosts and their associated microbes are largely the outcome of coevolution. Here, the authors show differences in the intestinal microbiome of hybrids compared with pure species of house mice, which suggests that host–microbiome interactions contribute to the evolution of host species.
- Jun Wang
- , Shirin Kalyan
- & John F. Baines
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PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes
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