Data Analysis

Top ZOTUs

Data Filtering

Taxa-Filtering

Since we are only interested in eukaryotes, I removed all ZOTU assigne to bacteria. Furthermore, I also removed all ZOTUs with missing annoations at kingdom, phylum or class level. With these filter steps we reduce the number of ZOTUs to 174 (2.5%) but we keep 90% of the data. These bacterial related and unknown ZOUTs are rare and we keep the most adundant ZOTUs.

Data Set	ZOTU	Sample	Data Removed
full set	7298	368	0.0%
- bacteria	2115	368	7.2%
- kingdom	2115	368	7.2%
- phylum	217	368	9.4%
- class	174	368	10.0%

Sequencing-Depth

The number of counts per sample ranges from 8 to 91,157 with a mean of 23,434 and a median of 20,450. It is important to remove samples with low counts (sequencing-depth) because we underestimate diversity.

Rare Fraction Curve

There is a strong correlation between sequencing depth and diversity.

Anova: Observed ~ Depth + BAFU + Canton + Riverside

             Df Sum Sq Mean Sq F value     Pr(>F)    
Depth         1    656   655.7  20.153 0.00001055 ***
BAFU         91   6350    69.8   2.145 0.00000112 ***
Riverside     2      7     3.5   0.108      0.898    
Residuals   273   8882    32.5

Remove "Failed" Samples

Sample below 500 total counts are removed. With this filtering step we reduce the number of samples to 351 (-17). Although there is still a correlation between observed diversity and sequencing depth is is less prominent.

Anova: Observed ~ Depth + BAFU + Canton + Riverside

             Df Sum Sq Mean Sq F value     Pr(>F)    
Depth         1    145  145.01   4.741     0.0304 *  
BAFU         91   6040   66.38   2.170 0.00000102 ***
Riverside     2      0    0.19   0.006     0.9937    
Residuals   256   7830   30.59

Anova: Fisher ~ Depth + BAFU + Canton + Riverside
             Df Sum Sq Mean Sq F value     Pr(>F)    
Depth         1   0.84  0.8431   1.686      0.195    
BAFU         91  91.93  1.0102   2.020 0.00000879 ***
Riverside     2   0.01  0.0072   0.014      0.986    
Residuals   256 128.05  0.5002                       

Anova: Shannon ~ Depth + BAFU + Canton + Riverside
Depth         1   0.31  0.3127   1.290         0.257    
BAFU         91  56.20  0.6176   2.548 0.00000000388 ***
Riverside     2   0.59  0.2943   1.214         0.299    
Residuals   256  62.04  0.2424

Alpha diversity

Family Composition

Salmonidae

Leuciscidae

more soon ...