Evolutionary biology

  • Article
    | Open Access

    Here the authors sequence 16S rRNA and the more variable gyrase B protein-coding gene to profile the gut microbiome of captive great apes, which together with analysis of wild apes and humans, reveal a displacement of bacterial strains normally restricted to their wild conspecifics with those that are otherwise restricted to humans.

    • Alex H. Nishida
    •  & Howard Ochman
  • Article
    | Open Access

    Perilla is a young allotetraploid species within the mint family Lamiaceae. Here, the authors assemble the genomes of a tetraploid species and its diploid progenitor, characterize the incipient diploidization of the tetraploid, conduct population genetics analyses, and identify loci associate with pigmentation and oil content.

    • Yujun Zhang
    • , Qi Shen
    •  & Shilin Chen
  • Article
    | Open Access

    Historical interbreeding between Neanderthals and humans should leave signatures of historical demographics in modern human genomes. Analysing the size distribution of Neanderthal fragments in non-African genomes suggests consistent differences in the generation interval across Eurasia, and that this could explain mutational spectrum variation.

    • Moisès Coll Macià
    • , Laurits Skov
    •  & Mikkel Heide Schierup
  • Article
    | Open Access

    Intricate color patterns are a defining aspect of morphological diversity in the Felidae. Here the authors apply morphological and single-cell gene expression analysis to fetal skin of domestic cats to identify when, where, and how, during fetal development, felid color patterns are established.

    • Christopher B. Kaelin
    • , Kelly A. McGowan
    •  & Gregory S. Barsh
  • Article
    | Open Access

    Analyses of both natural and experimental evolution suggest that adaptation depends on the evolutionary past and adaptive potential decreases over time. Here, by tracking yeast adaptation with DNA barcoding, the authors show that such evolutionary phenomena can be observed even after a single adaptive step.

    • Dimitra Aggeli
    • , Yuping Li
    •  & Gavin Sherlock
  • Article
    | Open Access

    How ecological divergence causes reproductive isolation between populations in close contact remains poorly understood at the genomic level. This study presents a clinal investigation based on whole-genome sequencing to characterize reproductive isolation between threespine stickleback adapted to contiguous but ecologically different lake and stream habitats.

    • Quiterie Haenel
    • , Krista B. Oke
    •  & Daniel Berner
  • Article
    | Open Access

    The mutational effects of chemotherapies on healthy cells are unclear. Here, the authors show that the mutational signature of platinum-based drugs -but not 5-fluorouracil- is detectable in secondary acute myeloid leukemia, implying that the clonal expansion begins after the start of therapy.

    • Oriol Pich
    • , Albert Cortes-Bullich
    •  & Nuria Lopez-Bigas
  • Article
    | Open Access

    We lack a comprehensive understanding of how Neanderthal ancestry influences human traits. This study finds that regions with Neanderthal ancestry are broadly depleted of trait-associated variation; yet, introgressed variants likely contributed to human adaptation in a few traits, like skin color and immune response modulation.

    • Evonne McArthur
    • , David C. Rinker
    •  & John A. Capra
  • Article
    | Open Access

    Without understanding the genetic architecture of inbreeding depression, its effects are hard to pinpoint. Long-term data from wild Soay sheep shows that inbreeding manifests in long runs of homozygosity, which made up nearly half of the genome in the most inbred individuals with severe fitness consequences.

    • M. A. Stoffel
    • , S. E. Johnston
    •  & J. M. Pemberton
  • Article
    | Open Access

    Selection on alleles contributing to human evolution is not well understood. Here, the authors investigate positive selection on skin barrier adaptation, identifying a selective sweep on involucrin alleles associated with migration out of Africa, and confirming enhancer regulatory effects with functional assays.

    • Mary Elizabeth Mathyer
    • , Erin A. Brettmann
    •  & Cristina de Guzman Strong
  • Article
    | Open Access

    The genus Miscanthus has great potential for bio-energy production due to its high biomass yield and strong stress resistance. Here, the authors report the genome assembly of the diploid M. lutarioriparius, showing it has an allotetraploid origin and an expanded number of genes in families related to stress resistance.

    • Jiashun Miao
    • , Qi Feng
    •  & Bin Han
  • Article
    | Open Access

    The mutations underlying sexually selected traits like the red fins on a male medaka fish can be hard to pinpoint. Using a new genome, transcriptomics and gene editing, Ansai et al. find that the gene csf1 causes male fins to be red, which attracts females and, surprisingly, is less attractive to predators.

    • Satoshi Ansai
    • , Koji Mochida
    •  & Jun Kitano
  • Article
    | Open Access

    Koalas are susceptible to neoplasms, which are related to infection with the Koala retrovirus. Here, the authors use DNA sequencing to show that the retroviral insertion sites cluster near known cancer genes and demonstrate a high mutational load associated with the germline invasion of the virus.

    • Gayle K. McEwen
    • , David E. Alquezar-Planas
    •  & Alex D. Greenwood
  • Article
    | Open Access

    Hybrid zones are windows into the evolutionary process. Semenov et al. find that the head plumage differences between white wagtail subspecies have a simple genetic basis involving two small genetic regions, in which partially dominant and epistatic interactions help to explain how this sexual signal has become decoupled from other plumage traits.

    • Georgy A. Semenov
    • , Ethan Linck
    •  & Scott A. Taylor
  • Article
    | Open Access

    The genomic details of adaptation to extreme environments remain challenging to characterize. Using new methods to analyze flies experimentally evolved to survive extreme O2 conditions, the authors find a surprising level of synchronicity in selective sweeps, de novo mutations and adaptive recombination events.

    • Arya Iranmehr
    • , Tsering Stobdan
    •  & Gabriel G. Haddad
  • Article
    | Open Access

    Sequencing and mapping of long repetitive regions can be challenging due to technical difficulties in sequencing and assembly of the sequence data. Here authors report the complete sequences of subtelomeric homologous (SH) regions of the fission yeast Schizosaccharomyces pombe to reveal highly polymorphic and hot spots for genome variation features.

    • Yusuke Oizumi
    • , Takuto Kaji
    •  & Junko Kanoh
  • Article
    | Open Access

    Ancient, asexual lineages are rare as a lack of recombination is usually an evolutionary dead end. Here, authors compare complete genomes of 11 individual bdelloid rotifers that suggest evidence of regular genetic exchange between individuals in a species that was previously thought to be asexual.

    • Olga A. Vakhrusheva
    • , Elena A. Mnatsakanova
    •  & Alexey S. Kondrashov
  • Article
    | Open Access

    Leviviruses are phages with ssRNA genomes that encode a protein (Sgl) that induces host autolysis by interfering with bacterial cell wall synthesis. Identification of sgl genes is complicated by their small size and lack of sequence similarity. Here, Chamakura et al. use bioinformatic and experimental approaches to identify sgl genes in 244 leviviral genomes.

    • Karthik R. Chamakura
    • , Jennifer S. Tran
    •  & Ry Young
  • Article
    | Open Access

    Dioecy has evolved independently from hermaphroditic ancestors in different plant lineages. Here, the authors assemble Populus deltoides male and female genomes, and show the putative roles of a femaleness gene and a maleness gene in sex determination, which suggests independent evolution in different poplar species.

    • Liangjiao Xue
    • , Huaitong Wu
    •  & Tongming Yin
  • Article
    | Open Access

    Azaleas are one of the most diverse ornamental plants and have cultural and economic importance. Here, the authors report a chromosome-scale genome assembly for the primary ancestor of the azalea cultivar Rhododendro simsi and identify transcription factors that may function in flower coloration at different stages.

    • Fu-Sheng Yang
    • , Shuai Nie
    •  & Jian-Feng Mao
  • Article
    | Open Access

    Tibetan adaptation to the high-altitude environment represents a case of natural selection during recent human evolution. Here the authors investigated the chromatin and transcriptional landscape of umbilical endothelial cells from Tibetan and Han Chinese donors and provide genome-wide characterization of the hypoxia regulatory network associated high-altitude adaptation.

    • Jingxue Xin
    • , Hui Zhang
    •  & Bing Su
  • Article
    | Open Access

    Principal component analysis is often used in studies of ancient DNA, but does not account for the age of the samples. Here, the authors present a factor analysis (FA) which corrects for this by including the effect of allele frequency drift over time.

    • Olivier François
    •  & Flora Jay
  • Article
    | Open Access

    Amino acid propensities at sites change over evolutionary time, due to epistatically interacting sites or environmental changes. Here, the authors develop an approach to distinguish between these, and model the fitness dynamics of each, then annotate indicative sites in vertebrate and insect genomes.

    • A. V. Stolyarova
    • , E. Nabieva
    •  & G. A. Bazykin
  • Article
    | Open Access

    Bats are a likely reservoir of zoonotic coronaviruses (CoVs). Here, analyzing bat CoV sequences in China, the authors find that alpha-CoVs have switched hosts more frequently than betaCoVs, identify a bat family and genus that are highly involved in host-switching, and define hotspots of CoV evolutionary diversity.

    • Alice Latinne
    • , Ben Hu
    •  & Peter Daszak
  • Article
    | Open Access

    A fraction of mammalian CTCF binding sites fall within transposable elements (TEs) but their contribution to the evolution of 3D chromatin structure is unknown. Here the authors investigate the effect of TE-driven CTCF binding site expansions on chromatin looping in humans and mice, and provide evidence that TEs contribute to cell-specific and species-specific chromatin looping diversity and variable gene regulation in mammalian genomes.

    • Adam G. Diehl
    • , Ningxin Ouyang
    •  & Alan P. Boyle
  • Article
    | Open Access

    Local adaptation contributes to plant colonization across extreme environmental gradients. Here, the authors reconstruct the colonization history of Lotus japonicus in Japan and identify extreme genetic signatures of local adaptation to a cold climate using genome resequencing and common garden experiments.

    • Niraj Shah
    • , Tomomi Wakabayashi
    •  & Stig Uggerhøj Andersen
  • Article
    | Open Access

    Relatively little is known about the complexity of regulatory evolution accompanying polyploid crop domestication. Here, using reciprocal hybrids between wild and domesticated allotetraploid cotton lines, the authors catalog cis and trans regulatory variants and show their equivalent effects on cotton fiber domestication.

    • Ying Bao
    • , Guanjing Hu
    •  & Jonathan F. Wendel
  • Article
    | Open Access

    The Chloropicophyceae represent an important group of green algae in tropical oceans, but there is only limited genomic resource available. Here, the authors present the genome sequence of Chloropicon primus, revealing a diploid structure and the presence of a propionate detoxification pathway.

    • Claude Lemieux
    • , Monique Turmel
    •  & Jean-François Pombert
  • Article
    | Open Access

    Studying how genetic variants in different genes interact and their combinatorial output is experimentally and analytically challenging. Here, the authors quantify the effects of more than 5000 mutation pairs in the yeast GAL regulatory system, finding that many combinations can be predicted with statistical models.

    • Aaron M. New
    •  & Ben Lehner
  • Article
    | Open Access

    Sexual selection has the potential to either increase or decrease absolute fitness. Here, Cally et al. perform a meta-analysis of 65 experimental evolution studies and find that sexual selection on males tends to increase fitness, especially in females evolving under stressful conditions.

    • Justin G. Cally
    • , Devi Stuart-Fox
    •  & Luke Holman
  • Article
    | Open Access

    The Caucasus mountain range has impacted on the culture and genetics of the wider region. Here, the authors generate genome-wide SNP data for 45 Eneolithic and Bronze Age individuals across the Caucasus, and find distinct genetic clusters between mountain and steppe zones as well as occasional gene-flow.

    • Chuan-Chao Wang
    • , Sabine Reinhold
    •  & Wolfgang Haak
  • 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