Questions related to Benthic Ecology
My colleague has just asked me for advice regarding analyzing his BRUV (baited remote underwater video) dataset. It's a video camera fixed on a structure, used to record marine fishes passing by or attracted to the attached bait. It resulted in a wide dataset of species assemblage (lots of zeroes, lots of species columns). He has generated an NMDS ordination plot and ANOSIM to analyze his species assemblage dataset. He sees a spatial (geographic) separation of species composition through these methods.
Now, he wants to understand what drives this assemblage. He has additional benthic composition dataset (% coral, sand, rubble, etc.), current strength, depth, and more abiotic data. His coauthor is suggesting fitting envfit vectors on their NMDS and use the p-value of said vectors. I don't think this is a good idea, but I'm not well versed in this topic so I couldn't explain it sophisticatedly. I think because the vectors are "retrofitted" onto the ordination, the p-values are therefore not explanatory toward the species assemblage.
The alternative I could think of is running PERMANOVA or a model. The problem with the former is that the benthic composition dataset are related to each other (7 different variables, but all add up to 100%) so they're not independent of each other.
I'm wondering if anyone has any solution to this/or can add to the explanation. Would it be reliable to run a PERMANOVA? Should he be transforming his benthic composition dataset first? Or would he be better off creating a model, and if yes, which kind?
For community studies like species succession, variation in composition, especially for plankton and benthos, what are the appropriate statistical methods? One such method is MDS with cluster overlay. Similarly what else can be applied for such studies?
This is a real dbRDA plot using real invertebrate abundance data (taxa-station matrix) with environmental data (substrate characteristics-station matrix) as predictor variables. The plot is produced in PRIMER v.7. Invertebrate data is 4th root transformed, Bray-Curtis similarity was used. Environmental data is normalized, Euclidean distance was used.
My question is: why is the vector overlay not centered at 0,0 in the plot? Interpreting this plot, one would conclude that every sampling station within the study area has values below the mean for predictor variables 2 and 13, which is impossible. Why would the center of the vector overlay be displaced -40 units? How can this be? Why is the plot centered on the dbRDA2 axis but the dbRDA1 axis?
Please let me know if anyone needs more information. Thank you!
I am working with intertidal muddy sediments. In one of my sites the sediment was extremely muddy (high % of silt), oxic layer was shallow, and there were a lot of oligochaetes.
I would like to know how deep into the sediment they live/go, and in what areas of the sediment column they feed.
Does anyone have literature that I could study?
I am not understanding very well the dynamic of benthic exchange in coastal sites and if is a process that normally can occurrs fast (hours to days) or slowly (weeks to decades)?
I need this information to understand the variability of concentration in long-lived and short lived Radium isotopes in a coastal aquifer
This sediment dwelling cnidarian was found within a benthic sediment grab at 170m depth north east of the Shetland Islands in the North Sea. Can anyone suggest a particular species?
Any help would be very much appreciated,
It is hypothesized that harpacticoid copepods are the only meiofaunal organisms to develop larval stages because their nauplii share the same habitat as the adults. I am interested to know whether the nauplii (larvae) and copodite stages of harpacticoid copepods are pelagic or benthic compared to calanoid or cyclopoid copepods?
After reading several articles I am a bit confused concerning the benthic species taken into account for the calculation of species richness and index like I2EC. In the description of I2EC (Grall & Glemarec, 2003) it is mentioned that fixed epifauna should not be counted. What about the vagile epifauna such as many molluscs of hard substrates (Nassarius, Chitons ...) ? I don’t understand why they are listed in mudflat case. What about Serpulidae species like Spirobranchus ?
Concerning the AMBI, normally used in soft sediment habitats, the list of ecological groups contains species like: Balanus trigonus, Nassarius sp., Actinia sp., Tethya sp., Polycarpa sp.
Looks like every study has its own recipe, and it is not possible to know which benthic species are taken into account by the authors for the calculation of each index.
In my opinion, different indices (AMBI, I2EC) must use different lists (infauna with or without epifauna), and each list should be clearly detailled to ensure reproductibility and comparison.
Can anyone enlighten me on this subject ?
I am trying to analyse the degrees of influence of a few environmental factors on benthic mollusc assemblage structure using DistLM and dbRDA plots. After selecting the best model, I have used a forward-stepping selection proceedure based on Bray-Curtis distance measures to run both adj R^2and AIC selection criteria tests. Two things are odd - the results of both marginal tests came out almost identical for both adj R^2 and AIC, and there are no factors/values listed at all for either of the sequential tests! What have I done/what should I have done?
I'm measuring the shrimp diversity using diversity indexes such as Shannon, Simpson, Pielou and Simpson's dominance. I sampled three different sites during three seasons, so I have a total of 9 values for each index. My question is which statistical analysis could I use for testing if there is a significant difference between those values due to the sampling site or season or both?. Or if there is no need to use them and just make my conclusions based on the raw values of the indexes. Thank you for your attention. Best regards
I am developing a project investigation the effect of electromagnetic fields on benthic infauna, especially with respect to array and export cables associated with offshore energy installations . It would give my rationale some weight if I could provide existing measurements of EMF strength at the benthic in operational developments, does anybody know of any papers or monitoring reports that could help with this?
Can anybody explain possible effects of estuarine mixing on benthic distribution, especially salinity and feeding behavior?
Which zone would be the benefit of high diversity?
I want to compare each communities' respiration (as measured in-situ in benthic chambers), per gram organic biomass. The problem is that biomass is order of magnitude different between communities and variations in biomass are much larger than variations in respiration between communities.
i.e. when subtracting a number by a large value = small value; when subtracting a small value = large value.
If I could, I would have done a controlled lab experiment using the same amount of biomass from each community and get rid of that artifact.
My question is:
Can I transform the biomass values in order to minimize variation between communities and - artifact? I don't care much about the actual values - I would just like to compare between them (which respires the most/least per gram organic biomass?)
also, which transformation should be used?: respiration is measured by the change in DIC concentration over time in side incubation chambers.
I expect that production of DIC over time will increase with increasing organic biomass inside the chamber, however I'm not sure how these variables behave. I expect it not to be linear. Possibly logarithmic, however I can't really do a manipulative experiment to check that.
Is anyone familiar with a study that used this kind of normalization using transformed data? Who can I cite?
Can foraminiferal paleontologists or interested colleagues help me to identify this species of agglutinated benthonic foraminifera from Paleogene of Egypt??
I suppose it is new species of Gaudryina...or not??
please be calm with my attached photos as i took it by my camera not attached with microscope,, so it may be low in resolution. Thank you.
Anything about their recovery as a community, the succession in assemblage, and their function in the recovery of the reef as a whole.
I'm looking at using meiofauna community data from eDNA analysis for benthic environmental monitoring. I would like to filter the eDNA dataset to exclude non-benthic taxa but am struggling to find a source with this information.
Can anyone suggest a database or publication detailing meiobenthic taxonomic groups which I could use to filter the eDNA data.
About 10 individuals of this unusal species were found in a benthic sample of the Great Belt area (Baltic Sea) with water depth around 40 m and a salinity around 25 psu. Unfortunately I have no idea what taxonomical group it could be. Our first idea was, it is a part of a medusae, however, all individuals have the same shape and seem to be complete. For a priapulid it is quite unusal "open".
recently from benthic samples we were able to collect interesting microgastropods (all less than 4 mm). There are six species attached herewith for identification. 4th species is that of a Nassarid and the first species looks like a Turritellid. Please help me to identify the species. All were collected in depths less than 10 meters.
I want to know the genus and species name for one of my friends, if possible.
The scale of each microscopic image is 200 μm.The images became re-size to upload. if you need to have more resolution, I can upload your mentioned fauna separately.
Thank you very much for your help.
They are found occasionally in grab samples from Kara and Laptev seas. Pictures of paraffin embedded cross sections stained by hematoxylin and eosin.
Thanks in advance.
I am interested to see if there has been any work on the ability of crustaceans and polychaetes to detect electromagnetic emissions from other organisms' nervous systems. This would be of interest in my study of epibenthic predators that burrow when prey is located as well as burrowing organisms that may retreat deeper when predators are detected. Any leads are appreciated!
All the best,
I picked the animal from benthic sample collected at the depth of about 40-50m in southern central Vietnam offshore waters. The size is 4-5mm. Thank you very much.
The research project will be based on: To investigate the effect of pollution to benthic fauna. Please any help to clarify myself with my project
Isolated from estuarine area (10 ppt) by agar plating (f/2 medium). Black small colonies formed after 4 weeks. The size of cells varies from 8 to 20 micron. Cells are attached together and benthic in culture.
I performed a multiple choice experiment to assess the food preference of the sea urchin Paracentrotus lividus in relation to 5 different food items. I have 15 replicates, each represented by a tank where the 5 food items were simultaneously offered to 1 sea urchin. For each tank, I measured the consumption of each food item after 48h.
Given the lack of independence within each replicate (the consumption of one food depends on the presence of other food sources), I would use a multivariate approach. The problem is that no treatments have been included in my experimental design (all replicates have the same condition) and it makes difficult choosing a proper statistical approach. Any suggestions?
I am currently modelling the potential distribution of the invasive Caprella mutica and native species of Caprellidae (for starters C. linearis) in the North Sea. From my own work I have obtained several offshore samples in the Dutch part of the North Sea. Furthermore I have received data from colleagues in other countries, but the total dataset is still very small. From literature I have obtained hundreds of presence-only observations (e.g. from Cook et al., 2007). But I found hardly any presence-absence data of Caprellidae.
Is there anyone that has this type of data from the North Sea and is interested in sharing this? Thank you for reading my question!
I'm seeking information on the pH of urchin digestive tracts or stomachs under standard conditions (e.g. not acidified conditions). I'm aware there are values for larvae (Stumpp et al 2013) but, again, I need values for adults.
Alternatively, I also need pH values for digestive tracts of bivalve larvae. I have values for adults. Any help on this would be much appreciated!
Hello, I am looking for recent (~1990s and forward) literature on invertebrate-moss associations in inland water ecosystems (lakes, streams, wetlands, canals, etc.). Articles should focus on fully submerged or semi-aquatic moss and/or invertebrate species. Articles in journals would be preferred, but easy-to-cite grey lit (e.g., USEPA technical reports) also would be appreciated -- anything that could stand in a soon-to-be-submitted manuscript that will have to pass through peer-review. Also, any important literature citation on invertebrate-moss associations from other habitats (i.e., terrestrial), recent or historical, would be greatly appreciated. Thanks a lot!
I am currently studying different species of starfish in Sogod Bay, Southern Leyte, Philippines as part of our Marine Biodiversity Project.
Please see attached picture.
I'm working on bioactivity of seaweeds. I have taken 5 kg amount of seaweed, extracted in the respective solvent, filtered and evaporated but I don't know that how much quantity of extracted material is required to isolate all compounds.
I analysed some of my data from Caspian Sea basin. these data comprised form hard substrate of macrobenthic communities. I attached the results. in the attached file Time (1,2,3, and 4) represent season and Site (1 to 8) represent sampling sites.
anyone can help me to understand the results?
I surveyed 4 sites (A, B, C and D) during six times along a year. On each site I measured abundance in six sampling transects. I have a total of 36 sampling units on each site.
Sites A and B are very impacted and sites C and D are reference with almost no human disturbance but topography is different A=C ≠ B=D (i.e. A and C present steep slope; B and D present gentle slope). I have 3 factors: Time (6 levels); Impact (2 levels) and Topography (2 levels). Data found to be normal and homocedastic. I´m interested in determining the relative contribution of Human disturbance and Topography to abundance variation of this species.
Is it possible lumping data together in order to perform two ANOVAS to determine the effect size attributed to each factor and then compare them?
I mean to perform a bifactorial ANOVA grouping data to compare Impact versus Reference sites and to calculate the effect size with its confidence intervals. To perform another bifactorial ANOVA grouping data to compare Gentle slope versus Steep slope and to calculate the effect size with its confidence intervals. Then comparing the effect size for each analysis in order to determine the relative contribution to variation of each factor
Note that: 1) variation due to time should be the same for both ANOVA; 2) in the first ANOVA the two sites on each level present different topography; 3) in the second ANOVA the two sites on each level present different disturbance.
- If it’s not possible to do that, there is any other alternative to determine relative contribution of Impact and Topography to variations in abundance with this sampling design?
Benthic realm and its biotic composition is highly important in glacio-marine fjords, specially when considering the cryosphere dynamics and the resulting phenomena (sedimentation, resuspension, freshwater influx, inter alia).
Also, in Antarctic seasonal bays (i.e. Mackellar Inlet (King George Island, South Shetlands), where I've sampled macrobenthic communities for previous research (see: http://goo.gl/YOy16D)) pelagic realm also plays a key role in terms of primary production and its consequent influence on higher trophic levels.
It's certain that analysing the benthic composition is more predictive when trying to speculate future scenarios. I presumably assume that the Mackellar Inlet is mainly a benthic-controlled system. Nevertheless, in order to be sure of this hypothesis I should go further through an integrated analysis of both realms.
The protocol that my colleagues usually execute is: macrobenthic survey (van Veen grab 0.05m2), collect plankton with plankton nets, and measure abiotic variables like temperature, pH, conductivity, turbidity and marine currents patterns (speed & direction).
I'd like to know if there's any specific protocol pointing straightforward to my question. What other measurements should I consider?
Thanks for the help. Cheers.
∞BSc. Bernabé Moreno
Can I have information or links on all information of (ecology, spatial distribution, and biology) of echinodermata of the Mediterranean sea?
- Biodiversity of echinodermata fauna.
- All research or articles of Paul Pallary.