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Second, molecular systematics can help us distinguish between forms that are morphologically similar but are in fact ancient, unrelated lineages with little or no gene flow between them. One example is Darwin's fox (Dusicyon fulvipes) on Chiloé Island in Chile. Some scientists had considered Darwin's fox a small race of the common South American grey-fox species Dusicyon griseus, on the basis of morphological similarities. Chiloé island is only 5 km off the coast and likely was connected to the mainland during the last glaciation (about 13,000 years ago), which would have created opportunities for gene flow between Darwin's and grey foxes. However, genetic analyses of Darwin's fox and other South American fox species suggest that Darwin's fox is at least as divergent from the grey fox as the grey fox is from another well-recognized fox species, the culpeo fox (Dusicyon culpaeus), and that Darwin's fox probably evolved from the first immigrant foxes into South America 2–3 million years ago. Recently, a small population of Darwin's foxes was found on mainland Chile, and they were shown to be quite genetically divergent from the grey fox but closely related to the population on Chiloé island. This suggests little or no present or historical gene flow between Darwin's and grey foxes, and it supports the distinctiveness of Darwin's fox as a separate species (Wayne 1996).

Third, systematic analyses of genetic characters can provide an objective means of identifying evolutionarily distinct lineages among closely related groups. The Iberian lynx, Lynx pardinus, is considered to be the most vulnerable cat in the world. Its remaining populations are highly fragmented and of limited size. The species status of the Iberian lynx is complicated: Some consider it to be a geographic variant of the Eurasian lynx, Lynx lynx, and others consider it to be a distinct species. Because the taxonomic status of the Iberian lynx is important to the establishment of an effective management plan for lynxes in general, a molecular-systematic study was conducted recently (Beltran and others 1996). The results of this study revealed a close relationship between the Canadian lynx (Lynx canadensis) and the Eurasian lynx, but the Iberian lynx is evolutionarily more distinct. Thus, these molecular data give validity to the concept that the Iberian lynx is a phylogetically distinct species that deserves separate consideration for conservation.

Molecular Phylogeography—
Where do those Conservation Units Reside?

Once we decide what groupings of organisms are distinct and worthy of separate efforts at conservation (that is, we identify our CUs), it becomes critical to determine the geographic location of important subsets of individuals within each CU. In other words, where will we focus our conservation efforts to preserve a CU or species?

The use of molecular systematics in a geographic context can contribute to answers to this question in two ways. First, detailed studies of intraspecific (within-species) variation can identify the geographic limits of either a CU or what Moritz (1994) calls a management unit (MU). Second, patterns of intraspecific phylogenies of unrelated groups of organisms may assist in identifying geographic regions