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18 results for “green crab”
Data from: European green crab predation in a Washington State estuary revealed with DNA metabarcoding
<p><strong>Fisher, MC, Grason, EW, Stote, A, Kelly, RP, Litle, K, & PS McDonald. (in review). <em>Invasive European green crab (</em>Carcinus maenas<em>) predation in a Washington State estuary revealed with DNA metabarcoding. </em></strong></p> <p>Sequencing data files produced for Fisher et al. (in review) on an Illumina MiSeq (2x300bp) targeting a 418bp DNA sequence in the mitochondrial cytochrome C oxidase subunit I gene (cox1 or COI) Folmer region. Data are demultiplexed but otherwise un-processed. Sample data sheets used to load each sequencing run are included as excel spreadsheets in the appropriate zipped folder. The metadata file contains sample (green crab stomach / mock community) metadata and corresponding MiSeq run number(s). </p> <p>Associated lab protocols are available on Github (<a href="https://github.com/mfisher5/Green-crab-dDNA/tree/main/doc" target="_blank" rel="noopener">Green-Crab-dDNA</a>)</p> <p>---</p> <p>Abstract: Predation by invasive species can threaten local ecosystems and economies. The European green crab (<em>Carcinus maenas</em>), one of the most widespread marine invasive species, is an effective predator associated with clam and crab population declines outside of its native range. In the U.S. Pacific Northwest, green crab has recently increased in abundance and expanded its distribution, generating concern for estuarine ecosystems and associated aquaculture production. However, regionally-specific information on the trophic impacts of invasive green crab is very limited. We compared the stomach contents of green crabs collected on shellfish aquaculture beds versus natural intertidal sloughs in Willapa Bay, Washington, to provide the first in-depth description of European green crab diet at a particularly crucial time for regional management. We first identified putative prey items using DNA metabarcoding of stomach content samples. We compared diet composition across sites using prey presence/absence and an index of species-specific relative abundance. For eight prey species, we also calibrated metabarcoding data to quantitatively compare DNA abundance between prey items, and to describe an ‘average’ green crab diet at an intertidal slough and an actively cultivated Manila clam bed. From the stomach contents of 61 green crabs, we identified 54 unique taxa belonging to nine phyla. The stomach contents of crabs collected from cultivated Manila clam beds were significantly different from the stomach contents of crabs collected at natural intertidal sloughs. Across all sites, arthropods were the most frequently detected prey, with the native hairy shore crab (<em>Hemigrapsus oregonensis</em>) the single most common prey item. Of the eight species included in the quantitative model, two ecologically-important native species – the sand shrimp (<em>Crangon franciscorum</em>) and the Pacific staghorn sculpin (<em>Leptocottus armatus</em>) – were the most abundant in crab stomach contents, when present. In addition to providing timely information on green crab diet, our research demonstrates the novel application of a recently developed model for more quantitative DNA metabarcoding. This represents another step in the ongoing evolution of DNA-based diet analysis towards producing the quantitative data necessary for modeling invasive species impacts.</p>
Github Repository for: European green crab predation in a Washington State estuary revealed with DNA metabarcoding
<p><strong>Fisher, MC, Grason, EW, Stote, A, Kelly, RP, Litle, K, & PS McDonald. (2024).<em> </em>Invasive European green crab (<em>Carcinus maenas</em>) predation in a Washington State estuary revealed with DNA metabarcoding. DOI:10.1371/journal.pone.0302518<em><br></em></strong></p> <p>Github release v1.1 of the repository for Fisher et al. 2024, "European green crab predation in a Washington State estuary revealed with DNA metabarcoding." For the most updated repository, see: <a href="https://github.com/mfisher5/Green-crab-dDNA/tree/main/doc">github.com/mfisher5/Green-crab-dDNA</a></p> <p>Contains the code and minimum dataset necessary to replicate study findings.</p> <p> </p> <p>---</p> <p>Abstract: Predation by invasive species can threaten local ecosystems and economies. The European green crab (<em>Carcinus maenas</em>), one of the most widespread marine invasive species, is an effective predator associated with clam and crab population declines outside of its native range. In the U.S. Pacific Northwest, green crab has recently increased in abundance and expanded its distribution, generating concern for estuarine ecosystems and associated aquaculture production. However, regionally-specific information on the trophic impacts of invasive green crab is very limited. We compared the stomach contents of green crabs collected on shellfish aquaculture beds versus natural intertidal sloughs in Willapa Bay, Washington, to provide the first in-depth description of European green crab diet at a particularly crucial time for regional management. We first identified putative prey items using DNA metabarcoding of stomach content samples. We compared diet composition across sites using prey presence/absence and an index of species-specific relative abundance. For eight prey species, we also calibrated metabarcoding data to quantitatively compare DNA abundance between prey items, and to describe an ‘average’ green crab diet at an intertidal slough and an actively cultivated Manila clam bed. From the stomach contents of 61 green crabs, we identified 54 unique taxa belonging to nine phyla. The stomach contents of crabs collected from cultivated Manila clam beds were significantly different from the stomach contents of crabs collected at natural intertidal sloughs. Across all sites, arthropods were the most frequently detected prey, with the native hairy shore crab (<em>Hemigrapsus oregonensis</em>) the single most common prey item. Of the eight species included in the quantitative model, two ecologically-important native species – the sand shrimp (<em>Crangon franciscorum</em>) and the Pacific staghorn sculpin (<em>Leptocottus armatus</em>) – were the most abundant in crab stomach contents, when present. In addition to providing timely information on green crab diet, our research demonstrates the novel application of a recently developed model for more quantitative DNA metabarcoding. This represents another step in the ongoing evolution of DNA-based diet analysis towards producing the quantitative data necessary for modeling invasive species impacts.</p>
Fig 2 in The effect of sulphur goatfish, sesarma, and green mussel as feed on the growth and survival of mud crab (Scylla paramamosain) in recirculation systems
Fig 2: Histogram of Survival Growth Rate (SGR)
Fig 1 in The effect of sulphur goatfish, sesarma, and green mussel as feed on the growth and survival of mud crab (Scylla paramamosain) in recirculation systems
Fig 1: Histogram of Food Conversion Ratio (FCR) Calculation
Fig 3 in The effect of sulphur goatfish, sesarma, and green mussel as feed on the growth and survival of mud crab (Scylla paramamosain) in recirculation systems
Fig 3: Histogram of Survival Rate (SR)
Data from: Genomic evidence of hybridization between two independent invasions of European green crab (Carcinus maenas) in the Northwest Atlantic
Invasive species have been associated with significant negative impacts in their introduced range often outcompeting native species, yet the long-term evolutionary dynamics of biological invasions are not well understood. Hybridization, either among waves of invasion or between native and introduced populations, could alter the ecological and evolutionary impacts of invasions yet has rarely been studied in marine invasive species. The European green crab (Carcinus maenas) invaded eastern North America twice from northern and southern locations in its native range. Here we examine the frequency of hybridization among these two distinct invasions at locations from New Jersey, USA to Newfoundland, Canada using restriction-site associated DNA sequencing (RAD-seq), microsatellite loci, and COI mtDNA sequences. We used Bayesian clustering and hybrid assignment analyses to investigate hybridization between the northern and southern populations. Of the samples analyzed, six locations contained at least one hybrid individual, while two locations were characterized by extensive hybridization, with 95% of individuals collected from Placentia Bay, Newfoundland being hybrids (mostly F2), and 90% of individuals from Kejimkujik, Nova Scotia being classified as hybrids, mostly backcrosses to the northern ecotype. The presence of both F2 hybrids and backcrossed individuals suggests that these hybrids are viable and introgression is occurring between invasions. Our results provide insight into the demographic and evolutionary consequences of hybridization between independent invasions, and will inform the management of green crabs in eastern North America.
Data from: Genome-wide evidence of environmentally mediated secondary contact of European green crab (Carcinus maenas) lineages in eastern North America
Genetic-environment associations are increasingly revealed through population genomic data and can occur through a number of processes, including secondary contact, divergent natural selection, or isolation-by-distance. Here we investigate the influence of the environment, including seasonal temperature and salinity, on the population structure of the invasive European green crab (Carcinus maenas) in eastern North America. Green crab populations in eastern North America are associated with two independent invasions, previously shown to consist of distinct northern and southern ecotypes, with a contact zone in southern Nova Scotia, Canada. Using a RAD-seq panel of 9137 genome-wide SNPs, we detected 41 SNPs (0.49%) whose allele frequencies were highly correlated with environmental data. A principal components analysis of 25 environmental variables differentiated populations into northern, southern, and admixed sites in concordance with the observed genomic spatial structure. Furthermore, a spatial principal components analysis conducted on genomic and geographic data revealed a high degree of global structure (p<0.0001) partitioning a northern and southern ecotype. Redundancy and partial redundancy analyses revealed that among the environmental variables tested, winter sea surface temperature had the strongest association with spatial structuring, suggesting that it is an important factor defining range and expansion limits of each ecotype. Understanding environmental thresholds associated with intraspecific diversity will facilitate the ability to manage current and predict future distributions of this aquatic invasive species.
Data from: RAD sequencing reveals genomewide divergence between independent invasions of the European green crab (Carcinus maenas) in the Northwest Atlantic
Genomic studies of invasive species can reveal both invasive pathways and functional differences underpinning patterns of colonization success. The European green crab (Carcinus maenas) was initially introduced to eastern North America nearly 200 years ago where it expanded northwards to eastern Nova Scotia. A subsequent invasion to Nova Scotia from a northern European source allowed further range expansion, providing a unique opportunity to study the invasion genomics of a species with multiple invasions. Here, we use restriction-site-associated DNA sequencing-derived SNPs to explore fine-scale genomewide differentiation between these two invasions. We identified 9137 loci from green crab sampled from 11 locations along eastern North America and compared spatial variation to mitochondrial COI sequence variation used previously to characterize these invasions. Overall spatial divergence among invasions was high (pairwise FST ~0.001 to 0.15) and spread across many loci, with a mean FST ~0.052 and 52% of loci examined characterized by FST values >0.05. The majority of the most divergent loci (i.e., outliers, ~1.2%) displayed latitudinal clines in allele frequency highlighting extensive genomic divergence among the invasions. Discriminant analysis of principal components (both neutral and outlier loci) clearly resolved the two invasions spatially and was highly correlated with mitochondrial divergence. Our results reveal extensive cryptic intraspecific genomic diversity associated with differing patterns of colonization success and demonstrates clear utility for genomic approaches to delineating the distribution and colonization success of aquatic invasive species.
Targeted Next Generation Sequencing data for European Green Crab
<p class="western"><span>In the northeast Pacific Ocean there is high interest in developing eDNA-based survey methods to aid management of invasive populations of European green crab (<i>Carcinus maenas</i>). Expected benefits are improved sensitivity for early detection of secondary spread and to assess the outcome of eradication efforts. A new eDNA-based approach we term 'Targeted Next Generation Sequencing (tNGS)' is introduced here and shown to improve detection relative to qPCR at sites with lower green crab CPUE values measured by trapping. DNA standards (gBlock) with starting molecule copies that were 10- to 100- times lower than the qPCR limit of detection returned significant numbers of sequencing reads, which in our field assessments translated to a 7% - 10% increase in detection probability from tNGS relative to qPCR at sites with lower CPUE. We also found the number of sequencing reads from tNGS was significantly correlated with green crab CPUE whereas Ct values from qPCR were not. When sources of variation were partitioned for each assay, we found the difference between mean within-site and mean between-site variation was much larger and had non-overlapping confidence intervals for tNGS relative to qPCR, suggesting the former may offer more power for detecting spatial variation in eDNA availability. Results presented here indicate this approach is suitable for species of known low abundances where a positive detection has high economic or environmental consequences. Any species with an existing qPCR assay can be easily tested with a tNGS assay. We conclude with a discussion on the fit for purpose applications of tNGS vs. qPCR on how to best apply molecular surveys in management programs.</span></p>
Data from: Temporal dynamics of the genetic clines of invasive European green crab (Carcinus maenas) in eastern North America
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Data from: RAD sequencing reveals genomewide divergence between independent invasions of the European green crab (Carcinus maenas) in the Northwest Atlantic
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Analytical validation and field testing of a specific qPCR assay for environmental DNA detection of invasive European green crab - Collected and Generated Data
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Data from: Genome-wide evidence of environmentally mediated secondary contact of European green crab (Carcinus maenas) lineages in eastern North America
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Data from: Mitochondrial genotype influences the response to cold stress in the European green crab Carcinus maenas
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Data from: Genomic evidence of hybridization between two independent invasions of European green crab (Carcinus maenas) in the Northwest Atlantic
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Targeted Next Generation Sequencing data for European Green Crab
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Data from: A novel pathway of nutrient absorption in crustaceans: branchial amino acid uptake in the green shore crab (Carcinus maenas)
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Effects of elevated seawater pCO2 on gene expression patterns in the gills of the green crab, Carcinus maenas
GEO Series GSE28870. Carcinus maenas. 24 samples. Type: Expression profiling by array.
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