Holobionts and ecological speciation: the intestinal microbiota of lake whitefish species pairs

Microbiome

Table 2 Summary of weighted UniFrac and the PERMANOVA test statistics

Comparison	Lakes/effects	UniFrac	PERMANOVA
Comparison	Lakes/effects	WSig	F value	R2	Pr (> F)
Both whitefish species microbiota-water bacterial communities (sequence dataset)	Water-whitefish	< 0.0010	33.834	0.185	< 0.0010
	Lakes	–	2.774	0.061	< 0.0010
	Water-whitefish*lake	–	1.278	0.028	0.074
	Cliff	< 0.0010	3.818	0.124	< 0.0010
	East	< 0.0010	6.910	0.210	< 0.0010
	Indian	< 0.0010	6.653	0.172	< 0.0010
	Témiscouata	< 0.0010	6.218	0.182	< 0.0010
	Webster	< 0.0010	7.341	0.269	< 0.0010
Dwarf-normal whitefish microbiota (sequence dataset)	Species	< 0.0010	2.273	0.019	0.002
	Lakes	–	2.812	0.096	< 0.0010
	Species*lake	–	1.493	0.051	0.0021
	Cliff	< 0.0010	1.931	0.081	0.006
	East	< 0.0010	1.821	0.092	0.019
	Indian	< 0.0010	0.913	0.037	0.530
	Témiscouata	< 0.0010	1.848	0.077	0.025
	Webster	< 0.0010	1.396	0.104	0.145
Dwarf-normal whitefish microbiota (PICRUSt results)	Species	–	0.448	0.003	0.697
	Lake	–	6.761	0.200	< 0.0010
	Species*lake	–	2. 273	0.067	0.016
	Cliff	–	0.152	0.007	0.958
	East	–	1.642	0.083	0.114
	Indian	–	0.413	0.017	0.793
	Témiscouata	–	5.052	0.186	0.019
	Webster	–	2.562	0.176	0.108

Three comparisons are shown: (i) comparison within and between lakes for the whitefish microbiota (dwarf and normal) and the water bacterial communities, (ii) comparison within and between lakes for the dwarf whitefish microbiota and the normal whitefish microbiota, and (iii) comparison of the PICRUSt results between dwarf and normal microbiota for all lakes combined and for each lake. For the three comparisons, we tested the lake effect and the interaction between the bacterial communities (water, dwarf, and normal whitefish) using PERMANOVA. UniFrac test is based on beta diversity and cannot be done with PICRUSt results

ISSN: 2049-2618