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96 results for “scalloped”
Chromosome-level genome assembly of the bay scallop Argopecten irradians
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Data from: Identifying patterns of dispersal, connectivity, and selection in the sea scallop, Placopecten magellanicus, using RAD-seq derived SNPs
Understanding patterns of dispersal and connectivity among marine populations can directly inform fisheries conservation and management. Advances in high-throughput sequencing offer new opportunities for estimating marine connectivity. We used Restriction-site Associated DNA sequencing to examine dispersal and realized connectivity in the sea scallop Placopecten magellanicus, an economically important marine bivalve. Based on 245 individuals sampled range-wide at 12 locations from Newfoundland to the Mid-Atlantic Bight we identified and genotyped 7163 Single Nucleotide Polymorphisms; 112 (1.6%) were identified as outliers potentially under directional selection. Bayesian clustering revealed a discontinuity between northern and southern samples and latitudinal clines in allele frequencies were observed in 42.9% of the outlier loci and in 24.6% of neutral loci. Dispersal estimates derived using these clines and estimates of linkage disequilibrium imply limited dispersal; 373.1 ± 407.0 km (mean ± SD) for outlier loci and 641.0 ± 544.6 km (mean ± SD) for neutral loci. Our analysis suggests restricted dispersal compared to the species range (>2000 km) and that dispersal and effective connectivity differ. These observations support the hypothesis that limited effective dispersal structures scallop populations along eastern North America. These findings can help refine the appropriate scale of management and conservation in this commercially valuable species.
Data from: Fine-scale temperature associated genetic structure between inshore and offshore populations of sea scallop (Placopecten magellanicus)
In the northwest Atlantic Ocean, sea scallop (Placopecten magellanicus) have been characterized by a latitudinal genetic cline with a breakpoint between northern and southern genetic clusters occurring at ~45°N along eastern Nova Scotia, Canada. Using 96 diagnostic single nucleotide polymorphisms (SNPs) capable of discriminating between northern and southern clusters, we examined fine-scale genetic structure of scallops among 27 sample locations, spanning the largest geographic range evaluated in this species to date (~37-51°N). Here, we confirmed previous observations of northern and southern groups, but we show that the boundary between northern and southern clusters is not a discrete latitudinal break. Instead, at latitudes near the previously described boundary, we found unexpected patterns of fine-scale genetic structure occurring between inshore and offshore sites. Scallops from offshore sites, including St. Pierre Bank and the eastern Scotian Shelf, clustered with southern stocks, whereas inshore sites at similar latitudes clustered with northern stocks. Our analyses revealed significant genetic divergence across small spatial scales (i.e., 129 to 221 km distances), and that spatial structure over large and fine scales was strongly associated with temperature during seasonal periods of thermal minima. Clear temperature differences between inshore and offshore locations may explain the fine-scale structuring observed, such as why southern lineages of scallop occur at higher latitudes in deeper, warmer offshore waters. Our study supports growing evidence that fine-scale population structure in marine species is common, often environmentally associated, and that consideration of environmental and genomic data can significantly enhance the identification of marine diversity and management units.
Data from: Emerging patterns of genetic variation in the New Zealand endemic scallop Pecten novaezelandiae
Both historical and contemporary processes influence the genetic structure of species, but the relative roles of such processes are still difficult to access. Population genetic studies of species with recent evolutionary histories such as the New Zealand endemic scallop Pecten novaezelandiae (<1 Ma) permit testing of the effects of recent processes affecting gene flow and shaping genetic structure. In addition, studies encompassing the entire distributional range of species can provide insight into colonization processes. Analyses of genetic variation in P. novaezelandiae (952 individuals from 14 locations, genotyped at 10 microsatellite loci) revealed a weak but significant regional structure across the distributional range of the species, as well as latitudinal gradients of genetic diversity and differentiation: estimates of migration rates supported these patterns. Our results suggest that the observed genetic structure and latitudinal gradients reflect a stepping-stone model of colonization (north to south) and emerging divergence of populations as a result of ongoing limitations to gene flow and insufficient time to reach migration–drift equilibrium. The low levels of interpopulation and interregional genetic differentiation detected over hundreds of kilometres reflect the recent evolutionary history of P. novaezelandiae and stand in contrast to patterns reported for other evolutionary older species at the same spatial scale. The outcomes of this study contribute to a better understanding of evolutionary processes influencing the genetic variation of species and provide vital information on the genetic structure of P. novaezelandiae.
Data from: Conservation genetics of the scalloped hammerhead shark in the Pacific coast of Colombia
Previous investigations of the population genetics of the scalloped hammerhead sharks (Sphyrna lewini) in the Eastern Tropical Pacific have lacked information about nursery areas. Such areas are key to promoting conservation initiatives that can protect young sharks from threats such as overfishing. Here, we investigated the genetic diversity, phylogeography, and connectivity of S. lewini found in 3 areas of Colombia's Pacific coast: around Malpelo Island and in 2 National Natural Parks on the Colombian Pacific mainland (Sanquianga and Ensenada de Utría). We analyzed mtDNA control region (CR) sequences and genotyped 15 microsatellite loci in 137 samples of adults and juveniles. The mtDNA analyses showed haplotypes shared between the Colombian Pacific individuals sampled in this investigation and other areas in the Eastern Tropical Pacific, the Indo-Pacific, and with sequences previously reported in Colombia (Buenaventura Port), as well as 4 unique haplotypes. Population assignment and paternity analyses detected 3 parent–offspring pairs between Malpelo and Sanquianga and 1 between Malpelo and Utría. These results indicate high genetic connectivity between Malpelo Island and the Colombian Pacific coast, suggesting that these 2 areas are nurseries for S. lewini. This is, to our knowledge, the first evidence of nursery areas identified for the scalloped hammerhead shark anywhere in the world. Additional conservation planning may be required to protect these nursery habitats of this endangered shark species.
Data from: Stock enhancement or sea ranching? Insights from monitoring the genetic diversity, relatedness and effective size in a seeded great scallop population (Pecten maximus)
The mass release of hatchery-propagated stocks raises numerous questions concerning its efficiency in terms of local recruitment and effect on the genetic diversity of wild populations. A seeding program, consisting of mass release of hatchery-produced juveniles in the local naturally occurring population of great scallops (Pecten maximus L.), was initiated in the early 1980s in the Bay of Brest (France). The present study aims at evaluating whether this seeding program leads to actual population enhancement, with detectable effects on genetic diversity and effective population size, or consists of sea ranching with limited genetic consequences on the wild stock. To address this question, microsatellite-based genetic monitoring of three hatchery-born and naturally recruited populations was conducted over a 5-year period. Results showed a limited reduction in allelic richness but a strong alteration of allelic frequencies in hatchery populations, while genetic diversity appeared very stable over time in the wild populations. A temporal increase in relatedness was observed in both cultured stock and wild populations. Effective population size (Ne) estimates were low and variable in the wild population. Moreover, the application of the Ryman-Laikre model suggested a high contribution of hatchery-born scallops to the reproductive output of the wild population. Overall, the data suggest that the main objective of the seeding program, which is stock enhancement, is fulfilled. Moreover, gene flow from surrounding populations and/or the reproductive input of undetected sub-populations within the bay may buffer the Ryman-Laikre effect and ensure the retention of the local genetic variability.
Data for Scallop (Pecten maximus) Identification in Natural Marine Habitats: A NetHarn Model Approach.
<p>The data have been divided into distinct training and testing subsets, each encompassing still images corresponding to individual stations along with their respective annotations or predictions as CSV files.</p><p>This research explores the potential of Artificial Intelligence (AI), specifically the NetHarn model provided by the VIAME toolkit, to identify and count king and queen scallops from towed underwater video transects. The study utilizes video footage from NatureScot, captured using custom camera systems (DDV and miniDDV), providing a diverse dataset with variations in habitat, image quality, and camera specifications. Necessary details from the original report by Pascoe et al. (2021) are provided in the manuscript.</p><p>Pasco, G., James, B., Burke, L., Johnston, C., Orr, K., Clarke, J., Thorburn, J., Boulcott, P., Kent, F., Kamphausen, L. and Sinclair, R. (2021) 'Engaging the Fishing Industry in Marine Environmental Survey and Monitoring Scottish Marine and Freshwater Science Vol 12 No 3'. doi:10.7489/12365-1</p>
Supplemental documents for: Temperature-associated selection linked to putative chromosomal inversions in king scallop (Pecten maximus)
<p>The genomic landscape of divergence – the distribution of differences among populations or species across the genome – is increasingly characterized to understand the role that microevolutionary forces such as natural selection and recombination play in causing and maintaining genetic divergence. This line of inquiry has also revealed chromosome structure variation to be an important factor shaping the landscape of adaptive genetic variation. Due to a high prevalence of chromosome structure variation and the strong pressure for local adaptation necessitated by their sessile nature, bivalve molluscs are an ideal taxon for exploring the relationship between chromosome structure variation and local adaptation. Here, we report a population genomic survey of king scallop (<em>Pecten</em> <em>maximus</em>) across its natural range in the northeastern Atlantic Ocean, utilizing a recent chromosome-level genome assembly. We report the presence of at least three large (12-22 Mb), putative chromosomal inversions associated with sea surface temperature and whose frequencies are in contrast to neutral population structure. These results highlight a potentially large role for recombination-suppressing chromosomal inversions in local adaptation and suggest a hypothesis to explain the maintenance of differences in reproductive timing found at relatively small spatial scales across king scallop populations.</p>
Fig. 7 in Untangling the diversity and evolution of tentacles in scallops, oysters, and their relatives (Bivalvia: Pteriomorphia)
Fig. 7 Middle fold tentacles (MFT) in Pectinida. Proximal (arrows) and distal (arrowheads) submarginal tentacles in Limidae (a–e), Dimyidae (f), Plicatulidae (g), Anomiidae (h–j), Spondylidae (k), Propeamussiidae (l), and Pectinidae (m–p). Longitudinal grooves are indicated by ">". Scale bars = 1 mm. a Limatula hodgsoni (USNM882395). b Lima lima USNM754383. c Acesta oophaga (USNM1263635). d Ctenoides scaber (USNM833716). e Limaria orbignyi (SBMNH19892). f Dimya argentea
Fig. 6 in Untangling the diversity and evolution of tentacles in scallops, oysters, and their relatives (Bivalvia: Pteriomorphia)
Fig. 6 Middle fold tentacles (MFT) in Ostreida. Submarginal tentacles in Ostreidae (a–d) and Gryphaeidae (e–f) and marginal tentacles in Malleidae (g), Pteriidae (h), Isognomonidae (i), Margaritidae (j), and Vulsellidae (k–l). Submarginal tentacles include proximal (arrows) and distal (arrowheads) tentacles (a–f). Marginal tentacles are indicated by arrows in g–l. Scale bars = 1 mm. a Ostrea edulis (USNM836256). b Crassostrea virginica (USNM804279). c Dendostrea folium (USNM802346). d Striostrea prismatica (SBMNH211884). e Hyotissa hyotis (MCZ378999). f Neopycnodonte cochlear (MCZ379076). g Malleus candeanus (MCZ340681). h Pteria hirundo (ZUECBIV1401). i Isognomon isognomum (MZSP54988). j Pinctada imbricata (MZSP106549). k Vulsella minor (USNM896263). l Electroma alacorvi (USNM801689)
Fig. 5 in Untangling the diversity and evolution of tentacles in scallops, oysters, and their relatives (Bivalvia: Pteriomorphia)
Fig. 5 Inner fold tentacles (IFT) in Pectinida. Marginal tentacles in Spondylidae (a–c) and submarginal in Pectinidae (d–o). Scale bars = 1 mm. a Schematic representation of marginal IFT (arrows), as observed in b and c. b Spondylus americanus (USNM833744). c Spondylus squamosus (USNM793728). d Schematic representation of submarginal IFT (arrowheads) in a single row, as observed in e–g. e Euvola raveneli (USNM801009). f Amusium sp. (USNM804083). g Crassodoma gigantea (SBMNH466682). h Schematic representation of submarginal
Fig. 3 in Untangling the diversity and evolution of tentacles in scallops, oysters, and their relatives (Bivalvia: Pteriomorphia)
Fig. 3 Tentacle evolution in Pteriomorphia (Bivalvia). Maximum likelihood estimations of inner fold tentacles (IFT) in a and middle fold tentacles (MFT) in b. The clade Pteriomorphia is indicated by the gray box. Family names are in black, superfamily names in gray, and orders in bold. Likelihood proportions for ancestral states (presence and absence) are indicated in pie charts. a Four independent gains of IFT: in the ancestor of Pectinidae, in the ancestor of Spondylidae, in the ancestor of Plicatulidae, and in the ancestor of all Ostreida. b Two independent gains of MFT: in the ancestor of Pectinida + Limida and in the ancestor of the clade Ostreoidea + Pterioidea
Figure 3 in Morphological convergence of shell shape in distantly related scallop species (Mollusca: Pectinidae)
Figure 3. Principal component plot of shell shape variation for specimens used in this study. The first three principal component (PC) axes explain 75.8% of the total variation in shell shape (PC1 = 57.3%; PC2 = 11.6%; PC3 = 6.9%). (A) Shape variation along PC1 and PC2 with photographs of representative individuals for each species. Scale bars = 1 cm. (B) Shape variation along PC1 and PC3. Species are designated as: Amusium pleuronectes (blue squares), 'Amusium' balloti (blue circles), Argopecten irradians (red squares), Argopecten purpuratus (red circles), Chlamys behringiana (green triangles), Caribachlamys sentis (green diamonds), Pseudamussium septemradiatus (white inverted triangles).
Figure 2 in Morphological convergence of shell shape in distantly related scallop species (Mollusca: Pectinidae)
Figure 2. Maximum likelihood estimation of ancestral behaviours using a symmetrical likelihood model (Mk1) on an independently derived multigene Bayesian majority-rule consensus tree. Pie diagrams show character states and their proportion at each node. Taxa highlighted in blue represent long-distance swimming species; taxa in bold represent the seven species examined in our quantitative morphometric analyses of shell shape.
Figure 1 in Morphological convergence of shell shape in distantly related scallop species (Mollusca: Pectinidae)
Figure 1. Three-dimensional surface scan of the left valve of a representative scallop, with the positions of 506 landmarks and semilandmarks indicated. Fixed landmarks are shown as numbered, open circles (Landmark 1: ventroposterior auricle, 2: dorsoposterior auricle, 3: umbo, 4: dorsoanterior auricle, 5: ventroanterior auricle), semilandmarks along the ventral edge of the valve are shown as closed circles, and surface semilandmarks on the scallop valve are shown as grey circles. Dorso-ventral and antero-posterior axes are provided.
Data for: Warming and hypoxia reduce performance and survival of northern bay scallops, Argopecten irradians irradians, amid a fishery collapse
<p>Populations of the northern bay scallop, <em>Argopecten</em> <em>irradians</em> <em>irradians</em>, across the northeast US have recently experienced severe declines. Here we used high-resolution satellite-based temperature records, long-term temperature and dissolved oxygen records, field and laboratory experiments, and high-frequency measures of scallop cardiac activity in an ecosystem setting to quantify decadal summer warming and assess the vulnerability of northern bay scallops to thermal- and hypoxic-stress across their geographic distribution. This set of files contains the raw data analyzed for this study. The data are grouped into relevant subfolders: Commercial Landings Data; Field Deployment Data; Gonad Index Data; Laboratory Data; Optical Infrared Sensor Data; Remote Sensing Data.</p>
Anatomical Feasibility of an Off-the-shelf Scalloped Stent-graft for Infrarenal Abdominal Aneurysm With a Hostile Neck
ClinicalTrials.gov study NCT05150873. IPD Sharing: NO. Countries: 1. Publications: 10.
Clinical Effectiveness of an Off-the-shelf Single REnal Scalloped sTent-graft for HOstile NEck Infrarenal Abdominal Aortic Aneurysm
ClinicalTrials.gov study NCT05609539. IPD Sharing: Not stated. Countries: 1. Publications: 15.
Data from: Identifying patterns of dispersal, connectivity, and selection in the sea scallop, Placopecten magellanicus, using RAD-seq derived SNPs
Open the record for dataset details and reuse information.
Data from: Fine-scale temperature associated genetic structure between inshore and offshore populations of sea scallop (Placopecten magellanicus)
Open the record for dataset details and reuse information.
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