De Novo Characterization of the Timema Cristinae Transcriptome Facilitates Marker Discovery and Inference of Genetic Divergence
Molecular Ecology Resources (2012) doi: 10.1111/j.1755-0998.2012.03121.x De novo characterization of the Timema cristinae transcriptome facilitates marker discovery and inference of genetic divergence AARON A. COMEAULT,* MATHEW SOMMERS,* TANJA SCHWANDER,† C. ALEX BUERKLE,‡ TIMOTHY E. FARKAS,* PATRIK NOSIL* and THOMAS L. PARCHMAN‡ *Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80303, USA, †Center for Ecology and Evolutionary Studies, University of Groningen, 9700CC Groningen, The Netherlands, ‡Department of Botany, University of Wyoming, Laramie, WY 82071, USA Abstract Adaptation to different ecological environments can promote speciation. Although numerous examples of such ‘ecological speciation’ now exist, the genomic basis of the process, and the role of gene flow in it, remains less understood. This is, at least in part, because systems that are well characterized in terms of their ecology often lack genomic resources. In this study, we characterize the transcriptome of Timema cristinae stick insects, a system that has been researched intensively in terms of ecological speciation, but for which genomic resources have not been previously developed. Specifically, we obtained >1 million 454 sequencing readsthatassembledinto84937contigsrepresenting approximately 18 282 unique genes and tens of thousands of potential molecular markers. Second, as an illustration of their utility, we used these geno- mic resources to assess multilocus genetic divergence within both an ecotype pair and a species pair of Timema stick insects. The results suggest variable levels of genetic divergence and gene flow among taxon pairs and genes and illustrate afirststeptowardsfuturegenomicworkinTimema. Keywords: gene flow, isolation with migration, next-generation sequencing, speciation, transcriptome Received 3 November 2011; revision received 6 January 2012; accepted 13 January 2012 Introduction resources (some notable exceptions aside, such as three- spine stickleback; Peichel et al.
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