New sequencing technologies, the development of genomics tools, and their applications in evolutionary arachnology

• Published in: The Journal of arachnology 2014-01, Vol.42 (1), p.1-15
• Main Authors: Brewer, Michael S., Cotoras, Darko D., Croucher, Peter J. P., Gillespie, Rosemary G.
• Format: Article
• Language: English
• Subjects: adaptation; Arachnida; biogeography; bioinformatics; DNA; DNA sequencing; Genes; Genetic aspects; Genetic research; genome; Genomes; Genomics; high-throughput nucleotide sequencing; Invited Review; Next-generation sequencing; Nucleotide sequencing; Phylogenetics; phylogeny; Population genetics; selection; Sequencing; Spiders; Technology; transcriptome; Transcriptomes; Zoological research
• ISSN: 0161-8202; 1937-2396
• DOI: 10.1636/M13-78.1

Molecular genetic tools have been a boon to arachnologists for decades and used to study many unique aspects of arachnid biology including genomics, phylogenetics, population genetics, and biogeography. These tools have evolved over time and now provide myriad methods for exploring evolutionary questions. Early tools, while still useful under the proper circumstances, are giving way to a new generation of DNA sequencing technologies. These new platforms yield impressive amounts of data at a fraction of the cost of traditional techniques. Herein, we discuss the history and future of molecular evolutionary arachnology in terms of available genetic/genomic tools and their potential applications, strengths, weaknesses, and relative costs. Next-generation sequencing (NGS) platforms are varied in their methods and potential uses, making high-throughput sequencing studies focusing on a wide array of questions tractable. To date, relatively few studies have employed NGS technologies using arachnids, but many could benefit from using them. Because no model species exist within the class Arachnida, we have a limited understanding of arachnid genomics. With the ever-advancing nature of sequencing technologies and bioinformatics, arachnologists can relatively easily implement NGS studies to bridge the gaps in our understanding and open avenues for deeper and more powerful experiments. To this end, we discuss examples of applications of NGS technologies focusing on arachnid taxa. Despite the allure of acquiring massive quantities of sequence data, we should recognize the limitations of existing NGS technologies and not forsake pre-NGS methods when these technologies could adequately address our questions.