I've had bioinformatics data from sequencing company but am struggling with the beta diversity analysis. I have 2 fish, one was fed a mixed diet (X) and the other fed a wood diet (W). I sent off the fore, mid and hind gut for analysis from both fish. So I have XF, XM, XH, WF, WM, WH.
In the beta diversity result the within group compares X vs X, W vs W and W vs X and I have the same for between groups.
I would expect within groups to compare the areas of the gut of the X fed fish and same for the W fed fish. And the between groups to compare the fore gut of the X and W fish and so on.
Can anyone shed light on the fact I have analysis for W vs X for within group and W vs W and X vs X for between groups?
See: Ecology Letters, (2006) 9: 683–693.
I hope this helps!
Andrew :-)
Dear Caroline,
I do not understand how beta diversity was or even could be calculated in your case. Please give some more information on the data sets that were used for the beta diversity analysis.
Thanks, Roland
Dear Marden
from your given problem I could not follow your line of questioning. because your problem does not deals with any sort of beta diversity within or between the groups. it is a foolish idea.
With regards
Sunit Mitra
I agree some of it is bizarre, I think the bioinformatics company just runs the same analysis for all microbial samples whether appropriate or not!
In the case of microbial diversity in the food or gut content, the calculation of beta-diversity might be a meaningful question. But I do not yet understand which diversity (species, nutrient particels, ...) you want to analyse in your experiment, sorry.
I am trying to look at any difference in fungal diversity within the gut of a wood fed fish and a mixed fed (algal pellets) fish. Then to see if there are differences between the fungal species found in the fore, mid and hind gut. What indigenous species are found in the gut of wood fed fish, what lignocellulose degrading fungal species are found in the guts of fish fed a wood diet compared to that of the mixed fed diet.
Like I said I only have one fish fed on each diet
Thanks for the information, Caroline. If you want to estimate the differences or dissimilarities in fungal species composition, I would suggest to calculate some similarity indices such as Jaccard index of fungal species composition between and within groups (beta-diversity is not appropriate here).
Hi Caroline,
I think you may agree to increase your knowledge about biostatistics.
Download these manuscripts, they are free. Read and Then we will solve your question easily.
https://www.cell.com/heliyon/fulltext/S2405-8440(18)38688-2
https://www.cell.com/heliyon/fulltext/S2405-8440(19)35821-9
However, the result of the beta diversity ( Whittaker) is a pairwise comparison. It is used to compare between two or more groups or communities. So there is no between groups or within groups. These words may apply for ANOVA, if the analysis is suitable for your case. Yes, it takes time with everybody to know how to do the right thing; Best regards.
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