I see where you are coming from, Smokemaster, but it is very clear that the genus Capsicum originated in South America, was passed up through Central America and into Mexico. At one point in history there was likely to be a single prototypical species that others evolved from. It`s a bit like saying Humans originated in Africa. They did, but they colonized the rest of the world and developed different characteristics through adaptation to different climates over many thousands of years.
Capsicum species probably spread and evolved over a very long time, probably 100,000 years or more. Archaeologists have found Capsicum seeds with human remains that are around 7500BC. Once they became a cultivated then the hands of humans selected for particular traits. 9500+ years of selecting and sharing seeds.
DNA testing has been done a lot on chills, for more than 20 years, both wild species and domesticated varieties. There was a lot of discussion as whether C.annuum, C.chinense and C.frutescens were distinct species or not. DNA analysis says they are distinct, but a number of Landraces have genes from more than one species, e.g. Bhut jolokia.
Here is a papper on the genetic diversity in C.annuum,
http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0056200
The widely cultivated pepper, Capsicum spp., important as a vegetable and spice crop world-wide, is one of the most diverse crops. To enhance breeding programs, a detailed characterization of Capsicum diversity including morphological, geographical and molecular data is required. Currently, molecular data characterizing Capsicum genetic diversity is limited. The development and application of high-throughput genome-wide markers in Capsicum will facilitate more detailed molecular characterization of germplasm collections, genetic relationships, and the generation of ultra-high density maps. We have developed the Pepper GeneChip® array from Affymetrix for polymorphism detection and expression analysis inCapsicum. Probes on the array were designed from 30,815 unigenes assembled from expressed sequence tags (ESTs). Our array design provides a maximum redundancy of 13 probes per base pair position allowing integration of multiple hybridization values per position to detect single position polymorphism (SPP). Hybridization of genomic DNA from 40 diverse C. annuum lines, used in breeding and research programs, and a representative from three additional cultivated species (C. frutescens, C. chinense and C. pubescens) detected 33,401 SPP markers within 13,323 unigenes. Among the C. annuum lines, 6,426 SPPs covering 3,818 unigenes were identified. An estimated three-fold reduction in diversity was detected in non-pungent compared with pungent lines, however, we were able to detect 251 highly informative markers across these C. annuum lines. In addition, an 8.7 cM region without polymorphism was detected around Pun1 in non-pungent C. annuum. An analysis of genetic relatedness and diversity using the software Structure revealed clustering of the germplasm which was confirmed with statistical support by principle components analysis (PCA) and phylogenetic analysis. This research demonstrates the effectiveness of parallel high-throughput discovery and application of genome-wide transcript-based markers to assess genetic and genomic features among Capsicum annuum.
Here`s another one,
Genome. 1995 Apr;38(2):224-31.
A survey of DNA polymorphism within the genus Capsicum and the fingerprinting of pepper cultivars.
Prince JP,
Lackney VK,
Angeles C,
Blauth JR,
Kyle MM.
Source
Department of Plant Breeding and Biometry, Cornell University, Ithaca, NY 14853, USA.
Abstract
Interspecific genetic variation was examined in the genus Capsicum based on shared restriction fragments in Southern analyses. Four distinct clusters were delineated among 21 accessions of cultivated and wild pepper (C. annuum, C. baccatum, C. chacoense, C. chinense, and C. frutescens). Three tight clusters comprised of accessions belonging to C. annuum, C. frutescens, and C. baccatum, respectively, were formed, along with a fourth cluster comprised of one accession each of C. chinense and C. chacoense. All accessions were differentiated by this technique, and the clusters corresponded closely to previous morphology-based classification. Sufficient DNA polymorphism exists among these accessions that segregating populations useful for restriction fragment length polymorphism (RFLP) mapping could be constructed using any two pepper accessions as parents. Regression analysis indicates that genetic distance is a good predictor (R2 = 0.872) of the level of mappable DNA polymorphism in Capsicum. Intraspecific variability was examined among four C. annuum cultivars (NuMex R Naky, Jupiter, Perennial, and Criollo de Morelos 334) using both RFLPs and randomly amplified polymorphic DNA (RAPDs), allowing a comparative evaluation of the two techniques. Seventeen percent of the clones used singly in RFLP analyses were sufficient for the differentiation of these varieties, as were 12.5% of the RAPD PCR amplifications. Dendrograms constructed from RFLP and RAPD analyses of the intraspecific data are similar but not identical. Southern analysis and RAPD PCR should be useful for DNA fingerprinting and the discrimination of closely related C. annuum genotypes.
