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Evolution and Population Genomics of Loliginid Squids

  • Author(s): Cheng, Samantha Hue Tone
  • Advisor(s): Barber, Paul H
  • et al.
Abstract

Globally, rampant harvesting practices have left vital marine resources in sharp decline precipitating a dramatic loss of the biodiversity and threatening the health and viability of natural populations. To protect these crucial resources and ecosystems, a comprehensive assessment of biodiversity, as well as a rigorous understanding of the mechanisms underlying it, is urgently needed. As global finfish fisheries decline, harvest of cephalopod fisheries, squid, in particular, has exponentially increased. However, while much is known about the evolution and population dynamics of teleost fishes, much less is understood about squids. This dissertation provides a robust, in-depth examination of these mechanisms in commercially important squids using a novel approach combining genetics and genomics methods. In the first chapter, a suite of genetic markers is used to thoroughly examine the distribution and evolution of a species complex of bigfin reef squid (Sepioteuthis cf. lessoniana) throughout the global center of marine biodiversity, the Coral Triangle, and adjacent areas. Phylogenetic analyses and species delimitation methods unequivocally demonstrate the presence of at least three cryptic lineages sympatrically distributed throughout the region. While these putative species are reciprocally monophyletic, they are difficult to distinguish morphologically and little is known about how they differ in life history and ecology. To this end, in chapter 2, patterns of population structure over the Coral Triangle and adjacent regions were examined using genetic and genomic methods to identify important processes shaping both genetic and demographic connectivity in two of these cryptic species. Using both mitochondrial DNA (cytochrome oxidase subunit 1) and genome-wide single nucleotide polymorphisms (generated from restriction site associated digest (RAD) sequencing), we find strong, but discordant, patterns of population structure between these sympatric sibling taxa suggesting contrasting dispersal life histories. Moreover, detection of putative outlier loci highlights the possible role of selective pressures from regional environmental differences in shaping ongoing divergence. Given the fine-scale resolution achieved in chapter 2 with using RAD sequencing, in chapter 3, we apply these methods to examine potential population structure in the highly valuable market squid fishery (Doryteuthis opalescens) in California. This fishery has long been hypothesized to be two separate stocks due to different spawning peaks and areas. Using genome-wide SNPs and a rigorous temporal sampling scheme, we determined that northern and southern regions do not represent two distinct spatial stocks. Rather, complex patterns of temporal population structure lend support to continual spawning of genetically distinct cohorts at both sites throughout the 2014 harvest season. Collectively, these results demonstrate that squid biodiversity and population structure is much more complex than previously thought. Through the use of genetic and genomic technologies, we can delineate populations and identify the mechanisms driving connectivity to provide key information for fisheries management and conservation.

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