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Data Intensive Ecology

Edited by Dr Christopher Lortie, Dr Noah Lottig, Dr Mark Schildhauer, and Dr Xin Zhou

As the ecology community expands, it is now adopting new ways of making sense of the plethora of data produced from diverse approaches, including ocean research, eco-genomics, limnology, and macrosystems ecology, through more integrative means – improving our understanding of biology in a broader sense. This also presents new challenges, including data hosting and sharing to improve collaborations between multiple disciplines within ecology, and to improve reproducibility and data reuse. GigaScience is proud to present this comprehensive and forward-looking series, which will highlight new advances, applications, and challenges, and serve to promote and improve data sharing and reproducibility in ecology science.

This collection of articles has not been sponsored and articles have undergone the journal’s standard peer-review process. The Guest Editors declare no competing interests.

View all collections published in GigaScience.

  1. Research

    Circadian rhythms have significant effects on leaf-to-canopy scale gas exchange under field conditions

    Molecular clocks drive oscillations in leaf photosynthesis, stomatal conductance, and other cell and leaf-level processes over ~24 h under controlled laboratory conditions. The influence of such circadian regu...

    Víctor Resco de Dios, Arthur Gessler, Juan Pedro Ferrio, Josu G. Alday, Michael Bahn, Jorge del Castillo, Sébastien Devidal, Sonia García-Muñoz, Zachary Kayler, Damien Landais, Paula Martín-Gómez, Alexandru Milcu, Clément Piel, Karin Pirhofer-Walzl, Olivier Ravel, Serajis Salekin…

    GigaScience 2016 5:43

    Published on: 20 October 2016

  2. Data Note

    A picture is worth a thousand data points: an imagery dataset of paired shrub-open microsites within the Carrizo Plain National Monument

    Carrizo Plain National Monument (San Joaquin Desert, California, USA) is home to many threatened and endangered species including the blunt-nosed leopard lizard (Gambelia sila). Vegetation is dominated by annual ...

    Taylor J. Noble, Christopher J. Lortie, Michael Westphal and H. Scott Butterfield

    GigaScience 2016 5:40

    Published on: 27 September 2016

  3. Data Note

    Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database

    Microbial inhabitants of soils are important to ecosystem and planetary functions, yet there are large gaps in our knowledge of their diversity and ecology. The ‘Biomes of Australian Soil Environments’ (BASE) ...

    Andrew Bissett, Anna Fitzgerald, Thys Meintjes, Pauline M. Mele, Frank Reith, Paul G. Dennis, Martin F. Breed, Belinda Brown, Mark V. Brown, Joel Brugger, Margaret Byrne, Stefan Caddy-Retalic, Bernie Carmody, David J. Coates, Carolina Correa, Belinda C. Ferrari…

    GigaScience 2016 5:21

    Published on: 18 May 2016

  4. Review

    Mitochondrial metagenomics: letting the genes out of the bottle

    ‘Mitochondrial metagenomics’ (MMG) is a methodology for shotgun sequencing of total DNA from specimen mixtures and subsequent bioinformatic extraction of mitochondrial sequences. The approach can be applied to...

    Alex Crampton-Platt, Douglas W. Yu, Xin Zhou and Alfried P. Vogler

    GigaScience 2016 5:15

    Published on: 22 March 2016

  5. Commentary

    Simulating social-ecological systems: the Island Digital Ecosystem Avatars (IDEA) consortium

    Systems biology promises to revolutionize medicine, yet human wellbeing is also inherently linked to healthy societies and environments (sustainability). The IDEA Consortium is a systems ecology open science i...

    Neil Davies, Dawn Field, David Gavaghan, Sally J. Holbrook, Serge Planes, Matthias Troyer, Michael Bonsall, Joachim Claudet, George Roderick, Russell J. Schmitt, Linda Amaral Zettler, Véronique Berteaux, Hervé C. Bossin, Charlotte Cabasse, Antoine Collin, John Deck…

    GigaScience 2016 5:14

    Published on: 17 March 2016

  6. Research

    Evaluating a multigene environmental DNA approach for biodiversity assessment

    There is an increasing demand for rapid biodiversity assessment tools that have a broad taxonomic coverage. Here we evaluate a suite of environmental DNA (eDNA) markers coupled with next generation sequencing ...

    Alexei J. Drummond, Richard D. Newcomb, Thomas R. Buckley, Dong Xie, Andrew Dopheide, Benjamin CM Potter, Joseph Heled, Howard A. Ross, Leah Tooman, Stefanie Grosser, Duckchul Park, Nicholas J. Demetras, Mark I. Stevens, James C. Russell, Sandra H. Anderson, Anna Carter…

    GigaScience 2015 4:46

    Published on: 6 October 2015

  7. Commentary

    Standardizing metadata and taxonomic identification in metabarcoding studies

    High-throughput sequencing-based metabarcoding studies produce vast amounts of ecological data, but a lack of consensus on standardization of metadata and how to refer to the species recovered severely hampers...

    Leho Tedersoo, Kelly S. Ramirez, R Henrik Nilsson, Aivi Kaljuvee, Urmas Kõljalg and Kessy Abarenkov

    GigaScience 2015 4:34

    Published on: 31 July 2015

  8. Review

    Building a multi-scaled geospatial temporal ecology database from disparate data sources: fostering open science and data reuse

    Although there are considerable site-based data for individual or groups of ecosystems, these datasets are widely scattered, have different data formats and conventions, and often have limited accessibility. A...

    Patricia A. Soranno, Edward G. Bissell, Kendra S. Cheruvelil, Samuel T. Christel, Sarah M. Collins, C. Emi Fergus, Christopher T. Filstrup, Jean-Francois Lapierre, Noah R. Lottig, Samantha K. Oliver, Caren E. Scott, Nicole J. Smith, Scott Stopyak, Shuai Yuan, Mary Tate Bremigan, John A. Downing…

    GigaScience 2015 4:28

    Published on: 1 July 2015

  9. Commentary

    The ocean sampling day consortium

    Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the w...

    Anna Kopf, Mesude Bicak, Renzo Kottmann, Julia Schnetzer, Ivaylo Kostadinov, Katja Lehmann, Antonio Fernandez-Guerra, Christian Jeanthon, Eyal Rahav, Matthias Ullrich, Antje Wichels, Gunnar Gerdts, Paraskevi Polymenakou, Giorgos Kotoulas, Rania Siam, Rehab Z Abdallah…

    GigaScience 2015 4:27

    Published on: 19 June 2015