Population Genetics of the Teleost Orange Roughy, Hoplostethus Atlanticus, and Insights into their Visual Adaptations to the Deep-Sea Environment

<p>The orange roughy, Hoplostethus atlanticus, has been one of the main targeted species in deep-sea fisheries worldwide. It occurs at depths of 450 – 1800 m and is abundant off the coasts of New Zealand, Australia, Namibia, Chile, and in the Northeast Atlantic Ocean. Like many other deep-sea fishes, orange roughy is vulnerable to over exploitation because they grow slow reaching maturity at about 30 years and live for more than 100 years. Their fecundity is low, which means they have low productivity. The individuals form predictable and dense spawning aggregations close to seamounts, plateaus and canyons. The trawl fishery for orange roughy started in seamounts around New Zealand in the late 1970s and progressively expanded off the coast of other countries and to the high seas (out of any Economic Exclusive Zone). Most stocks have been fished down to or below 30% pre-exploitation levels; as a consequence, fisheries have been closed or catches largely reduced. Currently, the only large scale fisheries operate off New Zealand. For effective fisheries management it is essential to define real biological units or “stocks”. There has been considerable research into the levels of population differentiation of orange roughy using a range of techniques at different geographic scales to attempt to differentiated stocks. However, there is no consensus about the level of connectivity among populations. In the present study, I investigated the levels of population differentiation in orange roughy using two types of neutral molecular markers at a global and fine-scales. Both markers revealed high levels of genetic diversity which is likely related with historically large population sizes. The analyses of 546 cytochrome c oxidase subunit I (COI) sequences revealed a lack of global genetic differentiation among samples from New Zealand, Australia, Namibia, and Chile. However, low but significant differentiation was found between the Southern hemisphere sites and two Northeast Atlantic sites. Mismatch distribution and Bayesian analyses indicated the occurrence of expansion events in orange roughy during the Pleistocene period. A data set of nine microsatellite DNA loci genotyped from 812 individuals, showed a predominant lack of significant genetic differentiation across the Tasman Sea and at a fine-scale around New Zealand. At a global scale, differentiation was low but significant across the Southern hemisphere; and the highest values of differentiation were detected between the Southern hemisphere sites and the Northeast Atlantic Ocean. The predominant lack of differentiation at the regional and fine-scale and the low differentiation within the Southern hemisphere is probably the result of stepping-stone dispersal of long-lived adults that are able to spawn many times in their life. Most orange roughy studies have been oriented to fisheries aspects, but other kind of studies as the genetic divergence and phylogenetic relationships among Hoplostethus species are lacking. Using available COI sequences, I conducted a phylogenetic study including H. atlanticus, H. crassispinus, H. gigas, H. japonicus H. latus, and H. mediterraneus. As expected, the inter species divergence was much higher than the intra species divergence. Phylogenetics analyses showed that H. latus, H. crassispinus, H. japonicus, and H. mediterraneus form a separate clade from H. atlanticus and H. gigas. The position of H. gigas was not well defined with the nucleotide data. However, at the amino acid level, non-synonymous substitutions differentiated H. atlanticus from all the other species. This was correlated with morphological characteristics presented elsewhere. A candidate gene approach was attemped using the rhodopsin gene; however, there was almost no variation among partial sequences of individuals from distant sites. Instead, this gene was used to investigate the molecular basis for visual adaptations in orange roughy to the bathypelagic light environment. It is known that certain amino acid replacements in the rhodopsin gene of vertebrates shift the λmax value of the pigment to perceive different light conditions. To compare and identify critical amino acid sites that are known to be involved in spectral tuning, I obtained partial rhodopsin sequences of other 18 marine teleost habiting at different depths (1 – 1,175 m) and, thus, different light environments. A phylogenetic analysis was conducted to determine whether particular rhodopsin gene sequences correlate with the depths occupied by the species. I identified four critical amino acid replacements that have been involved in the spectral tuning of rod pigments. Orange roughy presented the same amino acid combination at two critical sites already reported for the deep-sea congener silver roughy, which was not found in any of the other species. This likely reflects an adaptation to the light available (i.e. bioluminescence) in the bathypelagic environment. The phylogeny was weakly related to the maximum depth of the species, probably because there are selectively neutral (i.e. inherited by ancestry) and non-neutral changes (i.e. influenced by natural selection) among the rhodopsin sequences of the species being considered.</p>

Population Genetics of the Teleost Orange Roughy, Hoplostethus Atlanticus, and Insights into their Visual Adaptations to the Deep-Sea Environment

<p>The orange roughy, Hoplostethus atlanticus, has been one of the main targeted species in deep-sea fisheries worldwide. It occurs at depths of 450 – 1800 m and is abundant off the coasts of New Zealand, Australia, Namibia, Chile, and in the Northeast Atlantic Ocean. Like many other deep-sea fishes, orange roughy is vulnerable to over exploitation because they grow slow reaching maturity at about 30 years and live for more than 100 years. Their fecundity is low, which means they have low productivity. The individuals form predictable and dense spawning aggregations close to seamounts, plateaus and canyons. The trawl fishery for orange roughy started in seamounts around New Zealand in the late 1970s and progressively expanded off the coast of other countries and to the high seas (out of any Economic Exclusive Zone). Most stocks have been fished down to or below 30% pre-exploitation levels; as a consequence, fisheries have been closed or catches largely reduced. Currently, the only large scale fisheries operate off New Zealand. For effective fisheries management it is essential to define real biological units or “stocks”. There has been considerable research into the levels of population differentiation of orange roughy using a range of techniques at different geographic scales to attempt to differentiated stocks. However, there is no consensus about the level of connectivity among populations. In the present study, I investigated the levels of population differentiation in orange roughy using two types of neutral molecular markers at a global and fine-scales. Both markers revealed high levels of genetic diversity which is likely related with historically large population sizes. The analyses of 546 cytochrome c oxidase subunit I (COI) sequences revealed a lack of global genetic differentiation among samples from New Zealand, Australia, Namibia, and Chile. However, low but significant differentiation was found between the Southern hemisphere sites and two Northeast Atlantic sites. Mismatch distribution and Bayesian analyses indicated the occurrence of expansion events in orange roughy during the Pleistocene period. A data set of nine microsatellite DNA loci genotyped from 812 individuals, showed a predominant lack of significant genetic differentiation across the Tasman Sea and at a fine-scale around New Zealand. At a global scale, differentiation was low but significant across the Southern hemisphere; and the highest values of differentiation were detected between the Southern hemisphere sites and the Northeast Atlantic Ocean. The predominant lack of differentiation at the regional and fine-scale and the low differentiation within the Southern hemisphere is probably the result of stepping-stone dispersal of long-lived adults that are able to spawn many times in their life. Most orange roughy studies have been oriented to fisheries aspects, but other kind of studies as the genetic divergence and phylogenetic relationships among Hoplostethus species are lacking. Using available COI sequences, I conducted a phylogenetic study including H. atlanticus, H. crassispinus, H. gigas, H. japonicus H. latus, and H. mediterraneus. As expected, the inter species divergence was much higher than the intra species divergence. Phylogenetics analyses showed that H. latus, H. crassispinus, H. japonicus, and H. mediterraneus form a separate clade from H. atlanticus and H. gigas. The position of H. gigas was not well defined with the nucleotide data. However, at the amino acid level, non-synonymous substitutions differentiated H. atlanticus from all the other species. This was correlated with morphological characteristics presented elsewhere. A candidate gene approach was attemped using the rhodopsin gene; however, there was almost no variation among partial sequences of individuals from distant sites. Instead, this gene was used to investigate the molecular basis for visual adaptations in orange roughy to the bathypelagic light environment. It is known that certain amino acid replacements in the rhodopsin gene of vertebrates shift the λmax value of the pigment to perceive different light conditions. To compare and identify critical amino acid sites that are known to be involved in spectral tuning, I obtained partial rhodopsin sequences of other 18 marine teleost habiting at different depths (1 – 1,175 m) and, thus, different light environments. A phylogenetic analysis was conducted to determine whether particular rhodopsin gene sequences correlate with the depths occupied by the species. I identified four critical amino acid replacements that have been involved in the spectral tuning of rod pigments. Orange roughy presented the same amino acid combination at two critical sites already reported for the deep-sea congener silver roughy, which was not found in any of the other species. This likely reflects an adaptation to the light available (i.e. bioluminescence) in the bathypelagic environment. The phylogeny was weakly related to the maximum depth of the species, probably because there are selectively neutral (i.e. inherited by ancestry) and non-neutral changes (i.e. influenced by natural selection) among the rhodopsin sequences of the species being considered.</p>

Draft Genome Sequence of Salegentibacter sp. Strain BDJ18, a Plankton-Associated Bacterium in the Northeast Atlantic Ocean

Salegentibacter sp. strain BDJ18 was isolated from a plankton-associated seawater sample from the northeast Atlantic Ocean. We report its draft genome assembly, which includes genes potentially important for microbial interactions in the marine environment.

Regional patterns of δ 13 C and δ 15 N for European common cuttlefish ( Sepia officinalis ) throughout the Northeast Atlantic Ocean and Mediterranean Sea

Stable isotope compositions of carbon and nitrogen (expressed as δ 13 C and δ 15 N) from the European common cuttlefish ( Sepia officinalis ) were measured in order to evaluate the utility of using these natural tracers throughout the Northeast Atlantic Ocean and Mediterranean Sea (NEAO-MS). Mantle tissue was obtained from S. officinalis collected from 11 sampling locations spanning a wide geographical coverage in the NEAO-MS. Significant differences of both δ 13 C and δ 15 N values were found among S. officinalis samples relative to sampling location. δ 13 C values did not show any discernable spatial trends; however, a distinct pattern of lower δ 15 N values in the Mediterranean Sea relative to the NEAO existed. Mean δ 15 N values of S. officinalis in the Mediterranean Sea averaged 2.5‰ lower than conspecifics collected in the NEAO and showed a decreasing eastward trend within the Mediterranean Sea with the lowest values in the most eastern sampling locations. Results suggest δ 15 N may serve as a useful natural tracer for studies on the population structure of S. officinalis as well as other marine organisms throughout the NEAO-MS.

Modelling collective navigation via non-local communication

Collective migration occurs throughout the animal kingdom, and demands both the interpretation of navigational cues and the perception of other individuals within the group. Navigational cues orient individuals towards a destination, while it has been demonstrated that communication between individuals enhances navigation through a reduction in orientation error. We develop a mathematical model of collective navigation that synthesizes navigational cues and perception of other individuals. Crucially, this approach incorporates uncertainty inherent to cue interpretation and perception in the decision making process, which can arise due to noisy environments. We demonstrate that collective navigation is more efficient than individual navigation, provided a threshold number of other individuals are perceptible. This benefit is even more pronounced in low navigation information environments. In navigation ‘blindspots’, where no information is available, navigation is enhanced through a relay that connects individuals in information-poor regions to individuals in information-rich regions. As an expository case study, we apply our framework to minke whale migration in the northeast Atlantic Ocean, and quantify the decrease in navigation ability due to anthropogenic noise pollution.

Tracking the rising extinction risk of sharks and rays in the Northeast Atlantic Ocean and Mediterranean Sea

The loss of biodiversity is increasingly well understood on land, but trajectories of extinction risk remain largely unknown in the ocean. We present regional Red List Indices (RLIs) to track the extinction risk of 119 Northeast Atlantic and 72 Mediterranean shark and ray species primarily threatened by overfishing. We combine two IUCN workshop assessments from 2003/2005 and 2015 with a retrospective backcast assessment for 1980. We incorporate predicted categorisations for Data Deficient species from our previously published research. The percentage of threatened species rose from 1980 to 2015 from 29 to 41% (Northeast Atlantic) and 47 to 65% (Mediterranean Sea). There are as many threatened sharks and rays in Europe as there are threatened birds, but the threat level is nearly six times greater by percentage (41%, n = 56 of 136 vs. 7%, n = 56 of 792). The Northeast Atlantic RLI declined by 8% from 1980 to 2015, while the higher-risk Mediterranean RLI declined by 13%. Larger-bodied, shallow-distributed, slow-growing species and those with range boundaries within the region are more likely to have worsening status in the Northeast Atlantic. Conversely, long-established, severe threat levels obscure any potential relationships between species’ traits and the likelihood of worsening IUCN status in the Mediterranean Sea. These regional RLIs provide the first widespread evidence for increasing trends in regional shark and ray extinction risk and underscore that effective fisheries management is necessary to recover the ecosystem function of these predators.

Dispersal ability, habitat characteristics, and sea-surface circulation shape population structure of Cingula trifasciata (Gastropoda: Rissoidae) in the remote Azores Archipelago

Background In the marine realm, dispersal ability is among the major factors shaping the distribution of species. In the Northeast Atlantic Ocean, the Azores Archipelago is home to a multitude of marine invertebrates which, despite their dispersal limitations, maintain gene flow among distant populations, with complex evolutionary and biogeographic implications. The mechanisms and factors underlying the population dynamics and genetic structure of non-planktotrophic gastropods within the Azores Archipelago and related mainland populations are still poorly understood. The rissoid Cingula trifasciata is herewith studied to clarify its population structure in the Northeast Atlantic Ocean and factors shaping it, with a special focus in intra-archipelagic dynamics. Results Coupling microsatellite genotyping by amplicon sequencing (SSR-GBAS) and mitochondrial datasets, our results suggest the differentiation between insular and continental populations of Cingula trifasciata, supporting previously raised classification issues and detecting potential cryptic diversity. The finding of connectivity between widely separated populations was startling. In unique ways, dispersal ability, habitat type, and small-scale oceanographic currents appear to be the key drivers of C. trifasciata’s population structure in the remote Azores Archipelago. Dispersal as non-planktotrophic larvae is unlikely, but its small-size adults easily engage in rafting. Although the typical habitat of C. trifasciata, with low hydrodynamics, reduces the likelihood of rafting, individuals inhabiting algal mats are more prone to dispersal. Sea-surface circulation might create dispersal pathways for rafts, even between widely separated populations/islands. Conclusions Our results show that gene flow of a marine non-planktotrophic gastropod within a remote archipelago can reveal unanticipated patterns, such that the understanding of life in such areas is far from well-understood. We expect this work to be the starting of the application of SSR-GBAS in other non-model marine invertebrates, providing insights on their population dynamics at distinct geographical scales and on hidden diversity. How transversal is the role played by the complex interaction between functional traits, ecological features, and sea-surface circulation in the population structure of marine invertebrates can be further addressed by expanding this approach to more taxa.

Growth patterns of the lanternfish Ceratoscopelus maderensis in the western Mediterranean Sea

The age and growth patterns of the mesopelagic fish Ceratoscopelus maderensis (family Myctophidae) of the western Mediterranean Sea were described throughout its entire life cycle (from larvae to adult stages) using the sagittae otoliths of 59 individuals collected in December 2009. Three characteristic zones were identified along the cross-section of the sagittae (larval, metamorphic and juvenile-adult zones). Assuming growth rings as daily increments, the age of the analysed individuals (from 3.5 to 64 mm standard length [SL]) would range from 7 to 332 days. The relationship between the number of increments and the fish SL was fitted to a von Bertalanffy growth model (SL=70.5899Å~(1–exp(–0.0501(t+2.6705))). The growth pattern of C. maderensis in the western Mediterranean Sea was similar to that reported for this species in the northeast Atlantic Ocean. Though from a body size of 40-45 mm SL, growth rates declined more slowly in individuals from the western Mediterranean Sea, growth differences between these individuals and those from the northeast Atlantic Ocean were not statistically significant. This study provides new insights into the age and growth patterns of one of the most abundant mesopelagic fish species in the Mediterranean Sea that have clear implications for the study and management of marine ecosystems.