Covariation and phenotypic integration in chemical communication displays: biosynthetic constraints and eco-evolutionary implications.

Chemical communication is ubiquitous. The identification of conserved structural elements in visual and acoustic communication is well established, but comparable information on chemical communication displays (CCDs) is lacking. We assessed the phenotypic integration of CCDs in a meta-analysis to characterize patterns of covariation in CCDs and identified functional or biosynthetically constrained modules. Poorly integrated plant CCDs (i.e. low covariation between scent compounds) support the notion that plants often utilize one or few key compounds to repel antagonists or to attract pollinators and enemies of herbivores. Animal CCDs (mostly insect pheromones) were usually more integrated than those of plants (i.e. stronger covariation), suggesting that animals communicate via fixed proportions among compounds. Both plant and animal CCDs were composed of modules, which are groups of strongly covarying compounds. Biosynthetic similarity of compounds revealed biosynthetic constraints in the covariation patterns of plant CCDs. We provide a novel perspective on chemical communication and a basis for future investigations on structural properties of CCDs. This will facilitate identifying modules and biosynthetic constraints that may affect the outcome of selection and thus provide a predictive framework for evolutionary trajectories of CCDs in plants and animals.

Allopolyploidy, diversification, and the Miocene grassland expansion.

The role of polyploidy, particularly allopolyploidy, in plant diversification is a subject of debate. Whole-genome duplications precede the origins of many major clades (e.g., angiosperms, Brassicaceae, Poaceae), suggesting that polyploidy drives diversification. However, theoretical arguments and empirical studies suggest that polyploid lineages may actually have lower speciation rates and higher extinction rates than diploid lineages. We focus here on the grass tribe Andropogoneae, an economically and ecologically important group of C4 species with a high frequency of polyploids. A phylogeny was constructed for ca. 10% of the species of the clade, based on sequences of four concatenated low-copy nuclear loci. Genetic allopolyploidy was documented using the characteristic pattern of double-labeled gene trees. At least 32% of the species sampled are the result of genetic allopolyploidy and result from 28 distinct tetraploidy events plus an additional six hexaploidy events. This number is a minimum, and the actual frequency could be considerably higher. The parental genomes of most Andropogoneae polyploids diverged in the Late Miocene coincident with the expansion of the major C4 grasslands that dominate the earth today. The well-documented whole-genome duplication in Zea mays ssp. mays occurred after the divergence of Zea and Sorghum. We find no evidence that polyploidization is followed by an increase in net diversification rate; nonetheless, allopolyploidy itself is a major mode of speciation.

The potential for crop to wild hybridization in eggplant (Solanum melongena; Solanaceae) in southern India.

UNLABELLED: • PREMISE OF THE STUDY: In India and elsewhere, transgenic Bt eggplant (Solanum melongena) has been developed to reduce insect herbivore damage, but published studies of the potential for pollen-mediated, crop- to- wild gene flow are scant. This information is useful for risk assessments as well as in situ conservation strategies for wild germplasm.• METHODS: In 2010-2014, we surveyed 23 populations of wild/weedy eggplant (Solanum insanum; known as wild brinjal), carried out hand-pollination experiments, and observed pollinators to assess the potential for crop- to- wild gene flow in southern India.• KEY RESULTS: Wild brinjal is a spiny, low-growing perennial commonly found in disturbed sites such as roadsides, wastelands, and sparsely vegetated areas near villages and agricultural fields. Fourteen of the 23 wild populations in our study occurred within 0.5 km of cultivated brinjal and at least nine flowered in synchrony with the crop. Hand crosses between wild and cultivated brinjal resulted in seed set and viable F1 progeny. Wild brinjal flowers that were bagged to exclude pollinators did not set fruit, and fruit set from manual self-pollination was low. The exserted stigmas of wild brinjal are likely to promote outcrossing. The most effective pollinators appeared to be bees (Amegilla, Xylocopa, Nomia, and Heterotrigona spp.), which also were observed foraging for pollen on crop brinjal.• CONCLUSION: Our findings suggest that hybridization is possible between cultivated and wild brinjal in southern India. Thus, as part of the risk assessment process, we assume that transgenes from the crop could spread to wild brinjal populations that occur nearby.

Genetic diversity and population structure of wild/weedy eggplant (Solanum insanum, Solanaceae) in southern India: implications for conservation.

UNLABELLED: • PREMISE OF THE STUDY: Crop wild relatives represent important genetic resources for crop improvement and the preservation of native biodiversity. Eggplant (Solanum melongena), known as brinjal in India, ranks high among crops whose wild gene pools are underrepresented in ex situ collections and warrant urgent conservation. Knowledge of outcrossing rates and patterns of genetic variation among wild populations can aid in designing strategies for both in situ and ex situ preservation.• METHODS: We used 14 microsatellite (simple sequence repeat) markers to examine genetic diversity, population structure, and outcrossing in 10 natural populations of wild/weedy eggplant (S. insanum = S. melongena var. insanum) and three cultivated populations in southern India.• KEY RESULTS: Multilocus FST analyses revealed strong differentiation among populations and significant isolation by distance. Bayesian model-based clustering, principal coordinate analysis, and hierarchical cluster analysis grouped the wild/weedy populations into three major clusters, largely according to their geographic origin. The three crop populations were similar to each other and grouped with two wild/weedy populations that occurred nearby. Outcrossing rates among the wild/weedy populations ranged from 5-33%, indicating a variable mixed-mating system.• CONCLUSION: Geographic isolation has played a significant role in shaping the contemporary patterns of genetic differentiation among these populations, many of which represent excellent candidates for in situ conservation. In two cases, close genetic affinity between cultivars and nearby wild/weedy populations suggests that gene flow has occurred between them. To our knowledge, this is the first study investigating population-level patterns of genetic diversity in wild relatives of eggplant.

Quantitative trait loci analysis of flowering time related traits identified in recombinant inbred lines of cowpea (Vigna unguiculata).

Flowering time is a major adaptive trait in plants and an important selection criterion in the breeding for genetic improvement of crop species. QTLs for the time of flower opening and days to flower were identified in a cross between a short duration domesticated cowpea (Vigna unguiculata (L.) Walp.) variety, 524B, and a relatively long duration wild accession, 219-01. A set of 159 F7 lines was grown under greenhouse conditions and scored for the flowering time associated phenotypes of time of flower opening and days to flower. Using a LOD threshold of 2.0, putative QTLs were identified and placed on a linkage map consisting of 202 SSR markers and four morphological loci. A total of five QTLs related to the time of flower opening were identified, accounting for 8.8%-29.8% of the phenotypic variation. Three QTLs for days to flower were detected, accounting for 5.7%-18.5% of the phenotypic variation. The major QTL of days to flower and time of flower opening were both mapped on linkage group 1. The QTLs identified in this study provide a strong foundation for further validation and fine mapping for developing an efficient way to restrain the gene flow between the cultivated and wild plants.

Genetic structure and mating system of wild cowpea populations in West Africa.

BACKGROUND: Cowpea is a highly inbred crop. It is part of a crop-weed complex, whose origin and dynamics is unknown, which is distributed across the African continent. This study examined outcrossing rates and genetic structures in 35 wild cowpea (Vigna unguiculata ssp. unguiculata var. spontanea) populations from West Africa, using 21 isozyme loci, 9 of them showing polymorphism. RESULTS: Outcrossing rates ranged from 1% to 9.5% (mean 3.4%), which classifies the wild cowpea breeding system as primarily selfing, though rare outcrossing events were detected in each population studied. Furthermore, the analyses of both the genetic structure of populations and the relationships between the wild and domesticated groups suggest possibilities of gene flow that are corroborated by field observations. CONCLUSIONS: As expected in a predominantly inbred breeding system, wild cowpea shows high levels of genetic differentiation and low levels of genetic diversity within populations. Gene flow from domesticated to wild cowpea does occur, although the lack of strong genetic swamping and modified seed morphology in the wild populations suggest that these introgressions should be rare.

Isolation, phylogeny and evolution of the SymRK gene in the legume genus Lupinus L.

SymRK is one of the key genes involved in initial steps of legume symbiotic association with fungi (mycorrhization) and nitrogen-fixing bacteria (nodulation). A large portion of the sequence encoding the extracellular domain of SYMRK was obtained for 38 lupine accessions and 2 outgroups in order to characterize this region, to evaluate its phylogenetic utility, and to examine whether its molecular evolutionary pattern is correlated with rhizobial diversity and specificity in Lupinus. The data suggested that, in Lupinus, SymRK is a single copy gene that shows good phylogenetic potential. Accordingly, SymRK provided additional support to previous molecular phylogenies, and shed additional light on relationships within the Old World group of Lupinus, especially among the African species. Similar to results of other studies, analyses of SymRK sequences were unable to resolve placement of the Florida unifoliolate lineage, whose relationship was weakly supported to either the Old or the New World lupines. Our data are consistent with strong purifying selection operating on SymRK in Lupinus, preserving rather than diversifying its function. Thus, although SymRK was demonstrated to be a vital gene in the early stages of the root-bacterial symbiotic associations, no evidence from present analyses indicate that this gene is involved in changes in rhizobial specificity in Lupinus.

Vigna (Leguminosae) sensu lato: the names and identities of the American segregate genera.

PREMISE OF STUDY: The legume genus Vigna and close relatives have highly elaborated floral morphologies that involve the coiling, bending, and intricate connection of flower parts. Banners, levers, platforms, and pumps have evolved that attract pollinators and then manipulate their movement. Given this three-dimensional floral complexity, the taxonomy of Vigna and relatives has been confounded by the study of mostly two-dimensional museum specimens. A molecular phylogenetic analysis was undertaken in the effort to resolve long-standing taxonomic questions centered on floral morphology. METHODS: The phylogenetic analysis included cpDNA trnK and nuclear ribosomal ITS/5.8S (ITS) sequence variation. The American species were comprehensively sampled and outgroups included Old World relatives. KEY RESULTS: The trnK and ITS data analyses concurred in resolving six well-supported clades of American Vigna that are most closely related to other American genera: Dolichopsis, Macroptilium, Mysanthus, Oryxis, Oxyrhynchus, Phaseolus, Ramirezella, and Strophostyles. These 14 American clades ranked here as genera are resolved as sister to a clade comprising the mainly Old World species of Vigna. CONCLUSIONS: American Vigna clades were reassigned to the genera Ancistrotropis, Cochliasanthus, Condylostylis, Leptospron, Sigmoidotropis, and the newly described Helicotropis. Vigna sensu stricto in the Americas now includes relatively few and mostly pantropical species. Elaborate floral asymmetries are readily used to apomorphically diagnose nearly all of the American genera. The age estimates of the extant diversification of the American and its Old World sister clade are approximately coeval at ca. 6-7 million yr, which belies much greater floral variation in the Americas.

Long-distance pollen flow assessment through evaluation of pollinator foraging range suggests transgene escape distances.

Foraging range, an important component of bee ecology, is of considerable interest for insect-pollinated plants because it determines the potential for outcrossing among individuals. However, long-distance pollen flow is difficult to assess, especially when the plant also relies on self-pollination. Pollen movement can be estimated indirectly through population genetic data, but complementary data on pollinator flight distances is necessary to validate such estimates. By using radio-tracking of cowpea pollinator return flights, we found that carpenter bees visiting cowpea flowers can forage up to 6 km from their nest. Foraging distances were found to be shorter than the maximum flight range, especially under adverse weather conditions or poor reward levels. From complete flight records in which bees visited wild and domesticated populations, we conclude that bees can mediate gene flow and, in some instances, allow transgene (genetically engineered material) escape over several kilometers. However, most between-flower flights occur within plant patches, while very few occur between plant patches.

Impact of violated high-dose refuge assumptions on evolution of Bt resistance.

Transgenic crops expressing Bacillus thuringiensis (Bt) toxins have been widely and successfully deployed for the control of target pests, while allowing a substantial reduction in insecticide use. The evolution of resistance (a heritable decrease in susceptibility to Bt toxins) can pose a threat to sustained control of target pests, but a high-dose refuge (HDR) management strategy has been key to delaying countervailing evolution of Bt resistance. The HDR strategy relies on the mating frequency between susceptible and resistant individuals, so either partial dominance of resistant alleles or nonrandom mating in the pest population itself could elevate the pace of resistance evolution. Using classic Wright-Fisher genetic models, we investigated the impact of deviations from standard refuge model assumptions on resistance evolution in the pest populations. We show that when Bt selection is strong, even deviations from random mating and/or strictly recessive resistance that are below the threshold of detection can yield dramatic increases in the pace of resistance evolution. Resistance evolution is hastened whenever the order of magnitude of model violations exceeds the initial frequency of resistant alleles. We also show that the existence of a fitness cost for resistant individuals on the refuge crop cannot easily overcome the effect of violated HDR assumptions. We propose a parametrically explicit framework that enables both comparison of various field situations and model inference. Using this model, we propose novel empiric estimators of the pace of resistance evolution (and time to loss of control), whose simple calculation relies on the observed change in resistance allele frequency.

Dominant inheritance of field-evolved resistance to Bt corn in Busseolafusca.

Transgenic crops expressing Bacillus thuringiensis (Bt) toxins have been adopted worldwide, notably in developing countries. In spite of their success in controlling target pests while allowing a substantial reduction of insecticide use, the sustainable control of these pest populations is threatened by the evolution of resistance. The implementation of the "high dose/refuge" strategy for managing insect resistance in transgenic crops aims at delaying the evolution of resistance to Bt crops in pest populations by promoting survival of susceptible insects. However, a crucial condition for the "high dose/refuge" strategy to be efficient is that the inheritance of resistance should be functionally recessive. Busseolafusca developed high levels of resistance to the Bt toxin Cry 1Ab expressed in Bt corn in South Africa. To test whether the inheritance of B. fusca resistance to the Bt toxin could be considered recessive we performed controlled crosses with this pest and evaluated its survival on Bt and non-Bt corn. Results show that resistance of B. fusca to Bt corn is dominant, which refutes the hypothesis of recessive inheritance. Survival on Bt corn was not lower than on non-Bt corn for both resistant larvae and the F1 progeny from resistant × susceptible parents. Hence, resistance management strategies of B. fusca to Bt corn must address non-recessive resistance.

Regulatory considerations surrounding the deployment of Bt-expressing cowpea in Africa: report of the deliberations of an expert panel.

Cowpea (Vigna unguiculata spp unguiculata) is adapted to the drier agro-ecological zones of West Africa where it is a major source of dietary protein and widely used as a fodder crop. Improving the productivity of cowpea can enhance food availability and security in West Africa. Insect predation--predominately from the legume pod borer (Maruca vitrata), flower thrips (Megalurothrips sjostedti) and a complex of pod-sucking bugs (e.g., Clavigralla spp)--is a major yield-limiting factor in West African cowpea production. Dramatic increases in yield are shown when M. vitrata is controlled with insecticides. However, availability, costs, and safety considerations limit pesticides as a viable option for boosting cowpea production. Development of Bt-cowpea through genetic modification (GM) to control the legume pod borer is a promising approach to cowpea improvement. Cowpea expressing the lepidopteran-active Cry1Ab protein from Bacillus thuringiensis is being developed as a first generation Bt-cowpea crop for West Africa. Appropriate stewardship of Bt-cowpea to assure its sustainability under West African conditions is critical to its successful development. A first step in this process is an environmental risk assessment to determine the likelihood and magnitude of adverse effects of the Cry1Ab protein on key environmental protection goals in West Africa. Here we describe the results of an expert panel convened in 2009 to develop the problem formulation phase for Bt-cowpea and to address specific issues around gene flow, non-target arthropods, and insect resistance management.