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| Open AccessRedefining the treponemal history through pre-Columbian genomes from Brazil
Reconstruction of four Treponema pallidum genomes associated with human remains from around 2,000 years ago suggests that T. pallidum existed in the Americas and diverged to its modern subspecies before the fifteenth century European contact with the Americas.
- Kerttu Majander
- , Marta Pla-Díaz
- & Verena J. Schuenemann
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Article |
A weakly structured stem for human origins in Africa
An analysis of models of human populations in Africa, using some newly sequenced genomes, finds that human origins in the continent can best be described by a weakly structured stem model.
- Aaron P. Ragsdale
- , Timothy D. Weaver
- & Simon Gravel
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Article
| Open AccessEvolution of the germline mutation rate across vertebrates
Using sequencing and comparing high-coverage genomes, the germline mutation rates across vertebrates are quantified.
- Lucie A. Bergeron
- , Søren Besenbacher
- & Guojie Zhang
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Article
| Open AccessGenetic insights into the social organization of Neanderthals
Genetic data for 13 Neanderthals from 2 Middle Palaeolithic sites in the Altai Mountains of southern Siberia presented provide insights into the social organization of an isolated Neanderthal community at the easternmost extent of their known range.
- Laurits Skov
- , Stéphane Peyrégne
- & Benjamin M. Peter
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Article |
Dairying, diseases and the evolution of lactase persistence in Europe
Examination of archaeological pottery residues and modern genes suggest that environmental conditions, subsistence economics and pathogen exposure may explain selection for lactase persistence better than prehistoric consumption of milk.
- Richard P. Evershed
- , George Davey Smith
- & Mark G. Thomas
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Article
| Open AccessPleistocene sediment DNA reveals hominin and faunal turnovers at Denisova Cave
Ancient mitochondrial DNA from sediments reveals the sequence of Denisovan, Neanderthal and faunal occupation of Denisova Cave, and evidence for the appearance of modern humans at least 45,000 years ago.
- Elena I. Zavala
- , Zenobia Jacobs
- & Matthias Meyer
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Article
| Open AccessInitial Upper Palaeolithic humans in Europe had recent Neanderthal ancestry
Genome-wide data for the three oldest known modern human remains in Europe, dated to around 45,000 years ago, shed light on early human migrations in Europe and suggest that mixing with Neanderthals was more common than is often assumed.
- Mateja Hajdinjak
- , Fabrizio Mafessoni
- & Svante Pääbo
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Article
| Open AccessGiant lungfish genome elucidates the conquest of land by vertebrates
A chromosome-quality genome of the lungfish Neoceratodus fosteri sheds light on the development of obligate air-breathing and the gain of limb-like gene expression in lobed fins, providing insights into the water-to-land transition in vertebrate evolution.
- Axel Meyer
- , Siegfried Schloissnig
- & Manfred Schartl
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Article |
Innovations present in the primate interneuron repertoire
Single-nucleus RNA-sequencing analyses of brain from humans, macaques, marmosets, mice and ferrets reveal diverse ways that interneuron populations have changed during evolution.
- Fenna M. Krienen
- , Melissa Goldman
- & Steven A. McCarroll
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Article
| Open AccessSix reference-quality genomes reveal evolution of bat adaptations
Reference-quality genomes for six bat species shed light on the phylogenetic position of Chiroptera, and provide insight into the genetic underpinnings of the unique adaptations of this clade.
- David Jebb
- , Zixia Huang
- & Emma C. Teeling
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Article |
Dynamic RNA acetylation revealed by quantitative cross-evolutionary mapping
A method termed ac4C-seq is introduced for the transcriptome-wide mapping of the RNA modification N4-acetylcytidine, revealing widespread temperature-dependent acetylation that facilitates thermoadaptation in hyperthermophilic archaea.
- Aldema Sas-Chen
- , Justin M. Thomas
- & Schraga Schwartz
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Article |
A positively selected FBN1 missense variant reduces height in Peruvian individuals
In an ethnically diverse group of Peruvian individuals, the population-specific, missense variant in FBN1 (E1297G) is associated with lower height and shows evidence of positive selection within the Peruvian population.
- Samira Asgari
- , Yang Luo
- & Soumya Raychaudhuri
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Article |
The dental proteome of Homo antecessor
Analyses of the proteomes of dental enamel from Homo antecessor and Homo erectus demonstrate that the Early Pleistocene H. antecessor is a close sister lineage of later Homo sapiens, Neanderthal and Denisovan populations in Eurasia.
- Frido Welker
- , Jazmín Ramos-Madrigal
- & Enrico Cappellini
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The strength and pattern of natural selection on gene expression in rice
Phenotypic selection analysis is used to estimate the type and strength of selection that acts on more than 15,000 transcripts in rice (Oryza sativa), which provides insight into the adaptive evolutionary role of selection on gene expression.
- Simon C. Groen
- , Irina Ćalić
- & Michael D. Purugganan
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Article |
A sensory appendage protein protects malaria vectors from pyrethroids
The leg-enriched sensory appendage protein, SAP2, confers pyrethroid resistance to Anopheles gambiae, through high-affinity binding of pyrethroid insecticides; an observed selective sweep in field mosquitoes mirrors the increasing resistance reported in Africa.
- Victoria A. Ingham
- , Amalia Anthousi
- & Hilary Ranson
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Article |
Frequent mutations that converge on the NFKBIZ pathway in ulcerative colitis
In patients with ulcerative colitis, chronic inflammation can lead to remodelling of the colorectal epithelium through positive selection of clones with mutations in genes related to IL-17 signalling, which, however, might be negatively selected during colitis-associated carcinogenesis.
- Nobuyuki Kakiuchi
- , Kenichi Yoshida
- & Seishi Ogawa
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Letter |
Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny
Palaeoproteomic analysis of dental enamel from an Early Pleistocene Stephanorhinus resolves the phylogeny of Eurasian Rhinocerotidae, by enabling the reconstruction of molecular evolution beyond the limits of ancient DNA preservation.
- Enrico Cappellini
- , Frido Welker
- & Eske Willerslev
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Letter |
Non-photosynthetic predators are sister to red algae
Species of the eukaryotic phylum Rhodelphidia are non-photosynthetic, flagellate predators with gene-rich genomes, in contrast to their closely related sister lineage—the red algae—which are immotile, typically photoautotrophic and have relatively small intron-poor genomes and reduced metabolism.
- Ryan M. R. Gawryluk
- , Denis V. Tikhonenkov
- & Patrick J. Keeling
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Letter |
Pluripotency and the origin of animal multicellularity
Comparison of transcriptomes, cell fates and behaviour of three primary cell types from the sponge Amphimedon queenslandica with choanoflagellates and other unicellular holozoans suggests that the first animal cells transitioned between multiple states.
- Shunsuke Sogabe
- , William L. Hatleberg
- & Bernard M. Degnan
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Transposon molecular domestication and the evolution of the RAG recombinase
Identification of the changes that converted a transposase to a recombinase sheds light on the evolution of the vertebrate adaptive immune system.
- Yuhang Zhang
- , Tat Cheung Cheng
- & David G. Schatz
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Letter |
Age estimates for hominin fossils and the onset of the Upper Palaeolithic at Denisova Cave
Bayesian modelling of chronometric, stratigraphic and genetic data from Denisova Cave provides a chronological framework for understanding Neanderthal and Denisovan presence at the site, as well as interactions between these groups.
- Katerina Douka
- , Viviane Slon
- & Tom Higham
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Article |
Age-related remodelling of oesophageal epithelia by mutated cancer drivers
In physiologically normal epithelia, age-related expansion of clones that carry mutations in NOTCH1 and other driver genes is accelerated by risk factors for developing oesophageal squamous cell carcinoma, such as alcohol consumption or smoking.
- Akira Yokoyama
- , Nobuyuki Kakiuchi
- & Seishi Ogawa
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Letter |
Pairwise and higher-order genetic interactions during the evolution of a tRNA
Mutagenesis of a yeast tRNA shows that the effects of mutations and how they interact varies both in magnitude and sign between genotypes.
- Júlia Domingo
- , Guillaume Diss
- & Ben Lehner
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Letter |
Reconstructing the genetic history of late Neanderthals
Genetic similarity among late Neanderthals is predicted well by their geographical location, and although some of these Neanderthals were contemporaneous with early modern humans, their genomes show no evidence of recent gene flow from modern humans.
- Mateja Hajdinjak
- , Qiaomei Fu
- & Janet Kelso
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Review Article |
The evolution of Ebola virus: Insights from the 2013–2016 epidemic
A comprehensive review of how analysis of genome sequences provided insights into the origins, evolution and spread of Ebola virus during the 2013–2016 epidemic in West Africa.
- Edward C. Holmes
- , Gytis Dudas
- & Kristian G. Andersen
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Letter |
Genomic insights into the peopling of the Southwest Pacific
Analysis of ancient DNA from four individuals who lived in Vanuatu and Tonga between 2,300 and 3,100 years ago suggests that the Papuan ancestry seen in present-day occupants of this region was introduced at a later date.
- Pontus Skoglund
- , Cosimo Posth
- & David Reich
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Letter |
Genomic analyses inform on migration events during the peopling of Eurasia
Whole-genome sequencing of individuals from 125 populations provides insight into patterns of genetic diversity, natural selection and human demographic history during the peopling of Eurasia and finds evidence for genetic vestiges of an early expansion of modern humans out of Africa in Papuans.
- Luca Pagani
- , Daniel John Lawson
- & Mait Metspalu
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Letter |
Cloche is a bHLH-PAS transcription factor that drives haemato-vascular specification
The zebrafish cloche gene is required for the formation of most endothelial and haematopoietic cells, however, it has been difficult to isolate; this study reveals that cloche encodes a PAS-domain-containing bHLH transcription factor, and a mammalian orthologue can partially rescue cloche mutants, indicating a possible conserved role in mammals.
- Sven Reischauer
- , Oliver A. Stone
- & Didier Y. R. Stainier
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Letter |
The gene cortex controls mimicry and crypsis in butterflies and moths
Wing colour patterning of multiple species in the butterfly genus Heliconius is controlled by differential expression of the gene cortex, a member of a conserved family of cell cycle regulators.
- Nicola J. Nadeau
- , Carolina Pardo-Diaz
- & Chris D. Jiggins
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Article |
The genetic history of Ice Age Europe
Analysis of ancient genomic data of 51 humans from Eurasia dating from 45,000 to 7,000 years ago provides insight into the population history of pre-Neolithic Europe and support for recurring migration and population turnover in Europe during this period.
- Qiaomei Fu
- , Cosimo Posth
- & David Reich
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Letter |
Nuclear DNA sequences from the Middle Pleistocene Sima de los Huesos hominins
Nuclear DNA sequences from Middle Pleistocene Sima de los Huesos hominins show they were more closely related to Neanderthals than to Denisovans, and indicate a population divergence between Neanderthals and Denisovans that predates 430,000 years ago.
- Matthias Meyer
- , Juan-Luis Arsuaga
- & Svante Pääbo
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Article |
Ancient gene flow from early modern humans into Eastern Neanderthals
It is known that there was gene flow from Neanderthals to modern humans around 50,000 years ago; now, analysis of a Neanderthal genome from the Altai Mountains in Siberia reveals evidence of gene flow 100,000 years ago in the other direction—from early modern humans to Neanderthals.
- Martin Kuhlwilm
- , Ilan Gronau
- & Sergi Castellano
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Letter |
Polygenic evolution of a sugar specialization trade-off in yeast
An evolutionary trade-off of unprecedented genetic complexity in the glucose/galactose utilization regulatory pathway across several long-diverged species of Saccharomyces.
- Jeremy I. Roop
- , Kyu Chul Chang
- & Rachel B. Brem
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Article |
Re-engineering the zinc fingers of PRDM9 reverses hybrid sterility in mice
PRDM9 is a DNA-binding protein that controls the position of double-strand breaks in meiosis, and the gene that encodes it is responsible for hybrid infertility between closely related mouse species; this hybrid infertility is eliminated by introducing the zinc-finger domain sequence from the human version of the PRDM9 gene, a change which alters both the position of double-strand breaks and the symmetry of PRDM9 binding and suggests that PRDM9 may have a more general but transient role in the early stages of speciation.
- Benjamin Davies
- , Edouard Hatton
- & Peter Donnelly
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Letter |
Sex reversal triggers the rapid transition from genetic to temperature-dependent sex
The first report of reptile sex reversal in the wild and rapid transition between genetic and environmental sex determination in the Australian bearded dragon (Pogona vitticeps)
- Clare E. Holleley
- , Denis O'Meally
- & Arthur Georges
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Letter |
Polyploidy can drive rapid adaptation in yeast
In vitro evolution experiments on haploid, diploid, and tetraploid yeast strains show that adaptation is faster in tetraploids, providing direct quantitative evidence that in some environments polyploidy can accelerate evolutionary adaptation.
- Anna M. Selmecki
- , Yosef E. Maruvka
- & David Pellman
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Article
| Open AccessConservation of trans-acting circuitry during mammalian regulatory evolution
Mouse genomic footprinting reveals conservation of transcription factor (TF) recognition repertoires and trans-regulatory circuitry despite massive turnover of DNA elements that contact TFs in vivo.
- Andrew B. Stergachis
- , Shane Neph
- & John A. Stamatoyannopoulos
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Letter |
Calcisponges have a ParaHox gene and dynamic expression of dispersed NK homeobox genes
A study of the genomes of calcisponges shows that they contain at least one ParaHox gene, adding weight to the ‘ghost locus’ hypothesis that Hox and ParaHox genes were present in the earliest animal ancestor, but subsequently lost in some sponge lineages.
- Sofia A. V. Fortunato
- , Marcin Adamski
- & Maja Adamska
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Letter |
An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons
The authors show that two primate-specific genes encoding KRAB domain containing zinc finger proteins, ZNF91 and ZNF93, have evolved during the last 25 million years to repress retrotransposon families that emerged during this time period; according to the new data KZNF gene expansion limits the activity of newly emerged retrotransposons, which subsequently mutate to evade repression.
- Frank M. J. Jacobs
- , David Greenberg
- & David Haussler
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Article
| Open AccessThe genomic substrate for adaptive radiation in African cichlid fish
Genomes and transcriptomes of five distinct lineages of African cichlids, a textbook example of adaptive radiation, have been sequenced and analysed to reveal that many types of molecular changes contributed to rapid evolution, and that standing variation accumulated during periods of relaxed selection may have primed subsequent diversification.
- David Brawand
- , Catherine E. Wagner
- & Federica Di Palma
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Letter
| Open AccessComparative analysis of regulatory information and circuits across distant species
A map of genome-wide binding locations of 165 human, 93 worm and 52 fly transcription-regulatory factors (almost 50% presented for the first time) from diverse cell types, developmental stages, or conditions reveals that gene-regulatory properties previously observed for individual factors may be general principles of metazoan regulation that are well preserved.
- Alan P. Boyle
- , Carlos L. Araya
- & Michael Snyder
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Letter |
Climate change selects for heterozygosity in a declining fur seal population
Three decades of data on Antarctic fur seals show that reduced prey availability due to climate change leads to selection for increased heterozygosity in breeding females.
- Jaume Forcada
- & Joseph Ivan Hoffman
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Letter |
Horizontal genome transfer as an asexual path to the formation of new species
The formation of a new species can occur by an asexual mechanism by transfer of entire nuclear genomes between plant cells as shown by the creation of a new allopolyploid plant from parental herbaceous and woody plant species, this mechanism is a potential new tool for crop improvement.
- Ignacia Fuentes
- , Sandra Stegemann
- & Ralph Bock
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Article |
Genome-defence small RNAs exapted for epigenetic mating-type inheritance
The molecular basis for mating-type determination in the ciliate Paramecium has been elucidated, revealing a novel function for a class of small RNAs — these scnRNAs are typically involved in reprogramming the Paramecium genome during sexual reproduction by recognizing and excising transposable elements, but they are now found to be co-opted to switch off expression of the newly identified mating-type gene mtA by excising its promoter, and to mediate epigenetic inheritance of mating types across sexual generations.
- Deepankar Pratap Singh
- , Baptiste Saudemont
- & Eric Meyer
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Letter |
Mitoflash frequency in early adulthood predicts lifespan in Caenorhabditis elegans
In Caenorhabditis elegans, mitochondrial activity as measured by the frequency of the mitochondrial flash in young adult animals is a powerful predictor of lifespan across genetic, environmental and stochastic factors.
- En-Zhi Shen
- , Chun-Qing Song
- & Meng-Qiu Dong
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Letter |
A mitochondrial genome sequence of a hominin from Sima de los Huesos
A full mitochondrial genome from a 400,000-year-old Middle Pleistocene hominin from Spain unexpectedly reveals a close relationship to Denisovans, a sister group to the Neanderthals, raising interesting questions about the origins of Neanderthals and Denisovans.
- Matthias Meyer
- , Qiaomei Fu
- & Svante Pääbo
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Letter |
Differential L1 regulation in pluripotent stem cells of humans and apes
Induced pluripotent stem-cell characterization reveals phenotypical differences between humans and non-human primates (NHPs): gene expression analysis shows differences in the regulation of long interspersed element-1 (L1) transposons, and in the expression of L1-restricting genes APOBEC3B and PIWIL2, correlating with higher L1 mobility in NHPs; this indicates that L1 mobility differences may have differentially shaped the human and NHP genomes.
- Maria C. N. Marchetto
- , Iñigo Narvaiza
- & Fred H. Gage
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Letter |
Life history trade-offs at a single locus maintain sexually selected genetic variation
Wild Soay sheep rams with large horns have more offspring, yet there is considerable genetic variation at RXFP2, a locus strongly implicated in horn size (with different alleles conferring either large or small horns); this study finds that although the larger horn allele leads to more offspring, the smaller horn allele leads to increased survival, meaning heterozygous rams (which develop medium-sized horns) have high reproductive success and survival, providing a rare example of heterozygote advantage.
- Susan E. Johnston
- , Jacob Gratten
- & Jon Slate
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Letter
| Open AccessGenomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga
The genome of the asexual rotifer Adineta vaga lacks homologous chromosomes; instead, its allelic regions are rearranged and sometimes found on the same chromosome in a palindromic fashion, a structure reminiscent of the primate Y chromosome and of other mitotic lineages such as cancer cells.
- Jean-François Flot
- , Boris Hespeels
- & Karine Van Doninck