Collections-based research in the genomic era

Abstract

Biological collections are at the front line of biodiversity research, informing taxonomy, evolution, conservation and sustainable livelihoods. In April 2014, we organised a meeting at the Linnean Society (UK) discussing the impact of next‐generation sequencing (NGS) methods on collections‐based research. Here, we explore the main themes of this meeting and outline the incredible potential of NGS to reinvent collections‐based research. Among the many opportunities at the interface of genomics and collections, we focus specifically on (1) the genomic characterisation of biological collections, (2) the enhancement and development of DNA‐based identification, (3) the tree of life and (4) interdisciplinary research addressing the most pressing environmental challenges of our times. Across the world, biological collections are at risk, primarily due to declining funding and shifts in scientific fashions. We encourage all users of collections to embrace the genomic era, not only because of the unparalleled scientific potential that it presents, but also because new cross‐disciplinary synergies will reinvigorate and secure the collections for future generations.

Herbarium genomics: skimming and plastomics from archival specimens

“…Where in the pre-NGS, polymerase chain reaction (PCR), era fragmented template DNA represented a major roadblock to successful amplification, the opposite is now true. Indeed next-generation sequencing has opened up tremendous possibilities for sequencing museum specimens, not only because of its increased output and power, but also because of the ever-decreasing costs (Millar et al 2008;Metzker 2010;Glenn 2011;Rowe et al 2011;Buerki and Baker 2016).…”

An assessment of sampling biases across studies of diel activity patterns in marine ray-finned fishes (Actinopterygii)

“…Likewise, the phylogenetic bias of underrepresented cryptic taxa is also sure to change with the continual accumulation of new studies sampling taxa highlighted here as underrepresented , Yang et al 2015, Miller et al 2016. Given that tissue biopsies of the thousands of marine fish species sampled in phylogenetic analyses are often deposited in the world's natural history collections (Wandeler et al 2007, Buerki andBaker 2016), researchers will soon be able to integrate next generation sequencing techniques with this steady accumulation of phylogenetic and behavioral data to place shifts in diel activity patterns into a genomic perspective.…”

Molecular ecology studies of species radiations: current research gaps, opportunities and challenges

“…We expect that targeted resequencing will greatly help students and researchers of species radiations to overcome the challenge of sequencing many individuals, populations and species for fairly large numbers of functionally interesting genome regions. As they effectively enrich genomic DNA templates for the chosen targets, capture approaches are expected to be useful for recovering genomic information from tissues that contain only minute amounts of DNA, as is typically the case for museum or herbarium specimens (Buerki & Baker 2016). Thus, sequence capture holds great promise for the rapid assessment of genomic diversity across a wide range of spatial, temporal and taxonomic scales.…”

“…Notably, sequence capture is known to be practicable even for biological samples yielding only minute amounts of DNA, even if partially degraded (Mamanova et al 2010;Meyer & Kircher 2010). This is relevant for the study of 'recalcitrant' nonmodel species posing difficulties during DNA extraction, and even more so for projects based on biological material from herbaria and museum collections (Buerki & Baker 2016). We anticipate that herbaria (and museum collections more generally) will play crucial roles in facilitating research on broadscale patterns of genomic diversity and diversification, given their richness of preserved specimens that yield fragmented DNA suitable for NGS techniques.…”