Genomic analysis of the four ecologically distinct cactus host populations of Drosophila mojavensis

BACKGROUND

Relationships between an organism and its environment can be fundamental in the understanding how populations change over time and species arise. Local ecological conditions can shape variation at multiple levels, among these are the evolutionary history and trajectories of coding genes. This study examines the rate of molecular evolution at protein-coding genes throughout the genome in response to host adaptation in the cactophilic Drosophila mojavensis. These insects are intimately associated with cactus necroses, developing as larvae and feeding as adults in these necrotic tissues. Drosophila mojavensis is composed of four isolated populations across the deserts of western North America and each population has adapted to utilize different cacti that are chemically, nutritionally, and structurally distinct.

RESULTS

High coverage Illumina sequencing was performed on three previously unsequenced populations of D. mojavensis. Genomes were assembled using the previously sequenced genome of D. mojavensis from Santa Catalina Island (USA) as a template. Protein coding genes were aligned across all four populations and rates of protein evolution were determined for all loci using a several approaches.

CONCLUSIONS

Loci that exhibited elevated rates of molecular evolution tend to be shorter, have fewer exons, low expression, be transcriptionally responsive to cactus host use and have fixed expression differences across the four cactus host populations. Fast evolving genes were involved with metabolism, detoxification, chemosensory reception, reproduction and behavior. Results of this study give insight into the process and the genomic consequences of local ecological adaptation.

Untangling the Hypogeococcus pungens species complex (Hemiptera: Pseudococcidae) for Argentina, Australia, and Puerto Rico based on host plant associations and genetic evidence

Hypogeococcus pungens, a mealybug native of southern South America, is devastating native cacti in Puerto Rico and threatening cactus diversity in the Caribbean, and potentially in Central and North America. The taxonomic status of H. pungens is controversial since it has been reported feeding not only on Cactaceae but also on other plant families throughout its distribution range. However, in Australia, where the species had been exported from Argentina to control weedy American cacti, it was never found on host plants other than Cactaceae. These conflicting pieces of evidence not only cast doubt on the species identity that invaded Puerto Rico, but also have a negative impact on the search for natural enemies to be used in biological control programs against this pest. Here we present reproductive incompatibility and phylogenetic evidences that give support to the hypothesis that H. pungens is a species complex in which divergence appears to be driven by the host plants. The nuclear EF1α and 18S and the mitochondrial COI genes were used as markers to evaluate the phylogenetic relationships among H. pungens populations collected in Argentina, Australia and Puerto Rico feeding on Cactaceae and/or Amaranthaceae. Additionally, we conducted reciprocal crosses between mealybugs from both hosts. Species delimitation analysis revealed two well-supported putative species within H. pungens, one including mealybugs feeding on Amaranthaceae (H. pungens sensu stricto), and a new undescribed species using Cactaceae as hosts. Additionally, we found asymmetric reproductive incompatibility between these putative species suggesting recent reproductive isolation. The Bayesian species delimitation also suggested that the Australian mealybug population may derive from another undescribed species. Overall, the patterns of genetic differentiation may be interpreted as the result of recent speciation events prompted by host plant shifts. Finally, the finding of a single haplotype in the Puerto Rico population suggests only one invasive event. We still need to identify the geographical origin of the pest in order to enable the use of biological control to reduce the threat to cacti diversity in the Caribbean.

Genetic variation amongst biotypes of Dactylopius tomentosus

The tomentose cochineal scale insect, Dactylopius tomentosus (Lamarck) (Hemiptera: Dactylopiidae), is an important biological control agent against invasive species of Cylindropuntia (Caryophyllales: Cactaceae). Recent studies have demonstrated that this scale is composed of host-affiliated biotypes with differential host specificity and fitness on particular host species. We investigated genetic variation and phylogenetic relationships among D. tomentosus biotypes and provenances to examine the possibility that genetic diversity may be related to their host-use pattern, and whether their phylogenetic relationships would give insights into taxonomic relatedness of their host plants. Nucleotide sequence comparison was accomplished using sequences of the mitochondrial cytochrome c oxidase I (COI) gene. Sequences of individuals from the same host plant within a region were identical and characterized by a unique haplotype. Individuals belonging to the same biotype but from different regions had similar haplotypes. However, haplotypes were not shared between different biotypes. Phylogenetic analysis grouped the monophyletic D. tomentosus into 3 well-resolved clades of biotypes. The phylogenetic relationships and clustering of biotypes corresponded with known taxonomic relatedness of their hosts. Two biotypes, Fulgida and Mamillata, tested positive for Wolbachia (α-Proteobacteria), a common endosymbiont of insects. The Wolbachia sequences were serendipitously detected by using insect-specific COI DNA barcoding primers and are most similar to Wolbachia Supergroup F strains. This study is the first molecular characterization of cochineal biotypes that, together with Wolbachia sequences, contribute to the better identification of the biotypes of cochineal insects and to the biological control of cacti using host-specific biotypes of the scale.

Host plant adaptation in Drosophila mettleri populations

The process of local adaptation creates diversity among allopatric populations, and may eventually lead to speciation. Plant-feeding insect populations that specialize on different host species provide an excellent opportunity to evaluate the causes of ecological specialization and the subsequent consequences for diversity. In this study, we used geographically separated Drosophila mettleri populations that specialize on different host cacti to examine oviposition preference for and larval performance on an array of natural and non-natural hosts (eight total). We found evidence of local adaptation in performance on saguaro cactus (Carnegiea gigantea) for populations that are typically associated with this host, and to chemically divergent prickly pear species (Opuntia spp.) in a genetically isolated population on Santa Catalina Island. Moreover, each population exhibited reduced performance on the alternative host. This finding is consistent with trade-offs associated with adaptation to these chemically divergent hosts, although we also discuss alternative explanations for this pattern. For oviposition preference, Santa Catalina Island flies were more likely to oviposit on some prickly pear species, but all populations readily laid eggs on saguaro. Experiments with non-natural hosts suggest that factors such as ecological opportunity may play a more important role than host plant chemistry in explaining the lack of natural associations with some hosts.

Bacteria associated with Copestylum (Diptera, Syrphidae) larvae and their cactus host Isolatocereus dumortieri

We describe the gut bacterial diversity inhabiting two saprophagous syrphids and their breeding substrate (decayed tissues of the columnar cactus Isolatocereus dumortieri). We analyzed the gut microbiota of Copestylum latum (scooping larvae that feed on decayed cactus tissues) and Copestylum limbipenne (whose larvae can also feed on semiliquid tissues) using molecular techniques. DNA was extracted from larval guts and cactus tissues. The V1-V3 region of the 16S rRNA genes was amplified and sequenced. A total of 31079 sequences were obtained. The main findings are: C. limbipenne is dominated by several Enterobacteriaceae, including putative nitrogen-fixing genera and pectinolitic species and some denitrifying species, whereas in C. latum unclassified Gammaproteobacteria predominate. Decayed tissues have a dominant lactic acid bacterial community. The bacterial communities were more similar between larval species than between each larva and its breeding substrate. The results suggest that the gut bacterial community in these insects is not strongly affected by diet and must be dependent on other factors, such as vertical transmission, evolutionary history and host innate immunity.

Determination of biotypes of Dactylopius tomentosus (Hemiptera: Dactylopiidae) and insights into the taxonomic relationships of their hosts, Cylindropuntia spp

Host specialization to form biotypes is common among phytophagous insects, and it has been hypothesised that biotypes of Dactylopius tomentosus L. (Hemiptera: Dactylopiidae) occur. D. tomentosus is an important biological control agent for Cylindropuntia cacti when they occur as weeds. Additionally, there is uncertainty surrounding the taxonomic status of some species of Cylindropuntia. This study aimed to confirm the existence of D. tomentosus biotypes and to assess whether host specialization can help to resolve this systematic uncertainty. For this study, the host specificity and performance of ten provenances of D. tomentosus collected from C. cholla, C. fulgida var. fulgida, C. imbricata, C. f. var. mamillata, C. rosea and C. tunicata and reared on C. cholla, C. fulgida var. fulgida, C. imbricata and C. rosea were investigated. Five life-history parameters were measured including: crawler development time and survival, female development time, and the weight and number of eggs produced by females. Results revealed significant variation in host specificity with provenances either thriving, surviving or dying on the different hosts, thus demonstrating the existence of biotypes. Also, host specificity was related to host species and not to the geographic locality from which either the host or provenance was sourced. These findings suggest that the characteristics of Cylindropuntia species may differ sufficiently, there by presenting different selection pressures that induce and sustain distinct biotypes of D. tomentosus. The observed host use patterns of the biotypes separated the plant species into two groups that accorded with known phylogenetic relationships among Cylindropuntia species, suggesting that biotypes can be used to elucidate their taxonomic relatedness. Besides advancing our knowledge of the ecology and evolution of D. tomentosus, these novel findings have important implications for the biological control of Cylindropuntia species.

Genetics of incipient speciation in Drosophila mojavensis. I. Male courtship song, mating success, and genotype x environment interactions

Few studies have examined genotype by environment (GxE) effects on premating reproductive isolation and associated behaviors, even though such effects may be common when speciation is driven by adaptation to different environments. In this study, mating success and courtship song differences among diverging populations of Drosophila mojavensis were investigated in a two-environment quantitative trait locus (QTL) analysis. Baja California and mainland Mexico populations of D. mojavensis feed and breed on different host cacti, so these host plants were used to culture F2 males to examine host-specific QTL effects and GxE interactions influencing mating success and courtship songs. Linear selection gradient analysis showed that mainland females mated with males that produced songs with significantly shorter L(long)-IPIs, burst durations, and interburst intervals. Twenty-one microsatellite loci distributed across all five major chromosomes were used to localize effects of mating success, time to copulation, and courtship song components. Male courtship success was influenced by a single detected QTL, the main effect of cactus, and four GxE interactions, whereas time to copulation was influenced by three different QTLs on the fourth chromosome. Multiple-locus restricted maximum likelihood (REML) analysis of courtship song revealed consistent effects linked with the same fourth chromosome markers that influenced time to copulation, a number of GxE interactions, and few possible cases of epistasis. GxE interactions for mate choice and song can maintain genetic variation in populations, but alter outcomes of sexual selection and isolation, so signal evolution and reproductive isolation may be slowed in diverging populations. Understanding the genetics of incipient speciation in D. mojavensis clearly depends on cactus-specific expression of traits associated with courtship behavior and sexual isolation.

Functional genomics of cactus host shifts in Drosophila mojavensis

Understanding the genetic basis of adaptation to novel environments remains one of the major challenges confronting evolutionary biologists. While newly developed genomic approaches hold considerable promise for addressing this overall question, the relevant tools have not often been available in the most ecologically interesting organisms. Our study organism, Drosophila mojavensis, is a cactophilic Sonoran Desert endemic utilizing four different cactus hosts across its geographical range. Its well-known ecology makes it an attractive system in which to study the evolution of gene expression during adaptation. As a cactophile, D. mojavensis oviposits in the necrotic tissues of cacti, therefore exposing larvae and even adults to the varied and toxic compounds of rotting cacti. We have developed a cDNA microarray of D. mojavensis to examine gene expression associated with cactus host use. Using a population from the Baja California population we examined gene expression differences of third instar larvae when reared in two chemically distinct cactus hosts, agria (Stenocereus gummosus, native host) vs. organpipe (Stenocereus thurberi, alternative host). We have observed differential gene expression associated with cactus host use in genes involved in metabolism and detoxification.

Triatominae et Cactaceae : un risque pour la transmission de la Trypanosomose américaine dans le péridomicile (nord-est du Brésil)

Field observations carried in semi-arid Brazil Northeast point out the frequent association, in the peridomiciliary space, between a cactus, Cereus jamacaru, the occurrence of nests in its branches and the occurrence of two species of insects vectors of Trypanosoma cruzi, pathogenic agent of Chagas disease: Rhodnius neglectus and Triatoma pseudomaculata. The analysis of the architectural variables of this Cactaceae shows that the presence of nests, and thus of insects, depends on the traditional practices of management of this cactus. This study underlines the relevance of an integrated approach of the ecology of Triatominae for the identification of factors of risk.

Genotype by environment interactions in viability and developmental time in populations of cactophilic Drosophila

The genetic and ecological basis of viability and developmental time differences between Drosophila buzzatii and D. koepferae were analysed using the isofemale line technique. Several isofemale lines were sampled from pairs of allopatric/sympatric populations of each species. Flies were reared in media prepared with decaying tissues of two of the main natural cactus hosts of each species. This experimental design enabled us to evaluate the relative contribution of phenotypic plasticity, genetic variation and genotype by environment interaction (G x E) to total phenotypic variation for two fitness traits, viability and developmental time. Our results revealed significant G x E in both traits, suggesting that the maintenance of genetic variation can be explained, at least in part, by diversifying selection in different patches of a heterogeneous environment in both species. However, the relative importance of the factors involved in the G x E varied between traits and populations within species. For viability, the G x E can be mainly attributed to changes in the rank order of lines across cacti. However, the pattern was different for developmental time. In D. buzzatii the G x E can be mainly accounted for by changes in among line variance across cacti, whereas changes in the rank order of lines across cacti was the main component in D. koepferae. These dissimilar patterns of variation between traits and species suggest that the evolutionary forces shaping genetic variation for developmental time and viability vary between populations within species and between species.

INTEGRATING QUALITY AND QUANTITY OF MUTUALISTIC SERVICE TO CONTRAST ANT SPECIES PROTECTINGFEROCACTUS WISLIZENI

Generalized, facultative mutualisms are often characterized by great variation in the benefits provided by different partner species. This variation may be due to differences among species in the quality and quantity of their interactions, as well as their phenology. Many plant species produce extrafloral nectar, a carbohydrate-rich resource, to attract ant species that can act as "bodyguards" against a plant's natural enemies. Here, we explore differences in the quality and quantity of protective service that ants can provide a plant by contrasting the four most common ant visitors to Ferocactus wislizeni, an extrafloral nectary-bearing cactus in southern Arizona. The four species differ in abundance when tending plants, and in the frequency at which they visit plants. By adding surrogate herbivores (Manduca sexta caterpillars) to plants, we demonstrate that all four species recruit to and attack potential herbivores. However, their per capita effectiveness in deterring herbivores (measured as the inverse of the number of workers needed to remove half of the experimentally added caterpillars) differs. Using these among-species differences in quality (per capita effectiveness) and quantity (number of workers that visit a plant and frequency of visitation), we accurately predicted the variation in fruit production among plants with different histories of ant tending. We found that plant benefits (herbivore removal and maturation of buds and fruits) typically saturated at high levels of ant protection, although plants could be "well defended" via different combinations of interaction frequency, numbers of ant workers per interaction, and per capita effects. Our study documents variation among prospective mutualists, distinguishes the components of this variation, and integrates these components into a predictive measure of protection benefit to the plant. The method we used to average saturating benefits over time could prove useful for quantifying overall service in other mutualisms.

A mass collection of Triatoma ryckmani (Hemiptera: Reduviidae) from Stenocereus Eichlamii (Cactaceae) in the semiarid region of Guatemala

A population of 216 specimens of Stenocereus eichlamii (Cactaceae, Subfamily Cereoideae) was surveyed for Triatoma ryckmani (vector of Chagas disease) in a one hectare plot of semiarid habitat in Guatemala. Out of 44 plants that had dead and dry sections, 24 plants had a total of 103 specimens of T. ryckmani. In comparison with other areas of Guatemala, T ryckmani is well established in the semiarid ecosystem (Infestation index 54.5, density = 2.3 and crowding index 4.3). The insects were mainly found (52.4%) in the dead portions of S. eichlamii 2.0 to 3.2 m above the ground (X2 = 26.0, P < 0.00001), followed by dry cactus sections between 3.2 and 5.0 m (35.9%). They were less frequent 0.2 to 2.0 m above the ground. A considerable proportion (75.7%) had no aparent blood in their digestive systems. To determine the presence of flagellates, 43 of the bugs were dissected, but none were found. This is the first report on T. ryckmani population dynamics in this habitat.

Relationships between necrotic cactus availability and population size in a cactophilic Drosophila (Diptera, Drosophilidae) located on a sandstone table hill in Brazil

Drosophila gouveai is a cactophilic species endemic to South America. In southeast Brazil it is found on summits of isolated hills, which apparently are current refugia resulting from climatic changes during the Quaternary Period. It breeds only in necrotic cactus cladodes of Pilosocereus machrisii. Temporal differences in necrotic cactus availability could have a great impact upon D. gouveai population size, and could thus influence its evolutionary history. We analyzed the relationship between necrotic cactus availability and population size of D. gouveai. The fluctuation in the population size, variation in necrotic cactus availability and exploitation of this resource by larvae were surveyed bimonthly for one year on a sandstone table hill in central-south Brazil. Temporal necrotic cactus availability did not vary significantly, though in June there was a moderate decrease Larval populations were highest in October and December. The D. gouveai population size was highest in February and remained relatively stable the rest of the year. The observed fluctuation in population size was not a function of temporal necrotic cactus availability in quantitative terms.