Natural variation in gene expression between wild and weedy populations of Helianthus annuus

The molecular genetic changes underlying the transformation of wild plants into agricultural weeds are poorly understood. Here we use a sunflower cDNA microarray to detect variation in gene expression between two wild (non-weedy) Helianthus annuus populations from Utah and Kansas and four weedy H. annuus populations collected from agricultural fields in Utah, Kansas, Indiana, and California. When grown in a common growth chamber environment, populations differed substantially in their gene expression patterns, indicating extensive genetic differentiation. Overall, 165 uni-genes, representing approximately 5% of total genes on the array, showed significant differential expression in one or more weedy populations when compared to both wild populations. This subset of genes is enriched for abiotic/biotic stimulus and stress response proteins, which may underlie niche transitions from the natural sites to agricultural fields for H. annuus. However, only a small proportion of the differentially expressed genes overlapped in multiple wild vs. weedy comparisons, indicating that most of the observed expression changes are due to local adaptation or neutral processes, as opposed to parallel genotypic adaptation to agricultural fields. These results are consistent with an earlier phylogeographic study suggesting that weedy sunflowers have evolved multiple times in different regions of the United States and further indicate that the evolution of weedy sunflowers has been accompanied by substantial gene expression divergence in different weedy populations.     

Rapid evolutionary divergence and ecotypic diversification of germination behavior in weedy rice populations

Feral plants have evolved from well-studied crops, providing good systems for elucidation of how weediness evolves. As yet, they have been largely neglected for this purpose. The evolution of weediness can occur by simple back mutations in domestication genes (domestication in reverse). Whether the evolutionary steps to weediness always occur in reverse remains largely unknown. We examined seed germination behavior in recently evolved weedy rice (Oryza sativa f. spontanea) populations and their coexisting cultivars in eastern and north-eastern China to address whether 'dedomestication' is the simple reverse of domestication. We found that these weedy populations did not diverge from their progenitors by reverting to the pre-domestication trait of seed dormancy. Instead, they have evolved a novel mechanism to avoid growing in inappropriate environments via changes in critical temperature cues for seed germination. Furthermore, we found evidence for subsequent ecotypic divergence of these populations such that the critical temperature for germination correlates with the local habitat temperature at latitudinal gradients. The origins of problematic plant species, weeds and invasives, have already been studied in detail. These plants can thus be used as systems for studying rapid evolution. To determine whether and how that evolution is adaptive, experiments such as those described here can be performed.     

All roads lead to weediness: Patterns of genomic divergence reveal extensive recurrent weedy rice origins from South Asian Oryza

Weedy rice (Oryza spp.), a weedy relative of cultivated rice (O. sativa), infests and persists in cultivated rice fields worldwide. Many weedy rice populations have evolved similar adaptive traits, considered part of the ‘agricultural weed syndrome’, making this an ideal model to study the genetic basis of parallel evolution. Understanding parallel evolution hinges on accurate knowledge of the genetic background and origins of existing weedy rice groups. Using population structure analyses of South Asian and US weedy rice, we show that weeds in South Asia have highly heterogeneous genetic backgrounds, with ancestry contributions both from cultivated varieties (aus and indica) and wild rice. Moreover, the two main groups of weedy rice in the USA, which are also related to aus and indica cultivars, constitute a separate origin from that of Asian weeds. Weedy rice populations in South Asia largely converge on presence of red pericarps and awns and on ease of shattering. Genomewide divergence scans between weed groups from the USA and South Asia, and their crop relatives are enriched for loci involved in metabolic processes. Some candidate genes related to iconic weedy traits and competitiveness are highly divergent between some weed‐crop pairs, but are not shared among all weed‐crop comparisons. Our results show that weedy rice is an extreme example of recurrent evolution, and suggest that most populations are evolving their weedy traits through different genetic mechanisms.     

Italian weedy rice—A case of de‐domestication?

Weedy rice is a representative of the extensive group of feral weeds that derive from crops, but has returned to the lifestyle of a wild species. These weeds develop either from a hybridization of crops with wild relatives (exoferality), or by mutation of crops to weedy forms (endoferality). Due to the close relation of weed and crop, the methods for weed‐targeted containment are limited to date. A deeper understanding of the development of such weeds might help to design more efficient and sustainable approaches for weed management. Weedy rice poses a serious threat to rice yields worldwide. It is widely accepted that weedy rice has originated independently in different regions all over the world. However, details of its evolution have remained elusive. In the current study, we investigated the history of weedy rice in northern Italy, the most important rice‐growing area in Europe. Our approach was to analyze genes related to weedy traits (SD1, sh4, Rc) in weedy rice accessions compared to cultivars, and to integrate these results with phenotypic and physiological data, as well as historical information about rice farming in Italy. We arrive at a working model for the timeline of evolution of weedy rice in Italy indicating that both exoferality and endoferality acted as forces driving the development of the diverse weedy rice populations found in the region today. Models of weed evolution can help to predict the direction which weed development might take and to develop new, sustainable methods to control feral weeds.     

Origins of weedy rice revealed by polymorphisms of chloroplast DNA sequences and nuclear microsatellites

Conspecific weeds that permanently infest worldwide agroecosystems are evolved from their crop species. These weeds cause substantial problems for crop production by competing for resources in agricultural fields. Weedy rice represents such a conspecific weed infesting rice ecosystems, and causing tremendous rice yield losses owing to its strong competitiveness and abundant genetic diversity, likely resulted from its complex origins. Here, we report the use of chloroplast DNA (cpDNA) fingerprints to determine whether weedy rice is evolved from its wild (exo‐feral) or cultivated (endo‐feral) rice progenitor as the maternal donor in recent hybridization events. In addition, we also applied nuclear simple sequence repeat (SSR) markers to confirm the exo‐feral or endo‐feral origins of weedy rice accessions determined by the cpDNA fingerprints. We found that the studied weedy rice accessions evolved either from their wild or cultivated rice progenitor, as the maternal donor, based on the cpDNA network and structure analyses. Combined analyses of cpDNA and nuclear SSR markers indicated that a much greater proportion of weedy rice accessions had the endo‐feral origin. In addition, results from the genetic structure of nuclear SSR markers indicated that weedy rice accessions from the endo‐feral pathway are distinctly associated with either indica or japonica rice cultivars, suggesting their complex origins through crop–weed introgression. The complex pathways of origin and evolution could greatly promote genetic diversity of weedy rice. Therefore, innovative methods should be developed for effective weedy rice control.     

Malaysian weedy rice shows its true stripes: wild Oryza and elite rice cultivars shape agricultural weed evolution in Southeast Asia

Weedy rice is a close relative of domesticated rice (Oryza sativa) that competes aggressively with the crop and limits rice productivity worldwide. Most genetic studies of weedy rice have focused on populations in regions where no reproductively compatible wild Oryza species occur (North America, Europe and northern Asia). Here, we examined the population genetics of weedy rice in Malaysia, where wild rice (O. rufipogon) can be found growing in close proximity to cultivated and weedy rice. Using 375 accessions and a combined analysis of 24 neutral SSR loci and two rice domestication genes (sh4, controlling seed shattering, and Bh4, controlling hull colour), we addressed the following questions: (i) What is the relationship of Malaysian weedy rice to domesticated and wild rice, and to weedy rice strains in the USA? (ii) To what extent does the presence of O. rufipogon influence the genetic and phenotypic diversity of Malaysian weeds? (iii) What do the distributions of sh4 and Bh4 alleles and associated phenotypes reveal about the origin and contemporary evolution of Malaysian weedy rice? Our results reveal the following: independent evolutionary origins for Malaysian weeds and US strains, despite their very close phenotypic resemblance; wild‐to‐weed gene flow in Malaysian weed populations, including apparent adaptive introgression of seed‐shattering alleles; and a prominent role for modern Malaysian cultivars in the origin and recent proliferation of Malaysian weeds. These findings suggest that the genetic complexity and adaptability of weedy crop relatives can be profoundly influenced by proximity to reproductively compatible wild and domesticated populations.     

Structure and evolution of plant disease resistance genes

This article reviews recent advances that shed light on plant disease resistance genes, beginning with a brief overview of their structure, followed by their genomic organization and evolution. Plant disease resistance genes have been exhaustively investigated in terms of their structural organization, sequence evolution and genome distribution. There are probably hundreds of NBS-LRR sequences and other types of R-gene-like sequences within a typical plant genome. Recent studies revealed positive selection and selective maintenance of variation in plant resistance and defence-related genes. Plant resistance genes are highly polymorphic and have diverse recognition specificities. R-genes occur as members of clustered gene families that have evolved through duplication and diversification. These genes appear to evolve more rapidly than other regions of the genome, and domains such as the leucine-rich repeat, are subject to adaptive selection     

Molecular evolution of the rice blast resistance gene Pi-ta in invasive weedy rice in the USA

The Pi-ta gene in rice has been effectively used to control rice blast disease caused by Magnaporthe oryzae worldwide. Despite a number of studies that reported the Pi-ta gene in domesticated rice and wild species, little is known about how the Pi-ta gene has evolved in US weedy rice, a major weed of rice. To investigate the genome organization of the Pi-ta gene in weedy rice and its relationship to gene flow between cultivated and weedy rice in the US, we analyzed nucleotide sequence variation at the Pi-ta gene and its surrounding 2 Mb region in 156 weedy, domesticated and wild rice relatives. We found that the region at and around the Pi-ta gene shows very low genetic diversity in US weedy rice. The patterns of molecular diversity in weeds are more similar to cultivated rice (indica and aus), which have never been cultivated in the US, rather than the wild rice species, Oryza rufipogon. In addition, the resistant Pi-ta allele (Pi-ta) found in the majority of US weedy rice belongs to the weedy group strawhull awnless (SH), suggesting a single source of origin for Pi-ta. Weeds with Pi-ta were resistant to two M. oryzae races, IC17 and IB49, except for three accessions, suggesting that component(s) required for the Pi-ta mediated resistance may be missing in these accessions. Signatures of flanking sequences of the Pi-ta gene and SSR markers on chromosome 12 suggest that the susceptible pi-ta allele (pi-ta), not Pi-ta, has been introgressed from cultivated to weedy rice by out-crossing.     

Polyploidy: its consequences and enabling role in plant diversification and evolution

BackgroundMost, if not all, green plant (Virdiplantae) species including angiosperms and ferns are polyploids themselves or have ancient polyploid or whole genome duplication signatures in their genomes. Polyploids are not only restricted to our major crop species such as wheat, maize, potato and the brassicas, but also occur frequently in wild species and natural habitats. Polyploidy has thus been viewed as a major driver in evolution, and its influence on genome and chromosome evolution has been at the centre of many investigations. Mechanistic models of the newly structured genomes are being developed that incorporate aspects of sequence evolution or turnover (low-copy genes and regulatory sequences, as well as repetitive DNAs), modification of gene functions, the re-establishment of control of genes with multiple copies, and often meiotic chromosome pairing, recombination and restoration of fertility.ScopeWorld-wide interest in how green plants have evolved under different conditions – whether in small, isolated populations, or globally – suggests that gaining further insight into the contribution of polyploidy to plant speciation and adaptation to environmental changes is greatly needed. Forward-looking research and modelling, based on cytogenetics, expression studies, and genomics or genome sequencing analyses, discussed in this Special Issue of the Annals of Botany, consider how new polyploids behave and the pathways available for genome evolution. They address fundamental questions about the advantages and disadvantages of polyploidy, the consequences for evolution and speciation, and applied questions regarding the spread of polyploids in the environment and challenges in breeding and exploitation of wild relatives through introgression or resynthesis of polyploids.ConclusionChromosome number, genome size, repetitive DNA sequences, genes and regulatory sequences and their expression evolve following polyploidy – generating diversity and possible novel traits and enabling species diversification. There is the potential for ever more polyploids in natural, managed and disturbed environments under changing climates and new stresses.     

The long and the short of it: SD1 polymorphism and the evolution of growth trait divergence in U.S. weedy rice

Growth-related traits, such as greater height, greater biomass, faster growth rate and early flowering, are thought to enhance competitiveness of agricultural weeds. However, weedy rice, a conspecific weed of cultivated rice (Oryza sativa L.), displays variation for growth traits. In the United States, separately evolved weedy rice groups have been shown to share genomic identity with exotic domesticated cultivars. Through a common garden experiment, we investigated whether growth trait divergence has occurred among U.S. weeds and their putative cultivated progenitors. We also determined polymorphism patterns in the growth candidate gene, SD1, to assess its possible role in the evolution of divergent phenotypes. We found considerable growth trait variation among weed groups, suggesting that growth trait convergence is not evident among weedy populations. Phenotypic divergence of weedy rice from cultivated ancestors is most apparent for flowering time. Introgression of a chromosomal block containing the SD1 allele from tropical japonica, the predominant U.S. rice cultivar, was detected in one weedy rice population and is associated with a change in growth patterns in this group. This study demonstrates the role of introgressive hybridization in evolutionary divergence of an important weed.     

A harvest of weeds yields insight into a case of contemporary evolution

When Charles Darwin was exploring the idea of evolution via natural selection, he looked to domesticated species, with the opening chapter of The Origin of Species titled ‘Variation Under Domestication’ (Darwin 1859 ). Domesticated species such as crops are a great example of artificial selection, which Darwin realized was analogous to natural selection. But growing among those carefully selected crop varieties are the unwelcome and unwanted plants we call weeds. Despite the importance of weeds and long‐standing interest in their evolution (Baker 1974 ), we still know little about how agricultural weeds evolve, and we often fail to take evolution into account when attempting to manage them (Neve et al. 2009 ). Agricultural weeds are subjected to the unique conditions of farm fields, such as frequent soil disturbance and the addition of water and nutrients. They are also confronted with aggressive attempts at their removal via herbicides and mechanical means. As such, they are under intense demographic and selective pressure and can potentially rapidly evolve in response. In this issue of Molecular Ecology, Kuester and co‐authors make a rare attempt to understand contemporary evolution in an agricultural weed (Kuester et al. 2016 ). They do so using the powerful resurrection approach of comparing ancestors and descendants under common conditions (Franks et al. 2008 ). They sampled multiple populations of the weedy plant Ipomoea purpurea at two points in time. A comparison of these greenhouse‐grown ancestor and descendent populations showed that, over time, populations had lost significant levels of neutral genetic diversity, consistent with genetic bottlenecks. The authors also found a slight increase, on average, of resistance to the herbicide glyphosate, which is the active ingredient in Roundup^®. This work is one of a growing number of studies demonstrating rapid evolution in natural populations (Thompson 2013 ) and also reveals evidence of both selection and drift in populations of an agricultural weed.     

Weed genomics: new tools to understand weed biology

In spite of the large yield losses that weeds inflict on crops, we know little about the genomics of economically important weed species. Comparative genomics between plant model species and weeds, map-based approaches, genomic sequencing and functional genomics can play vital roles in understanding and dissecting weedy traits of agronomically important weed species that damage crops. Weed genomics research should increase our understanding of the evolution of herbicide resistance and of the basic genetics underlying traits that make weeds a successful group of plants. Here, we propose specific weed candidates as genomic models, including economically important plants that have evolved herbicide resistance on several occasions and weeds with good comparative genomic qualities that can be anchored to the genomics of Arabidopsis and Oryza sativa.     

Structural variation and evolution of a defense-gene cluster in natural populations of Aegilops tauschii

Genetic mapping and sequencing of plant genomes have been useful for investigating eukaryotic chromosome structural organization. In many cases, analyses have been limited in the number of representatives sampled from specific groups. The degree of intraspecific genome diversity remains in question. The possibility exists that a single model genome may have limited utility for identifying genes in related members of the species or genus. Crop improvement programs have particular interests in disease resistance genes that are harbored by wild relatives of modern cultivated crops. These genes are evolutionarily dynamic and under selective pressure by a broad range of pathogenic organisms. Using resistance gene analogs as models for gene evolution, intraspecific genome comparisons were made among populations of wild diploid wheat (Aegilops tauschii). We observed that deletion haplotypes are occurring frequently and independently in the genome. Haplotypes are geographically correlated and maintenance of gene complements in localized populations indicates selective advantage. Furthermore, deletion haplotypes are not detrimental to plant health, since genes without adaptive value in alternate environments are eliminated from the genome. Deletion haplotypes appear to be a common form of allelic variation in plants, and we address the consequences on genome restructuring and gene evolution. Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

Genetic diversity and origin of weedy rice (Oryza sativa f. spontanea) populations found in North-eastern China revealed by simple sequence repeat (SSR) markers

BACKGROUND AND AIMS: Weedy rice (Oryza sativa f. spontanea) is one of the most notorious weeds occurring in rice-planting areas worldwide. The objectives of this study are to determine the genetic diversity and differentiation of weedy rice populations from Liaoning Province in North-eastern China and to explore the possible origin of these weedy populations by comparing their genetic relationships with rice varieties (O. sativa) and wild rice (O. rufipogon) from different sources. METHODS: Simple sequence repeat (SSR) markers were used to estimate the genetic diversity of 30 weedy rice populations from Liaoning, each containing about 30 individuals, selected rice varieties and wild O. rufipogon. Genetic differentiation and the relationships of weedy rice populations were analysed using cluster analysis (UPGMA) and principle component analysis (PCA). KEY RESULTS: The overall genetic diversity of weedy rice populations from Liaoning was relatively high (H(e) = 0.313, I = 0.572), with about 35 % of the genetic variation found among regions. The Liaoning weedy rice populations were closely related to rice varieties from Liaoning and japonica varieties from other regions but distantly related to indica rice varieties and wild O. rufipogon. CONCLUSIONS: Weedy rice populations from Liaoning are considerably variable genetically and most probably originated from Liaoning rice varieties by mutation and intervarietal hybrids. Recent changes in farming practices and cultivation methods along with less weed management may have promoted the re-emergence and divergence of weedy rice in North-eastern China.     

The origins of weedy rice

Where do weeds come from? How do they evolve from nonweedy ancestors? In this issue of Molecular Ecology, Londo and Schaal examine the origin of weedy rice (Oryza sativa) populations in the USA. Analysing nuclear DNA sequence and microsatellite data, they show the importance of parallel evolution, hybridization, gene flow, and migration in the evolution of these weeds.     

Impact of interspecific hybridization between crops and weedy relatives on the evolution of flowering time in weedy phenotypes

Background

Like conventional crops, some GM cultivars may readily hybridize with their wild or weedy relatives. The progressive introgression of transgenes into wild or weedy populations thus appears inevitable, and we are now faced with the challenge of determining the possible evolutionary effects of these transgenes. The aim of this study was to gain insight into the impact of interspecific hybridization between transgenic plants and weedy relatives on the evolution of the weedy phenotype.

Methodology/Principal Findings

Experimental populations of weedy birdseed rape (Brassica rapa) and transgenic rapeseed (B. napus) were grown under glasshouse conditions. Hybridization opportunities with transgenic plants and phenotypic traits (including phenological, morphological and reproductive traits) were measured for each weedy individual. We show that weedy individuals that flowered later and for longer periods were more likely to receive transgenic pollen from crops and weed×crop hybrids. Because stem diameter is correlated with flowering time, plants with wider stems were also more likely to be pollinated by transgenic plants. We also show that the weedy plants with the highest probability of hybridization had the lowest fecundity.

Conclusion/Significance

Our results suggest that weeds flowering late and for long periods are less fit because they have a higher probability of hybridizing with crops or weed×crop hybrids. This may result in counter-selection against this subset of weed phenotypes, and a shorter earlier flowering period. It is noteworthy that this potential evolution in flowering time does not depend on the presence of the transgene in the crop. Evolution in flowering time may even be counter-balanced by positive selection acting on the transgene if the latter was positively associated with maternal genes promoting late flowering and long flowering periods. Unfortunately, we could not verify this association in the present experiment.     

Phenotypic selection for dormancy introduced a set of adaptive haplotypes from weedy into cultivated rice

Association of seed dormancy with shattering, awn, and black hull and red pericarp colors enhances survival of wild and weedy species, but challenges the use of dormancy genes in breeding varieties resistant to preharvest sprouting. A phenotypic selection and recurrent backcrossing technique was used to introduce dormancy genes from a wild-like weedy rice to a breeding line to determine their effects and linkage with the other traits. Five generations of phenotypic selection alone for low germination extremes simultaneously retained dormancy alleles at five independent QTL, including qSD12 (R(2) > 50%), as determined by genome-wide scanning for their main and/or epistatic effects in two BC(4)F(2) populations. Four dormancy loci with moderate to small effects colocated with QTL/genes for one to three of the associated traits. Multilocus response to the selection suggests that these dormancy genes are cumulative in effect, as well as networked by epistases, and that the network may have played a "sheltering" role in maintaining intact adaptive haplotypes during the evolution of weeds. Tight linkage may prevent the dormancy genes from being used in breeding programs. The major effect of qSD12 makes it an ideal target for map-based cloning and the best candidate for imparting resistance to preharvest sprouting.     

The role of Bh4 in parallel evolution of hull colour in domesticated and weedy rice

The two independent domestication events in the genus Oryza that led to African and Asian rice offer an extremely useful system for studying the genetic basis of parallel evolution. This system is also characterized by parallel de‐domestication events, with two genetically distinct weedy rice biotypes in the US derived from the Asian domesticate. One important trait that has been altered by rice domestication and de‐domestication is hull colour. The wild progenitors of the two cultivated rice species have predominantly black‐coloured hulls, as does one of the two U.S. weed biotypes; both cultivated species and one of the US weedy biotypes are characterized by straw‐coloured hulls. Using Black hull 4 (Bh4) as a hull colour candidate gene, we examined DNA sequence variation at this locus to study the parallel evolution of hull colour variation in the domesticated and weedy rice system. We find that independent Bh4‐coding mutations have arisen in African and Asian rice that are correlated with the straw hull phenotype, suggesting that the same gene is responsible for parallel trait evolution. For the U.S. weeds, Bh4 haplotype sequences support current hypotheses on the phylogenetic relationship between the two biotypes and domesticated Asian rice; straw hull weeds are most similar to indica crops, and black hull weeds are most similar to aus crops. Tests for selection indicate that Asian crops and straw hull weeds deviate from neutrality at this gene, suggesting possible selection on Bh4 during both rice domestication and de‐domestication.     

Introgression from cultivated rice influences genetic differentiation of weedy rice populations at a local spatial scale

Hybridization and introgression can play an important role in genetic differentiation and adaptive evolution of plant species. For example, a conspecific feral species may frequently acquire new alleles from its coexisting crops via introgression. However, little is known about this process. We analyzed 24 weedy rice (Oryza sativa f. spontanea) populations and their coexisting rice cultivars from northern Italy to study their genetic differentiation, outcrossing, and introgression based on microsatellite polymorphisms. A total of 576 maternal plants representing 24 weedy populations were used to estimate their genetic differentiation, and 5,395 progeny (seedlings) derived from 299 families of 15 selected populations were included to measure outcrossing rates. Considerable genetic differentiation (F _st = 0.26) was detected among weedy rice populations, although the differentiation was not associated with the spatial pattern of the populations. Private alleles (28%) were identified in most populations that exhibited a multiple cluster assignments, indicating stronger genetic affinities of some weedy populations. Outcrossing rates were greatly variable and positively correlated (R ² = 0.34, P = 0.02) with the private alleles of the corresponding populations. Paternity analysis suggested that ~15% of paternal specific alleles, a considerable portion of which was found to be crop-specific, were acquired from the introgression of the coexisting rice cultivars. Frequent allelic introgression into weedy populations resulting from outcrossing with nearby cultivars determines the private alleles of local feral populations, possibly leading to their genetic differentiation. Introgression from a crop may play an important role in the adaptive evolution of feral populations.     

In situ management and domestication of plants in Mesoamerica

BACKGROUND AND AIMS: Ethnobotanical studies in Mexico have documented that Mesoamerican peoples practise systems of in situ management of wild and weedy vegetation directed to control availability of useful plants. In situ management includes let standing, encouraging growing and protection of individual plants of useful species during clearance of vegetation, which in some cases may involve artificial selection. The aim of this study was to review, complement and re-analyse information from three case studies which examined patterns of morphological, physiological and genetic effects of artificial selection in plant populations under in situ management in the region. METHODS: Information on wild and in situ managed populations of the herbaceous weedy plants Anoda cristata and Crotalaria pumila, the tree Leucaena esculenta subsp. esculenta and the columnar cacti Escontria chiotilla, Polaskia chichipe and Stenocereus stellatus from Central Mexico was re-analysed. Analyses compared morphology and frequency of morphological variants, germination patterns, and population genetics parameters between wild and managed in situ populations of the species studied. Species of columnar cacti are under different management intensities and their populations, including cultivated stands of P. chichipe and S. stellatus, were also compared between species. KEY RESULTS: Significant differences in morphology, germination patterns and genetic variation documented between wild, in situ managed and cultivated populations of the species studied are associated with higher frequencies of phenotypes favoured by humans in managed populations. Genetic diversity in managed populations of E. chiotilla and P. chichipe is slightly lower than in wild populations but in managed populations of S. stellatus variation was higher than in the wild. However, genetic distance between populations was generally small and influenced more by geographic distance than by management. CONCLUSIONS: Artificial selection operating on in situ managed populations of the species analysed is causing incipient domestication. This process could be acting on any of the 600-700 plant species documented to be under in situ management in Mesoamerica. In situ domestication of plants could be relevant to understand early processes of domestication and current conditions of in situ conservation of plant genetic resources.