期刊
GENETICS
卷 204, 期 2, 页码 513-529出版社
GENETICS SOCIETY AMERICA
DOI: 10.1534/genetics.116.191973
关键词
gene insertion/deletion; indel rates; maximum likelihood; unobserved data
资金
- National Science Foundation Graduate Research Fellowship Program [DGE-1256259]
- National Institutes of Health National Research Service Award [T32 GM07215]
- National Institutes of Health [R01AI113287]
- National Sciences and Engineering Research Council [140221-10]
Lateral gene transfer is an important mechanism for evolution among bacteria. Here, genome-wide gene insertion and deletion rates are modeled in a maximum-likelihood framework with the additional flexibility of modeling potential missing data. The performance of the models is illustrated using simulations and a data set on gene family phyletic patterns from Gardnerella vaginalis that includes an ancient taxon. A novel application involving pseudogenization/genome reduction magnitudes is also illustrated, using gene family data from Mycobacterium spp. Finally, an R package called indelmiss is available from the Comprehensive R Archive Network at https://cran.r-project.org/package=indelmiss, with support documentation and examples.
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