Dimensions in marine biodiversity: Traditional and molecular approaches to unraveling the mysteries of the deep

Abstract

Biodiversity research is a critical field for addressing global change and species loss. Understanding patterns of species distribution and community composition is fundamental to many other aspects of biology and conservation, and molecular approaches are increasingly central to such work. Here I explored three separate but related dimensions in biodiversity research: infrastructure, taxonomy, and exploration. DNA barcoding is a critical component of the infrastructure underlying conservation and biodiversity research, yet public reference databases are incomplete. I used genome skimming to sequence complete mitogenomes and nuclear ribosomal repeats to build comprehensive barcode reference databases for marine fishes, with all sequences matched to voucher specimens housed in natural history collections. Results affirm that genome skimming is an efficient and cost-effective method to generate multiple commonly used barcoding loci simultaneously. This approach has great potential for future projects and to facilitate completing barcode reference databases for marine fishes. Robust molecular resources can also illuminate previously unknown biodiversity and its origins. I used DNA barcoding combined with integrated molecular-phylogeographic-taxonomic methods to reveal and describe a new species of combtooth blenny, named Cirripectes matatakaro. The distribution and phylogenetic position of the new species helped uncover the evolutionary origins of a closely related Hawaiian endemic, showing that it most likely arose via colonization from the Central/Southern Pacific through the Line Islands and possibly Johnston Atoll. In addition to revealing previously undescribed species, molecular biodiversity approaches can be used to explore new habitats. Mesophotic coral ecosystems (MCEs) are coral reef communities found from 30–150 m depth. I used environmental DNA (eDNA) metabarcoding to investigate patterns of community composition across the tree of life from the surface to ~100 m on Hawaiʻi Island. I found a transition zone at 45–60 m, where shallow reef communities give way to distinctly mesophotic assemblages, for a broad range of invertebrates and eukaryotes but not for fishes. I attribute this finding to the higher mobility of fishes, although methodological limitations may contribute as well. Since the invertebrate communities below 45 m are taxonomically distinct, they are seemingly unlikely to act as refugia to reseed depleted shallow reefs over ecological timescales. Together, this work examines three avenues in biodiversity research and provides insight into genetic infrastructure, the importance and relevance of traditional taxonomy, and the application of new technologies to marine exploration.