Understanding the process of evolution is one of the great challenges in biology. Cave animals are one group with immense potential to address the mechanisms of evolutionary change. Amazingly, similar morphological alterations, such as enhancement of sensory systems and the loss of eyes and pigmentation, have evolved multiple times in a diverse assemblage of cave animals. Our goal is to develop an invertebrate model to study cave evolution so that, in combination with a previously established vertebrate cave system, we can address genetic questions concerning evolutionary parallelism and convergence. We chose the isopod crustacean, Asellus aquaticus, and generated a genome-wide linkage map for this species. Our map, composed of 117 markers, of which the majority are associated with genes known to be involved in pigmentation, eye, and appendage development, was used to identify loci of large effect responsible for several pigmentation traits and eye loss. Our study provides support for the prediction that significant morphological change can be mediated through one or a few genes. Surprisingly, we found that within population variability in eye size occurs through multiple mechanisms; eye loss has a different genetic basis than reduced eye size. Similarly, again within a population, the phenotype of albinism can be achieved by two different genetic pathways-either by a recessive genotype at one locus or doubly recessive genotypes at two other loci. Our work shows the potential of Asellus for studying the extremes of parallel and convergent evolution-spanning comparisons within populations to comparisons between vertebrate and arthropod systems.arthropods | regressive evolution | subterranean | mapping C ave animals have long interested biologists because of their bizarre and other-worldly appearance. Common characteristics of cave animals include the absence or great reduction of eyes, the elimination or near disappearance of pigmentation, and the elongation of limbs (1). These characteristics can be found in cave animals as diverse as salamanders, fish, spiders, shrimp, beetles, and collembolans. Most studies looking at the genetic basis of parallel or convergent evolution examine either closely related species with the same phenotypes or independently evolved populations of the same species with similar phenotypes (reviewed in ref.2). The cave system, however, is unique in that we can examine, and eventually compare, the genetic and molecular basis for the loss of eyes and pigmentation in vastly different (i.e., both invertebrate and vertebrate) taxa.A vertebrate cave fish, Astyanax mexicanus, has been established as an emerging model species for genetic and developmental analyses (reviewed in refs. 3 and 4). Mapping, using this species, has identified regions of the genome that are responsible for caveassociated morphological changes (5, 6). We decided to develop an invertebrate cave model that will provide an independent example of cave adaptation. Of the invertebrates, crustaceans have been particularly succ...