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      Odonata (dragonflies and damselflies) as a bridge between ecology and evolutionary genomics

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          Abstract

          Odonata (dragonflies and damselflies) present an unparalleled insect model to integrate evolutionary genomics with ecology for the study of insect evolution. Key features of Odonata include their ancient phylogenetic position, extensive phenotypic and ecological diversity, several unique evolutionary innovations, ease of study in the wild and usefulness as bioindicators for freshwater ecosystems worldwide. In this review, we synthesize studies on the evolution, ecology and physiology of odonates, highlighting those areas where the integration of ecology with genomics would yield significant insights into the evolutionary processes that would not be gained easily by working on other animal groups. We argue that the unique features of this group combined with their complex life cycle, flight behaviour, diversity in ecological niches and their sensitivity to anthropogenic change make odonates a promising and fruitful taxon for genomics focused research. Future areas of research that deserve increased attention are also briefly outlined.

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          Most cited references212

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          Climate change, adaptation, and phenotypic plasticity: the problem and the evidence

          Many studies have recorded phenotypic changes in natural populations and attributed them to climate change. However, controversy and uncertainty has arisen around three levels of inference in such studies. First, it has proven difficult to conclusively distinguish whether phenotypic changes are genetically based or the result of phenotypic plasticity. Second, whether or not the change is adaptive is usually assumed rather than tested. Third, inferences that climate change is the specific causal agent have rarely involved the testing – and exclusion – of other potential drivers. We here review the various ways in which the above inferences have been attempted, and evaluate the strength of support that each approach can provide. This methodological assessment sets the stage for 11 accompanying review articles that attempt comprehensive syntheses of what is currently known – and not known – about responses to climate change in a variety of taxa and in theory. Summarizing and relying on the results of these reviews, we arrive at the conclusion that evidence for genetic adaptation to climate change has been found in some systems, but is still relatively scarce. Most importantly, it is clear that more studies are needed – and these must employ better inferential methods – before general conclusions can be drawn. Overall, we hope that the present paper and special issue provide inspiration for future research and guidelines on best practices for its execution.
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            Applications of next generation sequencing in molecular ecology of non-model organisms.

            As most biologists are probably aware, technological advances in molecular biology during the last few years have opened up possibilities to rapidly generate large-scale sequencing data from non-model organisms at a reasonable cost. In an era when virtually any study organism can 'go genomic', it is worthwhile to review how this may impact molecular ecology. The first studies to put the next generation sequencing (NGS) to the test in ecologically well-characterized species without previous genome information were published in 2007 and the beginning of 2008. Since then several studies have followed in their footsteps, and a large number are undoubtedly under way. This review focuses on how NGS has been, and can be, applied to ecological, population genetic and conservation genetic studies of non-model species, in which there is no (or very limited) genomic resources. Our aim is to draw attention to the various possibilities that are opening up using the new technologies, but we also highlight some of the pitfalls and drawbacks with these methods. We will try to provide a snapshot of the current state of the art for this rapidly advancing and expanding field of research and give some likely directions for future developments.
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              Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing.

              We present a de novo assembly of a eukaryote transcriptome using 454 pyrosequencing data. The Glanville fritillary butterfly (Melitaea cinxia; Lepidoptera: Nymphalidae) is a prominent species in population biology but had no previous genomic data. Sequencing runs using two normalized complementary DNA collections from a genetically diverse pool of larvae, pupae, and adults yielded 608,053 expressed sequence tags (mean length = 110 nucleotides), which assembled into 48,354 contigs (sets of overlapping DNA segments) and 59,943 singletons. BLAST comparisons confirmed the accuracy of the sequencing and assembly, and indicated the presence of c. 9000 unique genes, along with > 6000 additional microarray-confirmed unannotated contigs. Average depth of coverage was 6.5-fold for the longest 4800 contigs (348-2849 bp in length), sufficient for detecting large numbers of single nucleotide polymorphisms. Oligonucleotide microarray probes designed from the assembled sequences showed highly repeatable hybridization intensity and revealed biological differences among individuals. We conclude that 454 sequencing, when performed to provide sufficient coverage depth, allows de novo transcriptome assembly and a fast, cost-effective, and reliable method for development of functional genomic tools for nonmodel species. This development narrows the gap between approaches based on model organisms with rich genetic resources vs. species that are most tractable for ecological and evolutionary studies.
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                Author and article information

                Contributors
                018014223152 , seth.bybee@byu.edu
                acordoba@iecologia.unam.mx
                katie.duryea@biol.lu.se
                ryo-futahashi@aist.go.jp
                bengt.hansson@biol.lu.se
                m.o.lorenzo.carballa@gmail.com
                rjs360@psu.edu
                Robby.Stoks@bio.kuleuven.be
                antony.suvorov@gmail.com
                Erik.Svensson@biol.lu.se
                Janne.Swaegers@bio.kuleuven.be
                takahashi.yum@gmail.com
                Phillip.Watts@oulu.fi
                maren.wellenreuther@gmail.com
                Journal
                Front Zool
                Front. Zool
                Frontiers in Zoology
                BioMed Central (London )
                1742-9994
                10 October 2016
                10 October 2016
                2016
                : 13
                : 46
                Affiliations
                [1 ]Brigham Young University, Provo, UT 84606 USA
                [2 ]Departmento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Apdo, Postal 70-275, Ciudad Universitaria, 04510 Mexico City, Mexico
                [3 ]Evolutionary Ecology Unit, Department of Biology, Lund University, 223 62 Lund, Sweden
                [4 ]Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Central 6, Tsukuba, Ibaraki 305-8566 Japan
                [5 ]Institute of Integrative Biology, Biosciences Building, University of Liverpool, Crown Street, Liverpool, L69 7ZB UK
                [6 ]Departments of Entomology and Biology, Pennsylvania State University, University Park, PA 16802 USA
                [7 ]Laboratory of Aquatic Ecology, Evolution and Conservation, Department of Biology, University of Leuven, 3000 Leuven, Belgium
                [8 ]Department of Biology, Brigham Young University, LSB 4102, Provo, UT 84602 USA
                [9 ]Division of Ecology and Evolutionary Biology, Graduate School of Life Sciences, Tohoku University, 6-3, Aoba, Aramaki, Aoba, Sendai, Miyagi 980-8578 Japan
                [10 ]Department of Ecology, University of Oulu, Oulu, 90014 Finland
                [11 ]Plant and Food Research Limited, Nelson, 7010 New Zealand
                Author information
                http://orcid.org/0000-0001-6224-6303
                Article
                176
                10.1186/s12983-016-0176-7
                5057408
                27766110
                fc9e1776-352c-413d-b81f-da227bdca6af
                © The Author(s). 2016

                Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

                History
                : 2 March 2016
                : 16 September 2016
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/100000076, Directorate for Biological Sciences;
                Award ID: IOS 1457237
                Award ID: NESCent Catalysis
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100005739, Universidad Nacional Autónoma de México;
                Award ID: No. IN302115
                Award Recipient :
                Funded by: KULeuven Excellence Center Financing
                Award ID: PF/2010/07
                Award Recipient :
                Funded by: FWO
                Award ID: PF/2010/07
                Award Recipient :
                Funded by: Linnaeus centre CAnMove at Lund University
                Categories
                Review
                Custom metadata
                © The Author(s) 2016

                Animal science & Zoology
                ngs,ancient insects,complex life cycle,naiad,climate change,polymorphism,flight,ecological genomics

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