Using microsatellite and MHC variation to identify species, ESUs, and MUs in the endangered Sonoran topminnow

Highly variable loci can provide insight into the recognition of species, e volutionarily significant units (ESUs) and management units (MUs). In gener al, the ESU and MU categories are thought to be reflective of adaptive diff erences between them. Here we examine this premise by presenting a comprehe nsive examination of genetic variation for both microsatellite loci and a m ajor histocompatibility complex (MHC) locus, thought to be of adaptive sign ificance, in the endangered Sonoran topminnow. The extent of variation for the microsatellite loci and the MHC gene within the 13 populations of the G ila topminnow is highly correlated, suggesting that nonselective factors ha ve played an important role in influencing variation within and between pop ulations for the MHC locus. Therefore, using all of these loci, we found th at the eight natural populations of the Gila topminnow fell into two differ ent ESUs, one of which had four different MUs. The source of the Boyce Thom pson sample, a population that was used extensively for restocking, appeare d to be Monkey Spring. The source of the Watson Wash population also appear ed to be Monkey Spring (or Boyce Thompson). The newly colonized Santa Cruz River population, which had the most genetic variation of any Gila topminno w population, appeared to descend primarily from Sonoita Creek populations. The Yaqui topminnow, presently considered another subspecies of the Sonora n topminnow, was very distinct for-both microsatellite (only two of 25 alle les found in the Yaqui were in any of the Gila topminnow samples) and MHC a lleles (nonoverlapping sets of alleles for the two groups). As a result, it appeared that the taxonomic status of the two subspecies should be re-eval uated and that full species status for Gila and Yaqui topminnows was approp riate. There was evidence for the importance of long-term selection at the MHC locus in the higher rate of nonsynonymous than synonymous substitution. In addition, there appeared to have been a duplication of the MHC locus th at was present in most of the fish in six of the natural populations of the Gila topminnow.