Evolutionary genetics articles within Nature

Featured

  • Letter |

    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

  • Letter |

    A detailed analysis of fly wing phenotypes reveals a strong positive relationship between variation produced by mutation, standing genetic variation, and evolutionary rate over the past 40 million years.

    • David Houle
    • , Geir H. Bolstad
    •  & Thomas F. Hansen

  • Article |

    Parental care in mice evolves through multiple genetic changes; one candidate is vasopressin, the reduced expression of which promotes parental nest-building behaviour in monogamous mice.

    • Andres Bendesky
    • , Young-Mi Kwon
    •  & Hopi E. Hoekstra

  • Article
    | Open Access

    Genomic and molecular analyses of Clunio marinus timing strains suggest that modulation of alternative splicing of Ca2+/calmodulin-dependent kinase II represents a mechanism for evolutionary adaptation of circadian timing.

    • Tobias S. Kaiser
    • , Birgit Poehn
    •  & Kristin Tessmar-Raible

  • Letter |

    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

  • Article |

    Whole-genome sequencing of 264 clones sampled from 12 Escherichia coli populations evolved over 50,000 generations under identical culture conditions is used to characterize the patterns and dynamics of genome evolution over time.

    • Olivier Tenaillon
    • , Jeffrey E. Barrick
    •  & Richard E. Lenski

  • Letter |

    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

  • Letter |

    In a comparison between replicate sexual and asexual populations of Saccharomyces cerevisiae, sexual reproduction increases fitness by reducing clonal interference and alters the type of mutations that get fixed by natural selection.

    • Michael J. McDonald
    • , Daniel P. Rice
    •  & Michael M. Desai

  • Article |

    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

  • Article |

    The first genome-wide scan for selection using ancient DNA, based on data from 230 West Eurasians dating between to 6500 and 300 bc and including new data from 163 individuals among which are 26 Neolithic Anatolians, provides a direct view of selection on loci associated with diet, pigmentation and immunity.

    • Iain Mathieson
    • , Iosif Lazaridis
    •  & David Reich

  • Article |

    This study reports exome sequencing of samples from 538 individuals with chronic lymphocytic leukaemia (CLL), including 278 collected as part of a prospective clinical trial; recurrently mutated genes are identified and pathways involved in CLL are highlighted, as well as their evolution in progression and disease relapse.

    • Dan A. Landau
    • , Eugen Tausch
    •  & Catherine J. Wu

  • Letter |

    Experimentally transplanting guppies to evolve in a novel, predator-free environment reveals that the direction of plasticity in gene expression is usually opposite to the direction of adaptive evolution; that is, those genes whose expression changes are disadvantageous are more strongly selected upon than those whose changes are advantageous.

    • Cameron K. Ghalambor
    • , Kim L. Hoke
    •  & Kimberly A. Hughes

  • Letter |

    An analysis of 16 health-related quantitative traits in approximately 350,000 individuals reveals statistically significant associations between genome-wide homozygosity and four complex traits (height, lung function, cognitive ability and educational attainment); in each case increased homozygosity associates with a decreased trait value, but no evidence was seen of an influence on blood pressure, cholesterol, or ten other cardio-metabolic traits.

    • Peter K. Joshi
    • , Tonu Esko
    •  & James F. Wilson

  • Letter |

    Analysis of DNA from a 37,000–42,000-year-old modern human from Romania reveals that 6–9% of the genome is derived from Neanderthals, with the individual having a Neanderthal ancestor as recently as four to six generations back.

    • Qiaomei Fu
    • , Mateja Hajdinjak
    •  & Svante Pääbo

  • Letter |

    Quantifying activity of cis-regulatory sequences controlling gene expression shows that selection on expression noise has a greater impact on sequence variation than selection on mean expression level.

    • Brian P. H. Metzger
    • , David C. Yuan
    •  & Patricia J. Wittkopp

  • Article |

    Comprehensive genome sequencing of 120 individuals representing all of the Darwin’s finch species and two close relatives reveals important discrepancies with morphology-based taxonomy, widespread hybridization, and a gene, ALX1, underlying variation in beak shape.

    • Sangeet Lamichhaney
    • , Jonas Berglund
    •  & Leif Andersson

  • Letter |

    Documented cases of horizontal gene transfer from bacteria to eukaryotes are rare, but now, not only is a new class of transferred genes identified, the function of one representative is also demonstrated in its new setting, where it controls bacterial growth.

    • Seemay Chou
    • , Matthew D. Daugherty
    •  & Joseph D. Mougous

  • Article |

    The mosquito Aedes aegypti includes two subspecies, one of which shows a preference for biting humans, whereas the other prefers to bite non-human animals; genetic analysis reveals that changes in the mosquito odorant receptor Or4 contribute to the behavioural difference—in human-preferring mosquitoes, Or4 is more highly expressed and more sensitive to sulcatone, a compound present at high levels in human odour.

    • Carolyn S. McBride
    • , Felix Baier
    •  & Leslie B. Vosshall

  • Letter |

    A comparative analysis of bacterial growth and genetic phenotypes using hundreds of genome-scale metabolic models reveals a two-stage evolutionary process that consists of a rapid initial phenotypic diversification followed by a slow long-term divergence.

    • Germán Plata
    • , Christopher S. Henry
    •  & Dennis Vitkup

  • Article |

    The high-quality genome sequence of a 45,000-year-old modern human from Siberia reveals that gene flow from Neanderthals into the ancestors of this individual had already occurred about 7,000 to 13,000 years earlier; genomic comparisons show that he belonged to a population that lived close in time to the separation of populations in east and west Eurasia and that may represent an early modern human radiation out of Africa that has no direct descendants today.

    • Qiaomei Fu
    • , Heng Li
    •  & Svante Pääbo

  • Article |

    The monarch butterfly, well known for its spectacular annual migration across North America, is shown by genome sequencing of monarchs from around the world to have been ancestrally migratory and to have dispersed out of North America to occupy its current broad distribution; the authors also discovered signatures of selection associated with migration within loci implicated in flight muscle function, leading to greater flight efficiency.

    • Shuai Zhan
    • , Wei Zhang
    •  & Marcus R. Kronforst

  • Article
    | Open Access

    The genome of the gibbon, a tree-dwelling ape from Asia positioned between Old World monkeys and the great apes, is presented, providing insights into the evolutionary history of gibbon species and their accelerated karyotypes, as well as evidence for selection of genes such as those for forelimb development and connective tissue that may be important for locomotion through trees.

    • Lucia Carbone
    • , R. Alan Harris
    •  & Richard A. Gibbs

  • Letter
    | Open Access

    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

  • Article |

    Traits responsible for recent niche divergence between sympatric threespine stickleback species are subjected to forward genetic analysis; additive variation at several loci across the genome accounts for most of the genetic basis of ecological divergence, with a further role for epistatic interactions that disadvantage hybrids.

    • Matthew E. Arnegard
    • , Matthew D. McGee
    •  & Dolph Schluter

  • Article |

    A study comparing the Y chromosome across mammalian species reveals that selection to maintain the ancestral dosage of homologous X–Y gene pairs preserved a handful of genes on the Y chromosome while the rest were lost; the survival of broadly expressed dosage-sensitive regulators of gene expression suggest that the human Y chromosome is essential for male viability.

    • Daniel W. Bellott
    • , Jennifer F. Hughes
    •  & David C. Page

  • Letter |

    The phenomenon of sex-limited mimicry is phylogenetically widespread in the swallowtail butterfly genus Papilio — now, a single gene, doublesex, is shown to control supergene mimicry, a finding that is in contrast to the long-held view that supergenes are likely to be controlled by a tightly linked cluster of loci.

    • K. Kunte
    • , W. Zhang
    •  & M. R. Kronforst

  • Article |

    A computational approach for predicting the future evolution of the human influenza virus, based on population-genetic data of previous strains, is presented; this model holds promise for improving vaccine strain selection for seasonal influenza.

    • Marta Łuksza
    •  & Michael Lässig

  • Letter |

    In the modern human genome, elevated Neanderthal ancestry is found at genes affecting keratin filaments, suggesting that gene flow with Neanderthals helped modern humans to adapt to non-African environments; deficiencies of Neanderthal ancestry are also found, particularly on the X chromosome and in genes expressed highly in testes, suggesting that some Neanderthal mutations were not tolerated on a modern human genetic background as they reduced male fertility.

    • Sriram Sankararaman
    • , Swapan Mallick
    •  & David Reich

  • Letter |

    A complete pre-agricultural European human genome from a ∼7,000-year-old Mesolithic skeleton suggests the existence of a common genomic signature across western and central Eurasia from the Upper Paleolithic to the Mesolithic, and ancestral alleles in several skin pigmentation genes suggest that the light skin of modern Europeans was not yet ubiquitous in Mesolithic times.

    • Iñigo Olalde
    • , Morten E. Allentoft
    •  & Carles Lalueza-Fox

  • Article |

    Evolutionary study of long noncoding RNA (lncRNA) repertoires and expression patterns in 11 tetrapod species identifies approximately 11,000 primate-specific lncRNAs and 2,500 highly conserved lncRNAs, including approximately 400 genes that are likely to have ancient origins; many lncRNAs, particularly ancient ones, are actively regulated and may function mainly in embryonic development.

    • Anamaria Necsulea
    • , Magali Soumillon
    •  & Henrik Kaessmann

  • Article |

    A complete genome sequence is presented of a female Neanderthal from Siberia, providing information about interbreeding between close relatives and uncovering gene flow events among Neanderthals, Denisovans and early modern humans, as well as establishing substitutions that became fixed in modern humans after their separation from the ancestors of Neanderthals and Denisovans.

    • Kay Prüfer
    • , Fernando Racimo
    •  & Svante Pääbo

  • Letter |

    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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