Population genomics of three deep-sea cephalopod species reveals connectivity between the Gulf of Mexico and northwestern Atlantic Ocean

Highlights

• Genetic methods were used to study population dynamics in three deep-sea cephalopods from the Gulf of Mexico and the northern Atlantic Ocean.

• Genetic diversity is lowest in Cranchia scabra which appears to be in a population growth stage, and highest in Vampyroteuthis infernalis.

• Two distinct populations of V. infernalis were observed but they do not appear to be the result of ocean-basin vicariance.

• The genetic connectivity across these populations suggests resilience to disturbance from localized events in the Gulf of Mexico.

Abstract

Despite the ecological importance of deep-sea cephalopods, little is known about their genetic diversity or population dynamics. The cephalopod species Cranchia scabra, Pyroteuthis margaritifera, and Vampyroteuthis infernalis are commonly collected in midwater samples from both the Gulf of Mexico and northwestern Atlantic Ocean but, despite their common appearance in trawls and important roles in marine food webs, no genetic studies of population connectivity exist for these species. Here, Sanger sequencing of three conserved genetic loci and ddRADseq techniques were used to examine population genetic dynamics in these deep-sea species. Genetic diversity is lowest in C. scabra, which appears to be in a population growth stage, and highest in V. infernalis. Population structure was unique to V. infernalis but does not appear to be the result of ocean-basin vicariance, thus possible alternative explanations are explored, specifically environmental variation in dissolved oxygen. The genetic connectivity between these geographically disparate sites suggests these three cephalopod species could be resilient to localized environmental disturbances in the Gulf of Mexico.

Introduction

Molecular approaches are powerful tools to investigate life history and population dynamics in enigmatic species, such as cephalopods (e.g. Dai et al., 2012; Vecchione et al., 2015; Judkins et al., 2016). This is especially true for midwater offshore species, which are difficult to collect and cannot be kept alive for study onshore. These difficulties have resulted in a paucity of information about their natural history (Hoving et al., 2014). Until recently, studies involving large samples of oceanic cephalopods in the Gulf of Mexico have been limited (Judkins et al., 2013, 2016). With so few specimens available, population genetics/genomics studies can provide unprecedented insight into the state and flux of diversity in these elusive species and allow us to make inferences regarding their life histories (Domínguez-Contreras et al., 2018).

Ecologically, cephalopods are crucial links in the world oceans: as predators of nekton and zooplankton, and as major food sources for nektonic fishes and mammals (Judkins, 2009). Cephalopod life-history strategies (high growth rates and short lifespans) allow them to contend with rapidly changing environmental conditions such as extreme climate change and anthropogenic influences like overfishing, pollution, etc. (Doubleday et al., 2016). Less is known about the impact of other aspects of life history (e.g., reproduction rates, development, migration patterns, diets, and diel vertical migratory (DVM) behavior) on cephalopod survival and adaptation (Hoving et al., 2014).

This study targets three cosmopolitan deep-sea cephalopod species with differing DVM behaviors: Cranchia scabra Leach, 1817 (Cranchiidae) (Fig. 1A), Pyroteuthis margaritifera (Ruppell, 1844) (Enoploteuthidae) (Fig. 1B), and Vampyroteuthis infernalis Chun, 1903 (Vampyroteuthidae) (Fig. 1C). These three species are abundant in the Gulf of Mexico and the western North Atlantic Ocean. Geographically, C. scabra is found in tropical and sub-tropical oceans worldwide (Jereb and Roper, 2010; Young and Mangold, 2016). In the Gulf, C. scabra occupies a large section of the water column, from the surface down to 1500 m depth (Fig. 1D), with little evidence of ontogenetic shift or vertical migration (Judkins and Vecchione, 2020, in press). Pyroteuthis margaritifera, the small (<5 cm mantle length) jewel Enope squid, is found throughout the water column in the North Atlantic and the Gulf, vertically migrating from the upper mesopelagic zone (~600 m depth) during the day to the surface and epipelagic zone at night (Young and Mangold, 2009) (Fig. 1E). Vampyroteuthis infernalis (the vampire squid) is found worldwide in tropical and temperate oceans (Jereb and Roper, 2010; Young, 2016), between 600 m–1500 m deep (Judkins and Vecchione, 2020, in press) (Fig. 1F).Vampire squid are unique in terms of reproductive cycle (evincing multiple reproductive cycles in their lifespan, instead of the single cycle characteristic of other coleoid cephalopods (Hoving et al., 2015)), and behavior (often passively feeding on marine snow in oxygen minimum zones (OMZs), unlike the active carnivory characteristic of other cephalopods (Hoving and Robison, 2012)). To date, only a few studies have examined large numbers of oceanic cephalopods in the Gulf of Mexico (Judkins et al., 2013, 2016) and, to date, no genetic studies have been undertaken to explore genetic connectivity or population dynamics in these three species.

Population genetic studies are sometimes the only realistic means of inferring life history and broader ecology of enigmatic species that are both difficult to observe and complicated to collect (Dai et al., 2012; Vecchione et al., 2015; Judkins et al., 2016; Domínguez-Contreras et al., 2018). Two metrics targeted in population genetics studies, genetic diversity and population structure, provide especially valuable information about the species at large, namely health and resilience, respectively (Cowen and Sponaugle, 2009; Danovaro et al., 2008; Hellberg et al., 2002; Hughes and Stachowicz, 2004). Genetic diversity is the number of alleles present within a population or species (Wright, 1931). Higher genetic diversity is characteristic of a healthy population, increasing a population's or species' ability to adapt to new environments or changing environmental conditions (Cowen and Sponaugle, 2009; Danovaro et al., 2008; Hughes and Stachowicz, 2004). Population structure can provide insight into historical gene flow, migration, and demography of a population, such as recent geographic separation or re-introduction and population size changes (Cowen et al., 2007). Ecologically, population structure can inform our understanding of species resilience: in the event of a localized perturbation, lack of structure among geographically separated groups can indicate gene flow between the affected group and a functional genetic reservoir outside the affected area (Cowen and Sponaugle, 2009; Hellberg et al., 2002).

This study focuses on the population genetics of three cephalopod species in the Gulf of Mexico and northwestern Atlantic. The biological importance of the Gulf of Mexico (Backus et al., 1977; Gartner, 1988; Sutton et al., 2017), in light of the frequent natural and anthropogenic perturbations it experiences (Kaiser, 2015; Soto et al., 2014; Murawski et al., 2018), is strong motivation for comparative study of population genetics in common Gulf species. Moreover, the information generated here fills a large and important data gap, namely by establishing reference states for the targeted species. Here, we define a “reference state” as a description of standing genetic variation and inferred connectivity in a species. Because so little is known about the biological impacts of the aforementioned disturbances, much less the rates and means of recovery, it is not possible to define a normal state or biological baseline with any degree of confidence.

To estimate this reference state, we used a powerful next-generation sequencing (NGS) method, double digest Restriction site Associated DNA sequencing (ddRADseq, as described by Peterson et al., 2012), in combination with traditional single-locus Sanger sequencing of three genes. This approach provided several notable benefits: Sanger data allowed us to decisively confirm species identifications with DNA barcoding and take advantage of analyses that have not yet been optimized for NGS, such as Tajima's D (Arnold et al., 2013). By conducting ddRADseq research in parallel, we were also able to complete the most comprehensive and statistically powerful analyses of genetic diversity and connectivity to date.

Utilizing this integrative approach, our overall objective was to improve our understanding of population dynamics of midwater cephalopods in the Gulf of Mexico and the northernwestern Atlantic by establishing reference states for three species (C. scabra, P. margaritifera, and V. infernalis). We sought to 1) describe the organization of genetic diversity within each species between the Gulf of Mexico and the Atlantic; 2) characterize the role of population connectivity in maintaining this organization; and 3) use these insights to make inferences about life history, ecology, and species health. To the best of our knowledge, the work we present here represents the first comparative population genomics study of deep-sea cephalopods.