RT Journal
A1 Doolittle, W. Ford
A1 Zhaxybayeva, Olga
T1 On the origin of prokaryotic species
JF Genome Research 
JO Genome Research 
YR 2009 
FD May 01 
VO 19 
IS 5 
SP 744 
OP 756 
DO 10.1101/gr.086645.108 
UL http://genome.cshlp.org/content/19/5/744.abstract 
AB The notion that all prokaryotes belong to genomically and phenomically cohesive clusters that we might legitimately call “species” is a contentious one. At issue are (1) whether such clusters actually exist; (2) what species definition might most reliably identify them, if they do; and (3) what species concept—by which is meant a genetic and ecological theory of speciation—might best explain species existence and rationalize a species definition, if we could agree on one. We review existing theories and some relevant data. We conclude that microbiologists now understand in some detail the various genetic, population, and ecological processes that effect the evolution of prokaryotes. There will be on occasion circumstances under which these, working together, will form groups of related organisms sufficiently like each other that we might all agree to call them “species,” but there is no reason that this must always be so. Thus, there is no principled way in which questions about prokaryotic species, such as how many there are, how large their populations are, or how globally they are distributed, can be answered. These questions can, however, be reformulated so that metagenomic methods and thinking will meaningfully address the biological patterns and processes whose understanding is our ultimate target.