318 Speciesrather than discuss all possible permutations and combinations. Later I shall appeal
to several current conceptions directly. Then we will consider three possible rea-
sons why microbes are not homogeneous and undifferentiated. The first is due to
stochastic processes of extinction and diversification, in what are called Branching
Random Walks.^103 The second is due to the lateral genetic exchange of parts of bac-
terial genomes and plasmids, and is called the Core Genome Hypothesis.^104 The
third is due to selection for adaptation to local fitness peaks maintaining a relatively
stable cluster of genomes and phenotypes. I shall then appeal to the notion devel-
oped initially for viral species by Manfred Eigen—the “quasispecies,” a collection of
close neighboring genomes. In the first instance, “microbial” (that is, asexual single-
celled) species form quasispecies.
Finally, I shall attempt to locate the different processes and species concepts in order
to draw a general point about asexual organisms, sexual organisms, and the evolution-
ary groups they form in different ways. I then will argue that the basic notion of “spe-
cies” is, in fact, the quasispecies, and that the definitions developed to serve metazoans
and metaphytes are secondary rather than primary conceptions of what species are.
What Are We Talking About?
The literature on microbial species refers to a number of groupings of organisms:
prokaryotes, protists, monerans, bacteria, and so on. There appears to be no sin-
gle term to cover them all, so I will here adopt “microbe” as a convenient label,
although it must not be thought that this implies microbes are a natural group. None
of these groups appear to be “natural” (which in a cladistic sense means monophy-
letic). Almost all of them are defined as some complement of Life after other groups,
eukaryotes, animals or metazoans, plants or metaphytes, and fungi, have been taken
out. In other words, “microbe” is a paraphyletic or polyphyletic group.
Under the “three-domain” hypothesis of Woese, the three multicellular “king-
doms” (animals, fungi, and plants) are small branches on a much larger tree, part of the
Eukaryota but not even the bulk of them.^105 Sex as we know it is a very restricted and
minor part of the diversity of life. “Prokaryotes” refers broadly to a group of organ-
isms that are basically not-eukaryotes.^106 Nowadays we refer instead to several groups:
Bacteria, Archaea, and Eukaryota. This privative classification is under challenge, and
many think that the three-domain deep phylogeny is an artifact of the genes used, and
that prokaryotes are indeed a monophyletic group.^107 Whether or not they are, one
(^103) Pie and Weitz 2005.
(^104) Dykhuizen and Green 1991, Dykhuizen 1998, Wertz et al. 2003, Coleman et al. 2006.
(^105) Woese 1998.
(^106) Pace 2006; but for a dissenting view see Martin and Koonin 2006.
(^107) See, for example, essays in Sapp 2005; particularly Doolittle 2005. Cavalier-Smith 2010 argues
that the Eukaryote/Prokaryote division is fundamental (the six-kingdom, two-empire classification).
Whitman 2009 accepts the three domains, but groups Archae and Bacteria as Prokaryota. Foster et al.
2009 make Eukaryota a sister group to Chrenarchaeota, and Euryarchaeota and Eubacteria sister
groups, thus making Archaebacteria paraphyletic. More recent work indicates what McInerney et al.
2015 call a “ring of life” scheme, cf. Lake 2015. None of this affects the point made here: that meta-
zoan eukaryotes with sexual reproduction are a tiny fraction of the tree of life. Thanks to Laurence
Moran for this information.