So, you want to use next-generation sequencing in marine systems? Insight from the Pan-Pacific Advanced Studies Institute

Abstract

The emerging field of next-generation sequencing (NGs) is rapidly expanding capabilities for cutting edge genomic research, with applications that can help meet marine conservation challenges of food security, biodiversity loss, and climate change. Navigating the use of these tools, however, is complex at best. Furthermore, applications of marine genomic questions are limited in developing nations where both marine biodiversity and threats to marine biodiversity are most concentrated. This is particularly true in southeast Asia. The first Pan-Pacific Advanced studies Institute (PacAsI) entitled "Genomic Applications to Marine science and resource Management in southeast Asia" was held in July 2012 in Dumaguete, Philippines, with the intent to draw together leading scientists from both sides of the Pacific Ocean to understand the potential of NGs in helping address the aforementioned challenges. Here we synthesize discussions held during the PacAsI to provide perspectives and guidance to help scientists new to NGs choose among the variety of available advanced genomic methodologies specifically for marine science questions.

Phylogeography unplugged: comparative surveys in the genomic era

“…Based on the arc of events described above, is this phase the end of history as we know it for single-locus studies in phylogeography? The latest advances into next generation sequencing have opened the gateway to rapid scientific advances, but we currently are limited by the computing power and analytical methods required to take full advantage of the new data and handle the massive increase in numbers of loci and sequence length , Willette et al 2014). …”

“…The great promise of genomic comparisons (Berner et al 2008, Hohenlohe et al 2011, Willette et al 2014) and occasional perils (Roesti et al 2012) continue to unfold. As genomic data become available, DNA segments can be parsed across selected and neutral panels of loci, and will likely reveal the main forces of local adaptation at work at the species and community levels (Bertness and Gaines 1993, Sotka 2005, Gaggiotti et al 2009, Nielsen et al 2009, Sanford and Kelly 2011.…”

Misidentification of bluefin tuna larvae: a call for caution and taxonomic reform

“…Fisheries organizations and multi-institutional larval surveys, plagued by sampling and species identification bias, have much to gain from this new technology. Although NGS techniques have been very expensive in the past, its cost is declining rapidly and new markets are opening up in the developing world (Willette et al 2014).…”

Magnificent dimensions, varied forms, and brilliant colors: the molecular ecology and evolution of the Indian and Pacific oceans

“…both Keyse et al (2014) andbowen et al (2014) stress the importance of research coordination and collaboration among laboratories to the advancement of Indo-Pacific marine science. Willette et al (2014a) complete this first trio of syntheses by looking forward to the application of massively parallel sequencing technologies to science and resource management in the Indo-Pacific region. They identify two major categories of questions that benefit from greater sequencing breadth across both individuals and genomes: population genomics and studies of local adaptation.…”

“…While there are a few groundbreaking examples of Indo-Pacific projects utilizing "second generation" methods (barshis et al 2013, toonen et al 2013), these technologies lie in the future for most molecular practitioners working in the Indo-Pacific region. Willette et al (2014a) accordingly provide advice for those who would like to add massively parallel sequencing to their toolkit, including textboxes outlining the basics for six specific methodologies ranging from rAD-seq to metagenomics. Finally, they align themselves with bowen et al (2014) by stressing that the scientific question should guide the use of sequencing technology, rather than vice versa.…”