Sequence diversity in the tetraploid Zea perennis and the closely related diploid Z. diploperennis: insights from four nuclear loci

Polyploidy has been an extremely common phenomenon in the evolutionary history of angiosperms. Despite this there are few data available to evaluate the effects of polyploidy on genetic diversity and to compare the relative effects of drift and selection in polyploids and related diploids. We investigated DNA sequence diversity at four nuclear loci (adh1, glb1, c1, and waxy) from the tetraploid Zea perennis and the closely related diploid Z. diploperennis. Contrary to expectations, we detected no strong evidence for greater genetic diversity in the tetraploid, or for consistent differences in the effects of either drift or selection between the tetraploid and the diploid. Our failure to find greater genetic diversity in Z. perennis may result from its relatively recent origin or demographic factors associated with its origin. In addition to comparing genetic diversity in the two species, we constructed genealogies to infer the evolutionary origin of Z. perennis. Although these genealogies are equivocal regarding the mode of origin, several aspects of these genealogies support an autotetraploid origin. Consistent with previous molecular data the genealogies do not, however, support the division of Zea into two sections, the section Zea and the section Luxuriantes.     

Molecular evolution of the wound-induced serine protease inhibitor wip1 in Zea and related genera

Plant defense mechanisms have been the subject of intensive investigation. However, little is known about their long-term evolutionary dynamics. We investigated the molecular diversity of a wound-induced serine protease inhibitor, wip1, in the genus Zea, as well as the divergence of wip1 among four genera, Zea, Tripsacum, Sorghum, and Oryza, in order to gain insight into the long-term evolution of plant defense. The specific objectives of this study were to determine (1) whether wip1 has a history of positive or balancing selection, as has been shown for genes involved in plant defense against pathogens, and (2) if the evolutionary histories of wip1 inhibitory loops, which come into closest contact with proteases, differ from the evolutionary history of other parts of this gene. The Zea polymorphism data are consistent with a neutral evolutionary history. In contrast, relative-rate tests suggest a nonneutral evolutionary history. This inconsistency may indicate that selection acting on wip1 is episodic or that wip1 evolves in response to selection favoring novel alleles. We also detected significant heterogeneity in the evolutionary rates of the two inhibitory loops of wip1-one inhibitory loop is highly conserved, whereas the second has diverged rapidly. Because these two inhibitory loops are predicted to have very similar biochemical functions, the significantly different evolutionary histories suggest that these loops have different ecological functions.     

Zea systematics: ribosomal ITS evidence

Ribosomal internal transcribed spacer (ITS) sequences were used to evaluate the phylogenetics of Zea and Tripsacum. Maximum likelihood and polymorphism parsimony were used for phylogenetic reconstructions. Zea ITS nucleotide diversity was high compared to other plant species, but approximately equivalent to other maize loci. Coalescence of ITS alleles was rapid relative to other nuclear loci; however, there was still much diversity within populations. Zea and Tripsacum form a clade clearly differentiated from all other Poaceae. Four Zea ITS pseudogenes were identified by phylogenetic position and nucleotide composition. The phylogenetic position of Z. mays ssp. huehuetenangensis was clearly established as basal to the other Z. mays. The ITS phylogeny disfavored a Z. luxurians and Z. diploperennis clade, which conflicted with some previous studies. The introgression of Z. mays alleles into Z. perennis and Z. diploperennis was also established. The ITS data indicated a near contemporary divergence of domesticated maize and its two closest wild relatives.      

Higher expression of induced defenses in teosintes (Zea spp.) is correlated with greater resistance to fall armyworm,Spodoptera frugiperda

Selection for plant traits important for agriculture can come at a high cost to plant defenses. While selecting for increased growth rate and yield, domestication and subsequent breeding may lead to weakened defenses and greater susceptibility of plants to herbivores. We tested whether expression of defense genes differed among maize, Zea mays ssp. mays L. (Poaceae), and its wild relatives Zea mays ssp. parviglumis Iltis & Doebley and Zea diploperennis Iltis et al. We used two populations of Z. mays ssp. parviglumis: one expected to express high levels of an herbivore resistance gene, wound‐inducible protein (wip1), and another expected to have low expression of wip1. To test whether maize and wild Zea differed in induction of defenses against Spodoptera frugiperda (Smith) (Lepidoptera: Noctuidae), we quantified expression of several genes involved in plant defense: wip1, maize protease inhibitor (mpi), pathogenesis‐related protein (PR‐1), and chitinase. Moreover, we compared growth, development, and survival of caterpillars on maize and wild Zea plants. We found that maize expressed low levels of all but one of the genes when attacked by caterpillars, whereas the wild relatives of maize expressed induced defense genes at high levels. Expression of wip1, in particular, was much greater in the Z. mays ssp. parviglumis population that we expected to naturally express high levels of wip1, with expression levels 29‐fold higher than in herbivore‐free plants. Elevated expression of defenses in wild plants was correlated with higher resistance to caterpillars. Larvae were 15–20% smaller on wild Zea compared with maize, developed 20% slower, and only 22% of them survived to pupation on Z. mays ssp. parviglumis with high levels of wip1. Our results suggest that domestication has inadvertently reduced the resistance of maize, and it is likely that expression of wip1 and other genes associated with defenses play an important role in this reduction in resistance.     

Genetic diversity and the evolutionary history of plant immunity genes in two species of Zea

Plant pathogenesis-related genes (PR genes) code for enzymes, enzyme inhibitors, and other peptides that confer resistance to pathogens and herbivores. Although several PR genes have been the subject of molecular population genetic analyses, a general understanding of their long-term evolutionary dynamics remains incomplete. Here we analyze sequence data from 17 PR genes from two closely related teosinte species of central Mexico. In addition to testing whether patterns of diversity at individual loci depart from expectations under a neutral model, we compared patterns of diversity at defense genes, as a class, to nondefense genes. In Zea diploperennis, the majority of defense genes have patterns of diversity consistent with neutral expectations while at least two genes showed evidence of recent positive selection consistent with arms-race models of antagonistic coevolution. In Zea mays ssp. parviglumis, by contrast, analyses of both defense and nondefense genes revealed strong and consistent departures from the neutral model, suggestive of nonequilibrium population dynamics or population structure. Nevertheless, we found a significant excess of replacement polymorphism in defense genes compared to nondefense genes. Although we cannot exclude relaxed selective constraint as an explanation, our results are consistent with temporally variable (transient or episodic) selection or geographically variable selection acting on parviglumis defense genes. The different patterns of diversity found in the two Zea species may be explained by parviglumis' greater distribution and population structure together with geographic variation in selection.     

Population genetics of duplicated disease-defense genes,hm1 and hm2, in maize (Zea mays ssp. mays L.) and its wild ancestor (Zea mays ssp. parviglumis)

Plant defense genes are subject to nonneutral evolutionary dynamics. Here we investigate the evolutionary dynamics of the duplicated defense genes hm1 and hm2 in maize and its wild ancestor Zea mays ssp. parviglumis. Both genes have been shown to confer resistance to the fungal pathogen Cochliobolus carbonum race 1, but the effectiveness of resistance differs between loci. The genes also display different population histories. The hm1 locus has the highest nucleotide diversity of any gene yet sampled in the wild ancestor of maize, and it contains a large number of indel polymorphisms. There is no evidence, however, that high diversity in hm1 is a product of nonneutral evolution. In contrast, hm2 has very low nucleotide diversity in the wild ancestor of maize. The distribution of hm2 polymorphic sites is consistent with nonneutral evolution, as indicated by Tajima's D and other neutrality tests. In addition, one hm2 haplotype is more frequent than expected under the equilibrium neutral model, suggesting hitchhiking selection. Both defense genes retain >80% of the level of genetic variation in maize relative to the wild ancestor, and this level is similar to other maize genes that were not subject to artificial selection during domestication.     

Specialist and generalist herbivores exert opposing selection on a chemical defense

* Plant defense traits often show high levels of genetic variation, despite clear impacts on plant fitness. This variation may be partly maintained by trade-offs in the defense against multiple herbivore species, for example between generalists and coevolved specialists. Despite a long-standing discussion in the literature on the subject, no study to date has specifically manipulated specialist and generalist herbivores independently of one another to determine whether the two guilds exert opposing selection pressures on specific defensive traits. * In two separate experiments, the dominant specialist and generalist herbivores of Brassica nigra were independently manipulated to test whether the composition of the herbivore community altered the direction of selection on a major defensive trait of the plant, sinigrin concentration. * It was found that generalist damage was negatively correlated but specialist loads were positively correlated with increasing sinigrin concentrations; and sinigrin concentration was favored when specialists were removed, disfavored (past an intermediate point) when generalists were removed and selectively neutral when plants faced both generalists and specialists.     

玉米近缘种中玉米着丝粒序列的FISH检测

为分析玉米着丝粒卫星DNA(CentC)和着丝粒反转录转座子(CRM)在玉米种的亚种及近缘种中的保守性,采用双色荧光原位杂交检测了这两种重复序列在墨西哥玉米、二倍体多年生类玉米、多年生类玉米、摩擦禾、薏苡、高粱中的存在和分布。CentC、CRM探针在墨西哥玉米、二倍体多年生类玉米和多年生类玉米的所有染色体的着丝粒区产生了强或较强的杂交信号, 而且不同染色体的杂交信号的强度存在差异, 表明两种玉米着丝粒重复序列在不同着丝粒中的数量不同; 此外, 部分着丝粒中的CentC和CRM信号的强度存在差异, 不完全重叠。CentC、CRM探针仅在摩擦禾的多数染色体的着丝粒区产生了弱的杂交信号。在薏苡和高粱中仅测检到主要分布在着丝粒区的较强或强的CRM信号。这些结果表明, CentC在玉米种的亚种间及玉蜀黍属的物种间高度保守, 在与玉蜀黍属亲缘关系最近的摩擦禾属物种中也具有较高的保守性; CRM在与玉蜀黍属亲缘关系较近和较远的禾本科种属中都具有保守性。     

Comparative analysis of quantitative trait loci controlling glucosinolates,myrosinase and insect resistance in Arabidopsis thaliana

Evolutionary interactions among insect herbivores and plant chemical defenses have generated systems where plant compounds have opposing fitness consequences for host plants, depending on attack by various insect herbivores. This interplay complicates understanding of fitness costs and benefits of plant chemical defenses. We are studying the role of the glucosinolate-myrosinase chemical defense system in protecting Arabidopsis thaliana from specialist and generalist insect herbivory. We used two Arabidopsis recombinant inbred populations in which we had previously mapped QTL controlling variation in the glucosinolate-myrosinase system. In this study we mapped QTL controlling resistance to specialist (Plutella xylostella) and generalist (Trichoplusia ni) herbivores. We identified a number of QTL that are specific to one herbivore or the other, as well as a single QTL that controls resistance to both insects. Comparison of QTL for herbivory, glucosinolates, and myrosinase showed that T. ni herbivory is strongly deterred by higher glucosinolate levels, faster breakdown rates, and specific chemical structures. In contrast, P. xylostella herbivory is uncorrelated with variation in the glucosinolate-myrosinase system. This agrees with evolutionary theory stating that specialist insects may overcome host plant chemical defenses, whereas generalists will be sensitive to these same defenses.     

Chromosome C-banding of the teosinte Zea nicaraguensis and comparison to other Zea species

The Nicaraguan teosinte Zea nicaraguensis was studied cytologically to determine its chromosome number and C-banding pattern. The C-banding pattern was compared with that of the close relative Zea luxurians as well as with Zea diploperennis and cultivated maize, Zea mays ssp. mays. Karyograms were constructed for the four Zea species. It is shown that Z. nicaraguensis, like most other Zea species, is a diploid with 2n=20 chromosomes. The C-banding pattern shows that Z. nicaraguensis is very similar to Z. luxurians and more similar to Z. luxurians than to Z. diploperennis and cultivated maize. Whether or not Z. nicaraguensis and Z. luxurians should be regarded as subspecies instead of individual species is, however, not possible to conclude from this study.     

Physical mapping of the 5S and 45S rDNA in teosintes

The physical locations of the 5S and 45S rDNA sequences were examined in three types of teosinte, Zea mays ssp. mexicana (2n = 20), Zea diploperennis (2n = 20) and Zea perennis (2n = 40) by biotinylated fluorescence in situ hybridization (FISH). The tested materials only showed one hybridization site of 5S rDNA on their genomes, but they were different in the position of the signals. The hybridization site of Zea mays ssp. mexicana was located on the long arm of chromosome 2, indicating that it is the same as the cultivated maize in the position of 5S rDNA, while the sites of Zea diploperennis and Zea perennis were on the short arms of other chromosomes. For 45S rDNA, one hybridization site was detected at secondary constriction region of the satellite chromosomes in Zea mays ssp. mexicana and Zea diploperennis, while in Zea perennis, besides the site located at the secondary constriction region, a second site on the short arm of another chromosome pair was observed. Our results provide additional evidence for Zea mays ssp. mexicana being a subspecies of Zea mays.     

Salivary proteins of spider mites suppress defenses in Nicotiana benthamiana and promote mite reproduction

Spider mites (Tetranychidae sp.) are widely occurring arthropod pests on cultivated plants. Feeding by the two‐spotted spider mite T. urticae, a generalist herbivore, induces a defense response in plants that mainly depends on the phytohormones jasmonic acid and salicylic acid (SA). On tomato (Solanum lycopersicum), however, certain genotypes of T. urticae and the specialist species T. evansi were found to suppress these defenses. This phenomenon occurs downstream of phytohormone accumulation via an unknown mechanism. We investigated if spider mites possess effector‐like proteins in their saliva that can account for this defense suppression. First we performed an in silico prediction of the T. urticae and the T. evansi secretomes, and subsequently generated a short list of candidate effectors based on additional selection criteria such as life stage‐specific expression and salivary gland expression via whole mount in situ hybridization. We picked the top five most promising protein families and then expressed representatives in Nicotiana benthamiana using Agrobacterium tumefaciens transient expression assays to assess their effect on plant defenses. Four proteins from two families suppressed defenses downstream of the phytohormone SA. Furthermore, T. urticae performance on N. benthamiana improved in response to transient expression of three of these proteins and this improvement was similar to that of mites feeding on the tomato SA accumulation mutant nahG. Our results suggest that both generalist and specialist plant‐eating mite species are sensitive to SA defenses but secrete proteins via their saliva to reduce the negative effects of these defenses.     

Attract and deter: a dual role for pyrrolizidine alkaloids in plant–insect interactions

Pyrrolizidine alkaloids (PAs) are the major defense compounds of plants in the Senecio genus. Here I will review the effects of PAs in Senecio on the preference and performance of specialist and generalist insect herbivores. Specialist herbivores have evolved adaptation to PAs in their host plant. They can use the alkaloids as cue to find their host plant and often they sequester PAs for their own defense against predators. Generalists, on the other hand, can be deterred by PAs. PAs can also affect survival of generalist herbivores. Usually generalist insects avoid feeding on young Senecio leaves, which contain a high concentration of alkaloids. Structurally related PAs can differ in their effects on insect herbivores, some are more toxic than others. The differences in effects of PAs on specialist and generalists could lead to opposing selection on PAs, which may maintain the genetic diversity in PA concentration and composition in Senecio species.     

Chemical and physical defenses against predators in Cystodytes (Ascidiacea)

Ascidians utilize both physical (spicules, tunic toughness) and chemical defenses (secondary metabolites, acidity) and suffer relatively little predation by generalist predators. The genus Cystodytes (Polycitoridae) is distributed widely in both tropical and temperate waters. Secondary metabolite composition, calcareous spicules and tunic acidity (pH < 1) may act as redundant defense mechanisms against predation in this genus. To assess the relative importance of chemical and physical defenses against predation in ascidians, we studied purple and blue morphs of Cystodytes from the western Mediterranean (formerly assigned to Cystodytes dellechiajei, but recently shown to belong to two different species), and a purple morph from Guam (USA), identified as Cystodytes violatinctus. Crude extracts, spicules, ascididemin (the major alkaloid of the blue morph) and acidity were used in feeding trials to evaluate chemical and physical defense mechanisms in Cystodytes spp. We performed feeding experiments in the field with a guild of generalist fish (mostly damselfish), and in the laboratory with a sea urchin and a puffer fish. Our results showed that all crude extracts and ascididemin significantly deterred fish predation, but not sea urchin predation. However, neither acidity alone nor spicules at natural concentrations deterred feeding. These results and other studies on sponges and gorgonians suggest that secondary metabolites are the primary means of defense against fish predators. Spicules and tunic acidity may perform other ecological roles and/or target certain specialist predators.     

Functionally different predators break down antipredator defenses of spider mites

Prey that lives with functionally different predators may experience enhanced mortality risk, because of conflicts between the specific defenses against their predators. Because natural communities usually contain combinations of prey and functionally different predators, examining risk enhancement with multiple predators may help to understand prey population dynamics. It is also important in an applied context: risk enhancement with multiple biological control agents could lead to successful suppression of pests. We examined whether risk enhancement occurs in the spider mite Tetranychus kanzawai Kishida (Acari: Tetranychidae) when exposed to two predator species: a generalist ant, Pristomyrmex punctatus Mayr (Hymenoptera: Formicidae), and a specialist predatory mite, Neoseiulus womersleyi Schicha (Acari: Phytoseiidae). We replicated microcosms that consisted of spider mites, ants, and predatory mites. Spider mites avoided generalist ants by staying inside their webs on leaf surfaces. In contrast, spider mites avoided specialist predatory mites that intruded into their webs by exiting the web, which obviously conflicts with the defense against ants. In the presence of both predators, enhanced mortality of spider mites was observed. A conflict occurred between the spider mites’ defenses: they seemed to move out of their webs and be preyed upon by ants. This is the first study to suggest that risk enhancement occurs in web‐spinning spider mites that are exposed to both generalist and specialist predator species, and to provide evidence that ants can have remarkable synergistic effects on the biological control of spider mites using specialist predatory mites.     

Relaxation of putative plant defenses in a tropical agroecosystem

Evidence of the effects of agriculture on natural systems is widespread, but potential evolutionary responses in nontarget species are largely uncharacterized. To explore whether exposure to agrochemicals may influence selective pressures and phenotypic expression in nonagricultural plant populations, we characterized the expression of putative antiherbivore defense phenotypes in three nonagricultural species found upstream and downstream of irrigated rice fields in Guanacaste Province, Costa Rica. We found that plants downstream of chemically intensive agriculture showed shifts toward reduced expression of putative antiherbivore defenses relative to upstream counterparts. In two of three tested species, leaf extracts from downstream plants were more palatable to a generalist consumer, suggesting a possible reduction of chemical defenses. In one species with multiple modes of putative defenses, we observed parallel reductions of three metrics of putative biotic and physical defenses. These reductions were concurrent with reduced herbivore damage on downstream plants. Together, these results suggest that agriculture has the potential to alter intraspecific phenotypic expression, ecological interactions, and natural selection in nontarget plant populations.     

Does habitat specialization shape the evolutionary potential of wild bird populations?

Because specialist species evolved in more temporally and spatially homogeneous environments than generalist species, they are supposed to experience less fluctuating selection. For this reason, we expect specialists to show lower overall genetic variation as compared to generalists. We also expect populations from specialist species to be smaller and more fragmented, with lower neutral genetic diversity. We tested these hypotheses by investigating patterns of genetic diversity along a habitat specialization gradient in wild birds, based on estimates of heritability, coefficients of variation of additive genetic variance, and heterozygosity available in the literature. We found no significant effect of habitat specialization on any of the quantitative genetic estimators but generalists had higher heterozygosity. This effect was mainly a consequence of the larger population size of generalists. Our results suggest that evolutionary potential does not differ at the population level between generalist and specialist species, but the trend observed in heterozygosity levels and population sizes may explain their difference in susceptibility to extinction.     

Maize Sh2 gene is constrained by natural selection but escaped domestication

In Zea mays L., we studied the molecular evolution of Shrunken2 (Sh2), a gene that encodes the large subunits of a major enzyme in endosperm starch biosynthesis, ADP-glucose pyrophosphorylase. We compared 4669 bp of the Sh2 coding region on 50 accessions of maize and teosinte. Very few nucleotide polymorphisms were found when compared with other genes in Z. mays, revealing an effect of purifying selection in the whole species that predates domestication. Additionally, the comparison of Sh2 sequences in all Z. mays subspecies and outgroups Z. diploperennis and Tripsacum dactyloides suggests the occurrence of an ancient selective sweep in the Sh2 3' region. The amount and nature of nucleotide diversity are similar in both maize and teosinte, confirming previous results that suggested that Sh2 has not been involved in maize domestication. The very low level of nucleotide diversity as well as the highly conserved protein sequence suggest that natural selection retained effective Sh2 allele(s) long before agriculture started, making human selection inefficient on this gene.     

Physical leaf defenses – altered by Zea life‐history evolution,domestication, and breeding – mediate oviposition preference of a specialist leafhopper

Plant anti‐herbivore defenses are known to be affected by life‐history evolution, as well as by domestication and breeding in the case of crop species. A suite of plants from the maize genus Zea (Poaceae) and the specialist herbivore Dalbulus maidis (DeLong & Wolcott) (Hemiptera: Cicadellidae) were used to test the hypothesis that anti‐herbivore defenses are affected by plant life‐history evolution and human intervention through domestication and breeding for high yield. The suite of plants included a maize (Zea mays ssp. mays L.) commercial hybrid, a maize landrace, two populations of the annual Balsas teosinte (Z. mays ssp. parviglumis Iltis & Doebley), and perennial teosinte (Z. diploperennis Iltis, Doebley & Guzman). Leaf toughness, pubescence, and oviposition preference were compared among the suite of host plants looking for effects of transitions in life history (i.e., from perennial to annual life cycle), domestication (i.e., from wild annual to domesticated annual), and breeding (i.e., from landrace to hybrid maize) on defense against D. maidis. Results on leaf toughness suggested that the life‐history and domestication transitions weakened the plant's resistance to penetration by the mouthparts and ovipositor of D. maidis, whereas results on pubescence suggested that this putative defense was strengthened with the breeding transition, contrary to expectations. Results on oviposition preference of D. maidis coincided with the expectation that life‐history and domestication transitions would lead to preference for Balsas teosinte over perennial teosinte, and of landrace maize over Balsas teosinte. Also, a negative correlation suggested that oviposition preference is significantly influenced by leaf toughness. Overall, the results suggested that Zea defenses against the specialist herbivore D. maidis were variably affected by plant life‐history evolution, domestication, and breeding, and that chemical defense may play a role in Zea defense against D. maidis because leaf toughness and pubescence only partially explained its host preferences.