Detailed Results of the PERMANOVA Analyses

Detailed results of the PERMANOVA analyses

conducted by Peršoh 2013: “Factors shaping community structure of endophytic fungi – evidence from the Pinus-Viscum-system” (Fungal Diversity)

1)PERMANOVA analyses of all samples

Permutational MANOVA

Resemblance worksheet

Data type: Similarity

Selection: All

Standardise Samples by Total

Resemblance: S17 Bray Curtis similarity

Sums of squares type: Type III (partial)

Fixed effects sum to zero for mixed terms

Permutation method: Permutation of residuals under a reduced model

Number of permutations: 10000

Factors

NameAbbrev.TypeLevels

SiteSiFixed 2 (Grain, Zirl)

DateDaFixed 3 (2011/10/09,2011/10/16, 2011/10/24)

PlantPlFixed 2 (Pinus, Viscum)

OrganOrFixed 2 (Leaf, Stem)

AgeAgFixed 3 (1, 2 , 3 years)

PERMANOVA table of results

Unique

Source df SS MSPseudo-FP(perm) perms P(MC)

Si 1 11189 11189 5,1414 0,0001 99320,0001

Pl 1 34509 34509 15,857 0,0001 99110,0001

Or 1 6020,86020,8 2,7665 0,0076 99050,0078

Ag 2 3899,21949,6 0,89583 0,5699 98790,5638

Da(Si) 1 7805,77805,7 3,5867 0,0012 99190,0016

SixPl 1 5236,75236,7 2,4062 0,0172 99300,0159

SixOr 1 2522,32522,3 1,159 0,273 99230,2772

SixAg 2 3134,91567,5 0,72023 0,8177 99130,8116

PlxOr 1 5694,45694,4 2,6165 0,0109 9922 0,011

PlxAg 2 4964,22482,1 1,1405 0,2748 98980,2766

OrxAg 2 5710,32855,2 1,3119 0,1513 9897 0,159

Da(Si)xPl 1 18714 18714 8,5992 0,0001 99390,0001

Da(Si)xOr 1 2011,12011,1 0,9241 0,4709 99200,4678

Da(Si)xAg 2 3029,9 1515 0,69612 0,841 98880,8361

SixPlxOr 1 1490,31490,3 0,6848 0,754 99190,7419

SixPlxAg 2 3512,61756,3 0,807 0,6902 99130,6923

SixOrxAg 2 2221,61110,8 0,51041 0,9844 98850,9813

PlxOrxAg** 1 1828,61828,6 0,84023 0,5651 99200,5616

Da(Si)xPlxOr 1 3139,33139,3 1,4425 0,1403 99200,1443

Da(Si)xPlxAg 2 2912,91456,4 0,66922 0,8725 99080,8727

Da(Si)xOrxAg 2 3635,91817,9 0,83533 0,6576 99070,6451

SixPlxOrxAg** 1 1644,51644,5 0,75563 0,6695 99360,6633

Da(Si)xPlxOrxAg** 1 2722,52722,5 1,251 0,2253 99110,2223

Res1362,9598E52176,3

Total1684,6204E5

** Term has one or more empty cells

Details of the expected mean squares (EMS) for the model

SourceEMS

Si1*V(Res) + 52,107*S(Si)

Pl1*V(Res) + 51,95*S(Pl)

Or1*V(Res) + 49,852*S(Or)

Ag1*V(Res) + 37,602*S(Ag)

Da(Si)1*V(Res) + 25,468*S(Da(Si))

SixPl1*V(Res) + 25,975*S(SixPl)

SixOr1*V(Res) + 24,926*S(SixOr)

SixAg1*V(Res) + 18,801*S(SixAg)

PlxOr1*V(Res) + 24,854*S(PlxOr)

PlxAg1*V(Res) + 18,773*S(PlxAg)

OrxAg1*V(Res) + 22,29*S(OrxAg)

Da(Si)xPl1*V(Res) + 12,659*S(Da(Si)xPl)

Da(Si)xOr1*V(Res) + 11,699*S(Da(Si)xOr)

Da(Si)xAg1*V(Res) + 8,8944*S(Da(Si)xAg)

SixPlxOr1*V(Res) + 12,427*S(SixPlxOr)

SixPlxAg1*V(Res) + 9,3865*S(SixPlxAg)

SixOrxAg1*V(Res) + 11,145*S(SixOrxAg)

PlxOrxAg1*V(Res) + 12,427*S(PlxOrxAg)

Da(Si)xPlxOr1*V(Res) + 5,8182*S(Da(Si)xPlxOr)

Da(Si)xPlxAg1*V(Res) + 4,4343*S(Da(Si)xPlxAg)

Da(Si)xOrxAg1*V(Res) + 5,3415*S(Da(Si)xOrxAg)

SixPlxOrxAg1*V(Res) + 6,2136*S(SixPlxOrxAg)

Da(Si)xPlxOrxAg1*V(Res) + 2,9091*S(Da(Si)xPlxOrxAg)

Res1*V(Res)

Construction of Pseudo-F ratio(s) from mean squares

SourceNumeratorDenominatorNum.dfDen.df

Si1*Si1*Res 1 136

Pl1*Pl1*Res 1 136

Or1*Or1*Res 1 136

Ag1*Ag1*Res 2 136

Da(Si)1*Da(Si)1*Res 1 136

SixPl1*SixPl1*Res 1 136

SixOr1*SixOr1*Res 1 136

SixAg1*SixAg1*Res 2 136

PlxOr1*PlxOr1*Res 1 136

PlxAg1*PlxAg1*Res 2 136

OrxAg1*OrxAg1*Res 2 136

Da(Si)xPl1*Da(Si)xPl1*Res 1 136

Da(Si)xOr1*Da(Si)xOr1*Res 1 136

Da(Si)xAg1*Da(Si)xAg1*Res 2 136

SixPlxOr1*SixPlxOr1*Res 1 136

SixPlxAg1*SixPlxAg1*Res 2 136

SixOrxAg1*SixOrxAg1*Res 2 136

PlxOrxAg1*PlxOrxAg1*Res 1 136

Da(Si)xPlxOr1*Da(Si)xPlxOr1*Res 1 136

Da(Si)xPlxAg1*Da(Si)xPlxAg1*Res 2 136

Da(Si)xOrxAg1*Da(Si)xOrxAg1*Res 2 136

SixPlxOrxAg1*SixPlxOrxAg1*Res 1 136

Da(Si)xPlxOrxAg1*Da(Si)xPlxOrxAg1*Res 1 136

Estimates of components of variation

SourceEstimateSq.root

S(Si) 172,97 13,152

S(Pl) 622,38 24,948

S(Or) 77,117 8,7816

S(Ag) -6,0292-2,4554

S(Da(Si)) 221,04 14,867

S(SixPl) 117,82 10,854

S(SixOr) 13,881 3,7257

S(SixAg) -32,385-5,6907

S(PlxOr) 141,55 11,897

S(PlxAg) 16,29 4,0361

S(OrxAg) 30,455 5,5186

S(Da(Si)xPl) 1306,4 36,144

S(Da(Si)xOr) -14,12-3,7576

S(Da(Si)xAg) -74,356 -8,623

S(SixPlxOr) -55,199-7,4296

S(SixPlxAg) -44,749-6,6894

S(SixOrxAg) -95,602-9,7776

S(PlxOrxAg) -27,98-5,2896

S(Da(Si)xPlxOr) 165,51 12,865

S(Da(Si)xPlxAg) -162,34-12,741

S(Da(Si)xOrxAg) -67,092 -8,191

S(SixPlxOrxAg) -85,589-9,2514

S(Da(Si)xPlxOrxAg) 187,74 13,702

V(Res) 2176,3 46,651

2)PERMANOVA analyses of samples from the 8 non-deviating plots

Permutational MANOVA

Resemblance worksheet

Data type: Similarity

Selection: All

Standardise Samples by Total

Resemblance: S17 Bray Curtis similarity

Sums of squares type: Type III (partial)

Fixed effects sum to zero for mixed terms

Permutation method: Permutation of residuals under a reduced model

Number of permutations: 10000

Factors

NameAbbrev.TypeLevels

SiteSiFixed 2 (Grain, Zirl)

DateDaFixed 3 (2011/10/09,2011/10/16, 2011/10/24)

PlantPlFixed 2 (Pinus, Viscum)

OrganOrFixed 2 (Leaf, Stem)

AgeAgFixed 3 (1, 2 , 3 years)

PERMANOVA table of results

Unique

Source df SS MSPseudo-FP(perm) perms P(MC)

Si 1 10530 10530 5,0284 0,0001 99430,0001

Pl 1 27948 27948 13,347 0,0001 99330,0001

Or 1 5740,85740,8 2,7415 0,0076 99230,0082

Ag 2 4942,72471,4 1,1802 0,2478 98970,2435

Da(Si) 1 6709,96709,9 3,2043 0,0039 99310,0042

SixPl 1 3023,73023,7 1,444 0,1429 9909 0,151

SixOr 1 2705,72705,7 1,2921 0,1976 99140,2155

SixAg 2 3478,61739,3 0,83061 0,6645 9899 0,652

PlxOr 1 5350,85350,8 2,5553 0,0119 99190,0126

PlxAg 2 5136,92568,4 1,2266 0,2112 99060,2144

OrxAg 2 5169,32584,7 1,2343 0,2037 98990,2135

Da(Si)xPl 1 13586 13586 6,4877 0,0001 99250,0001

Da(Si)xOr 1 2122 2122 1,0134 0,3855 99190,3909

Da(Si)xAg 2 3555,41777,7 0,84894 0,6325 99060,6285

SixPlxOr 1 2212,62212,6 1,0566 0,3513 99200,3604

SixPlxAg 2 2950,41475,2 0,70448 0,8277 9914 0,822

SixOrxAg 2 1687,5843,76 0,40293 0,9978 99020,9958

PlxOrxAg** 1 1580,91580,9 0,75496 0,6768 99500,6572

Da(Si)xPlxOr 1 1925,91925,9 0,91973 0,4865 99270,4811

Da(Si)xPlxAg 2 3291,11645,5 0,78582 0,7238 99210,7159

Da(Si)xOrxAg 2 2237,9 1119 0,53436 0,9698 98920,9638

SixPlxOrxAg** 1 2911,22911,2 1,3903 0,1635 9924 0,167

Da(Si)xPlxOrxAg** 1 3478,43478,4 1,6611 0,0899 99270,0884

Res1022,1359E5 2094

Total1343,6771E5

** Term has one or more empty cells

Details of the expected mean squares (EMS) for the model

SourceEMS

Si1*V(Res) + 42,262*S(Si)

Pl1*V(Res) + 42,47*S(Pl)

Or1*V(Res) + 40,767*S(Or)

Ag1*V(Res) + 30,817*S(Ag)

Da(Si)1*V(Res) + 20,933*S(Da(Si))

SixPl1*V(Res) + 21,235*S(SixPl)

SixOr1*V(Res) + 20,383*S(SixOr)

SixAg1*V(Res) + 15,409*S(SixAg)

PlxOr1*V(Res) + 20,48*S(PlxOr)

PlxAg1*V(Res) + 15,446*S(PlxAg)

OrxAg1*V(Res) + 18,152*S(OrxAg)

Da(Si)xPl1*V(Res) + 10,569*S(Da(Si)xPl)

Da(Si)xOr1*V(Res) + 9,7572*S(Da(Si)xOr)

Da(Si)xAg1*V(Res) + 7,4441*S(Da(Si)xAg)

SixPlxOr1*V(Res) + 10,24*S(SixPlxOr)

SixPlxAg1*V(Res) + 7,7229*S(SixPlxAg)

SixOrxAg1*V(Res) + 9,076*S(SixOrxAg)

PlxOrxAg1*V(Res) + 10,24*S(PlxOrxAg)

Da(Si)xPlxOr1*V(Res) + 4,9231*S(Da(Si)xPlxOr)

Da(Si)xPlxAg1*V(Res) + 3,7398*S(Da(Si)xPlxAg)

Da(Si)xOrxAg1*V(Res) + 4,4181*S(Da(Si)xOrxAg)

SixPlxOrxAg1*V(Res) + 5,12*S(SixPlxOrxAg)

Da(Si)xPlxOrxAg1*V(Res) + 2,4615*S(Da(Si)xPlxOrxAg)

Res1*V(Res)

Construction of Pseudo-F ratio(s) from mean squares

SourceNumeratorDenominatorNum.dfDen.df

Si1*Si1*Res 1 102

Pl1*Pl1*Res 1 102

Or1*Or1*Res 1 102

Ag1*Ag1*Res 2 102

Da(Si)1*Da(Si)1*Res 1 102

SixPl1*SixPl1*Res 1 102

SixOr1*SixOr1*Res 1 102

SixAg1*SixAg1*Res 2 102

PlxOr1*PlxOr1*Res 1 102

PlxAg1*PlxAg1*Res 2 102

OrxAg1*OrxAg1*Res 2 102

Da(Si)xPl1*Da(Si)xPl1*Res 1 102

Da(Si)xOr1*Da(Si)xOr1*Res 1 102

Da(Si)xAg1*Da(Si)xAg1*Res 2 102

SixPlxOr1*SixPlxOr1*Res 1 102

SixPlxAg1*SixPlxAg1*Res 2 102

SixOrxAg1*SixOrxAg1*Res 2 102

PlxOrxAg1*PlxOrxAg1*Res 1 102

Da(Si)xPlxOr1*Da(Si)xPlxOr1*Res 1 102

Da(Si)xPlxAg1*Da(Si)xPlxAg1*Res 2 102

Da(Si)xOrxAg1*Da(Si)xOrxAg1*Res 2 102

SixPlxOrxAg1*SixPlxOrxAg1*Res 1 102

Da(Si)xPlxOrxAg1*Da(Si)xPlxOrxAg1*Res 1 102

Estimates of components of variation

SourceEstimateSq.root

S(Si) 199,6 14,128

S(Pl) 608,77 24,673

S(Or) 89,455 9,4581

S(Ag) 12,245 3,4992

S(Da(Si)) 220,51 14,85

S(SixPl) 43,782 6,6168

S(SixOr) 30,01 5,4782

S(SixAg) -23,021 -4,798

S(PlxOr) 159,02 12,61

S(PlxAg) 30,715 5,5421

S(OrxAg) 27,029 5,199

S(Da(Si)xPl) 1087,3 32,974

S(Da(Si)xOr) 2,8657 1,6928

S(Da(Si)xAg) -42,494-6,5187

S(SixPlxOr) 11,583 3,4033

S(SixPlxAg) -80,128-8,9514

S(SixOrxAg) -137,76-11,737

S(PlxOrxAg) -50,109-7,0788

S(Da(Si)xPlxOr) -34,145-5,8433

S(Da(Si)xPlxAg) -119,92-10,951

S(Da(Si)xOrxAg) -220,7-14,856

S(SixPlxOrxAg) 159,61 12,634

S(Da(Si)xPlxOrxAg) 562,41 23,715

V(Res) 2094 45,761