Next generation molecular ecology.
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TLDR
Calling a special issue of Molecular Ecology that deals with next-generation sequencing ‘Next generation Molecular Ecology’ seems to be all too obvious, but as the contributions to this issue came in, it became increasingly clear that next- generation sequencing (NGS) is more than just a technical leap – it will result in a transformation of how molecular ecology as a discipline is thought.About:
This article is published in Molecular Ecology.The article was published on 2010-02-10 and is currently open access. It has received 99 citations till now.read more
Citations
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Field guide to next-generation DNA sequencers
TL;DR: T careful thought about the desired characteristics of these systems is warranted before purchasing or using any of them, and the major characteristics of each commercially available platform are summarized.
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Extent and scale of local adaptation in salmonid fishes: review and meta-analysis
TL;DR: The frequency with which foreign salmonid populations outperform local populations suggests that drift, gene flow and plasticity often limit or mediate LA, and future research will benefit from an integration of classical and molecular approaches.
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Estimates of Genetic Differentiation Measured by FST Do Not Necessarily Require Large Sample Sizes When Using Many SNP Markers
TL;DR: It is shown that the population sample size can be significantly reduced when using an appropriate estimator and a large number of bi-allelic genetic markers, and conservation genetic studies can now obtain almost the same statistical power as studies performed on model organisms using markers developed with next-generation sequencing.
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Single-nucleotide polymorphism (SNP) discovery and applications of SNP genotyping in nonmodel organisms.
TL;DR: The current supplemental issue contains 22 papers that underline the advantages of SNPs, advocate the need for SNP research in nonmodel organisms, and chart advances in discovery and applications.
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An emergent science on the brink of irrelevance: a review of the past 8 years of DNA barcoding
TL;DR: The consistent failure of DNA barcoding to recognize its limitations and evolve its methodologies is presented, reducing the usefulness of the data produced by the movement and throwing into doubt its ability to embrace NGS.
References
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Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water
Thorsten Stoeck,David Bass,Markus E. Nebel,Richard Christen,Meredith D. M. Jones,Hans-Werner Breiner,Thomas A. Richards +6 more
TL;DR: It is suggested that current understanding of the ecological complexity of protist communities, genetic diversity, and global species richness are severely limited by the sequence data hitherto available, and long‐tailed rank abundance curves suggest that the 454 sequencing approach provides improved access to rare genotypes.
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Diversity in a hidden world: potential and limitation of next‐generation sequencing for surveys of molecular diversity of eukaryotic microorganisms
Ralph Medinger,Ralph Medinger,Viola Nolte,Ram Vinay Pandey,Steffen Jost,Birgit Ottenwälder,Christian Schlötterer,Jens Boenigk +7 more
TL;DR: This report studied the diversity and the seasonal community turnover of alveolates in an oligotrophic freshwater lake by SSU amplicon sequencing with NGS as well as by classical morphological analysis, and proposes that rDNA‐based diversity studies need to be adjusted for confounding effects of copy number variation.
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Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises.
Simon Creer,Vera G. Fonseca,Dorota L. Porazinska,Robin M. Giblin-Davis,Way Sung,Deborah M. Power,Margaret Packer,Gary R. Carvalho,Mark Blaxter,P. J. D. Lambshead,W. K. Thomas +10 more
TL;DR: An overview of meiofaunal metagenetic analyses, ranging from sample preservation and DNA extraction to PCR, sequencing and the bioinformatic interrogation of multiple, independent samples using 454 Roche sequencing platforms, is provided.
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Ecogenomics: using massively parallel pyrosequencing to understand virus ecology.
Marilyn J. Roossinck,Prasenjit Saha,Graham B. Wiley,Jiaxi Quan,James D. White,Hongshing Lai,Felipe Chavarría,Guoan Shen,Bruce A. Roe +8 more
TL;DR: Using a strategy to isolate double‐stranded RNA from individual plants and convert this to cDNA with a unique four nucleotide Tag at each end, this technology will be extremely useful in understanding the full scope of plant virus biodiversity.
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The ‘Expansion–Contraction’ model of Pleistocene biogeography: rocky shores suffer a sea change?
Peter B. Marko,Jessica M. Hoffman,Sandra A. Emme,Tamara M. Mcgovern,Carson C. Keever,L. Nicole Cox +5 more
TL;DR: The results indicate that the LGM did not extirpate the majority of species in the northeastern Pacific; instead, regional persistence during the L GM appears a common biogeographic history for rocky‐shore organisms in this region.