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Supplemental material to:
Weak phylogenetic signal in physiological traits of methane-oxidizing bacteria
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Figure S1: Phylogenetic tree based on partial pmoA sequences.
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Figure S2: Phylogenetic tree based on 16S rRNA sequences.
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Table S1: P-values of tip shuffling randomization to test the presence of phylogenetic signal
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in continuous-valued traits.
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Table S2: The phylogenetic autocorrelation in physiological traits of MOB using the test of
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Abouheif (1999).
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Figure S1. Phylogenetic tree based on partial pmoA sequences (391bp). The tree was
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constructed by maximum likelihood (1000 data resamplings) with the “GTR” substitution
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model. Bootstrap values (1000 data resamplings) are shown with a closed square representing
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bootstrap values above 70. The outgroup is Nitrosococcus mobilis but not displayed in the
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tree. The scale bar represents 0.1 change per base position.
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Figure S2. Phylogenetic tree based on 16S rRNA sequences (1399bp). The tree was
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constructed by maximum likelihood (1000 data resamplings) with the “GTR” substitution
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model. Bootstrap values (1000 data resamplings) are shown with a closed square representing
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bootstrap values above 70. The outgroup is Nitrosococcus mobilis but not displayed in the
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tree. The scale bar represents 0.01 change per base position.
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Table S1. Average P-values of a tip shuffling randomizations from 1000 bootstrap trees using
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the maximum likelihood algorithm, significant values are highlighted in bold.
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Traits*
pmoA
16S rRNA
pHopt
0.016 ± 0.06
0.001 ± 0.00
pHrange
0.237 ± 0.14
0.008 ± 0.01
Tempopt
0.001 ± 0.00
0.002 ± 0.01
Temprange
0.200 ± 0.05
0.186 ± 0.08
GC
0.156 ± 0.15
0.001 ± 0.01
Speccell
0.121 ± 0.07
0.402 ± 0.13
Specliter
0.561 ± 0.08
0.620 ± 0.10
Kmapp
0.511 ± 0.08
0.376 ± 018
*pHopt: optimal pH value for growth, pHrange: pH range for growth, Tempopt: optimal
temperature for growth, Temprange: temperature range for growth, Speccell: specific
affinity per cell (10-12 l cell-1 h-1), Specliter: specific affinity per liter (l g-1 h-1), Kmapp:
Michaelis constant Km (apparent).
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Table S2. The phylogenetic signal in physiological traits of MOB using the test of Abouheif
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(1999), significant P-values are highlighted in bold.
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pmoA
16S rRNA
Traits*
Obs
Std Obs H0
P-value Obs
Std Obs H0
P-value
pHopt
0.45
3.74
greater
0.50
4.31
greater
0.005
0.002
pHrange
0.33
2.37
greater
0.29
2.10
greater
0.002
0.008
Tempopt
0.44
3.33
greater
0.44
3.30
greater
0.001
0.003
Temprange 0.10
0.77
greater
0.22
0.01
0.14
greater
0.42
GC
0.45
3.47
greater
0.45
3.16
greater
0.001
0.001
Speccell
0.08
0.48
greater
0.30
0.21
1.12
greater
0.15
Specliter
-0.15 -0.81
greater
0.77
0.25
1.28
greater
0.11
Kmapp
0.12
0.81
greater
0.20
0.16
1.13
greater
0.13
*pHopt: optimal pH value for growth, pHrange: pH range for growth, Tempopt: optimal
temperature for growth, Temprange: temperature range for growth, Speccell: specific
affinity per cell (10-12 l cell-1 h-1), Specliter: specific affinity per liter (l g-1 h-1), Kmapp:
Michaelis constant Km (apparent).
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