Mapping Geological Events and Nitrogen Fixation Evolution Onto the Timetree of the Evolution of Nitrogen-Fixation Genes.

"to study the evolution of bnf we reconstructed the phylogenetic tree of 1099 concatenated nif/vnf/anfhdk protein sequences ( fig 1 ); the sequence data are listed in supplementary data s1 supplementary material online and supplementary fig s1 supplementary material online is a detailed version of fig 1 .; we constructed ten timetrees from the phylogeny in fig 1 ( table 1 ); we provided 18 additional timetrees in supplementary data s1 and s2 supplementary material online.; we considered several calibration points according to previous studies ( table 1 and supplementary data s1 supplementary material online) and we described all our supplementary data supplementary material online.; we constructed multiple timetrees but some estimated time points are apparently too old or too young ( supplementary data s1 and s2 supplementary material online).; the molecular clock test and the rate correlation test also reveal differences in bnf evolution rates ( supplementary data s1 supplementary material online).; we indeed found that many nitrogen-fixing bacteria (in all groups) possess sod/sor genes ( supplementary data s1 supplementary material online supplementary fig s1 supplementary material online).; we collected environmental data ( supplementary data s1 supplementary material online) of thermophilic bacteria from bacdive ( ) and ncbi biosample ( ).; our data collection was as described previously ( ); the data are given in supplementary data s1 supplementary material online and each dataset is described in supplementary material online.; therefore about 38% to 44% of the genomes in the gtdb database r95 were from uncultured isolates ( supplementary data s1 supplementary material online).; the alignments (after trimming) can be found in supplementary data s3 supplementary material online.; the timetrees were computed using calibration points listed in table 1 and supplementary data s1 supplementary material online.; the raw timetree figures are given in supplementary data s2 supplementary material online and have detailed information in supplementary data s1 supplementary material online."

"Conflict of interest: The authors declare no competing interests."

"We thank Dr. Sudhir Kumar for advice on timetree analysis and Dr. John Wang, Dr. Ronnie G. Gicana, and Tien-Yu Wu for suggestions. This study was supported by Academia Sinica, Taiwan. Hong-Wei Pi was supported by a postdoctoral fellowship of Academia Sinica. We thank the National Center for High-performance Computing (NCHC) of Taiwan for providing computational resources."