Evolution

  • Article
    | Open Access

    XACT is a primate-specific TE-derived lncRNA that coats active X chromosomes in pluripotent cells and may contribute to species-specific regulation of X chromosome inactivation. Here, the authors investigate TEs associated with the XACT locus and identify a critical enhancer for its regulation, which evolved from an ancestral group of mammalian endogenous retroviruses, prior to the emergence of XACT.

    • Miguel Casanova
    • , Madeleine Moscatelli
    • , Louis Édouard Chauvière
    • , Christophe Huret
    • , Julia Samson
    • , Tharvesh Moideen Liyakat Ali
    • , Olga Rosspopoff
    •  & Claire Rougeulle
  • Article
    | Open Access

    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
    • , Chungkun Shih
    • , Alexandr P. Rasnitsyn
    • , Xing Xu
    • , Sha Chen
    • , Chen Wang
    •  & Dong Ren
  • Article
    | Open Access

    Relapse, reinfection and recrudescence can all cause recurrent infection after treatment of Plasmodium vivax malaria in endemic areas, but are difficult to distinguish. Here the authors show that they can be differentiated probabilistically and thereby demonstrate the high efficacy of primaquine treatment in preventing relapse.

    • Aimee R. Taylor
    • , James A. Watson
    • , Cindy S. Chu
    • , Kanokpich Puaprasert
    • , Jureeporn Duanguppama
    • , Nicholas P. J. Day
    • , Francois Nosten
    • , Daniel E. Neafsey
    • , Caroline O. Buckee
    • , Mallika Imwong
    •  & Nicholas J. White
  • Article
    | Open Access

    Photosynthesis generates reactive oxygen species that can damage cells. Here, the authors show that unicellular predators of photosynthetic prey have shared responses to photosynthetic oxidative stress and these may also have been important for the evolution of endosymbiosis.

    • Akihiro Uzuka
    • , Yusuke Kobayashi
    • , Ryo Onuma
    • , Shunsuke Hirooka
    • , Yu Kanesaki
    • , Hirofumi Yoshikawa
    • , Takayuki Fujiwara
    •  & Shin-ya Miyagishima
  • Article
    | Open Access

    The cerebellum is critical in sensory-motor control and is structurally diverse across vertebrates. Here, the authors investigate the evolutionary relationship between locomotory mode and cerebellum architecture across squamates by integrating study of gene expression, cell distribution, and 3D morphology.

    • Simone Macrì
    • , Yoland Savriama
    • , Imran Khan
    •  & Nicolas Di-Poï
  • Article
    | Open Access

    Siblings of those with autism spectrum disorder (ASD) have increased likelihood of ASD or related subclinical traits. Here, studying 253 ASD families, D’Abate et al. test the predictive value of genomic copy number variation involving ASD-associated loci, with confirmation in a second cohort.

    • L. D’Abate
    • , S. Walker
    • , R. K. C. Yuen
    • , K. Tammimies
    • , J. A. Buchanan
    • , R. W. Davies
    • , B. Thiruvahindrapuram
    • , J. Wei
    • , J. Brian
    • , S. E. Bryson
    • , K. Dobkins
    • , J. Howe
    • , R. Landa
    • , J. Leef
    • , D. Messinger
    • , S. Ozonoff
    • , I. M. Smith
    • , W. L. Stone
    • , Z. E. Warren
    • , G. Young
    • , L. Zwaigenbaum
    •  & S. W. Scherer
  • Article
    | Open Access

    Recent studies have suggested that hybridization can facilitate adaptive radiations. Here, the authors show that opportunity for hybridization differentiates Lake Mweru, where cichlids radiated, and Lake Bangweulu, where cichlids did not radiate despite ecological opportunity in both lakes.

    • Joana I. Meier
    • , Rike B. Stelkens
    • , Domino A. Joyce
    • , Salome Mwaiko
    • , Numel Phiri
    • , Ulrich K. Schliewen
    • , Oliver M. Selz
    • , Catherine E. Wagner
    • , Cyprian Katongo
    •  & Ole Seehausen
  • Article
    | Open Access

    The authors build a reference phylogeny of 10,575 evenly-sampled bacterial and archaeal genomes, based on 381 markers. The results indicate a remarkably closer evolutionary proximity between Archaea and Bacteria than previous estimates that used fewer “core” genes, such as the ribosomal proteins.

    • Qiyun Zhu
    • , Uyen Mai
    • , Wayne Pfeiffer
    • , Stefan Janssen
    • , Francesco Asnicar
    • , Jon G. Sanders
    • , Pedro Belda-Ferre
    • , Gabriel A. Al-Ghalith
    • , Evguenia Kopylova
    • , Daniel McDonald
    • , Tomasz Kosciolek
    • , John B. Yin
    • , Shi Huang
    • , Nimaichand Salam
    • , Jian-Yu Jiao
    • , Zijun Wu
    • , Zhenjiang Z. Xu
    • , Kalen Cantrell
    • , Yimeng Yang
    • , Erfan Sayyari
    • , Maryam Rabiee
    • , James T. Morton
    • , Sheila Podell
    • , Dan Knights
    • , Wen-Jun Li
    • , Curtis Huttenhower
    • , Nicola Segata
    • , Larry Smarr
    • , Siavash Mirarab
    •  & Rob Knight
  • Article
    | Open Access

    Viral genomic DNA is often modified to evade the host bacterial restriction system. Here the authors identified 2′-deoxy-7-deazaguanine modifications on phage DNA by comparative genomics and experimental validation, showing their role in genome protection.

    • Geoffrey Hutinet
    • , Witold Kot
    • , Liang Cui
    • , Roman Hillebrand
    • , Seetharamsingh Balamkundu
    • , Shanmugavel Gnanakalai
    • , Ramesh Neelakandan
    • , Alexander B. Carstens
    • , Chuan Fa Lui
    • , Denise Tremblay
    • , Deborah Jacobs-Sera
    • , Mandana Sassanfar
    • , Yan-Jiun Lee
    • , Peter Weigele
    • , Sylvain Moineau
    • , Graham F. Hatfull
    • , Peter C. Dedon
    • , Lars H. Hansen
    •  & Valérie de Crécy-Lagard
  • Article
    | Open Access

    Songbirds have extensive germline–soma genome differences due to developmental elimination of a germline-specific chromosome (GRC). Here, the authors show that the GRC contains dozens of expressed developmental genes, some of which have been on the GRC since the ancestor of all songbirds.

    • Cormac M. Kinsella
    • , Francisco J. Ruiz-Ruano
    • , Anne-Marie Dion-Côté
    • , Alexander J. Charles
    • , Toni I. Gossmann
    • , Josefa Cabrero
    • , Dennis Kappei
    • , Nicola Hemmings
    • , Mirre J. P. Simons
    • , Juan Pedro M. Camacho
    • , Wolfgang Forstmeier
    •  & Alexander Suh
  • Article
    | Open Access

    The neural tissues of coleoids have a greater fraction of nonsynonymous sites than synonymous sites subject to high levels of A-to-I RNA editing, a pattern thought to indicate widespread adaptive editing. Here the authors propose and provide evidence for an alternative, nonadaptive explanation.

    • Daohan Jiang
    •  & Jianzhi Zhang
  • 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
    • , Corrinne E. Grover
    • , Justin Conover
    • , Daojun Yuan
    •  & Jonathan F. Wendel
  • Article
    | Open Access

    Structural variants may be omitted in sequence analysis despite their importance in genome variation and phenotypic impact. Here the authors present GraphTyper2, which uses pangenome graphs to genotype structural variants using short-reads and can be applied in large-scale sequencing studies.

    • Hannes P. Eggertsson
    • , Snaedis Kristmundsdottir
    • , Doruk Beyter
    • , Hakon Jonsson
    • , Astros Skuladottir
    • , Marteinn T. Hardarson
    • , Daniel F. Gudbjartsson
    • , Kari Stefansson
    • , Bjarni V. Halldorsson
    •  & Pall Melsted
  • Article
    | Open Access

    A significant proportion of the molecular evolution of bacteria and archaea occurs through gene gain and loss. Here Iranzo et al. develop a mathematical model that explains observed differential patterns of sequence evolution vs. gene content evolution as a consequence of homologous recombination.

    • Jaime Iranzo
    • , Yuri I. Wolf
    • , Eugene V. Koonin
    •  & Itamar Sela
  • Article
    | Open Access

    The role of Africa in the global spread of highly pathogenic avian influenza (HPAI) is not well understood. Here, using evolutionary analyses, the authors show that Africa mainly acts as ecological sink for HPAI H5, and reveal varying paths of HPAI incursions either through domestic or wild birds.

    • Alice Fusaro
    • , Bianca Zecchin
    • , Bram Vrancken
    • , Celia Abolnik
    • , Rose Ademun
    • , Abdou Alassane
    • , Abdelsatar Arafa
    • , Joseph Adongo Awuni
    • , Emmanuel Couacy-Hymann
    • , M.’ Bétiégué Coulibaly
    • , Nicolas Gaidet
    • , Emilie Go-Maro
    • , Tony Joannis
    • , Simon Dickmu Jumbo
    • , Germaine Minoungou
    • , Clement Meseko
    • , Maman Moutari Souley
    • , Deo Birungi Ndumu
    • , Ismaila Shittu
    • , Augustin Twabela
    • , Abel Wade
    • , Lidewij Wiersma
    • , Yao P. Akpeli
    • , Gianpiero Zamperin
    • , Adelaide Milani
    • , Philippe Lemey
    •  & Isabella Monne
  • Article
    | Open Access

    Whether Australia’s Pleistocene megafauna extinctions were caused by climate change, humans, or both is debated. Here, the authors infer the spatio-temporal trajectories of regional extinctions and find that water availability mediates the relationship among climate, human migration and megafauna extinctions.

    • Frédérik Saltré
    • , Joël Chadoeuf
    • , Katharina J. Peters
    • , Matthew C. McDowell
    • , Tobias Friedrich
    • , Axel Timmermann
    • , Sean Ulm
    •  & Corey J. A. Bradshaw
  • Article
    | Open Access

    The nematode Halicephalobus mephisto has been found more than 1 km underground and can tolerate high heat and low oxygen. Here Weinstein et al. report the genome and transcriptome of H. mephisto and identify genomic innovations that likely are responsible for its tolerance to heat.

    • Deborah J. Weinstein
    • , Sarah E. Allen
    • , Maggie C. Y. Lau
    • , Mariana Erasmus
    • , Kathryn C. Asalone
    • , Kathryn Walters-Conte
    • , Gintaras Deikus
    • , Robert Sebra
    • , Gaetan Borgonie
    • , Esta van Heerden
    • , Tullis C. Onstott
    •  & John R. Bracht
  • Article
    | Open Access

    Whole genome sequencing (WGS) holds promise to solve a subset of Mendelian disease cases for which exome sequencing did not provide a genetic diagnosis. Here, Wells et al. report a supervised machine learning model trained on functional, mutational and structural features for rank-scoring and interpreting variants in non-coding regions from WGS.

    • Alex Wells
    • , David Heckerman
    • , Ali Torkamani
    • , Li Yin
    • , Jonathan Sebat
    • , Bing Ren
    • , Amalio Telenti
    •  & Julia di Iulio
  • Article
    | Open Access

    Exceptional alpine plant diversity exists in the Hengduan Mountains. Here, through genome assembly and population genomics studies, the authors find notable intraspecific divergence among Cushion willow populations isolated by the sky island-like habitats and consider it contributes to speciation and biodiversity.

    • Jia-hui Chen
    • , Yuan Huang
    • , Benjamin Brachi
    • , Quan-zheng Yun
    • , Wei Zhang
    • , Wei Lu
    • , Hong-na Li
    • , Wen-qing Li
    • , Xu-dong Sun
    • , Guang-yan Wang
    • , Jun He
    • , Zhuo Zhou
    • , Kai-yun Chen
    • , Yun-heng Ji
    • , Ming-ming Shi
    • , Wen-guang Sun
    • , Yong-ping Yang
    • , Ren-gang Zhang
    • , Richard J. Abbott
    •  & Hang Sun
  • Article
    | Open Access

    Whole genome duplication (WGD) presents new challenges to the establishment of optimal allelic combinations and to the meiotic machinery. Here, the authors show that adaptive gene flow from Arabidopsis arenosa could rescue the nascent A. lyrata from extinction following WGD.

    • Sarah Marburger
    • , Patrick Monnahan
    • , Paul J. Seear
    • , Simon H. Martin
    • , Jordan Koch
    • , Pirita Paajanen
    • , Magdalena Bohutínská
    • , James D. Higgins
    • , Roswitha Schmickl
    •  & Levi Yant
  • Article
    | Open Access

    Cucurbits fruits have diverse shapes and sizes, but their genomes evolution and genetic basis of diversity are unclear. Here, the authors show that the wax gourd genome has the most ancestral karyotype among cucurbits and identify candidate genes which contribute to large fruit size by comparative and population genomics analyses.

    • Dasen Xie
    • , Yuanchao Xu
    • , Jinpeng Wang
    • , Wenrui Liu
    • , Qian Zhou
    • , Shaobo Luo
    • , Wu Huang
    • , Xiaoming He
    • , Qing Li
    • , Qingwu Peng
    • , Xueyong Yang
    • , Jiaqing Yuan
    • , Jigao Yu
    • , Xiyin Wang
    • , William J. Lucas
    • , Sanwen Huang
    • , Biao Jiang
    •  & Zhonghua Zhang
  • Article
    | Open Access

    The ‘parliament of genes’ hypothesis suggests that selfish genetic elements will be counteracted by suppressors that maintain equal transmission of the rest of the genome. Here, the authors find support for this hypothesis using mathematical models to explore a range of different scenarios.

    • Thomas W. Scott
    •  & Stuart A. West
  • Article
    | Open Access

    The clonal origins of metastases and the timing of dissemination remains an open question for most cancer types. Using primary and metastatic samples taken from one colorectal cancer patient, Alves et al. use Bayesian phylogenetics to reconstruct the history of metastasis.

    • Joao M. Alves
    • , Sonia Prado-López
    • , José Manuel Cameselle-Teijeiro
    •  & David Posada
  • Article
    | Open Access

    Models of mate choice have mainly focused on the implications of female mate choice for reproductive isolation. Here, Aubier et al. develop a population genetic model of coevolution between female and male mate choice, which can lead the population to oscillate between assortative and random mating.

    • Thomas G. Aubier
    • , Hanna Kokko
    •  & Mathieu Joron
  • Article
    | Open Access

    The spatial structure of a population is often critical for the evolution of cooperation. Here, Allen and colleagues show that when spatial structure is represented by an isothermal graph, the effective number of neighbors per individual determines whether or not cooperation can evolve.

    • Benjamin Allen
    • , Gabor Lippner
    •  & Martin A. Nowak
  • Article
    | Open Access

    The proximal femur is key for understanding locomotion in primates. Here, the authors analyze the evolution of the proximal femur in catarrhines, including a new Aegyptopithecus fossil, and suggest that Old World monkeys and hominoids diverged from an ancestral state similar to Aegyptopithecus.

    • Sergio Almécija
    • , Melissa Tallman
    • , Hesham M. Sallam
    • , John G. Fleagle
    • , Ashley S. Hammond
    •  & Erik R. Seiffert
  • Article
    | Open Access

    Various approaches are being used for polygenic prediction including Bayesian multiple regression methods that require access to individual-level genotype data. Here, the authors extend BayesR to utilise GWAS summary statistics (SBayesR) and show that it outperforms other summary statistic-based methods.

    • Luke R. Lloyd-Jones
    • , Jian Zeng
    • , Julia Sidorenko
    • , Loïc Yengo
    • , Gerhard Moser
    • , Kathryn E. Kemper
    • , Huanwei Wang
    • , Zhili Zheng
    • , Reedik Magi
    • , Tõnu Esko
    • , Andres Metspalu
    • , Naomi R. Wray
    • , Michael E. Goddard
    • , Jian Yang
    •  & Peter M. Visscher
  • Article
    | Open Access

    How epigenetics coordinate with genetics to impact protein fitness is unknown. Here, using a Variation Spatial Profiling strategy and machine learning, the authors map HDAC impact on a full set of Niemann pick C1 disease variants to quantitate an unanticipated plasticity in central dogma.

    • Chao Wang
    • , Samantha M. Scott
    • , Kanagaraj Subramanian
    • , Salvatore Loguercio
    • , Pei Zhao
    • , Darren M. Hutt
    • , Nicole Y. Farhat
    • , Forbes D. Porter
    •  & William E. Balch
  • Article
    | Open Access

    Quorum sensing (QS) regulates production of ‘public goods’ by Pseudomonas aeruginosa, which releases toxic hydrogen cyanide to constrain QS-deficient cheaters. Here, Yan et al. show that QS-proficient strains protect themselves by producing a cyanide-insensitive enzyme in response to reactive oxygen species released by cheaters.

    • Huicong Yan
    • , Kyle L. Asfahl
    • , Na Li
    • , Feng Sun
    • , Junwei Xiao
    • , Dongsheng Shen
    • , Ajai A. Dandekar
    •  & Meizhen Wang
  • Article
    | Open Access

    Modern humans and Neanderthals coexisted in the Levant for tens of thousands of years before modern humans spread and replaced Neanderthals. Here, Greenbaum et al. develop a model showing that transmission of disease and genes can explain the maintenance and then collapse of this contact zone.

    • Gili Greenbaum
    • , Wayne M. Getz
    • , Noah A. Rosenberg
    • , Marcus W. Feldman
    • , Erella Hovers
    •  & Oren Kolodny
  • Article
    | Open Access

    Vertebrate telencephalon formation requires Foxg-Fgf8 cross-regulation, but while ascidians express Foxg in the neural plate, they lack a telencephalon. Here the authors show that Foxg loss does not affect ascidian brain formation, indicating that telencephalon evolution required recruitment of Fgf downstream of Foxg.

    • Boqi Liu
    •  & Yutaka Satou
  • Article
    | Open Access

    Hypoxia occurs at high altitude and in cancer. Here, the authors show that a gene involved in hypoxia, YTHDF1, underwent rapid evolution in Tibetans and their domestic animals, and find that the gene is amplified in some cancers and contributes to drug resistance in hypoxic conditions.

    • Yulin Shi
    • , Songqing Fan
    • , Mengge Wu
    • , Zhixiang Zuo
    • , Xingyang Li
    • , Liping Jiang
    • , Qiushuo Shen
    • , Peifang Xu
    • , Lin Zeng
    • , Yongchun Zhou
    • , Yunchao Huang
    • , Zuozhang Yang
    • , Jumin Zhou
    • , Jing Gao
    • , Hu Zhou
    • , Shuhua Xu
    • , Hongbin Ji
    • , Peng Shi
    • , Dong-Dong Wu
    • , Cuiping Yang
    •  & Yongbin Chen
  • Article
    | Open Access

    Rare genetic disorders (RGDs) often exhibit significant clinical variability among affected individuals. Here, Oetjens et al. systematically study the contribution of common genetic variation to variable expressivity of RGDs and find it is frequently influenced by polygenic factors identified in genome-wide association studies of relevant traits.

    • M. T. Oetjens
    • , M. A. Kelly
    • , A. C. Sturm
    • , C. L. Martin
    •  & D. H. Ledbetter
  • Article
    | Open Access

    Several cortical association areas have rapidly expanded in size during human evolution, including elements of the central cognitive default mode network (DMN). Here, the authors show that genes highly divergent between humans and other primates (HAR genes) are particularly expressed in these brain regions.

    • Yongbin Wei
    • , Siemon C. de Lange
    • , Lianne H. Scholtens
    • , Kyoko Watanabe
    • , Dirk Jan Ardesch
    • , Philip R. Jansen
    • , Jeanne E. Savage
    • , Longchuan Li
    • , Todd M. Preuss
    • , James K. Rilling
    • , Danielle Posthuma
    •  & Martijn P. van den Heuvel
  • Article
    | Open Access

    Widely distributed red algae have experienced massive genome reduction during evolution. Here, using an improved genome assembly of Porphyridium purpureum, Lee et al. show the role of endosymbiotic gene transfer in plastid evolution and the correlation between phycobilisome linker diversification and the red algal radiation.

    • JunMo Lee
    • , Dongseok Kim
    • , Debashish Bhattacharya
    •  & Hwan Su Yoon
  • Article
    | Open Access

    Based on single worm whole genome sequencing, the authors here characterise the global evolution of the gastrointestinal parasite Haemonchus contortus and identify genes that play a role in drug resistance as well as climate-driven adaptations involving an epigenetic regulator.

    • G. Sallé
    • , S. R. Doyle
    • , J. Cortet
    • , J. Cabaret
    • , M. Berriman
    • , N. Holroyd
    •  & J. A. Cotton
  • Article
    | Open Access

    Pumas are experiencing increased isolation as human persecution and habitat loss fragment the populations of this once widespread species. Here, the authors estimate the genomic consequences of this isolation by analyzing the genomes of ten pumas from across North and South America.

    • Nedda F. Saremi
    • , Megan A. Supple
    • , Ashley Byrne
    • , James A. Cahill
    • , Luiz Lehmann Coutinho
    • , Love Dalén
    • , Henrique V. Figueiró
    • , Warren E. Johnson
    • , Heather J. Milne
    • , Stephen J. O’Brien
    • , Brendan O’Connell
    • , David P. Onorato
    • , Seth P. D. Riley
    • , Jeff A. Sikich
    • , Daniel R. Stahler
    • , Priscilla Marqui Schmidt Villela
    • , Christopher Vollmers
    • , Robert K. Wayne
    • , Eduardo Eizirik
    • , Russell B. Corbett-Detig
    • , Richard E. Green
    • , Christopher C. Wilmers
    •  & Beth Shapiro
  • Article
    | Open Access

    Parental care can take many forms but how this diversity arises is not well understood. Here, the authors compile data for over 1300 amphibian species and show that different forms of care evolve at different rates, prolonged care can be easily reduced, and biparental care is evolutionarily unstable.

    • Andrew I. Furness
    •  & Isabella Capellini
  • Article
    | Open Access

    An understanding of the ancestral state of the neural crest (NC) gene regulatory network (GRN) gives insight into vertebrate evolution. Here, the authors use transcriptomic and chromatin accessibility analyses of the lamprey NC, as well as cross-species enhancer assays, to identify GRN elements conserved throughout vertebrates.

    • Dorit Hockman
    • , Vanessa Chong-Morrison
    • , Stephen A. Green
    • , Daria Gavriouchkina
    • , Ivan Candido-Ferreira
    • , Irving T. C. Ling
    • , Ruth M. Williams
    • , Chris T. Amemiya
    • , Jeramiah J. Smith
    • , Marianne E. Bronner
    •  & Tatjana Sauka-Spengler
  • Article
    | Open Access

    Date palm is an important fruit crop in the Middle East and North Africa. Here, the authors report an improved genome assembly of this species and perform GWAS mapping of sex determining region and 21 fruit traits using high density SNP data generated from re-sequencing of the mapping population.

    • Khaled M. Hazzouri
    • , Muriel Gros-Balthazard
    • , Jonathan M. Flowers
    • , Dario Copetti
    • , Alain Lemansour
    • , Marc Lebrun
    • , Khaled Masmoudi
    • , Sylvie Ferrand
    • , Michael I. Dhar
    • , Zoë A. Fresquez
    • , Ulises Rosas
    • , Jianwei Zhang
    • , Jayson Talag
    • , Seunghee Lee
    • , David Kudrna
    • , Robyn F. Powell
    • , Ilia J. Leitch
    • , Robert R. Krueger
    • , Rod A. Wing
    • , Khaled M. A. Amiri
    •  & Michael D. Purugganan
  • Article
    | Open Access

    Retrotransposition events have been linked to some human disorders. Here, Gardner et al. systematically search for mobile genetic elements (ME) in trio whole exome-sequencing datasets and ascertain 9 de novo MEs and further estimate genome-wide germline ME burden and constraint.

    • Eugene J. Gardner
    • , Elena Prigmore
    • , Giuseppe Gallone
    • , Petr Danecek
    • , Kaitlin E. Samocha
    • , Juliet Handsaker
    • , Sebastian S. Gerety
    • , Holly Ironfield
    • , Patrick J. Short
    • , Alejandro Sifrim
    • , Tarjinder Singh
    • , Kate E. Chandler
    • , Emma Clement
    • , Katherine L. Lachlan
    • , Katrina Prescott
    • , Elisabeth Rosser
    • , David R. FitzPatrick
    • , Helen V. Firth
    •  & Matthew E. Hurles
  • Article
    | Open Access

    The common carp is derived from recent whole genome duplication and represents a model for polyploid genome evolution, rare in vertebrates. Here, the authors generate and analyse chromosome-level reference genomes for common carp, and describe subgenome gene expression changes.

    • Peng Xu
    • , Jian Xu
    • , Guangjian Liu
    • , Lin Chen
    • , Zhixiong Zhou
    • , Wenzhu Peng
    • , Yanliang Jiang
    • , Zixia Zhao
    • , Zhiying Jia
    • , Yonghua Sun
    • , Yidi Wu
    • , Baohua Chen
    • , Fei Pu
    • , Jianxin Feng
    • , Jing Luo
    • , Jing Chai
    • , Hanyuan Zhang
    • , Hui Wang
    • , Chuanju Dong
    • , Wenkai Jiang
    •  & Xiaowen Sun
  • Article
    | Open Access

    Many molecular and physiological mechanisms in the regulation of fertility are shared between female and male mammals. Here, Lee et al. report an association of CNVs in CSMD1 with early idiopathic menopause in women and show that loss of Csmd1 leads to gonadal dysfunction in both male and female mice.

    • Arthur S. Lee
    • , Jannette Rusch
    • , Ana C. Lima
    • , Abul Usmani
    • , Ni Huang
    • , Maarja Lepamets
    • , Katinka A. Vigh-Conrad
    • , Ronald E. Worthington
    • , Reedik Mägi
    • , Xiaobo Wu
    • , Kenneth I. Aston
    • , John P. Atkinson
    • , Douglas T. Carrell
    • , Rex A. Hess
    • , Moira K. O’Bryan
    •  & Donald F. Conrad
  • Article
    | Open Access

    Although bistability is common in biology, it is very difficult to design de novo into synthetic systems. Here, the authors present an experimental and theoretical analysis of a chemical network that displays bistable behavior under certain far-from-equilibrium conditions, and map the parameter space in which bistability operates.

    • Indrajit Maity
    • , Nathaniel Wagner
    • , Rakesh Mukherjee
    • , Dharm Dev
    • , Enrique Peacock-Lopez
    • , Rivka Cohen-Luria
    •  & Gonen Ashkenasy
  • Article
    | Open Access

    Evolution of optimal gene expression in females is expected to be constrained by sexually-antagonistic selection on males. Here, Parker and colleagues show that gene expression has in fact become masculinized in female stick insects across five independent transitions to asexual reproduction.

    • Darren J. Parker
    • , Jens Bast
    • , Kirsten Jalvingh
    • , Zoé Dumas
    • , Marc Robinson-Rechavi
    •  & Tanja Schwander
  • Article
    | Open Access

    Little is known about the long-term dynamics of mesopelagic fish despite their large contribution to total fish biomass. Here, the authors analyze the Santa Barbara Basin otolith record and suggest that mesopelagic fish populations were large but fluctuated with surface climate over the last ~2000 years.

    • William A. Jones
    •  & David M. Checkley Jr.
  • Article
    | Open Access

    Methane metabolism by some lineages of Archaea contributes to the cycling of carbon on Earth. Here, the authors show high diversity of methyl-coenzyme M reductase (Mcr), a key enzyme associated with archaeal methane/alkane metabolism, in hot spring Archaea, and investigate their ecological roles and evolution.

    • Zheng-Shuang Hua
    • , Yu-Lin Wang
    • , Paul N. Evans
    • , Yan-Ni Qu
    • , Kian Mau Goh
    • , Yang-Zhi Rao
    • , Yan-Ling Qi
    • , Yu-Xian Li
    • , Min-Jun Huang
    • , Jian-Yu Jiao
    • , Ya-Ting Chen
    • , Yan-Ping Mao
    • , Wen-Sheng Shu
    • , Wael Hozzein
    • , Brian P. Hedlund
    • , Gene W. Tyson
    • , Tong Zhang
    •  & Wen-Jun Li