Table 1

Divergence Time Estimates Under Different Rates of Evolution.

Divergence of interest

Tree

Calculation

Method

Divergence time estimates from different proposed rates


Universal bacterial rate

in nature

Empirical E. coli rates

in culture

DONNA2/

strain 195

divergence

16S clock


Dehalogenimonas/Dehalococcoides MRCA

Splitstree

5

(1.9/28/33/34)

0.9

(0.4/5.3/6.2/6.3)

0.5

200-600

ML

3

(1.2/18/21/21)

0.5

(0.2/3.2/3.8/3.9)

0.3

Dehalococcoides MRCA

Splitstree

0.3

(0.14/2/2.4/2.4)

0.06

(0.03/0.37/0.44/0.44)

0.04

30-60

ML

0.4

(0.17/2.5/3/3)

0.08

(0.03/0.47/0.55/0.56)

0.04

ssrA-GI integration modules MRCA

ML

3

(1.1/16/19/19)

0.5

(0.2/3/3.5/3.6)

0.2

integration modules MRCA, vcr-GIs only

ML

1

(0.4/5.5/6.5/6.6)

0.2

(0.07/1/1.2/1.2)

0.08

vcrAB MRCA

ML

0.05

(0.02/0.27/0.31/0.32)

0.008

(0.03/0.47/0.55/0.56)

0.004

vcrAB, leader masked

ML

0.01

(0.004/0.057/0.067/0.068)

0.002

(0.001/0.010/0.012/0.013)

0.0009


Reported age estimates (left, no parenthesis) are based on the rate of evolution listed in the column header as well as the average Dehalococcoides doubling time from published values (2 days). All estimates are reported in units of 1 million years. Age estimates of the Dehalococcoides clade from the Splitstree consensus network are based on branch lengths of strains to the common network node. '16S clock' is based on 1-2% 16S rRNA gene divergence per 50 million years [83]. Values in parenthesis are results from different doubling time estimates: 0.8 days - the fastest reported doubling time for Dehalococcoides [6]; 11.71 days - anaerobic benthic sediment community doubling time [49]; 13.76 days - bacterial doubling time in anaerobic seawater [48]; 14 days - approximate doubling time of the strictly anaerobic annamox bacteria [47]. For the secondary calculations of age estimates, an extra significant digit has been reported to allow distinguishing of estimates.

McMurdie et al. BMC Genomics 2011 12:287   doi:10.1186/1471-2164-12-287

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