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A Reduction of "Species" Resolves the Species Problem ----- Jody Hey , January
1997
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A SIMPLE SYSTEM
Consider the reproduction of a single-celled asexual organism. To simplify,
focus solely on the replication of the DNA genome, and view the remainder
of the organism as the machinery of DNA replication. This simplification
follows from the genotype/phenotype relationship: the genotype is the information
for the organism and is replicated; while the phenotype is the organism and
is recreated each generation as a function of the genotype. The focus is
on the transmission of information, and much of this discussion should apply
in principle to any informational replicating system (Orgel, 1992).
Hereafter, "a DNA" will be used to refer explicitly to the molecule that
contains the genotype information and that is replicated in this simple system.
This choice of term is motivated by the same reasoning that lead Dawkins
to employ "replicator", which he defined as an "entity that interacts with
its world, including other replicators, in such a way that copies of itself
are made" (Dawkins, 1978). The word "gene" is avoided here, and by Dawkins
(1978), because of its conventional meaning as a single unit of function
in the expression of the phenotype. In this paper, a DNA is a contiguous
double stranded molecule that is a replicator. A DNA may be physically connected
to a longer contiguous stretch of DNA or it may correspond to a single
chromosome, depending on the context. A DNA sequence is a particular order
of the component nucleotides within a DNA and is not synonymous with a DNA.
The terminology also includes "DNAs" to refer to multiple pieces of homologous
DNA. In this context, "homologous" means that the different DNAs are related
by common ancestry and thus share a gene tree history (Fig. 1). A sample
of DNAs may include one or multiple sequences.
Fig. 1 The gene tree history of a sample of DNAs. The tree is a hypothetical
depiction of a true history, not to be taken as an example of a tree estimated
from data. Key features include: the directionality of time, from the past
to the present; branches; branch tips; and nodes, the junctions of branches.
Branch tips refer to different pieces of DNA that exist at the present moment.
The remainder of the diagram below the tips is a description of history.
The tip of the branch at the base of the tree is undefined because the true
history is not known beyond this point. Branches refer precisely to the
persistence of a DNA sequence through time. This persistence means at times
the physical persistence, but also includes numerous cases of replication
when it is the information in the sequence that persists. The nodes of the
tree refer precisely to those cases of DNA replication when both daughter
sequences that were produced are ancestors of sequences that are represented
as tips of branches.
Consider a DNA that undergoes replication to form two daughter DNAs, and
suppose that the replication depends upon both the DNA sequence and the local
environmental resources. After replication, the fates of the daughter DNAs
may be linked because they coexist under common circumstances and compete
for the same pool of resources. If resources are limiting and competition
occurs so that not all DNAs undergo replication, and if both daughter DNAs
and all of their descendants are subject to the same circumstances (i.e.
no mutational differences or geographical separations), then the long term
persistence of both groups of descendants is mutually exclusive. After some
time, perhaps after many rounds of replication, one group of descendants
will have replaced the other, or both will have been replaced by the descendants
of yet another DNA that also shares those circumstances.
Now consider that DNAs reside within organisms, and that the continuous random
replacement of DNAs by the descendants of others is caused by a random birth
and death process that happens within a group of organisms that share a finite
set of resources. With an allele-based model of genetic variation, the effects
of the random birth and death process within a population of organisms include
random changes in allele frequencies that lead to the random loss and fixation
of mutations. This process is called genetic drift. From a gene tree standpoint,
genetic drift is manifested as a randomly shifting pattern of coancestry
among a set of DNAs (Fig. 2). Consider the persistence through time of a
group of organisms that experience a random process of birth and death, and
then consider the gene tree, one DNA per organism, with the tips constantly
moving forward with time. The random death of some organisms means that some
gene tree tips do not persist, and the branches that lead to these tips disappear
from the gene tree history that remains for those DNAs that do persist and
replicate (Fig. 2). This shift forward in time of the pattern of ancestry
proceeds continuously, and at intervals will include forward jumps for the
most basal node representing the ancestor for an entire group of DNAs (Watterson,
1982).
Fig. 2 A gene tree at successive times under genetic drift. Asterisks at
branch tips at times A and B indicate sequences that did not persist to the
next time period. Solid lines at times B and C indicate branches that were
present at the previous time and still remain (and are now longer) in the
tree because of the persistence of DNAs at the branch tips. Dotted lines
at times B and C indicate new branches leading to DNAs that arose by replication
since the previous time period. All solid lines at times B and C correspond
to a line (solid or dotted) at the previous time, and all lines at times
A and B (solid or dotted) that do not lead to an asterisk, correspond to
a solid line at the next time.
Two kinds of events can cause the descendants of two daughter DNAs to not
be mutually exclusive. First, the daughters may differ because of mutation,
and this may cause differences in the circumstances of replication. Individuals
carrying the mutation may utilize resources in a different way so that they
do not compete directly with individuals not carrying the mutation. Second,
one daughter DNA and respective descendants may occur in a geographically
distinct location from other DNAs. Under both mutation and geographic separation,
the genetic drift experienced by the descendants of one DNA occurs partially
independently of that experienced by the descendants of the other. To describe
this in another way, the individual DNAs within a group compete more directly
with one another, and are more likely to be replaced by the descendants of
other DNAs within the same group than by the descendants of DNAs from the
other group. In this way both mutation and geographic separation can lead
to multiple groups of DNAs that are not mutually exclusive.
The model of replication that leads to multiple groups of DNAs that are not
mutually exclusive has three components: a DNA with a sequence that causes
replication; the possibility of mutations; and some kind of environmental
structure such that the pool of resources used by one group of DNAs need
not completely overlap those of another group of DNAs. This simple system
probably existed early in the origin of life, though the actual nucleic acid
may have been single stranded RNA (Gilbert, 1986). The model is also an
approximation, for the multicellular case, of the transition from the
reproductive cells of an organism in one generation to the reproductive cells
in a descendant organism in the next generation. For a group of multicellular
organisms, the appropriate gene tree history to consider is one in which
a single DNA has been taken from each organism. In this case many but not
all of the instances of DNA replication represented by branches on a gene
tree will have occurred during germ line development and somatic growth (to
the degree that somatic growth occurs prior to germ line development). The
remaining replication events along gene tree branches, and all those replications
represented by gene tree nodes, must have occurred within reproductive cells
that gave rise to gametes or offspring.
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© 1997 Jody Hey
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