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  • 1
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    NGS barcoding reveals high resistance of a hyperdiverse chironomid (Diptera) swamp fauna against invasion from adjacent freshwater reservoirs (2021)
    BioMed Central
    In:  http://aquaticcommons.org/id/eprint/25902 | 20794 | 2018-09-26 06:38:40 | 25902 | Department of Biological Sciences, National University of Singapore
    Details
    Publication Date: 2021-07-16
    Description: Background. Macroinvertebrates such as non-biting midges (Chironomidae: Diptera) are important components of freshwater ecosystems. However, they are often neglected in biodiversity and conservation research because invertebrate species richness is difficult and expensive to quantify with traditional methods. We here demonstrate that Next Generation Sequencing barcodes (“NGS barcodes”) can provide relief because they allow for fast and large-scale species-level sorting of large samples at low cost. Results. We used NGS barcoding to investigate the midge fauna of Singapore’s swamp forest remnant (Nee Soon Swamp Forest). Based on 〉 14.000 barcoded specimens, we find that the swamp forest maintains an exceptionally rich fauna composed of an observed number of 289 species (estimated 336 species) in a very small area (90 ha). We furthermore barcoded the chironomids from three surrounding reservoirs that are located in close proximity. Although the swamp forest remnant is much smaller than the combined size of the freshwater reservoirs in the study (90 ha vs. 〉 450 ha), the latter only contains 33 (estimated 61) species. We show that the resistance of the swamp forest species assemblage is high because only 8 of the 314 species are shared despite the close proximity. Moreover, shared species are not very abundant (3% of all specimens). A redundancy analysis revealed that ~ 21% of the compositional variance of midge communities within the swamp forest was explained by a range of variables with conductivity, stream order, stream width, temperature, latitude (flow direction), and year being significant factors influencing community structure. An LME analysis demonstrates that the total species richness decreased with increasing conductivity. Conclusion. Our study demonstrates that midge diversity of a swamp forest can be so high that it questions global species diversity estimates for Chironomidae, which are an important component of many freshwater ecosystems. We furthermore demonstrate that small and natural habitat remnants can have high species turnover and can be very resistant to the invasion of species from neighboring reservoirs. Lastly, the study shows how NGS barcodes can be used to integrate specimen- and species-rich invertebrate taxa in biodiversity and conservation research.
    Keywords: Ecology ; Environment ; Limnology
    Repository Name: AquaDocs
    Type: article , TRUE
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    Format: 31
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  • 2
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    A guide to the Thalassinidea (Crustacea: Malacostraca: Decapoda) of the South Atlantic Bight (2021)
    NOAA/National Marine Fisheries Service | Seattle, WA
    In:  http://aquaticcommons.org/id/eprint/2477 | 403 | 2011-09-29 19:06:51 | 2477 | United States National Marine Fisheries Service
    Details
    Publication Date: 2021-07-13
    Description: Ghost shrimp and mud shrimp in the decapod infraorder Thalassinidea are ecologically important members of manybenthic intertidal and shallow subtidal infaunal communities, largely due to the sediment filtration and mixing that result from their burrowing and feeding behavior. These activities considerably modify their immediate environment and have made these cryptic animals extremely interesting to scientists in terms of their behavior, ecology, and classification.Over 20 years ago, seven species of thalassinideans were known from the South Atlantic Bight (Cape Hatteras, NC to Cape Canaveral, FL). During this study, the examinationof extensive collections from the National Museum of Natural History (NMNH), the Southeastern Regional Taxonomic Center (SERTC), and regional institutions, resultedin the identification of 14 species of thalassinideanscurrently known to occur within this region. The family Axiidae is represented by three species: Axius armatus, Calaxius jenneri, and Paraxiopsis gracilimana; the Callianassidae by six: Biffarius biformis, B. cf. fragilis, Callichirus major, Cheramus marginatus, Gilvossius setimanus, and Necallianassa berylae; the Calocarididae by two: Calocaris templemani and Acanthaxius hirsutimanus; andthe families Laomediidae, Thomassiniidae, and Upogebiidae are each represented by one: Naushonia crangonoides, Crosniera wennerae, and Upogebia affinis, respectively. Anillustrated key is presented for species level identification and supplemental notes on the ecology, distribution, and taxonomy of the species are provided.(PDF file contains 38 pages.)
    Keywords: Ecology ; Management ; Fisheries
    Repository Name: AquaDocs
    Type: monograph
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  • 3
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    Genetic and morphological identification of pelagic juvenile rockfish collected from the Gulf of Alaska (2021)
    NOAA/National Marine Fisheries Service | Seattle, WA
    In:  http://aquaticcommons.org/id/eprint/2476 | 403 | 2014-02-21 01:10:02 | 2476 | United States National Marine Fisheries Service
    Details
    Publication Date: 2021-07-13
    Description: Pelagic juvenile rockfish (Sebastes spp.) collected in surveys designed to assess juvenile salmonids and other species in the Gulf of Alaska in 1998 and 2000–2003provide an opportunity to document the occurrence of the pelagic juveniles of several species of rockfish. Often, species identification of rockfish is difficult or impossible at this stage of development (~20 to 60 mm),and few species indigenous to Alaska waters have been described. Use of mitochondrial DNA markers for rockfish species allowed unequivocal identification of ten species (S. aleutianus, S. alutus, S. borealis, S. entomelas, S.flavidus, S. melanops, S. pinniger, S. proriger, S. reedi, and S. ruberrimus) in subsamples from the collections. Other specimens were genetically assignable to groups of two or three species. Sebastes borealis, S. crameri, and S. reedi were identified using morphological data. Combining genetic and morphological data allowed successful resolution of the other species as S. emphaeus, probably S. ciliatus (although S. polyspinis cannot be totally ruled out), and S. polyspinis. Many specimens were initially morphologically indistinguishable from S. alutus, and several morphological groups included fish geneticallyidentified as S. alutus. This paper details the characteristics of these pelagic juveniles to facilitate morphological identification of these species in future collections. (PDF file contains 32 pages.)
    Keywords: Ecology ; Management ; Fisheries
    Repository Name: AquaDocs
    Type: monograph
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  • 4
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    Emerging technologies for reef fisheries research and management [held during the 56th annual Gulf and Caribbean Fisheries Institute meeting in Tortola, British Virgin Islands, November 2003] (2021)
    NOAA/National Marine Fisheries Service | Seattle, WA
    In:  http://aquaticcommons.org/id/eprint/2480 | 403 | 2011-09-29 18:56:12 | 2480 | United States National Marine Fisheries Service
    Details
    Publication Date: 2021-07-13
    Description: This publication of the NOAA Professional Paper NMFS Seriesis the product of a special symposium on “Emerging Technologies for Reef Fisheries Research and Management” held during the 56th annual Gulf and Caribbean Fisheries Institute meeting in Tortola, British Virgin Islands, November 2003. The purpose of this collection is to highlight the diversity of questions and issues in reeffisheries management that are benefiting from applications of technology. Topics cover a wide variety of questions and issues from the study of individual behavior, distribution and abundance of groups and populations, and associations between habitats and fish and shellfish species.(PDF files contains 124 pages.)
    Keywords: Ecology ; Management ; Fisheries
    Repository Name: AquaDocs
    Type: monograph
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  • 5
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    A video method for quantifying size distribution, density, and three-dimensional spatial structure of reef fish spawning aggregations (2021)
    NOAA | Seattle, WA
    In:  http://aquaticcommons.org/id/eprint/2483 | 403 | 2011-09-29 18:56:32 | 2483 | United States National Marine Fisheries Service
    Details
    Publication Date: 2021-07-13
    Description: There is a clear need to develop fisheries independent methods to quantify individual sizes, density, and three dimensional characteristics of reef fish spawning aggregations for use in population assessments and to provide critical baseline data on reproductive life history of exploited populations. We designed, constructed, calibrated, and applied an underwater stereo-video systemto estimate individual sizes and three dimensional (3D) positions of Nassau grouper (Epinephelus striatus) at a spawning aggregation site located on a reef promontory on the western edge of Little Cayman Island, Cayman Islands, BWI, on 23 January 2003. The system consists of two free-running camcorders mounted on a meter-long bar and supported by a SCUBA diver. Paired video “stills” werecaptured, and nose and tail of individual fish observed in the field of view of both cameras were digitized using imageanalysis software. Conversion of these two dimensional screen coordinates to 3D coordinates was achieved through a matrix inversion algorithm and calibration data. Our estimate of mean total length (58.5 cm, n = 29) was in close agreement with estimated lengths from a hydroacousticsurvey and from direct measures of fish size using visual census techniques. We discovered a possible bias in lengthmeasures using the video method, most likely arising from some fish orientations that were not perpendicular with respect to the optical axis of the camera system. We observed 40 individuals occupying a volume of 33.3 m3, resulting in a concentration of 1.2 individuals m–3 with a mean (SD) nearest neighbor distance of 70.0 (29.7) cm. We promote the use of roving diver stereo-videography as a method to assess the size distribution, density, and 3D spatial structure of fish spawning aggregations.
    Keywords: Management ; Ecology ; Fisheries
    Repository Name: AquaDocs
    Type: book_section , TRUE
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    Format: 4-9
    Format: 124
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  • 6
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    Deepwater reef fishes and multibeam bathymetry of the Tortugas South Ecological Reserve, Florida Keys National Marine Sanctuary, Florida (2021)
    NOAA | Seattle, WA
    In:  http://aquaticcommons.org/id/eprint/2485 | 403 | 2011-09-29 18:56:48 | 2485 | United States National Marine Fisheries Service
    Details
    Publication Date: 2021-07-13
    Description: The Tortugas South Ecological Reserve, located along the margin of the southwest Florida carbonate platform, is part of the largest no-take marine reserve in the U.S. Established in July 2001, the reserve is approximately206 km2 in area, and ranges in depths from 30 m at Riley’s Hump to over 600 m at the southern edge of the reserve. Geological and biological information for the Tortugas South Reserve is lacking, and critical for management of the area. Bathymetric surveys were conducted with a Simrad EM 3000 multibeam echosounder at Riley’s Hump and Miller’s Ledge, located in the northern and central part of the reserve. Resulting data were used to produce basemaps to obtain geological ground truth and visual surveys ofbiological communities, including reef fishes. Visual surveys were conducted using SCUBA and the Phantom S2 Remotely Operated Vehicle (ROV) at Riley’s Hump. Visual surveys were conducted using the ROV and the Deepworker 2000 research submersible along Miller’s Ledge, withinand outside of the reserve. A total of 108 fishes were recorded during SCUBA, ROV, and submersible observations. Replicate survey transects resulted in over 50 fishesdocumented at Miller’s Ledge, and eight of the top ten most abundant species were planktivores. Many species of groupers, including scamp (Mycteroperca phenax), red grouper (Epinephelus morio), snowy grouper (E. niveatus), speckled hind (E. drummondhayi), and Warsaw grouper (E.nigritus), are present in the sanctuary. Numerous aggregations of scamp and a bicolor phase of the Warsaw grouper were observed, indicating the importance of Miller’s Ledge as a potential spawning location for both commercially important and rare deep reef species, and as a potential source of larval recruits for the Florida Keys and other deep reef ecosystems of Florida
    Keywords: Ecology ; Management ; Fisheries
    Repository Name: AquaDocs
    Type: book_section , TRUE
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    Format: 48-68
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  • 7
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    Nassau grouper (Epinephelus striatus) spawning aggregations: hydroacoustic surveys and geostatistical analysis (2021)
    NOAA | Seattle, WA
    In:  http://aquaticcommons.org/id/eprint/2484 | 403 | 2014-02-21 01:06:03 | 2484 | United States National Marine Fisheries Service
    Details
    Publication Date: 2021-07-13
    Description: With the near extinction of many spawning aggregations of large grouper and snapper throughout the Caribbean, Gulf of Mexico, and tropical Atlantic, we need to provide baselinesfor their conservation. Thus, there is a critical need to develop techniques for rapidly assessing the remaining known(and unknown) aggregations. To this end we used mobile hydroacoustic surveys to estimate the density, spatial extent, and total abundance of a Nassau grouper spawning aggregation at Little Cayman Island, Cayman Islands, BWI.Hydroacoustic estimates of abundance, density, and spatial extent were similar on two sampling occasions. The locationand approximate spatial extent of the Nassau grouper spawning aggregation near the shelf-break was corroborated by diver visual observations. Hydroacoustic density estimates were, overall, three-times higher than the average density observed by divers; however, we note that in some instances diver-estimated densities in localizedareas were similar to hydroacoustic density estimates. The resolution of the hydroacoustic transects and geostatisticalinterpolation may have resulted in over-estimates in fish abundance, but still provided reasonable estimates of total spatial extent of the aggregation. Limitations in bottom time for scuba and visibility resulted in poor coverage of the entire Nassau grouper aggregation and low estimatesof abundance when compared to hydroacoustic estimates. Although the majority of fish in the aggregation werewell off bottom, fish that were sometimes in close proximity to the seafloor were not detected by the hydroacoustic survey. We conclude that diver observations offish spawning aggregations are critical to interpretations of hydroacoustic surveys, and that hydroacoustic surveys provide a more accurate estimate of overall fish abundance and spatial extent than diver observations. Thus, hydroacoustics is an emerging technology that, when coupledwith diver observations, provides a comprehensive survey method for monitoring spawning aggregations of fish.
    Keywords: Ecology ; Management ; Fisheries
    Repository Name: AquaDocs
    Type: book_section , TRUE
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    Format: 18-25
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  • 8
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    Detecting fish aggregations from reef habitats mapped with high resolution side scan sonar imagery (2021)
    NOAA | Seattle, WA
    In:  http://aquaticcommons.org/id/eprint/2489 | 403 | 2011-09-29 18:56:59 | 2489 | United States National Marine Fisheries Service
    Details
    Publication Date: 2021-07-13
    Description: As part of a multibeam and side scan sonar (SSS) benthic survey of the Marine Conservation District (MCD) south of St. Thomas, USVI and the seasonal closed areas in St. Croix—Lang Bank (LB) for red hind (Epinephelus guttatus) and the Mutton Snapper (MS) (Lutjanus analis) area—we extracted signals from water column targets that represent individualand aggregated fish over various benthic habitats encountered in the SSS imagery. The survey covered a total of 18 km2 throughout the federal jurisdiction fishery management areas. The complementary set of 28 habitat classification digital maps covered a total of 5,462.3 ha;MCDW (West) accounted for 45% of that area, and MCDE (East) 26%, LB 17%, and MS the remaining 13%. With the exceptionof MS, corals and gorgonians on consolidated habitats were significantly more abundant than submerged aquatic vegetation (SAV) on unconsolidated sediments or unconsolidated sediments. Continuous coral habitat was the most abundant consolidated habitat for both MCDW and MCDE (41% and 43% respectively). Consolidated habitats in LB and MS predominantly consisted of gorgonian plain habitat with 95% and 83% respectively. Coral limestone habitat was more abundant than coral patch habitat; it was found near the shelf break in MS, MCDW, and MCDE. Coral limestone and coral patch habitats only covered LB minimally. The high spatial resolution (0.15 m) of the acquired imagery allowed the detection of differing fish aggregation (FA) types. Thelargest FA densities were located at MCDW and MCDE over coral communities that occupy up to 70% of the bottom cover.Counts of unidentified swimming objects (USOs), likely representing individual fish, were similar among locations and occurred primarily over sand and shelf edge areas. Fish aggregation school sizes were significantly smaller at MS than the other three locations (MCDW, MCDE, and LB). This study shows the advantages of utilizing SSS in determining fish distributions and density.
    Keywords: Ecology ; Management ; Fisheries
    Repository Name: AquaDocs
    Type: book_section , TRUE
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    Format: 88-104
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  • 9
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    Field guide to requiem sharks (Elasmobranchiomorphi: Carcharhinidae) of the Western North Atlantic (2021)
    NOAA/National Marine Fisheries Service | Seattle, WA
    In:  http://aquaticcommons.org/id/eprint/2503 | 403 | 2011-09-29 18:58:46 | 2503 | United States National Marine Fisheries Service
    Details
    Publication Date: 2021-07-13
    Description: Identification problems are common for many sharks due to a general lack of meristic characteristics that are typicallyuseful for separating species. Other than number of vertebrae and number and shape of teeth, identifications are frequently based on external features that are often shared among species. Identification problems in the field are most prevalent when live specimens are captured and releasing them with a minimum of stress is a priority (e.g., shark tagging programs). Identifications mustbe accurate and conducted quickly but this can be challenging, especially if specimens are very active or too large to be landed without physical damage. This field guide was designed primarily for use during field studies and presents a simplified method for identifying the 21 species of western North Atlantic Ocean sharks belonging to the family Carcharhinidae (carcharhinids). To assist with identifications a dichotomous key to Carcharhinidae was developed, and for the more problematic Carcharhinus species (12 species), separation sheets based on importantdistinguishing features were constructed. Descriptive text and illustrations provided in the species accounts were developed from field observations, photographs, andpublished references. (PDF file contains 36 pages.)
    Keywords: Ecology ; Management ; Fisheries
    Repository Name: AquaDocs
    Type: monograph
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  • 10
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    Spawning, egg development, and early life history dynamics of arrowtooth flounder (Atheresthes stomias) in the Gulf of Alaska (2021)
    NOAA/National Marine Fisheries Service | Seattle, WA
    In:  http://aquaticcommons.org/id/eprint/2478 | 403 | 2011-09-29 18:55:56 | 2478 | United States National Marine Fisheries Service
    Details
    Publication Date: 2021-07-13
    Description: Arrowtooth flounder (Atheresthes stomias) has the highest biomass of any groundfish species in the Gulf of Alaska, is a voracious predator of age 1 walleye pollock (Theragra chalcogramma), and is a major component in the diet of Steller sea lions (Eumetopias jubatus). Owing to its ecological importance in the Gulf of Alaska and the limitedinformation available on its reproduction, interest has intensified in describing its spawning and early life history.A study was undertaken in late January–February 2001–2003 in the Gulf of Alaska to obtain information on adult spawning location, depth distribution, and sexual maturity, and to obtain fertilized eggs for laboratory studies. Adults were found 200–600 m deep east of Kodiak Islandover the outer continental shelf and upper slope, and southwest along the shelf break to the Shumagin Islands. Most ripe females (oocytes extruded with light pressure)were found at 400 m and most ripe males (milt extruded with light pressure) were found at depths ≥450 m. Eggs werefertilized and incubated in the laboratory at 3.0°, 4.5°, and 6.0°C. Eggs were reared to hatching, but larvae did not survive long enough to complete yolk absorption and develop pigment. Eggs were staged according to morphological hallmarks and incubation data were used to produce a stage duration table and a regression model to estimate egg age based on water temperature and developmental stage.Arrowtooth flounder eggs (1.58–1.98 mm in diameter) were collected in ichthyoplankton surveys along the continentalshelf edge, primarily at depths ≥400 m. Early-stage eggs were found in tows that sampled to depths of ≥450 m. Larvae,which hatch between 3.9 and 4.8 mm standard length, increased in abundance with depth. Observations on arrowtooth flounder eggs and early-stage larvae wereused to complete the description of the published partial developmental series.(PDF file contains 34 pages.)
    Keywords: Ecology ; Management ; Fisheries
    Repository Name: AquaDocs
    Type: monograph
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