Cnemidophorus tigris punctilinealis of the Sonoran Desert and C. t. marmoratus of the Chihuahuan Desert contact each other and interbreed in the Animas Valley of southwestern New Mexico. More than 600 specimens have been examined from the contact region, and data on biochemical genetics (mitochondrial DNA haplotypes, protein electrophoresis of nuclear gene products), chromosomes, external morphology (coloration, size, scalation), reproduction, and fitness have been compared for three hybrid zones. Habitats in the contact region were mapped and photographed, and they are discussed in the context of vegetational changes during Pleistocene to Recent times, which affected the geographic distribution of these animals.

Data from mitochondrial DNA, allele frequencies at four protein loci (of 36 analyzed), and body coloration demonstrate that the areas of contact have steep, concordant, and coincident step-clines in which most gene exchange occurs in hybrid zones that are 3.2–7.8 km wide. Analyses of allele frequencies, genotype frequencies, and fixation indices (including Hardy-Weinberg equilibrium, linkage equilibrium, and cytonuclear equilibrium) indicate a population structure determined primarily by random mating and an absence of selection against hybrids. Estimates of gene flow indicate that the clines resulted from neutral secondary contact initiated with the newest reconnection of the Sonoran and Chihuahuan Deserts within the present interglacial episode, from 1000 to 5000 years ago. This timeframe is consistent with paleoecological data from packrat middens.

Analyses of karyotypes, morphology, reproduction, and physiology also fail to detect differences in fitness among lizards with various genotypes. Although it is possible that there are fitness differences that are too small to be detected by the sample sizes we employed, the data indicate that reproductive success, fitness, and the dynamics of populations within the hybrid zones presently are no different from those in nonhybrid populations. Earlier data, which suggested that one of the step-clines was moving, are not supported.

The clines are located in fragile semiarid habitats that are subject to desertification. Consequently, we present considerable data and dated photographs of habitats, precise locations of sampling sites, and local allele frequencies, so that future investigators can monitor changes in position, width, or dynamics of these hybrid zones.

In addition, the population genetics data are discussed in the context of the following: (1) absence of rare, apparently novel alleles forming in the hybrid zones; (2) genetic comparisons with additional subspecies of C. tigris (C. t. aethiops and C. t. septentrionalis); and (3) interspecific hybridization between C. tigris and other whiptail lizards of either bisexual or unisexual (parthenogenetic, clonal) species. Cnemidophorus tigris is one of the ancestors of some of the parthenogens, which are of hybrid origin, and our interest in their evolutionary history fuels our efforts to improve understanding of hybridization among whiptail lizards.