America's red gold: multiple lineages of cultivated cochineal in Mexico

Abstract

Cultivated cochineal (Dactylopius coccus) produces carminic acid, a valuable red dye used to color textiles, cosmetics, and food. Extant native D. coccus is largely restricted to two populations in the Mexican and the Andean highlands, although the insect's ultimate center of domestication remains unclear. Moreover, due to Mexican D. coccus cultivation's near demise during the 19th century, the genetic diversity of current cochineal stock is unknown. Through genomic sequencing, we identified two divergent D. coccus populations in highland Mexico: one unique to Mexico and another that was more closely related to extant Andean cochineal. Relic diversity is preserved in the crops of small-scale Mexican cochineal farmers. Conversely, larger-scale commercial producers are cultivating the Andean-like cochineal, which may reflect clandestine 20th century importation.

Keywords: Cochineal; Mexico; Peru; genomics; phylogeography.

Figure 1

Map depicting the competing Dactylopius coccus origin hypotheses: (A) D. coccus originated in Peru and subsequently spread to Mexico; (B) D. coccus evolved in Mexico and was later introduced to Peru, possibly after domestication. D. coccus sampling locations for the genomic analyses are also shown.

Figure 2

Condensed maximum-likelihood trees of Dactylopius coccus cytochrome c oxidase I (cox1) and 12S rRNA mitochondrial genes. Topology robustness was tested with 100 bootstrap replicates.

Figure 3

Relatedness between Oaxacan small-scale farm, Mexican commercial, and Peruvian commercial cochineal bulk samples. Principle component analysis (top row) separates the Oaxacan small-scale farm insects from the commercial specimens, with the first principle component explaining the majority of the variation (59.9% and 70.8% in the unfiltered and filtered SNP datasets, respectively). Identity-by-state analysis (bottom row) of these SNP datasets produces dendrograms with congruent topology.

Figure 4

Venn diagram depicting numbers of genomic SNPs unique to and shared between each bulk Dactylopius coccus sample.

Figure A1

Condensed maximum-likelihood tree of 797 partial Wolbachia ftsZ genes. The Wolbachia endosymbiont of Dactylopius coccus (strain “wCoc”) falls in clade B. Clade nomenclature follows Lo et al. . The tree was constructed under a Tamura–Nei substitution model with invariant sites and a gamma distribution for substitution rates (four gamma categories) and tested with 100 bootstrap replicates. Only clades supported by at least 50 replicates are noted.