pathway” or “allelic genealogy”) entirely suitable for phylogenetic or cladistic examination (20, 21).
Genealogical Pathways and Organismal Phytogenies. Phylogeny at the level of populations and species. Ever since the publication of Genetics and the Origin of Species, geography and demography have played key roles in most biological speciation scenarios (22). During the evolutionary sequence of events by which an extended reproductive community of organisms (a field for gene recombination) becomes sundered, a curtailment of population genetic exchange by environmental separation typically is envisioned as a necessary prerequisite for the eventual evolution of the intrinsic (genetic) reproductive isolating barriers (RIBs) that are the hallmark of the BSC (Fig. 1). The initial genomic sundering may involve sister populations distributed across broad areas (species D and E in Fig. 1), small founding populations on the periphery of a species’ range (species A) (23), or, in some cases (24), local syntopic populations separated by microhabit at (species B). In each case, population genomic differentiation facilitated by environmental impediments to interbreeding initiates or eventually may lead to an elaboration of intrinsic reproductive barriers. Biological speciation also can take place suddenly in small populations via reproductive sundering processes such as polyploidization, chromosomal rearrangements, or changes in the mating system (20). Species A and B in Fig. 1 could be interpreted as examples.
Each such geographic-demographic model yields logical predictions about the coarse-focus phytogeny for particular extant populations or biological species (25). For example, from a traditional perspective, taxa D and E (Fig. 1) are sister biological species that comprise a clade. On the other hand, the widely distributed species C that recently spawned a peripheral isolate A, or a syntopic species B, is paraphyletic with respect to each of these latter forms. As emphasized by Patton and Smith (26), most mechanisms of speciation currently advocated by evolutionary biologists “will result in paraphyletic taxa as long as reproductive isolation forms the basis for species definition.” Such statements pertain to the historical subdivisions of gene pools at the levels of species or well-demarcated populations. In reality, intermediate situations also exist in which biotic subdivisions display incomplete phylogenetic separation because of a semipermeability in the extrinsic or intrinsic barriers to genetic exchange.
Phylogeny at the level of alleles. In principle, any representation of phytogeny for separated populations or species might be examined under finer focus by reference to organismal pedigrees (Fig. 2). Ineluctably, pedigrees define extended pathways of genetic transmission that constitute rivulets in “the stream of heredity (that) makes phytogeny” (27). Consider, for example, the matrilineal pathway of transmission (F → F → F → F…, where F signifies female) for mitochondrial (mt) DNA (Fig. 3 Upper Left). All extant females in taxon E trace genealogically through female ancestors to a shared progenitress at t−5, those in D coalesce at t−9, and those in the D+E assemblage stem to a common ancestor at t−12. The great-great…-great matrilineal grandmother of all extant individuals in the pedigree existed at t−20. With respect to the mainlines in the A-C complex (which coalesce at t−11), C1 is paraphyletic to A, and C2 is paraphyletic to B. All such statements reflect the realities of allelic-level ancestry through heredity, as to be distinguished from any estimates of ancestry in empirical appraisals based on molecular or any other data.
Similarly, other gender-described classes of genealogical pathways can be envisioned. In any pedigree for sexually reproducing organisms, only four such transmission routes are mutually exclusive in every generation: the matrilineal pathway already mentioned; the patrilineal analogue (M → M → M → M…, where M signifies male; the route, for example, of the mammalian Y chromosome); and the generation-to-generation alternating reciprocal pathways “M → F → M → F…” and “F → M → F → M….” As traced through the organismal pedigree under consideration (Fig. 3), a comparison of these “independent” pathways illustrates two fundamental points. First, the coalescent trees for the