Evolutionary biology articles within Nature Communications

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  • Article
    | Open Access

    Turnovers in sex determination systems occur quite frequently, yet the evolutionary drivers of these turnovers are not well understood. Here, the authors study the sex determination systems in sticklebacks and propose chromosomal inversions as a possible driver of the evolution of sex determination.

    • Heini M. Natri
    • , Juha Merilä
    •  & Takahito Shikano

  • Article
    | Open Access

    The origin of Tibetan barley (qingke) has been a controversial issue for many years. Here, the authors conduct population genomics study to support that qingke is derived from eastern domesticated barley instead of Tibetan wild barley and suggest southern Tibetan Plateau as its introduction route.

    • Xingquan Zeng
    • , Yu Guo
    •  & Nyima Tashi

  • Article
    | Open Access

    Drought is a major factor limiting crop productivity. Here, via eQTL analysis and comparative genomics, the authors show compensatory evolution between trans-regulatory loci and transcription factor binding sites that shape the drought response networks in the model C4 grass Panicum hallii.

    • John T. Lovell
    • , Jerry Jenkins
    •  & Thomas E. Juenger

  • Article
    | Open Access

    Staphylococcus epidermidis is carried asymptomatically by virtually all humans but is also a major cause of nosocomial infection. Here, the authors study 141 isolates from healthy carriage and 274 isolates from clinical infections, and identify genes and genetic elements associated with pathogenicity.

    • Guillaume Méric
    • , Leonardos Mageiros
    •  & Samuel K. Sheppard

  • Article
    | Open Access

    Pyrenestes finches have a bill size polymorphism thought to be maintained by disruptive selection. Here, the authors identify a single candidate region, including insulin-like growth factor 1, differentiating small and large bill size morphs and a wider region differentiating the mega-billed morph.

    • Bridgett M. vonHoldt
    • , Rebecca Y. Kartzinel
    •  & Thomas B. Smith

  • Article
    | Open Access

    Humans increasingly depend on seafood for nutrition, but nutrient content is unknown for the vast majority of fish species. Here, the authors use phylogenetic analyses and data imputation to predict the nutrient content of fish that are under-studied but that could be of future dietary importance.

    • Bapu Vaitla
    • , David Collar
    •  & Christopher D. Golden

  • Article
    | Open Access

    De novo DNA methylation during mouse oogenesis occurs within transcribed regions. Here the authors investigate the role of species-specific long terminal repeats (LTRs)-initiated transcription units in regulating the oocyte methylome, identifying syntenic regions in mouse, rat and human with divergent DNA methylation associated with private LITs.

    • Julie Brind’Amour
    • , Hisato Kobayashi
    •  & Matthew C. Lorincz

  • Article
    | Open Access

    During ‘meiotic drive’, some chromosomes can bias their spindle orientation and thus be retained in the egg. Here, the authors find that this phenomenon can be driven by microtubule force asymmetry on chromosomes with differently sized centromeres and kinetochores.

    • Tianyu Wu
    • , Simon I. R. Lane
    •  & Keith T. Jones

  • Article
    | Open Access

    Dominance is difficult to measure in natural populations as it is confounded with fitness. Here, Huber et al. developed a new approach to co-estimate dominance and selection coefficients, and found that the observed relationship is best fit by a new model of dominance based on gene expression level.

    • Christian D. Huber
    • , Arun Durvasula
    •  & Kirk E. Lohmueller

  • Article
    | Open Access

    Ancient diapsids diverged into the lineages leading to turtles and birds over 250 million years ago. Here, the authors use genomic and molecular cytogenetic analyses of modern species to infer the genome structure of the diapsid common ancestor (DCA) and the changes occurring along the lineage to birds through theropod dinosaurs.

    • Rebecca E. O’Connor
    • , Michael N. Romanov
    •  & Darren K. Griffin

  • Article
    | Open Access

    Supergenes result from beneficial linkage and recombination suppression between two or more genes. Giraud and colleagues use whole genome sequencing data to show convergent evolution of supergenes on mating-type chromosomes in multiple closely-related fungal lineages.

    • Sara Branco
    • , Fantin Carpentier
    •  & Tatiana Giraud

  • Article
    | Open Access

    The genetic code for amino acids is nearly universal, and among eukaryotic nuclear genomes the only known reassignments are of codon CUG in yeasts. Here, the authors identify a third independent CUG transition in budding yeasts that is still ongoing with alternative tRNAs present in the genome.

    • Tadeusz Krassowski
    • , Aisling Y. Coughlan
    •  & Kenneth H. Wolfe

  • Article
    | Open Access

    Recent natural selection left signals in human genomes. Here, Okada et al. generate high-depth whole-genome sequence (WGS) data (25.9×) from 2,234 Japanese people of the BioBank Japan Project (BBJ), and identify signals of recent natural selection which overlap variants associated with human traits.

    • Yukinori Okada
    • , Yukihide Momozawa
    •  & Yoichiro Kamatani

  • Article
    | Open Access

    The American cockroach (Periplaneta americana) is an hemimetabolous insect with rapid growth, high fecundity, and remarkable tissue-regeneration capability. Here Li et al sequence its 3.38-Gb genome and perform the functional studies, yielding insights into its environmental adaptation and developmental plasticity.

    • Sheng Li
    • , Shiming Zhu
    •  & Shuai Zhan

  • Article
    | Open Access

    The population history of Europe is complex and its very north has not yet been comprehensively studied at a genetic level. Here, Mittnik et al. report genome-wide data from 38 ancient individuals from the Eastern Baltic, Russia and Scandinavia to analyse gene flow throughout the Mesolithic and Bronze Age.

    • Alissa Mittnik
    • , Chuan-Chao Wang
    •  & Johannes Krause

  • Article
    | Open Access

    Wolbachia causes cytoplasmic incompatibility (CI) between mosquitoes infected with different strains, but the genetic basis of observed CI diversity is unknown. Here, Bonneau et al. sequence Wolbachia from over 100 Culex pipiens lines and show that crossing types match variations of the toxin-antitoxin cidA-cidB genes.

    • Manon Bonneau
    • , Celestine Atyame
    •  & Mylène Weill

  • Article
    | Open Access

    In a subset of patients with chronic lymphocytic leukemia (CLL) treated with targeted agents, such as ibrutinib, drug resistant subclones emerge. Here, the authors report on transcriptional changes in CLL patients treated with ibrutinib and identify early clonal shifts associated with evolution of resistant clones.

    • Dan A. Landau
    • , Clare Sun
    •  & Catherine J. Wu

  • Article
    | Open Access

    African populations show a high level of genetic diversity and extensive regional admixture. Here, the authors sequence the whole genomes of 24 South African individuals of different ethnolinguistic origin and find substantive genomic divergence between two southeastern Bantu-speaking groups.

    • Ananyo Choudhury
    • , Michèle Ramsay
    •  & Michael S. Pepper

  • Article
    | Open Access

    The fertilization of an egg by more than one sperm is typically lethal. Here, via a novel reporter assay, Nakel et al. report the generation of triparental triploid Arabidopsis plants, implying that polyspermy is a plausible route toward polyploidy during plant evolution.

    • Thomas Nakel
    • , Dawit G. Tekleyohans
    •  & Rita Groß-Hardt

  • Article
    | Open Access

    Asexual reproduction is thought to be an evolutionary dead end in eukaryotes because deleterious mutations will not be purged effectively. Here, Brandt and colleagues show that anciently asexual oribatid mites in fact have reduced accumulation of deleterious mutations compared to their sexual relatives.

    • Alexander Brandt
    • , Ina Schaefer
    •  & Jens Bast

  • Article
    | Open Access

    Why genetic variants that confer risk for psychiatric disorders persist in the genome is an evolutionary conundrum. Here, Mullinset al. report association of polygenic risk for autism with having fewer children and polygenic risk for ADHD with higher reproductive fitness.

    • Niamh Mullins
    • , Andrés Ingason
    •  & Kari Stefansson

  • Article
    | Open Access

    A First Nation population declined after European contact, likely as a result of infectious disease. Here, researchers partner with indigenous communities to analyse ancient and modern Native American exomes, and find a shift in selection pressure on immune genes, correlated to European-borne epidemics.

    • John Lindo
    • , Emilia Huerta-Sánchez
    •  & Ripan S. Malhi

  • Article
    | Open Access

    Tarsiers occupy a key node between strepsirrhines and anthropoids in the primate phylogeny. Here, Warren and colleagues present the genome of Tarsius syrichta, including a survey of transposable elements, an unusual mitochondrial insertion, and evidence for positive gene selection.

    • Jürgen Schmitz
    • , Angela Noll
    •  & Wesley C. Warren

  • Article
    | Open Access

    The evolution of germ cell specification by maternal germ plasm has been proposed to accelerate vertebrate protein evolution by liberating selective constraints. Whittle and Extavour analyse global rates of protein evolution and find no support for this hypothesis in vertebrates or invertebrates.

    • Carrie A. Whittle
    •  & Cassandra G. Extavour

  • Article
    | Open Access

    A fundamental question in evolutionary biology is how complex innovations requiring multiple genetic changes arise. Here the authors provide lines of evidence that changing environments facilitate the adaptive evolution of complex metabolic innovations via stepwise acquisition of single reactions.

    • Balázs Szappanos
    • , Jonathan Fritzemeier
    •  & Balázs Papp

  • Article
    | Open Access

    The bulbus arteriosus is an organ unique to the heart of teleosts, composed of specialized smooth muscle. Here, the authors show that the gene elastin b, which regulates cell fate of cardiac precursor cells into smooth muscle, evolved after whole-genome duplication and neofunctionalization in teleosts.

    • Yuuta Moriyama
    • , Fumihiro Ito
    •  & Kazuko Koshiba-Takeuchi

  • Article
    | Open Access

    Papillary renal cell carcinoma (pRCC) is a subtype of kidney cancer characterized by highly variable clinical behaviour. Here the authors sequence either the genomes or exomes of 31 pRCCs and identify several genes in sub-clones and large copy number variants in major clones that may be important drivers of pRCC.

    • Michal Kovac
    • , Carolina Navas
    •  & Ian Tomlinson

  • Article
    | Open Access

    The evolution of genetic dominance in polymorphic traits remains poorly understood. Here, the authors show that distinct dominance mechanisms have evolved in association with supergene inversions controlling wing pattern in Heliconiusbutterflies, in response to strong selection favouring mimicry.

    • Yann Le Poul
    • , Annabel Whibley
    •  & Mathieu Joron

  • Article |

    The accumulation of genetic and epigenetic mutations in cancer cells can drive malignant growth. Here, the authors model the evolution of intratumoral diversity and examine the classification of driver and passenger mutations, heterogeneity within tumours, and the dynamics of tumour response to targeted therapies.

    • R. A. Gatenby
    • , J. J. Cunningham
    •  & J. S. Brown

  • Article
    | Open Access

    The jujube is a major dry fruit crop in China and is commonly used for medicinal purposes. Here the authors sequence the genome and transcriptome of the most widely cultivated jujube cultivar, Dongzao, and highlight the genetic and molecular basis of agronomically important jujube traits, such as vitamin C content.

    • Meng-Jun Liu
    • , Jin Zhao
    •  & Long-Hai Luo

  • Article |

    Genes of the major histocompatibility complex (MHC) are crucial for immune response, yet it is unclear what shapes their diversity at a community level. Here, the authors show that indirect effects among rodent hosts and their helminth parasites can play a crucial role in shaping host MHC diversity.

    • Shai Pilosof
    • , Miguel A. Fortuna
    •  & Jordi Bascompte

  • Article
    | Open Access

    The mechanisms underlying the emergence of novel morphological traits are largely unknown. Here, the authors show that cis-regulatory changes controlling the expression of the fhl2bpigmentation gene are associated with the evolution of egg-spots colour markings in the male fins of a group of cichlids.

    • M. Emília Santos
    • , Ingo Braasch
    •  & Walter Salzburger

  • Article
    | Open Access

    The Antarctic midge, Belgica antarctica, is the only insect endemic to Antarctica. Here, the authors sequence the B. antarcticagenome, the smallest insect genome yet reported, and suggest that genes involved in development, metabolism and stimuli response may have had a role in how this insect adapted to survive in such a harsh environment.

    • Joanna L. Kelley
    • , Justin T. Peyton
    •  & David L. Denlinger

  • Article
    | Open Access

    The Asian liver fluke is a parasitic worm that is linked to an increased risk of malignant cancer. Here, the authors sequence the draft genome and transcriptome of this fluke and provide insight into how the species has adapted to be able to survive in the bile duct.

    • Neil D. Young
    • , Niranjan Nagarajan
    •  & Robin B. Gasser

  • Article |

    Overexpression of a drug’s molecular target increases drug resistance in some cases. Here the authors show that overexpressing antibiotic targets in Escherichia colican cause positive and negative changes in drug resistance, depending on whether the drug induces harmful reactions involving its target.

    • Adam C. Palmer
    •  & Roy Kishony

  • Article |

    Males and females show unique patterns of gene expression, but it is unclear if this dimorphism is genetically constrained. Here, Hollis et al. use experimental evolution in Drosophila melanogasterto reveal unresolved conflict between the sexes over gene expression caused by sexual selection.

    • Brian Hollis
    • , David Houle
    •  & Laurent Keller

  • Article |

    The impact of horizontal gene transfer (HGT) on the evolution of higher eukaryotes is not fully understood. Here the authors suggest that the vertebrate vasodilator, adrenomedullin (ADM), was horizontally acquired by ticks and hypothesize that the HGT of ADM triggers the emergence of a new tick genus.

    • Shiroh Iwanaga
    • , Haruhiko Isawa
    •  & Masao Yuda

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