Domestication is one of the most fundamental changes in the evolution of human societies. The geographical origins of domesticated plants are inferred from archaeology, ecology and genetic data. Scenarios vary among species and include single, diffuse or multiple independent domestications. Cultivated plants present a panel of traits, the "domestication syndrome" that distinguish them from their wild relatives. It encompasses yield-, food usage-, and cultivation-related traits. Most genes underlying those traits are "masterminds" affecting the regulation of gene networks. Phenotypic convergence of domestication traits across species or within species between independently domesticated forms rarely coincides with convergence at the gene level. We review here current data/models that propose a protracted transition model for domestication and investigate the impact of mating system, life cycle and gene flow on the pace of domestication. Finally, we discuss the cost of domestication, pointing to the importance of characterizing adaptive functional variation in wild resources.

In plants, local adaptation across species range is frequent. Yet, much has to be discovered on its environmental drivers, the underlying functional traits and their molecular determinants. Genome scans are popular to uncover outlier loci potentially involved in the genetic architecture of local adaptation, however links between outliers and phenotypic variation are rarely addressed. Here we focused on adaptation of teosinte populations along two elevation gradients in Mexico that display continuous environmental changes at a short geographical scale. We used two common gardens, and phenotyped 18 traits in 1664 plants from 11 populations of annual teosintes. In parallel, we genotyped these plants for 38 microsatellite markers as well as for 171 outlier single nucleotide polymorphisms (SNPs) that displayed excess of allele differentiation between pairs of lowland and highland populations and/or correlation with environmental variables. Our results revealed that phenotypic differentiation at 10 out of the 18 traits was driven by local selection. Trait covariation along the elevation gradient indicated that adaptation to altitude results from the assembly of multiple co-adapted traits into a complex syndrome: as elevation increases, plants flower earlier, produce less tillers, display lower stomata density and carry larger, longer and heavier grains. The proportion of outlier SNPs associating with phenotypic variation, however, largely depended on whether we considered a neutral structure with 5 genetic groups (73.7%) or 11 populations (13.5%), indicating that population stratification greatly affected our results. Finally, chromosomal inversions were enriched for both SNPs whose allele

Premise Capsicum annuum (Solanaceae) was originally domesticated in Mexico, where wild (C. annuum var. glabriusculum) and cultivated (C. annuum var. annuum) chile pepper populations (>60 landraces) are common, and wild‐resembling individuals (hereafter semiwild) grow spontaneously in anthropogenic environments. Here we analyze the role of elevation and domestication gradients in shaping the genetic diversity in C. annuum from the state of Oaxaca, Mexico. Methods We collected samples of 341 individuals from 28 populations, corresponding to wild, semiwild (C. annuum var. glabriusculum) and cultivated C. annuum, and closely related species Capsicum frutescens and C. chinense. From the genetic variation of 10 simple sequence repeat (SSR) loci, we assessed the population genetic structure, inbreeding, and gene flow through variance distribution analyses, genetic clustering, and connectivity estimations. Results Genetic diversity (HE) did not differ across domestication levels. However, inbreeding coefficients were higher in semiwild and cultivated chiles than in wild populations. We found evidence for gene flow between wild populations and cultivated landraces along the coast. Genetic structure analysis revealed strong differentiation between most highland and lowland landraces. Conclusions Gene flow between wild and domesticated populations may be mediated by backyards and smallholder farms, while mating systems may facilitate gene flow between landraces and semiwild populations. Domestication and elevation may overlap in their influence on genetic differentiation. Lowland Gui'ña dani clustered with highland landraces perhaps due to the social history of the Zapotec peoples. In situ conservation may play an important role in preserving semiwild populations and private alleles found in landraces.

Aim: Domestication is an ongoing well-described process. However, while many have studied the changes domestication causes in the genetic landscape, few have explored the way domestication changes the geographic landscape in which the plants exist. Therefore, the goal of this study was to understand how the domestication status changed the suitable geographic space of chile pepper in its center of origin. Methods: Capsicum annuum is a major crop species globally whose domestication center, Mexico, has been well studied. This provides a unique opportunity to explore the degree to which ranges of different domestication classes diverged and how these ranges might be altered by climate change. To this end, we created ecological niche models for four domestication classes (wild, semiwild, landrace, modern cultivar) based on present climate and future climate scenarios for 2050, 2070, and 2090. Results: Considering present environment, we found substantial overlap in the geographic niches of all the domestication gradient categories. Yet, there were also clear unique environmental and geographic aspects to the current ranges. Wild and commercial varieties were at ease in desert conditions as opposed to landraces. With projections into the future, habitat was lost asymmetrically, with wild, semiwild and landraces at far greater risk than modern cultivars. Further, we identified areas where future suitability overlap between landraces and wilds is expected to decouple. Main conclusions: While range expansion is widely associated with domestication, there is little support of a constant niche expansion (either in environmental or geographical space) throughout the domestication gradient. However, a shift to higher altitudes with cooler climate was identified for landraces. The clear differences in environmental adaptation, such as higher mean diurnal range and precipitation seasonality along the domestication gradient classes and their future potential range shifts show the need to increase conservation efforts, particularly to preserve landraces and semiwild genotypes.

2In plants, local adaptation across species range is frequent. Yet, much has to 3 be discovered on its environmental drivers, the underlying functional traits and their 4 molecular determinants. Genome scans are popular to uncover outlier loci potentially 5 involved in the genetic architecture of local adaptation, however links between 6 outliers and phenotypic variation are rarely addressed. Here we focused on adaptation 7 of teosinte populations along two elevation gradients in Mexico that display 8 continuous environmental changes at a short geographical scale. We used two 9 common gardens, and phenotyped 18 traits in 1664 plants from 11 populations of 10 annual teosintes. In parallel, we genotyped these plants for 38 microsatellite markers 11 as well as for 171 outlier single nucleotide polymorphisms (SNPs) that displayed 12 excess of allele differentiation between pairs of lowland and highland populations 13 and/or correlation with environmental variables. Our results revealed that phenotypic 14 differentiation at 10 out of the 18 traits was driven by local selection. Trait covariation 15 along the elevation gradient indicated that adaptation to altitude results from the 16 assembly of multiple co-adapted traits into a complex syndrome: as elevation 17 increases, plants flower earlier, produce less tillers, display lower stomata density and 18 carry larger, longer and heavier grains. The proportion of outlier SNPs associating 19 with phenotypic variation, however, largely depended on whether we considered a 20 neutral structure with 5 genetic groups (73.7%) or 11 populations (13.5%), indicating 21 that population stratification greatly affected our results. Finally, chromosomal 22 inversions were enriched for both SNPs whose allele frequencies shifted along 23 elevation as well as phenotypically-associated SNPs. Altogether, our results are 24 consistent with the establishment of an altitudinal syndrome promoted by local 25 selective forces in teosinte populations in spite of detectable gene flow. Because 26 elevation mimics climate change through space, SNPs that we found underlying 27 phenotypic variation at adaptive traits may be relevant for future maize breeding. 28 29 Author summary 33 Across their native range species encounter a diversity of habitats promoting local 34 adaptation of geographically distributed populations. While local adaptation is 35widespread, much has yet to be discovered about the conditions of its emergence, the 36 targeted traits, their molecular determinants and the underlying ecological drivers. 37Here we employed a reverse ecology approach, combining phenotypes and genotypes, 38 to mine the determinants of local adaptation of teosinte populations distributed along 39 two steep altitudinal gradients in Mexico. Evaluation of 11 populations in two 40 common gardens located at mid-elevation pointed to adaptation via an altitudinal 41 multivariate syndrome, in spite of gene flow. We scanned genomes to identify loci 42 with allele frequencies shifts along elevation, a subset of whic...

Background Peppers, bell and chile, are a culturally and economically important worldwide. Domesticated Capsicum spp. are distributed globally and represent a complex of valuable genetic resources. Objectives Explore population structure and diversity in a collection of 467 peppers representing eight species, spanning the spectrum from highly domesticated to wild using 22,916 SNP markers distributed across the twelve chromosomes of pepper. Results These species contained varied levels of genetic diversity, which also varied across chromosomes; the species also differ in the size of genetic bottlenecks they have experienced. We found that levels of diversity negatively correlate to levels of domestication, with the more diverse being the least domesticated.