Virtual Issue: Plant Ecogenomics

Edited by Associate Editor Nate Swenson

April 2016

The editors of the Journal of Ecology are pleased to present this Virtual Issue on plant ecogenomics. The technical, computational and financial barriers that have previously limited the broad scale integration of information generated by massively parallel/next-generation sequencing technology into ecology have been substantially eroded. Ecology now stands at the brink of a revolution where our ability to quantify individual-level nucleotide and gene expression variation and microbiomes on non-model systems in experimental and field settings will generate fascinating new insights into mechanisms and outcomes of species interactions with their environments.

We have selected 9 papers that leverage DNA sequencing and/or 'omics approaches in ecology that have been published in the Journal of Ecology with 6 of these appearing in the last 2 years. The work spans a range of methodologies (e.g. pyrosequencing to microarrays) and topics (e.g. plant volatile emissions to root microbiomes). While some work focuses on well-known temperate model plant species or their close relatives, other work included in this Virtual Issue comes from less well-known lineages from the temperate zone to the tropics.

The integration of 'omics into ecology has generally been limited to a small set of model species or their close relatives and meta-genomics approaches. Presently, and certainly going forward, this will no longer be the case and much more emphasis will be placed on testing mechanistic ecological hypotheses using multiple non-model species. While we aim for this Virtual Issue is to generate discussions and to provide a sample of research published in this field, we hope the issue encourages future submissions to the Journal that use the most up to date methodoology and leverage large 'omic data from model and non-model organisms to address questions of broad interest to ecology. We invite you to visit the Journal's blog, as well as follow the Journal of Ecology on Twitter and Facebook.

Nate Swenson
Associate Editor, Journal of Ecology

Ecologically diverse and distinct neighbourhoods trigger persistent phenotypic consequences, and amine metabolic profiling detects them.
Françoise Hennion, Isabelle Litrico, Igor V. Bartish, Alexandra Weigelt, Alain Bouchereau, Andreas Prinzing

Divergent evolution in antiherbivore defences within species complexes at a single Amazonian site
María-José Endara, Alexander Weinhold, James E. Cox, Natasha L. Wiggins, Phyllis D. Coley, Thomas A. Kursar

Tree genotype mediates covariance among communities from microbes to lichens and arthropods
Louis J. Lamit, Posy E. Busby, Matthew K. Lau, Zacchaeus G. Compson, Todd Wojtowicz, Arthur R. Keith, Matthew S. Zinkgraf, Jennifer A. Schweitzer, Stephen M. Shuster, Catherine A. Gehring, Thomas G. Whitham

Relationships between adaptive and neutral genetic diversity and ecological structure and functioning: a meta-analysis
Raj Whitlock

Determinants of root-associated fungal communities within Asteraceae in a semi-arid grassland
Jeannine Wehner, Jeff R. Powell, Ludo A. H. Muller, Tancredi Caruso, Stavros D. Veresoglou, Stefan Hempel, Matthias C. Rillig

Temporal dynamics of plant–soil feedback and root-associated fungal communities over 100 years of invasion by a non-native plant
Nicola J. Day, Kari E. Dunfield, Pedro M. Antunes

Ecogenomic approach to the role of herbivore-induced plant volatiles in community ecology
Tjeerd A. L. Snoeren, Peter W. De Jong, Marcel Dicke

An ecologist's guide to ecogenomics
N. J Ouborg, W. H Vriezen

Ecogenomics of cleistogamous and chasmogamous flowering: genome-wide gene expression patterns from cross-species microarray analysis in Cardamine kokaiensis (Brassicaceae)
Shin-Ichi Morinaga, Atsushi J. Nagano, Saori Miyazaki, Minoru Kubo, Taku Demura, Hiroo Fukuda, Satoki Sakai, Mitsuyasu Hasebe

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