Volume 3 Issue 4, April 2019

Volume 3 Issue 4

Mushroom phylogeny

Mushroom-forming fungi (Agaricomycetes) have key roles in ecosystems, such as plant biomass degraders and mycorrhizal mutualists. There are over 21,000 species of mushroom-forming fungi, and they have diverse fruiting-body morphologies. These range from simple and crust-like to highly structured and gilled, such as Mycena interrupta (depicted). Analysis of the global diversity of these fungi reveals intriguing patterns, including a Jurassic explosion of both species number and morphological diversity.

See Varga et al.

Image: Stephen Axford. Cover Design: Tulsi Voralia.

Editorial

  • Editorial |

    The development of essential biodiversity variables offers the prospect of large-scale data synthesis and a smoother path from science to policy.

Correspondence

Comment & Opinion

  • World View |

    More, not less, international cooperation on conservation is in the interest of Brazilian farmers and wider Brazilian society, argues Bernardo B. N. Strassburg.

    • Bernardo B. N. Strassburg
  • Comment |

    The inauguration of Jair Bolsonaro as Brazil’s new president has heralded a rapid acceleration of the erosion of environmental protection measures in the country. Brazil’s scientific community should rally to provide evidence that this is economically and socially unwise.

    • Denis Abessa
    • , Ana Famá
    •  & Lucas Buruaem
  • Comment |

    Macroscopic organisms from the late Ediacaran period have often been described as failed experiments in the history of life. We argue that the field of Ediacaran palaeobiology should dispense with unhelpful historical classification schemes and embrace phylogenetic systematics if we are to establish the evolutionary relevance of these fossils.

    • Frances S. Dunn
    •  & Alexander G. Liu
  • Comment |

    New antibiotics are urgently needed to combat rising rates of resistance against all existing classes of antimicrobials. We highlight key issues that complicate the prediction of resistance evolution in the real world and outline the ways in which these can be overcome.

    • Michael A. Brockhurst
    • , Freya Harrison
    • , Jan-Willem Veening
    • , Ellie Harrison
    • , Grace Blackwell
    • , Zamin Iqbal
    •  & Craig Maclean
  • Obituary |

    Pioneer of evolutionary developmental biology and supportive mentor.

    • Gregory A. Wray
    •  & Eric S. Haag

News & Views

  • News & Views |

    Analysis of Phanerozoic vertebrate community richness suggests there have been constraints on tetrapod diversity dynamics over much of their evolutionary history.

    • Linda C. Ivany
    •  & Jesse Czekanski-Moir
  • News & Views |

    A study of habitat loss associated with global trade reveals growing impacts on bird biodiversity and carbon sequestration. Overall increases in impacts are driven by changing consumption patterns and human population increases — and may be even greater if land-use intensification is considered.

    • Tim Newbold
  • News & Views |

    Analysis of genomes, transcriptomes and proteomes from recently diverged rice species provides mechanistic insight into the process of de novo gene origination.

    • Erich Bornberg-Bauer
    •  & Brennen Heames
  • News & Views |

    Comparative analysis of microexons across bilaterians identifies a new protein domain associated with the evolutionary origin of microexon inclusion in neural tissues.

    • Rupert Faraway
    •  & Jernej Ule

Reviews

  • Perspective |

    Integrating fossil and geochemical records challenges the notion that the Ediacaran and Cambrian worlds were markedly distinct and places biotic and environmental change within a longer-term narrative.

    • Rachel Wood
    • , Alexander G. Liu
    • , Frederick Bowyer
    • , Philip R. Wilby
    • , Frances S. Dunn
    • , Charlotte G. Kenchington
    • , Jennifer F. Hoyal Cuthill
    • , Emily G. Mitchell
    •  & Amelia Penny
  • Perspective | | Open Access

    Changes in species distribution and abundance can be captured using essential biodiversity variables (EBVs). Here, the authors synthesize the data and approaches needed for EBVs that allow monitoring of populations in both space and time.

    • Walter Jetz
    • , Melodie A. McGeoch
    • , Robert Guralnick
    • , Simon Ferrier
    • , Jan Beck
    • , Mark J. Costello
    • , Miguel Fernandez
    • , Gary N. Geller
    • , Petr Keil
    • , Cory Merow
    • , Carsten Meyer
    • , Frank E. Muller-Karger
    • , Henrique M. Pereira
    • , Eugenie C. Regan
    • , Dirk S. Schmeller
    •  & Eren Turak
  • Perspective |

    Parasites’ biological rhythms coordinate their activities with both the external environment and the biotic environment of their host. Here, the authors discuss biological rhythms of both host and parasite from an ecological and evolutionary perspective.

    • Mary L. Westwood
    • , Aidan J. O’Donnell
    • , Charissa de Bekker
    • , Curtis M. Lively
    • , Marlene Zuk
    •  & Sarah E. Reece
  • Review Article |

    A review of current knowledge of the mosquito and vertebrate host species for Zika virus, mechanisms of vector-borne transmission, and the possible scenarios of recent Zika virus emergence and evolution, including potential spillback from urban to zoonotic cycles.

    • Gladys Gutiérrez-Bugallo
    • , Luis Augusto Piedra
    • , Magdalena Rodriguez
    • , Juan A. Bisset
    • , Ricardo Lourenço-de-Oliveira
    • , Scott C. Weaver
    • , Nikos Vasilakis
    •  & Anubis Vega-Rúa

Research

  • Brief Communication |

    Analysis of crow admixed genomes in a European hybrid zone shows that variation in hybrid colour phenotypes is explained by recessive epistasis between two pigmentation genes, which are targets of divergent selection.

    • Ulrich Knief
    • , Christen M. Bossu
    • , Nicola Saino
    • , Bengt Hansson
    • , Jelmer Poelstra
    • , Nagarjun Vijay
    • , Matthias Weissensteiner
    •  & Jochen B. W. Wolf
  • Article |

    Fossil lipid biomarkers previously thought to be diagnostic of sponges (and thus indicative of animal life) are found to be preserved in unicellular Rhizarian protists, questioning a pre-Cambrian origin of sponges.

    • Benjamin J. Nettersheim
    • , Jochen J. Brocks
    • , Arne Schwelm
    • , Janet M. Hope
    • , Fabrice Not
    • , Michael Lomas
    • , Christiane Schmidt
    • , Ralf Schiebel
    • , Eva C. M. Nowack
    • , Patrick De Deckker
    • , Jan Pawlowski
    • , Samuel S. Bowser
    • , Ilya Bobrovskiy
    • , Karin Zonneveld
    • , Michal Kucera
    • , Marleen Stuhr
    •  & Christian Hallmann
  • Article |

    Taphonomic experiments show that sedimentary flows constrained Ediacara biota preservation and that Ediacaran fossils do not necessarily reflect the external shape of the organism.

    • Ilya Bobrovskiy
    • , Anna Krasnova
    • , Andrey Ivantsov
    • , Ekaterina Luzhnaya (Serezhnikova)
    •  & Jochen J. Brocks
  • Article |

    Diversity within terrestrial tetrapod communities has risen by at most threefold over the last 300 million years, consistent with a constrained model of diversification.

    • Roger A. Close
    • , Roger B. J. Benson
    • , John Alroy
    • , Anna K. Behrensmeyer
    • , Juan Benito
    • , Matthew T. Carrano
    • , Terri J. Cleary
    • , Emma M. Dunne
    • , Philip D. Mannion
    • , Mark D. Uhen
    •  & Richard J. Butler
  • Article |

    The authors identify a strong positive relationship between mass and metabolic rate among insects, fish, amphibians, reptiles, birds and mammals, and show that the genetic and interspecific correlations between these traits are consistent with a pattern of multivariate selection.

    • Craig R. White
    • , Dustin J. Marshall
    • , Lesley A. Alton
    • , Pieter A. Arnold
    • , Julian E. Beaman
    • , Candice L. Bywater
    • , Catriona Condon
    • , Taryn S. Crispin
    • , Aidan Janetzki
    • , Elia Pirtle
    • , Hugh S. Winwood-Smith
    • , Michael J. Angilletta Jr
    • , Stephen F. Chenoweth
    • , Craig E. Franklin
    • , Lewis G. Halsey
    • , Michael R. Kearney
    • , Steven J. Portugal
    •  & Daniel Ortiz-Barrientos
  • Article |

    Analysing soil and rhizosphere microbial communities across a latitudinal gradient from southern to central Europe, the authors show that the belowground microbiomes of range-expanding plant species become more similar the further they are from their native range.

    • Kelly S. Ramirez
    • , L. Basten Snoek
    • , Kadri Koorem
    • , Stefan Geisen
    • , L. Janneke Bloem
    • , Freddy ten Hooven
    • , Olga Kostenko
    • , Nikos Krigas
    • , Marta Manrubia
    • , Danka Caković
    • , Debbie van Raaij
    • , Maria A. Tsiafouli
    • , Branko Vreš
    • , Tatjana Čelik
    • , Carolin Weser
    • , Rutger A. Wilschut
    •  & Wim H. van der Putten
  • Article |

    Using a multifactorial global change experiment, the authors show that warming grassland plots by +3 °C over 6 years accelerates the scaling rate of both taxonomic and phylogenetic diversity in soil bacterial and fungal communities.

    • Xue Guo
    • , Xishu Zhou
    • , Lauren Hale
    • , Mengting Yuan
    • , Daliang Ning
    • , Jiajie Feng
    • , Zhou Shi
    • , Zhenxin Li
    • , Bin Feng
    • , Qun Gao
    • , Linwei Wu
    • , Weiling Shi
    • , Aifen Zhou
    • , Ying Fu
    • , Liyou Wu
    • , Zhili He
    • , Joy D. Van Nostrand
    • , Guanzhou Qiu
    • , Xueduan Liu
    • , Yiqi Luo
    • , James M. Tiedje
    • , Yunfeng Yang
    •  & Jizhong Zhou
  • Article |

    Fitting a water quality index to survey-based estimates of coral resilience finds that reefs exposed to poor water quality are more resistant to bleaching but slower to recover from disturbance and more susceptible to disease outbreaks.

    • M. Aaron MacNeil
    • , Camille Mellin
    • , Sam Matthews
    • , Nicholas H. Wolff
    • , Timothy R. McClanahan
    • , Michelle Devlin
    • , Christopher Drovandi
    • , Kerrie Mengersen
    •  & Nicholas A. J. Graham
  • Article |

    Combining biophysical and economic models, the authors show that the impacts of land use on bird biodiversity and carbon sequestration have increased over the years 2000–2011, with cattle farming being a major driver of biodiversity loss.

    • Alexandra Marques
    • , Inês S. Martins
    • , Thomas Kastner
    • , Christoph Plutzar
    • , Michaela C. Theurl
    • , Nina Eisenmenger
    • , Mark A. J. Huijbregts
    • , Richard Wood
    • , Konstantin Stadler
    • , Martin Bruckner
    • , Joana Canelas
    • , Jelle P. Hilbers
    • , Arnold Tukker
    • , Karlheinz Erb
    •  & Henrique M. Pereira
  • Article |

    A comparison of communities of Anolis lizards across an elevation gradient in the Dominican Republic finds contrasting effects of habitat conversion in lowland and highland communities and suggests that warm-climate specialists dominate human-modified landscapes, even in cool macroclimates.

    • Luke O. Frishkoff
    • , Eveling Gabot
    • , George Sandler
    • , Cristian Marte
    •  & D. Luke Mahler
  • Article |

    Genomic analysis of Drosophila melanogaster populations that are found at different climatic extremes identifies a trade-off between resistance to a neonicitinoid pesticide and adaptation to thermotolerance, controlled by two major genes.

    • Alexandre Fournier-Level
    • , Robert T. Good
    • , Stephen A. Wilcox
    • , Rahul V. Rane
    • , Michelle Schiffer
    • , Wei Chen
    • , Paul Battlay
    • , Trent Perry
    • , Philip Batterham
    • , Ary A. Hoffmann
    •  & Charles Robin
  • Article | | Open Access

    A phylogenetic tree of 5,284 fungal species is used to infer patterns of extinction, diversification and morphological innovation in mushroom-forming fungi.

    • Torda Varga
    • , Krisztina Krizsán
    • , Csenge Földi
    • , Bálint Dima
    • , Marisol Sánchez-García
    • , Santiago Sánchez-Ramírez
    • , Gergely J. Szöllősi
    • , János G. Szarkándi
    • , Viktor Papp
    • , László Albert
    • , William Andreopoulos
    • , Claudio Angelini
    • , Vladimír Antonín
    • , Kerrie W. Barry
    • , Neale L. Bougher
    • , Peter Buchanan
    • , Bart Buyck
    • , Viktória Bense
    • , Pam Catcheside
    • , Mansi Chovatia
    • , Jerry Cooper
    • , Wolfgang Dämon
    • , Dennis Desjardin
    • , Péter Finy
    • , József Geml
    • , Sajeet Haridas
    • , Karen Hughes
    • , Alfredo Justo
    • , Dariusz Karasiński
    • , Ivona Kautmanova
    • , Brigitta Kiss
    • , Sándor Kocsubé
    • , Heikki Kotiranta
    • , Kurt M. LaButti
    • , Bernardo E. Lechner
    • , Kare Liimatainen
    • , Anna Lipzen
    • , Zoltán Lukács
    • , Sirma Mihaltcheva
    • , Louis N. Morgado
    • , Tuula Niskanen
    • , Machiel E. Noordeloos
    • , Robin A. Ohm
    • , Beatriz Ortiz-Santana
    • , Clark Ovrebo
    • , Nikolett Rácz
    • , Robert Riley
    • , Anton Savchenko
    • , Anton Shiryaev
    • , Karl Soop
    • , Viacheslav Spirin
    • , Csilla Szebenyi
    • , Michal Tomšovský
    • , Rodham E. Tulloss
    • , Jessie Uehling
    • , Igor V. Grigoriev
    • , Csaba Vágvölgyi
    • , Tamás Papp
    • , Francis M. Martin
    • , Otto Miettinen
    • , David S. Hibbett
    •  & László G. Nagy
  • Article |

    Analysis of high-quality genomes and transcriptomes of 13 closely related Oryza species coupled with proteomics finds about 50 de novo genes per million years.

    • Li Zhang
    • , Yan Ren
    • , Tao Yang
    • , Guangwei Li
    • , Jianhai Chen
    • , Andrea R. Gschwend
    • , Yeisoo Yu
    • , Guixue Hou
    • , Jin Zi
    • , Ruo Zhou
    • , Bo Wen
    • , Jianwei Zhang
    • , Kapeel Chougule
    • , Muhua Wang
    • , Dario Copetti
    • , Zhiyu Peng
    • , Chengjun Zhang
    • , Yong Zhang
    • , Yidan Ouyang
    • , Rod A. Wing
    • , Siqi Liu
    •  & Manyuan Long
  • Article |

    Microexons play a crucial role in neural development and are evolutionarily conserved. Comparing microexons across bilaterians, the authors find a new protein domain responsible for the evolution of neural specificity of microexons.

    • Antonio Torres-Méndez
    • , Sophie Bonnal
    • , Yamile Marquez
    • , Jonathan Roth
    • , Marta Iglesias
    • , Jon Permanyer
    • , Isabel Almudí
    • , Dave O’Hanlon
    • , Tanit Guitart
    • , Matthias Soller
    • , Anne-Claude Gingras
    • , Fátima Gebauer
    • , Fabian Rentzsch
    • , Benjamin J. Blencowe
    • , Juan Valcárcel
    •  & Manuel Irimia
  • Article |

    Social spider colonies composed of ‘bold’ individuals have greater foraging success than ‘shy’ colonies, but this advantage diminishes as their frequency in the neighbourhood increases.

    • Jonathan N. Pruitt
    • , Brendan L. McEwen
    • , Steven T. Cassidy
    • , Gabriella M. Najm
    •  & Noa Pinter-Wollman

Amendments & Corrections

  • Author Correction |

    • Jeffrey R. Smith
    • , Andrew D. Letten
    • , Po-Ju Ke
    • , Christopher B. Anderson
    • , J. Nicholas Hendershot
    • , Manpreet K. Dhami
    • , Glade A. Dlott
    • , Tess N. Grainger
    • , Meghan E. Howard
    • , Beth M. L. Morrison
    • , Devin Routh
    • , Priscilla A. San Juan
    • , Harold A. Mooney
    • , Erin A. Mordecai
    • , Thomas W. Crowther
    •  & Gretchen C. Daily
  • Author Correction |

    • Janet S. Prevéy
    • , Christian Rixen
    • , Nadja Rüger
    • , Toke T. Høye
    • , Anne D. Bjorkman
    • , Isla H. Myers-Smith
    • , Sarah C. Elmendorf
    • , Isabel W. Ashton
    • , Nicoletta Cannone
    • , Chelsea L. Chisholm
    • , Karin Clark
    • , Elisabeth J. Cooper
    • , Bo Elberling
    • , Anna Maria Fosaa
    • , Greg H. R. Henry
    • , Robert D. Hollister
    • , Ingibjörg Svala Jónsdóttir
    • , Kari Klanderud
    • , Christopher W. Kopp
    • , Esther Lévesque
    • , Marguerite Mauritz
    • , Ulf Molau
    • , Susan M. Natali
    • , Steven. F. Oberbauer
    • , Zoe A. Panchen
    • , Eric Post
    • , Sabine B. Rumpf
    • , Niels Martin Schmidt
    • , Edward Schuur
    • , Philipp R. Semenchuk
    • , Jane G. Smith
    • , Katharine N. Suding
    • , Ørjan Totland
    • , Tiffany Troxler
    • , Susanna Venn
    • , Carl-Henrik Wahren
    • , Jeffrey M. Welker
    •  & Sonja Wipf