Applications of next generation sequencing in molecular ecology of non-model organisms

Abstract

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.

The quest to resolve recent radiations: Plastid phylogenomics of extinct and endangered Hawaiian endemic mints (Lamiaceae)

“…With the development of next-generation sequencing technologies (NGS) it is now possible to generate large amounts of sequence data for non-model taxa (Ekblom and Galindo, 2011). Sequences of complete chloroplast genomes are now becoming available for many contemporary species (Moore et al, 2006), and phylogenetic analyses of complete chloroplast genomes have been found to substantially increase resolution in taxa that have undergone rapid radiations (Parks et al, 2009), bypassing previous trade-offs between the number of taxa and the number of nucleotides utilized (Martin et al, 2005;Soltis et al, 2004).…”

Genomic tools for new insights to variation, adaptation, and evolution in the salmonid fishes: a perspective for charr

“…Therefore, resources like SNP arrays have their strengths for simplicity, reproducing the same and known panel of markers in all experiments, and very low per genotype cost after initial set up. For example, if research requires a reduced set of key SNPs of interest to be replicated across a very high number of samples, one might generate a SNP array, primers for targeted genotyping (or sequencing), or sequence capture and enrichment followed by high coverage resequencing (Ekblom & Galindo, 2011). Using genome-wide marker discovery to identify those loci of interest can be an effective way of doing this, either from genotyping, genome resequencing, transcriptome sequencing, or a combination of approaches.…”

Origin of a cryptic lineage in a threatened reptile through isolation and historical hybridization

“…The capacity to produce genomic-scale data sets from nonmodel organisms has transformed our ability to characterize patterns of genetic diversity within species and understand the historical processes that generate such patterns (Ekblom and Galindo, 2011). Highthroughput sequencing technologies, novel cost-effective methods for constructing reduced representation libraries (that is, restriction siteassociated DNA sequencing (RADseq); and the development of statistical approaches that allow historical demographic analyses of these data (that is, Gutenkunst et al, 2009;Excoffier et al, 2013;Leaché et al, 2014) are important factors contributing to this transformation.…”