Two described subspecies. Subspecies designations have been based on morphological and plumage differences, and confirmed by molecular analyses (Bulgarella et al. 2012). L. s. specularioides has a red iris, smaller body size, and more brownish or blackish mottled plumage, whereas L. s. alticola possesses a yellow-orange iris, larger body size, and more uniform, washed out plumage with fewer breast spots (Phillips 1922−1926).
Overall body size of crested ducks differs between the two subspecies and between the sexes (Bulgarella et al. 2007). Male and female L. s. alticola are significantly larger than male and female L. s. specularioides. Larger bodied individuals are found at higher elevations in the Andes (3000–5000 m), with the coastal and inland specimens from Patagonia being smaller, and the Mendoza specimens being intermediate in size between the two populations.
Morphologically intermediate populations of crested ducks, such as those found in Mendoza, Argentina, might be interpreted as evidence for introgression between the two populations, i.e., Andean Crested Ducks in the north and Patagonian Crested Duck populations in the south (Navas and Bo 1998). Intermediate morphology might also be maintained by natural selection on body size of individuals locally adapted to inhabiting intermediate elevational environments.
Analysis of multilocus genetic variation revealed a significant pattern of genetic differentiation between lowland and highland populations of Crested Ducks. The FST values for six autosomal reference loci were consistent with a model of neutral evolution. Historical migration rates based on the joint estimate for the six introns averaged 2.6 effective migrants ⁄ generation into the highlands from the lowlands. By contrast, no migration was observed into the lowland population from the highlands following population divergence (Bulgarella et al. 2012).
Geographic analysis of gene flow documented a strong pattern of haemoglobin differentiation in the distinct environments that crested ducks inhabit. The mismatch in migration estimates between the globins and the autosomal introns likely reflect the more restricted movement of haemoglobin alleles along the elevational gradient relative to the neutral nuclear alleles. Four derived amino acid polymorphisms occurred at high frequencies in the highland population, whereas the lowland population generally lacked these alleles and was predominantly fixed for the ancestral haemoglobin alleles (Bulgarella et al. 2012).
Geographic variation in nuclear DNA was strikingly similar to the variation in morphometrics previously reported in Bulgarella et al. (2007). In the molecular analysis, we found reciprocally monophyletic lineages in mtDNA and diagnosable multilocus genotypes between highland and lowland populations. Furthermore, individuals from Mendoza were intermediate in size in the morphological study. Likewise, multilocus data indicated that Mendoza individuals carried a mix of highland and lowland genotypes (including individuals with admixed ancestry), suggesting that the two morphotypes interbreed within that region. These concordant results between mtDNA, nuclear DNA, and morphology indicate that Crested Ducks comprise at least two genetic populations, corresponding to subspecies designations, but that some gene flow occurs between them (Bulgarella et al. 2012).