Systematics of the North American menhadens: molecular evolutionary reconstructions in the genus Brevoortia (Clupeiformes: Clupeidae)

Evolutionary associations among the four North American species of menhadens (Brevoortia spp.) have not been thoroughly investigated. In the present study, classifications separating the four species into small-scaled and large-scaled groups were evaluated by using DNA data, and genetic associations within these groups were explored. Specifically, data from the nuclear genome (microsatellites) and the mitochondrial genome (mtDNA sequences) were used to elicit patterns of recent and historical evolutionary associations. Nuclear DNA data indicated limited contemporary gene flow among the species, and also indicated higher relatedness within the small-scaled and large-scaled menhadens than between these groups. Mitochondrial DNA sequences of the large-scaled menhadens indicated the presence of two ancestral lineages, one of which contained members of both species. This result may indicate genetic diver-gence (reproductive isolation) followed by secondary contact (hybridization) between these species. In contrast, a single ancestral lineage indicated incomplete genetic divergence between the small-scaled menhaden. These results are discussed in the context of the biology and demographics of each species.

An examination of spatial and temporal genetic variation in walleye pollock (Theragra chalcogramma) using allozyme, mitochondrial DNA, and microsatellite data

We used allozyme, microsatellite, and mitochondrial DNA (mtDNA) data to test for spatial and interannual genetic diversity in wall-eye pollock (Theragra chalcogramma) from six spawning aggregations representing three geographic regions: Gulf of Alaska, eastern Bering Sea, and eastern Kamchatka. Interpopulation genetic diversity was evident primarily from the mtDNA and two allozyme loci (SOD-2*, MPI*). Permutation tests ˆindicated that FST values for most allozyme and microsatellite loci were not significantly greater than zero. The microsatellite results suggested that high locus polymorphism may not be a reliable indicator of power for detecting population differentiation in walleye pollock. The fact that mtDNA revealed population structure and most nuclear loci did not suggests that the effective size of most walleye pollock populations is large (genetic drift is weak) and migration is a relatively strong homogenizing force. The allozymes and mtDNA provided mostly concordant estimates of patterns of spatial genetic variation. These data showed significant genetic variation between North American and Asian populations. In addition, two spawning aggregations in the Gulf of Alaska, in Prince William Sound, and off Middleton Island, appeared genetically distinct from walleye pollock spawning in the Shelikof Strait and may merit management as a distinct stock. Finally, we found evidence of interannual genetic variation in two of three North American spawning aggregations, similar in magnitude to the spatial variation among North American walleye pol-lock. We suggest that interannual genetic variation in walleye pollock may be indicative of one or more of the following factors: highly variable reproductive success, adult philopatry, source-sink metapopulation structure, and intraannual variation (days) in spawning timing among genetically distinct but spatially identical spawning aggregates.

Protected species aerial survey data collection and analysis in waters underlying the R-5306A airspace: final report submitted to US Marine Corps, MCAS Cherry Point

To be in compliance with the Endangered Species Act and the Marine Mammal Protection Act, the United States Department of the Navy is required to assess the potential environmental impacts of conducting at-sea training operations on sea turtles and marine mammals. Limited recent and area-specific density data of sea turtles and dolphins exist for many of the Navy’s operations areas (OPAREAs), including the Marine Corps Air Station (MCAS) Cherry Point OPAREA, which encompasses portions of Core and Pamlico Sounds, North Carolina. Aerial surveys were conducted to document the seasonal distribution and estimated density of sea turtles and dolphins within Core Sound and portions of Pamlico Sound, and coastal waters extending one mile offshore. Sea Surface Temperature (SST) data for each survey were extracted from 1.4 km/pixel resolution Advanced Very High Resolution Radiometer remote images. A total of 92 turtles and 1,625 dolphins were sighted during 41 aerial surveys, conducted from July 2004 to April 2006. In the spring (March – May; 7.9°C to 21.7°C mean SST), the majority of turtles sighted were along the coast, mainly from the northern Core Banks northward to Cape Hatteras. By the summer (June – Aug.; 25.2°C to 30.8°C mean SST), turtles were fairly evenly dispersed along the entire survey range of the coast and Pamlico Sound, with only a few sightings in Core Sound. In the autumn (Sept. – Nov.; 9.6°C to 29.6°C mean SST), the majority of turtles sighted were along the coast and in eastern Pamlico Sound; however, fewer turtles were observed along the coast than in the summer. No turtles were seen during the winter surveys (Dec. – Feb.; 7.6°C to 11.2°C mean SST). The estimated mean surface density of turtles was highest along the coast in the summer of 2005 (0.615 turtles/km², SE = 0.220). In Core and Pamlico Sounds the highest mean surface density occurred during the autumn of 2005 (0.016 turtles/km², SE = 0.009). The mean seasonal abundance estimates were always highest in the coastal region, except in the winter when turtles were not sighted in either region. For Pamlico Sound, surface densities were always greater in the eastern than western section. The range of mean temperatures at which turtles were sighted was 9.68°C to 30.82°C. The majority of turtles sighted were within water ≥ 11°C. Dolphins were observed within estuarine waters and along the coast year-round; however, there were some general seasonal movements. In particular, during the summer sightings decreased along the coast and dolphins were distributed throughout Core and Pamlico Sounds, while in the winter the majority of dolphins were located along the coast and in southeastern Pamlico Sound. Although relative numbers changed seasonally between these areas, the estimated mean surface density of dolphins was highest along the coast in the spring of 2006 (9.564 dolphins/km², SE = 5.571). In Core and Pamlico Sounds the highest mean surface density occurred during the autumn of 2004 (0.192 dolphins/km², SE = 0.066). The estimated mean surface density of dolphins was lowest along the coast in the summer of 2004 (0.461 dolphins/km², SE = 0.294). The estimated mean surface density of dolphins was lowest in Core and Pamlico Sounds in the summer of 2005 (0.024 dolphins/km², SE = 0.011). In Pamlico Sound, estimated surface densities were greater in the eastern section except in the autumn. Dolphins were sighted throughout the entire range of mean SST (7.60°C to 30.82°C), with a tendency towards fewer dolphins sighted as water temperatures increased. Based on the findings of this study, sea turtles are most likely to be encountered within the OPAREAs when SST is ≥ 11°C. Since sea turtle distributions are generally limited by water temperature, knowing the SST of a given area is a useful predictor of sea turtle presence. Since dolphins were observed within estuarine waters year-round and throughout the entire range of mean SST’s, they likely could be encountered in the OPAREAs any time of the year. Although our findings indicated the greatest number of dolphins to be present in the winter and the least in the summer, their movements also may be related to other factors such as the availability of prey. (PDF contains 28 pages)

Flower Garden Banks National Marine Sanctuary: A rapid assessment of coral, fish, and algae using the AGRRA Protocol

The Flower Garden Banks are topographic features on the edge of the continental shelf in the northwest Gulf of Mexico. These banks are approximately 175 km southeast of Galveston, Texas at 28° north latitude and support the northernmost coral reefs on the North American continental shelf. The East and West Flower Garden Banks (EFG and WFG) and Stetson Bank, a smaller sandstone bank approximately 110 km offshore, are managed and protected as the Flower Garden Banks National Marine Sanctuary (FGBNMS). As part of a region-wide initiative to assess coral reef condition, the benthic and fish communities of the EFG and WFG were assessed using the Atlantic and Gulf Rapid Reef Assessment (AGRRA) protocol. The AGRRA survey was conducted during a week-long cruise in August 1999 that was jointly sponsored by the FGBNMS and the Reef Environmental Education Foundation (REEF). A total of 25 coral transects, 132 algal quadrats, 24 fish transects, and 26 Roving Diver (REEF) surveys were conducted. These surveys revealed reefs with high coral cover, dominated by large, healthy corals, little macroalgae, and healthy fish populations. The percent live coral cover was 53.9 and 48.8 at the WFG and EFG, respectively, and the average colony diameter was 93 and 81 cm. Fish diversity was lower than most Caribbean reefs, but large abundances and size of many species reflected the low fishing pressure on the banks. The benthic and fish assemblages at the EFG and WFG were similar. Due to its near pristine conditions, the FGB data will prove to be a valuable component in the AGRRA database and its resulting scale of reef condition for the region. (PDF contains 22 pages.)

Deep reef fish surveys by submersible on Alderdice, McGrail, and Sonnier Banks in the Northwestern Gulf of Mexico

Submersible surveys at numerous reefs and banks in the northwestern Gulf of Mexico (NWGOM) were conducted as part of the Sustainable Seas Expedition (SSE) during July/August 2002 to identify reef fish communities, characterize benthic habitats, and identify deep coral reef ecosystems. To identify the spatial extent of hard bottom reef communities, the Flower Garden Banks National Marine Sanctuary (FGBNMS) and the U.S. Geological Survey (USGS) mapped approximately 2000 km2 of the Northwestern Gulf of Mexico (NWGOM) continental shelf during June 2002 with high-resolution multibeam bathymetry. Previous investigations conducted on the features of interest (with the exceptions of East and West Flower Garden and Sonnier Banks, accessible by SCUBA) had not been conducted since the 1970s and 1980s, and did not have the use of high-resolution maps to target survey sites. The base maps were instrumental in navigating submersibles to specific features at each study site during the Sustainable Seas Expedition (SSE)—a submersible effort culminating from a partnership between the National Atmospheric and Oceanic Administration (NOAA) and the National Geographic Society (NGS). We report the initial findings of our submersible surveys, including habitat and reef fish diversity at McGrail, Alderdice, and Sonnier Banks. A total of 120 species and 40,724 individuals were identified from video surveys at the three banks. Planktivorous fishes constituted over 87% by number for the three banks, ranging from 81.4% at Sonnier Banks to 94.3% at Alderdice Bank, indicating a direct link to pelagic prey communities, particularly in the deep reef zones. High numbers of groupers, snappers, jacks, and other fishery species were observed on all three features. These sites were nominated as Habitat Areas of Particular Concern (HAPC) by the Gulf of Mexico Fishery Council in March 2004. Data obtained during this project will contribute to benthic habitat characterization and assessment of the associated fish communities through future SCUBA, ROV, and submersible missions, and allow comparisons to other deep reef ecosystems found throughout the Gulf of Mexico and western Atlantic Ocean.

Report on the collection of salmon creel census data from Rivers Ribble and Hodder

The River Ribble bailiff team completed a total of 377 salmonid creel censuses by interviewing anglers fishing on the banks of the Rivers Ribble and Hodder during 1994. The study was undertaken for a number of reasons: (i) , To determine which areas of the river were fished by anglers. (ii) To ascertain which fishing methods were used in these areas. (iii) To identify the success of each fishing method within each area of the River Ribble system. In a limited 1993 sampling programme, 55 censuses were carried out. Results from these indicated that fishing with worm as bait was the most common method (39% of anglers interviewed) and also resulted in the greatest number of salmon being caught (61% of all salmon). The 1994 census data were collected from all areas of the Ribble system during the months of June to October. The data presented here are for anglers fishing for salmon only or for those fishing for salmon and sea trout at the same time. All of the fish caught were salmon.

Evolutionary associations between sand seatrout (Cynoscion arenarius) and silver seatrout (C. nothus) inferred from morphological characters, mitochondrial DNA, and microsatellite markers

The evolutionary associations between closely related fish species, both contemporary and historical, are frequently assessed by using molecular markers, such as microsatellites. Here, the presence and variability of microsatellite loci in two closely related species of marine fishes, sand seatrout (Cynoscion arenarius) and silver seatrout (C. nothus), are explored by using heterologous primers from red drum (Sciaenops ocellatus). Data from these loci are used in conjunction with morphological characters and mitochondrial DNA haplotypes to explore the extent of genetic exchange between species offshore of Galveston Bay, TX. Despite seasonal overlap in distribution, low genetic divergence at microsatellite loci, and similar life history parameters of C. arenarius and C. nothus, all three data sets indicated that hybridization between these species does not occur or occurs only rarely and that historical admixture in Galveston Bay after divergence between these species was unlikely. These results shed light upon the evolutionary history of these fishes and highlight the genetic properties of each species that are influenced by their life history and ecology.

Benthic invertebrates that form habitat on deep banks off southern California, with special reference to deep sea coral

There is increasing interest in the potential impacts that fishing activities have on megafaunal benthic invertebrates occurring in continental shelf and slope ecosystems. We examined how the structure, size, and high-density aggregations of invertebrates provided structural relief for fishes in continental shelf and slope ecosystems off southern California. We made 112 dives in a submersible at 32−320 m water depth, surveying a variety of habitats from high-relief rock to flat sand and mud. Using quantitative video transect methods, we made 12,360 observations of 15 structure-form-ing invertebrate taxa and 521,898 individuals. We estimated size and incidence of epizoic animals on 9105 sponges, black corals, and gorgonians. Size variation among structure-form-ing invertebrates was significant and 90% of the individuals were <0.5 m high. Less than 1% of the observations of organisms actually sheltering in or located on invertebrates involved fishes. From the analysis of spatial associations between fishes and large invertebrates, six of 108 fish species were found more often adjacent to invertebrate colonies than the number of fish predicted by the fish-density data from transects. This finding indicates that there may be spatial associations that do not necessarily include physical contact with the sponges and corals. However, the median distances between these six fish species and the invertebrates were not particularly small (1.0−5.5 m). Thus, it is likely that these fishes and invertebrates are present together in the same habitats but that there is not necessarily a functional relationship between these groups of organisms. Regardless of their associations with fishes, these invertebrates provide structure and diversity for continental shelf ecosystems off southern California and certainly deserve the attention of scientists undertaking future conservation efforts.

Progress toward a global genealogy of common carp (Cyprinus carpio L.) strains using mitochondrial nucleotide sequences data

As part of a study of genetic variation in the Vietnamese strains of the common carp (Cyprinus carpio L.) using direct DNA sequencing of mitochondrial control and ATPase6/8 gene regions, samples from a number of other countries were analyzed for comparison. Results show that the levels of sequence divergence in common carp is low on a global scale, with the Asian carp having the highest diversity while Koi and European carp are invariant. A genealogical analysis supports a close relationship among Vietnamese, Koi, Chinese Color and, to a lesser extent, European carp. Koi carp appear to have originated from a strain of Chinese red carp. There is considerable scope to extend this research through the analysis of additional samples of carp from around the world, especially from China, in order to generate a comprehensive global genealogy of common carp strains.

A point for comparison: the Flower Garden Banks National Marine Sanctuary

A reoccurring goal listed during the creation of Marine Protected Areas (MPAs) is to return the region to a former state. However, limited data is available that describes or characterizes this former condition. Data collected from ecosystems with comparatively limited anthropogenic impacts, can provide invaluable information in suggesting what former states may have looked like. One example is the Flower Garden Banks National Marine Sanctuary which is located 180 kilometers off the coast of Texas. These relatively isolated and pristine banks are capped by substantial scleractinian coral communities, forming excellent habitat for over 200 species of fish. While fishing is permitted, it is limited by difficulty of access. In 2006, NOAA’s Biogeography Branch, in collaboration with the Sanctuary, initiated the first quantitative assessment of fish resources throughout the diveable portions of the Sanctuary. The sampling design and methodologies employed were identical to those that the Branch has utilized in other more impacted regions of the US Caribbean. Initial analyses reveal that fish density and species richness at the Sanctuary were almost two times greater than that found within the US Caribbean and biomass was approximately six times higher. This was due in large part to the presence of sizeable piscivores of the genera Mycteroperca and Dermatolepis. The Sanctuary is one of few minimally impacted locations remaining within the Tropical Western Atlantic. As such, these findings should be considered when attempting to establish a former state or evaluate effectiveness of an MPA in meeting its management goals.

Population structure of king mackerel (Scomberomorus cavalla) around peninsular Florida, as revealed by microsatellite DNA

A total of 1006 king mackerel (Scomberomorus cavalla) representing 20 discrete samples collected between 1996 and 1998 along the east (Atlantic) and west (Gulf) coasts of Florida and the Florida Keys were assayed for allelic variation at seven nuclear-encoded microsatellites. No significant deviations from Hardy-Weinberg equilibrium expectations were found for six of the microsatellites, and genotypes at all microsatellites were independent. Allele distributions at each microsatellite were independent of sex and age of individuals. Homogeneity tests of spatial distributions of alleles at the microsatellites revealed two weakly divergent “genetic” subpopulations or stocks of king mackerel in Florida waters—one along the Atlantic coast and one along the Gulf coast. Homogeneity tests of allele distributions when samples were pooled along seasonal (temporal) boundaries, consistent with the temporal boundaries used currently for stock assessment and allocation of the king mackerel resource, were nonsignificant. The degree of genetic divergence between the two “genetic” stocks was small: on average, only 0.19% of the total genetic variance across all samples assayed occurred between the two regions. Cluster analysis, assignment tests, and spatial autocorrelation analysis did not generate patterns that were consistent with either geographic or spatial-temporal boundaries. King mackerel sampled from the Florida Keys could not be assigned unequivocally to either “genetic” stock. The genetic data were not consistent with current spatial-temporal boundaries employed in stock assessment and allocation of the king mackerel resource. The genetic differences between king mackerel in the Atlantic versus those in the Gulf most likely stem from reduced gene flow (migration) between the Atlantic and Gulf in relation to gene flow (migration) along the Atlantic and Gulf coasts of peninsular Florida. This difference is consistent with findings for other marine fishes where data indicate that the southern Florida peninsula serves (or has served) as a biogeographic boundary.

Genetic analysis of east and west coast populations of Penaeus monodon from India based on random amplified polymorphic DNA

The east and west coast populations of wild Penaeus monodon in India were genetically characterized by RAPD analysis using six highly polymorphic primers reported earlier. The average genetic similarities within populations, based on profiles generated by all the six primers, were 0.828 and 0.851 for the east and west coast populations, respectively, values with individual primers ranging from 0.744 to 0.889. The average genetic similarity between populations across all the primers was 0.774. The number of bands found to be polymorphic were 38 (51.35%) and 37 (50.68%) in the east and west coast populations, respectively. Primer 5 yielded the highest level of polymorphism (63.63%) in the east coast population whereas primer 3 yielded the lowest level of polymorphism (36.36%) in the west coast population. The study reveals the existence of genetic variation in P. monodon stocks providing scope for genetic improvement through selective breeding. It also provides baseline data for future work on population structure analysis of P. monodon.

Study morphologic, phylogenic relationships DNA barcoding of of identified decapod group (Crustacean) of Persian Gulf and Oman Sea.

Phylogenetic relationships among all described species (total of 12 taxa) of the decapoda, were examined with nucleotide sequence data from portions of mitochondrial gene and cytochrome oxidase subunit I (COI). The previous works on phylogeny proved that the mitochondrial COI gene in crustacean is a good discriminative marker at both inter- and intra-specific levels. We provide COI barcode sequences of commertial decapoda of Oman Sea, Persian Gulf, Iran. Industrial activities, ecologic considerations, and goals of the decapoda Barcode of Life campaign make it crucial that species of the south costal be identified. The reconstruction of evolut phylogeny of these species are crucial for revealing stock identity that can be used for the management of fisheries industries in Iran. Mitochondrial DNA sequences were used to reconstruct the phylogeny of the Penaeus species of marine shrimp. For this purpose, DNA was extracted using phenol- chloroform well as CTAB method. The evolutionary relationships among 12 species of the decapoda were examined using 610 bp of mitochondrial (mt) DNA from the cytochrome oxidase subunit I gene. Finally the cladograms were compared and the resulted phylogenetic trees confirmed that the Iran's species origin is Indo-west pacific species. Iran's species, which were not grouped with the other decapoda taxa seem to always form a sister clade with Indo-west pacific species with strong bootstrap support 100%. The result completely agrees with the previously defined species using morphological characters.However, we still lack any comprehensive and clear understanding of phylogenetic relationships in this group.