Strong seed-bank effects in bacterial evolution.
Bacterial genomes are mosaics with fragments showing distinct phylogenetic origins or even being unrelated to any other genetic information (ORFan genes). Thus the analysis of bacterial population genetics is in large part a collection of explanations for anomalies in relation to classical population genetic models such as the Wright-Fisher model and the Kingman coalescent that do not adequately describe bacterial population genetics, genomics or evolution. The concept of "species" as an evolutionary coherent biological group that is genetically isolated and shares genetic information through recombination among its members cannot be applied to any bacterial group. Recently, a simple probabilistic model considering the role of strong seed-bank effects in population genetics has been proposed by Blath et al. This model suggests the existence of a genetic pool with high diversity that is not subject to classical selection and extinction. We reason that certain bacterial population genetics anomalies could be explained by the prevalence of strong seed-bank effects among bacteria. To address this possibility we analyzed the genome of the bacterium Azotobacter vinelandii and show that genes that code for functions that are essential for the bacterium biology do not have a relation of ancestry with closely related bacteria, or are ORFan genes. The existence of essential genes that are not inherited from the most recent ancestor cannot be explained by classical population genetics models and is irreconcilable with the current view of genes acquired by horizontal transfer as being accessory or adaptive.
Technische Universität Berlin, TU Berlin, Fakultät II, Institut für Mathematik, MA 7-3, Strasse des 17. Juni 136, 10623 Berlin, Germany; Berlin Mathematical School, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apartado Postal 70228, 04510 DF, México.
Adrián
A
González-Casanova
Instituto de Ecología, A. C., Red de Estudios Moleculares Avanzados, Apartado Postal 63, 91000, Xalapa, Veracruz, México.
Eneas
E
Aguirre-von-Wobeser
Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apartado, México.
Guadalupe
G
Espín
Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Distrito Federal, México.
Luis
L
Servín-González
Technische Universität Berlin, TU Berlin, Fakultät II, Institut für Mathematik, MA 7-3, Strasse des 17. Juni 136, 10623 Berlin, Germany.
Noemi
N
Kurt
University of Warwick, Coventry, UK.
Dario
D
Spanò
Technische Universität Berlin, TU Berlin, Fakultät II, Institut für Mathematik, MA 7-3, Strasse des 17. Juni 136, 10623 Berlin, Germany. Electronic address: blath@math.tu-berlin.de.
Jochen
J
Blath
Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Distrito Federal, México. Electronic address: gloria@biomedicas.unam.mx.
Gloria
G
Soberón-Chávez
D016948:Azotobacter vinelandii / Q000235:genetics*; D019143:Evolution, Molecular; D016680:Genome, Bacterial / Q000502:physiology*; D008957:Models, Genetic
Bacterial population genetics; Long-range Wright-Fisher model