The authors used the program STRUCTURE to infer the origin of the weedy rice accessions and their possible history of hybridization. STRUCTURE uses a Bayesian approach to examine the relationships of multilocus genotypes of individuals by differences in allele frequency and the nature of linkage disequilibrium. In the United States, the vast majority of cultivars are japonica types, but STRUCTURE analysis assigned almost all of the US weedy accessions to two groups unallied with japonica. Blackhulled weedy rice and a few other accessions were almost identical to domesticated O. sativa indica var. Aus; strawhulled weedy rice and a few other accessions were classified with exoferal ancestry involving hybridization of O. sativa indica and wild O. rufipogon. Clearly, most of the US weedy rice populations evolved from the cultivated species, but it is also clear that evolution did not occur in the United States. These data as well as other historical data suggest that US weedy rice has an Asian origin. Yet another pathway for the origin of weedy rice has been described for its populations in Bhutan . In that country japonica rice cultivars predominate in the highlands while indica cultivars predominate in the lowlands. Ishikawa et al. compared lowland cultivars, highland cultivars, and weedy populations with regards to nine isozyme loci, a chloroplast genome deletion, and four microsatellite loci. They found clear genetic differentiation between japonica and indica cultivars, cannabis drying and at the same time, they found that the weedy populations had genotypes that had both combinations of both japonica-specific alleles and indica-specific alleles.
They report that they did not detect any alleles specific to wild relatives. Thus, their conclusion is that the weedy populations are lineages descended from japonica x indica hybrids. When Gressel named the different evolutionary pathways to ferality, he did not consider intercultivar hybridization. Following his lead, we call this particular pathway for Bhutanese weedy ricde ‘exo-endoferality’ because it is first a case of endoferality because all ancestors are domesticates, but also ‘exo-’ because intertaxon hybridization is a critical evolutionary step. All three of the above comprehensive studies present strong evidence for the origin of the vast majority of the weedy rice populations to be from cultivated rice. Interestingly, the data collected reveals a polyphyletic origin for weedy rice. Polyphylesis is now well-known to play a role in the evolution of many invasive lineages but it is not clear whether it is the rule for domesticate-derived pests. For three of the four discovered pathways, involving direct ancestry from indica and japonica, de-domestication likely occurred via the evolution of shattering due to either mutation or an epistatic recombination event. The most parsimonious pathway for the remaining exoferal lineage detected by Londo and Schaal is for O. rufipogon to have provided the allele or alleles for shattering.In terms of area planted, cereal rye is one of the world’s top 10 grain crops. Volunteer rye has occasionally been a serious agricultural weed problem throughout North America for about 100 years. However, by the early 1960s self-sustaining, naturalized weedy rye populations were identified as increasingly problematic as weeds of cultivated lands and invasives of uncultivated lands in the US states of Washington, Oregon, Idaho, and California.
As a weed of cultivated rye, it was so bad that ‘farmers … abandoned efforts to grow cultivated rye for human consumption’ . Subsequently, weedy rye has spread elsewhere in the western United States and the Canadian province of British Columbia . Western North American weedy rye was originally thought to be a hybrid derivative of cultivated rye and the wild perennial mountain rye [S. strictum C. Presl.]. However, subsequent genetic analysis of several populations of North American weedy rye with 14 allozyme and three microsatellite loci failed to detect any ancestry from S. strictum or any other wild Secale. Overall, the weedy populations are more similar to each other than to any one cultivar. Nonetheless, the invasive populations share a single lineage that apparently evolved directly from one or more cultivars of cereal rye . Just as in the case of rice, cultivated rye is non-shattering and has little dormancy, while its derivative has evolved dispersal by shattering. De-domestication of the non-shattering trait to shattering likely occurred via mutation or perhaps an epistatic recombination event. Interestingly, in this case, both the crop and the feral populations have little seed dormancy. Other traits such as smaller seed, smaller leaves, thinner culms, and delayed flowering have rapidly evolved in this lineage . It is not clear whether all of these traits contribute to its evolution as a plant pest, especially its invasiveness outside of agroecosystems. However, evolution of a change in flowering time relative to an ancestor can be a powerful reproductive isolating mechanism. In this case, it might have evolved under selection to frustrate maladaptive gene flow from the crop to the weedy lineage .Cultivated radish is an important vegetable whose root is consumed worldwide. The wild jointed charlock is a closely related species, separated from the cultigen by a chromosomal translocation and a suite of morphological characters. When the two co-occur in most of the world, spontaneously hybridization occurs to a limited extent, resulting in no more than highly localized hybrid swarms . In contrast, for almost 100 years, hybridization between the two Raphanus taxa in California has been more extensive . In the last 50 years, hybrid-derived wild Raphanus has invaded coastal plains and disturbed inland valleys along the Paci- fic edge of North America from the US state of Oregon south through California to the Mexican state of Baja California . It has also become a troublesome weed for agronomic crops. Experimental work on what is now known as ‘California wild radish’ has confirmed it to be a lineage descended from hybrids of R. sativus and R. raphanistrum. Hegde et al. compared California wild radish populations with cultivars of R. sativus and populations of R. raphanistrum. They used 10 allozyme loci as well as common garden experiments to characterize the three types. The allozyme data revealed that California wild radish populations were in Hardy-Weinberg equilibrium; that is, there was no evidence that pure individuals of the parental taxa had persisted in significant frequencies.
STRUCTURE analysis of the allozyme dataset confirmed that conclusion. STRUCTURE assigned the cultivated radish to one group and the jointed charlock individuals to another group. The individuals from the California wild radish populations were assigned at various levels of hybrid ancestry involving the first two groups. Multivariate analysis of morphological characters measured in their common garden experiments revealed that the standard phenotype of California wild radish is significantly different from both of its progenitors. Interestingly, its bolting date, flowering date, and hypocotyl width are intermediate to its progenitors; its fruit diameter and fruit length are the same as the cultigen; and its fruit weight transgresses both parents! A subsequent common garden experiment showed that in several, drying cannabis contrasting California environments, the hybrid lineage produced both more fruits per plant and more seeds per plant than either progenitor , including specific source cultivars and R. raphanistrum populations as determined from cpDNA analysis . Is there something special about California that permitted this rapid adaptive evolution to proceed in light of the fact that Raphanus hybrids elsewhere have proven to be evolutionary deadends? Another common garden experiment has given a tantalizing result. Synthetic, F4 generation hybrid lineages and their R. raphanistrum progenitors were grown in the field in Michigan and California. The hybrid lineages’ fitness was slightly inferior to R. raphanistrum in Michigan but in California they exhibited 22% greater survival and 270% greater lifetime fecundity .Evolutionary studies on weedy and/or invasive plants that have domesticated ancestors have been useful for detailing the phylogenetic history of such plants. More examples might exist. While accumulating our examples for Table 1, we encountered some cases for which the current evidence is too weak at this time to convincingly support or refute a crop origin for an invasive lineage. These are enumerated in Table 2. Likewise, we encountered examples of domesticated taxa that have become plant pests, but it is not clear whether these have evolved to become pests or are simply ecological opportunists . Consider the case of strawberry guava . The free-living version of this domesticated plant is considered by some to be one of the world’s worst invasive species , but no studies have examined whether the invasive strawberry guava populations are substantially genetically different from their domesticated progenitor. The majority of our entries in Table 1 are examples of remarkably rapid evolution, at least six of our problematic lineages evolved in less than a century. The comparison of progenitors and their wild descendants grown in a common environment reveals differences that may account for the success of the latter.Nonetheless, research on such systems has barely exploited their utility for evolutionary study in comparison with certain other plant pests, such as the large body of integrated ecological, physiological and genetic study employed to understand evolution of invasiveness in North American reed canarygrass by Molofsky and colleagues and references therein. In particular, invasives and weeds descended from domesticated plants are ripe for approaches to tease out the evolutionary pathway to their new lifestyle. How do they differ from their progenitors with respect to their ecological relationships with biotic enemies, that is, herbivores and disease-causing organisms? Are there any differences in their chemical or physical defenses? Genetic and genomic approaches, often used in concert with ethnobotanical data, have been successful in illuminating the evolution of crops from wild species under domestication . These approaches may prove to be equally powerful in investigating evolution in the other direction, the evolution of sustainable feral populations from domesticated species. Let’s consider some of these approaches. Refined cytogenetic tools for studying chromosomal evolution under domestication have expanded to include not only traditional chromosome banding, but also techniques using fluorescent in situ hybridization and genomic in situ hybridization . Despite the fact that many major crops are cytogenetically well-characterized, we are not aware of any studies that address whether and how chromosomal evolution has occurred under de-domestication. Even if a crop species hasn’t had its genome sequenced, it is likely to be well-mapped. Quantitative trait locus mapping has proven a powerful way to study the domestication-related genes by examining the co-segregation of a trait with markers to determining the number of loci, their chromosomal location, and their relative influence on the expression of that trait. For example, the first maize ‘domestication gene’, teosinte branched1 , was identified by QTL mapping . In the same way, crosses between plant pests and their crop progenitors can be made to examine the genetic basis of key ecological traits that correlate with invasive success . Evolutionary genomic approaches have proven particularly fruitful for identifying the genomic and genetic correlates of crop domestication, in particular, potential adaptive changes . For domesticated taxa that have had their genome sequenced, such as rice and sorghum, comparative evolutionary ecogenomic approaches with their descendants will be able to provide a sweeping view of what genomic changes have occurred in the evolution of invasives and/or weeds relative to their crop ancestor. As genome sequencing become both less expensive and easier to conduct , such approaches will become available for more species, but the descendants of domesticated taxa will still have the advantage of centuries of study. We end with a few intriguing questions based on the simple observation that crops and weeds often have a lot in common ecologically. First, with regard to crops and their weedy derivatives, we note that both grow in exactly the same location, but they are subjected to different selection regimes. How do weedy crop derivatives end up perceiving different selection pressures so that diverge in sympatry? Furthermore, how do they diverge given that they are likely to be swamped by gene flow from the initially more abundant crop? With regards to the latterquestion, it is clear that reproductive isolating barriers must evolve rapidly, perhaps explaining why our list of examples is short . And, at the same time, that would explain why phenological divergence has been noted for all of our examples descended from an outcrossing crop ancestor which would be subject to a rain of cross-compatible pollen, but not for all of those descended from a highly selfing crop ancestor for which relatively short distances should afford reproductive isolation. Second, both crops and weeds are often selected for a life in a disturbed habitat. Both characteristically grow densely in simple communities or even monocultures.