We used landmark-based geometric morphometric methods to describe patterns of body shape variation and shape covariation with size among populations of the threatened White Sands Pupfish (Cyprinodon tularosa), a species that occurs in dissimilar aquatic habitats. White Sands Pupfish populations include two genetically distinct, native populations that have been historically isolated in Salt Creek, a saline river, and Malpais Spring, a brackish spring. In addition, two populations were established approximately 30 years before this study by translocation of fish from Salt Creek to Lost River (a saline river) and Mound Spring (a brackish spring). We found significant body shape variation among populations and between males and females. Body shapes were more slender for females than for males and more slender for saline river populations than brackish spring populations. Introductions of pupfish to new habitats resulted in significant departures in body shape and shape allometry from the native Salt Creek population. Shape divergence was more pronounced for the Mound Spring population, which is consistent with a greater change in abiotic conditions. Although Mound Spring pupfish, like Malpais Spring pupfish, were more deep-bodied than saline river pupfish, differences in body shape and the level of sexual dimorphism were significant between the two brackish spring populations, indicating that deep-bodied shapes may be achieved from different anatomical configurations. The significant shape divergence of introduced populations warrants consideration for the conservation of this rare species, as creation of refuge populations for native stocks is a current management strategy.

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