Ecogographic distribution and adaptation
Capsicum baccatum displays a wide geographic distribution across the South American continent from the west coast to the east coast, and from Columbia in the north to Chile in the south. The variability of ecological and climatic conditions along the broad geographic range is extensive. This broad geographic range contributes to the great diversity found in C. baccatum and related cultivated and wild Capsicum genetic resources [18]. Wild and ancestral species of tomato, a related member of the Solanaceae, share an equally broad geographic distribution in South America from near sea level to over 3,300 m elevation, with habitat ranging from arid coastal lowlands to mesic uplands [19, 20]. Analogous to Capsicum genetic diversity, the Andean geography, varied ecological habitats and different climates have contributed to wild tomato diversity [21]. Temperature extremes, as well as the amount and distribution of precipitation are often limiting factors to distribution of wild forms of a species and to a lesser extent cultivated forms. Ecological clines, i.e. associations between climatic conditions and a plant’s morphological or genetic patterns, arise as a consequence of migration and adaptations.
The ecological distribution of the C. baccatum accessions evaluated in this study indicated that domesticated accessions occupied habitat with rainfall as low as 3 mm per year, probably because of the option for irrigation. Wild forms of the species were restricted to areas of higher rainfall since cultivation is lacking. Likewise, cool temperatures in summer may represent a barrier to the distribution of wild forms of C. baccatum, as only domesticated types are found in areas where the maximum temperatures remain below 25°C. Genetic variation for pepper tolerance to moderately cold temperatures has been reported [22]. Assessment of five species including C. annuum, C. frutescens, C. chinense, C. baccatum and C. pubescens, revealed significant differences in low temperature (13°C – 18°C) seed emergence between accessions within species and a significantly greater seedling emergence score at low temperature for an accession of C. baccatum var. pendulum relative to all species accessions evaluated [22]. Similar to pepper, cold tolerance has been identified in wild as well as domesticated accessions of related Solanaceous crops that are native to temperate parts of the world where they may experience low temperatures [23, 24]. For example, Solanum lycopersicum and S. habrochaites accessions native to Turkey and Peru, respectively, exhibited cold tolerance during seed germination as well as during vegetative growth [25].
Locally adapted populations of wild plant species typically differ in their responses to abiotic stresses, including extremes of moisture and temperature. Differences with respect to climatic factors between wild and domesticated forms of C. baccatum were not significant, possibly due to the low representation of wild accessions. Both wild and domesticated forms occur in areas with chilling or freezing temperatures; however, tolerance to low temperatures is likely more important for wild types which are perennial than for domestic forms that are grown seasonally. In climates with warmer temperatures, farmers had the opportunity to select for varieties with earlier flowering or shorterened fruit development time spanning the period from anthesis to fruit maturity. Despite the option for use of supplemental irrigation of cultivated forms, large fruit set in C. baccatum is only obtained in accessions collected from geographic areas with natural occurrence of high rainfall.
Apart from having its geographic center further west and north, the average annual temperature recorded for accessions in the western group is more than 1°C lower in comparison to accessions that comprise the eastern group. In addition, the annual rainfall as well as the precipitation amount during the warmest quarter is far less in the west in comparison to the east.
Variation of morphological traits in the wild and domesticated C. baccatum
The present study revealed a high level of morphologic diversity, compatible with a prior report cataloguing aspects of C. baccatum morphological diversity [26]. Our results demonstrate morphological differences between the eastern and western groups that delineate the distribution range of wild and domesticated botanical forms of C. baccatum. Fruit attributes that contribute to yield potential, e.g. fruit weight, width and wall thickness, were generally greater in domesticated accessions occupying the eastern range in comparison to accessions from the western group. The differences in these domestication traits are likely the result of human selection and may reflect differences in cultural preferences between east and west.
Fruit traits in the domesticated C. baccatum accessions have been subjected to human selection [2, 27, 28]. Multiple factor analysis, MANOVA and random forest correlation identified fruit morphology as the most important phenotypic variable in C. baccatum. Out of the 40 morphological traits evaluated, we identified yield attributes that include fruit weight, fruit length and peduncle length as most informative for discrimination between wild (C. baccatum var. baccatum) and domesticated (C. baccatum var. pendulum) accessions. Fruit weight is clearly greater in domesticated accessions, as a result of enhanced fruit length, width and thicker fruit walls. Fruit width has greater importance than fruit length in the discrimination between wild and domesticated types; however, cluster analysis suggested that fruit length has a greater impact on final fruit weight. Studies in related Solanaceous crops suggest that a relatively small number of genes may account for the variation that discriminate wild and domesticated fruit of C. baccatum. In tomato, six loci explain much of the difference in fruit size evident between small fruited wild tomato species and their domesticated large fruited counterparts [29]. Orthologs of a number of these genes also account for size differences between small fruited ancestral eggplant species and large fruited commercial eggplant cultivars [30].
Differences in fruit morphology have been utilized to differentiate C. baccatum var. baccatum from C baccatum var. pendulum[7, 31]. Subsequent analyses suggested that morphological differences between wild and domesticated types were not clear cut [2, 3]. While we demonstrated that fruit yield-related attributes are robust indicators of varietal status, significant differences between varietal forms were also evident for traits including fruit anthocyanin pigmentation and fruit persistence. Related fruit attributes such as mature red pod color and upright peduncle orientation which are generally considered unique to wild varieties for bolstering bird predation and seed dissemination, did not distinguish wild from domesticated forms. For example, we found a number of domesticated varieties with small, erect fruit, and conversely, also wild types with larger, pendant fruit. A plausible explanation for this result may be the fact that C. baccatum is used as spice, and the use as a spice does not necessarily require substantial remodeling of fruit morphological traits such as increasing the fruit size, which would have led to a downward orientation of the peduncle. Our analyses and the descriptive results reported by [26] demonstrate introgresion of morphological characters among the botanical varieties. Wild and domesticated forms of the species are interfertile. Thus, hybridization likely accounts for much of this assimilation, particularly for geneflow from domesticated to wild accessions. Cultivation discourages geneflow from wild to domesticated genepools [12].
While most wild accessions bear fruit that produce anthocyanin when immature, that trait has largely been lost through human intervention during development of domesticated forms. Similar to anthocyanin in fruit, violet corollas are absent in the domesticated pool. Whereas fruit anthocyanin has been lost in domesticated accessions due to human selection, violet corollas are lacking in the lineage that contributed to domesticated forms of the species. Violet corollas are a trait that is exclusive to C. baccatum var. praetermissum wild types from Brazil. Our prior genetic analysis demonstrated that this wild form of C. baccatum is distinct and has not contributed to the domesticated pool [12]. Cluster analyses suggested an early divergence of the C. baccatum var. praetermissum lineage prior to C. baccatum domestication.
Cluster analysis of morphological traits demonstrated that anthocyanin pigmentation in vegetative plant parts (nodes, stems) is correlated but independent of anthocyanin accumulation in fruit. These observations are consistent with inheritance studies demonstrating simple inheritance for fruit anthocyanin pigmentation in Capsicum reproductive tissues and a complex inheritance for pigmentation in vegetative tissue [32].
Overall, the degree of fruit pungency was positively associated with days to maturity. The latter was inversely related to both maximum temperature and annual temperature. Although relationships between the degree of pungency and climatic factors were not significant, accessions with the highest pungency scores more often originated from warmer climates. Environmental factors, natural or brought upon by human intervention, such as temperature, light and fertilization level at the time of fruit maturation can influence fruit capsaicinoid concentration and pungency level and contribute to significant genotype x environement effects for this attribute [33–35]. Capsaicinoids are secondary metabolites that serve to deter predation by mammals with little effect on seed dispersal by birds since they do not sense capsaicinoid pungency.
Plant height is reduced and stem number increased among domesticated accessions in the ‘western’ group as based on both cluster [12] and Bayesian spatial analysis. Our data suggest that this is not a function of higher altitudes and cooler temperatures in the western territories. In fact, at lower temperatures, more erect plant habits are observed with thereby increased plant height, which may be a consequence of direct or indirect local human selection. A study of global patterns in plant height found that a wide range of height strategies were present in cold, dry, low productivity systems, but a lack of very short species in wetter, warmer, more productive sites [36]. That study found that the best model for global patterns in plant height included just one variable, precipitation in the wettest month. The longer maturation time and the lower fruit set observed for western C. baccatum accessions may be a consesquence of adaptations to climatic differences among the regions occupied by the western and eastern groups, i.e. based on lower temperatures and annual rainfall in western territories. Fruit set increased with annual rainfall, and highest fruit set was only observed in regions with at least 1,000 mm annual rainfall. In warmer habitats, maturation time or days to maturity were reduced. Alternatively or in addition to a scenario shaped by natural selection forces, human selection pressures for higher fruit set and shorter maturation times in the east may also have been stronger in this region in comparison to the west. Both annual rainfall and annual temperature are reduced in the western territories. In a study of two wild Andean tomato species, [37] proposed that local, regional, and species-wide environmental conditions are responsible for phenotypic and physiological diversification. Supportive of our results, Nakazato et al. [37] identified temperature and precipitation gradients as the strongest trait–environment associations, suggesting that those climatic factors are predominant drivers of adaptive diversification, at least in wild types. Due to assimilation of morphological attributes between wild and domesticated forms of C. baccatum, the relative role of natural selection versus human selection as drivers of morphological traits in the domesticated pool cannot be estimated from the present data.
Spatial structure in domesticated C. baccatum
The domesticated C. baccatum germplasm was highly admixed and distributed across distant and ecologically diverse geographic regions. This is an indication that the domesticated C. baccatum remained well connected through gene flow. Over long distances, natural dispersal agents such as insects (pollen) and birds (seeds) likely play a less significant role for gene flow of domesticated material relative to human activities such as trade, because of much higher mobility based on the technical means of human transport [38]. A clear ‘immigrant’ identity was detected from the far end of the gene pool, i.e. among accessions that are separated by 3,000 km, demonstrating that human mediated, long-distance seed exchange occurred among distant regions. This result is in congruence with other domesticated crops such as beans [39] and maize [40] which exhibited significant seed-flow across long distances, in amounts and across distances where only transport by humans is possible. However, our results are contrary with a study of Mexican C. annuum populations [41], which suggested that human activities do not necessarily result in increased long distance gene flow relative to natural dispersal. The fact that ‘immigrants’ or introductions did not hybridize with local types indicates that: a) long-distance seed displacement occurred fairly recently; therefore, their genetic identity has not yet been obscured, or b) the specificities of the introduced types were maintained deliberately for their ethno-botanical purpose. Evidence for preservation of specific lineages within this C. baccatum germplasm was previously identified using AFLP markers for a group of accessions that form a distinct subclade nested within the predominantly Brazilian ‘eastern’ clade [12]. We called this group of Brazilian accessions the ‘umbilicatum’ clade as one of its member accessions was described as C. baccatum var. umbilicatum. This botanical variety was recently established [42]. This group exhibited greater divergence from the remainder of the accessions in the ‘eastern’ group, and was comprised of accessions from two areas of Brazil separated by over 1000 km. Conversely, other accessions in geographic proximity to ‘umbilicatum’ types were only distantly related to that subgroup. The role of ecological factors and agricultural selection in maintenance of landraces of pepper [43] and eggplant [44], Solanaceous relatives, have been reported.
Significant correlations were found between genetic and geographic distance with respect to the western and eastern subgroups of domesticated C. baccatum. Moreover, regional spatial structure was detected (within 100 km) in domesticated C. baccatum. The structure weakened after 100 km, although remained detectable up to almost 2,000 km. Adaptations to local ecological conditions may be responsible for regional differentiation. Our results are in congruence with a scenario of overlapping, short- to medium-distance trading units within the domesticated pool, which leave a signature of gradual decline in relatedness with increasing distance.
The observed spatial structure supports the conclusion that the distribution of C. baccatum var. pendulum genotypes is not random at the sampled geographical scale. Proximate genotypes tend to be more genetically similar than distant ones, consistent with the isolation by distance pattern of many other tropical species [37, 45–47].
Multiple domestication events were proposed for the species’ based on the pattern of AFLP genetic admixture between wild and domesticated forms [12]. Our current results for spatial population analysis revealed separation of the western and eastern groups coincident with the political borders for Peru/Bolivia and Paraguay/Brazil. Wild accessions from areas that today comprise Bolivia and Peru were proposed as progenitors to the domesticated germplasm from these regions (the ‘western’ group), whereas Paraguayan wild types showed associations with the domesticated accessions from the same area [12]. The present results based on Bayesian spatial clustering methodology also demonstrate that each of the two sub-gene pools (the western and eastern) is homogeneous; indicating that the significant spatial genetic structure in each sub-gene pool is not due to recent colonization. The observed isolation by distance event in these two sub-gene pools therefore further support the hypothesis that the cultivated C. baccatum was domesticated independently in two sites, one in the Andes highlands (Peru/Bolivia) band and the other in the lowland of Paraguay.