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?
Thank you
Dear Mohammad,
You can contact with Dr. Hassan Fazli in Caspian Sea Ecology Research Center though his telephone or Email as follows:
Regards
Jalil
The SIMPER analysis calculates the contribution of each species (%) to the dissimilarity between each two groups. It is calculated from the Bray-Curtiss dissimilarity matrix, the last two columns show the contributions for each species in descendant order, and it is accumulative. For instance, the results compare first the invertebrate community composition between seasons across the different sites, and then between sites across the different seasons. For example between seasons 1 and 2 the average dissimilarity of 40,3% indicates that the whole community differs in 40% between seasons 1 and 2. The species with higher percentage are those who determine the group dissimilarity, in this case the first two species account for more than 50% of the dissimilarity of your groups 1 and 2, and if you consider the third species all of them will account together for more than 60%. Then, you should infer that species x y and Z are more typical from the season 1 or 2 maybe because they are comparatively more abundant for one of the seasons, also some of them could be absent for the other season.
Similarly, when you compare the community between sites (1 to 8) you will find there are some characteristic species accounting for differences between each pair of environments, maybe they are much more abundant in one environment than another. Various of the average dissimilarities are rather low, maybe the community is very similar across several environments, although some dissimilarities are higher, such as between the sites 2 and 7 (51%) with the first two species accounting for more than 70% of the dissimilarity
You can also run the analysis with the similarities instead of the dissimilarities and maybe you will find interest results to compare.
I hope it helps
You might find a previous RG’s question related to SIMPER useful for you (see link at the end).
A good way to visualise your data (and SIMPER data in general) could be to do a plot of the % similarity in the y axis against, for example, season on the x-axis. You could compare the season 2 by 2 for each site.
Before using SIMPER, I would suggest to perform a MDS to visualise where you have differences, so that you can find with SIMPER how similar or dissimilar (100% = % similarity + % dissimilarity) are the different groups appearing with MDS, and identify which variables (in your case species of macrobenthos) explain the differences between groups (Contrib% = % of contribution for each variable).
https://www.researchgate.net/post/Can_anyone_help_me_in_understanding_and_clearly_interpreting_ANOSIM_Analysis_of_Similarityand_SIMPER_Similarity_percentage_analysisresults/1
SIMPER is used after the differences between factors are confirmed using an ANOSIM or PERMANOVA test, the factors sometimes or frequently are defined a priori (before to start the research or analysis) according to some geographical, physics or chemistry characteristics that show an effect on the community as a driver of its structure. If there is not a clear effect for any factor selected a priori SIMPROF test allows to observe groups with significant differences, without significant differences SIMPER analysis has no sense.
If there are the environmental information with Linktree analysis it is possible to obtain a factor more robust.
Mohammad Hasan, please, can you show me the code that you used?
Dear Mohammad,
Here is what you need, download it from the following URL, it is free
Article Ecological importance and sociological characters of fourtee...
The Author
Dear Mohammed
Please take guide line from "Effects of the invasive plant Xanthium
strumarium on diversity of native plant
species: A competitive analysis approach in
North and Northeast China" this published paper in PLOS one.
Thanks
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