Integrative taxonomy reveals six new species related to the Mediterranean corn stalk borerSesamia nonagrioides(Lefèbvre) (Lepidoptera, Noctuidae, Sesamiina)

Cryptic diversity begets challenges and opportunities in biodiversity research

How many species of life are there on Earth? This is a question that we want to know but cannot yet answer. Some scholars speculate that the number of species may reach 2.2 billion when considering cryptic diversity and that each morphology-based insect species may contain an average of 3.1 cryptic species. With nearly two million described species, such high estimates of cryptic diversity would suggest that cryptic species are widespread. The development of molecular species delimitation has led to the discovery of a large number of cryptic species, and cryptic biodiversity has gradually entered our field of vision and attracted more attention. This paper introduces the concept of cryptic species, how they evolve, and methods by which they may be discovered and confirmed, and provides theoretical and methodological guidance for the study of hidden species. A workflow of how to confirm cryptic species is provided. In addition, the importance and reliability of multi-evidence-based integrated taxonomy are reaffirmed as a way to better standardize decision-making processes. Special focus on cryptic diversity and increased funding for taxonomy is needed to ensure that cryptic species in hyperdiverse groups are discoverable and described. An increased focus on cryptic species in the future will naturally arise as more difficult groups are studied, and thereby, we may finally better understand the rules governing the evolution and maintenance of cryptic biodiversity.

Characterizing virulence differences in a parasitoid wasp through comparative transcriptomic and proteomic

BACKGROUND

Two strains of the endoparasitoid Cotesia typhae (Hymenoptera: Braconidae) present a differential parasitism success on the host, Sesamia nonagrioides (Lepidoptera: Noctuidae). One is virulent on both permissive and resistant host populations, and the other only on the permissive host. This interaction provides a very interesting frame for studying virulence factors. Here, we used a combination of comparative transcriptomic and proteomic analyses to unravel the molecular basis underlying virulence differences between the strains.

RESULTS

First, we report that virulence genes are mostly expressed during the pupal stage 24 h before adult emergence of the parasitoid. Especially, 55 proviral genes are up-regulated at this stage, while their expression is only expected in the host. Parasitoid gene expression in the host increases from 24 to 96 h post-parasitism, revealing the expression of 54 proviral genes at early parasitism stage and the active participation of teratocytes to the parasitism success at the late stage. Secondly, comparison between strains reveals differences in venom composition, with 12 proteins showing differential abundance. Proviral expression in the host displays a strong temporal variability, along with differential patterns between strains. Notably, a subset of proviral genes including protein-tyrosine phosphatases is specifically over-expressed in the resistant host parasitized by the less virulent strain, 24 h after parasitism. This result particularly hints at host modulation of proviral expression. Combining proteomic and transcriptomic data at various stages, we identified 8 candidate genes to support the difference in reproductive success of the two strains, one proviral and 7 venom genes, one of them being also produced within the host by the teratocytes.

CONCLUSIONS

This study sheds light on the temporal expression of virulence factors of Cotesia typhae, both in the host and in the parasitoid. It also identifies potential molecular candidates driving differences in parasitism success between two strains. Together, those findings provide a path for further exploration of virulence mechanisms in parasitoid wasps, and offer insights into host-parasitoid coevolution.

Cellular dynamics of host - parasitoid interactions: Insights from the encapsulation process in a partially resistant host

Cotesia typhae is an eastern African endoparasitoid braconid wasp that targets the larval stage of the lepidopteran stem borer, Sesamia nonagrioides, a maize crop pest in Europe. The French host population is partially resistant to the Makindu strain of the wasp, allowing its development in only 40% of the cases. Resistant larvae can encapsulate the parasitoid and survive the infection. This interaction provides a very interesting frame for investigating the impact of parasitism on host cellular resistance. We characterized the parasitoid ovolarval development in a permissive host and studied the encapsulation process in a resistant host by dissection and histological sectioning compared to that of inert chromatography beads. We measured the total hemocyte count in parasitized and bead-injected larvae over time to monitor the magnitude of the immune reaction. Our results show that parasitism of resistant hosts delayed encapsulation but did not affect immune abilities towards inert beads. Moreover, while bead injection increased total hemocyte count, it remained constant in resistant and permissive larvae. We conclude that while Cotesia spp virulence factors are known to impair the host immune system, our results suggest that passive evasion could also occur.

Species delimitation with limited sampling: An example from rare trapdoor spider genus Cyclocosmia (Mygalomorphae, Halonoproctidae)

The outcome of species delimitation depends on many factors, including conceptual framework, study design, data availability, methodology employed and subjective decision making. Obtaining sufficient taxon sampling in endangered or rare taxa might be difficult, particularly when non-lethal tissue collection cannot be utilized. The need to avoid overexploitation of the natural populations may thus limit methodological framework available for downstream data analyses and bias the results. We test species boundaries in rare North American trapdoor spider genus Cyclocosmia Ausserer (1871) inhabiting the Southern Coastal Plain biodiversity hotspot with the use of genomic data and two multispecies coalescent model methods. We evaluate the performance of each methodology within a limited sampling framework. To mitigate the risk of species over splitting, common in taxa with highly structured populations, we subsequently implement a species validation step via genealogical diversification index (gdi), which accounts for both genetic isolation and gene flow. We delimited eight geographically restricted lineages within sampled North American Cyclocosmia, suggesting that major river drainages in the region are likely barriers to dispersal. Our results suggest that utilizing BPP in the species discovery step might be a good option for datasets comprising hundreds of loci, but fewer individuals, which may be a common scenario for rare taxa. However, we also show that such results should be validated via gdi, in order to avoid over splitting.

High species diversity of Phintella and Phintella-like spiders (Araneae: Salticidae) in Vietnam revealed by DNA-based species delimitation analyses

Salticidae (jumping spiders) usually exhibit pronounced sexual dimorphism in adult morphology, particularly body coloration and size and shape of the first legs. Consequently, the male and female from the same species might be erroneously assigned to different species or even different genera, which could generate synonymies in classification if only morphological data were used. Phintella is a species-rich genus of Salticidae, which currently exhibits 76 named species. However, the male-female counterpart is unknown for nearly half of the species. In this study, we used a molecular approach to delineate the species boundaries for Phintella and Phintella-like specimens collected in Vietnam, using morphological information as supporting data. We used three gene fragments (mitochondrial COI, 16S-ND1, and nuclear 28S) and biogeographical considerations for species delimitation. A total of 22 putative species were recognized: 18 species of the genus Phintella, one species of the genus Lechia (L. squamata), and three species of the genus Phinteloides. Eleven undescribed species were discovered, of which seven have a male-female combination, two species have only males, and two species have only females. The crown age of Phintella was estimated at the Serravallian stage of the Miocene after the increase of species number around 16 MYA. The crown ages of most putative species recognized in this study were estimated in the Pleistocene, and the divergence among sister species likely occurred from the mid-Miocene to the Pliocene. Our ancestral range reconstruction results showed that the diversification of our ingroup was governed by progressive dispersal events, i.e., Phintella and their related species in Vietnam diversified while expanding their range on the continent. Our results provide fundamental biodiversity data for a high-diversity genus in Vietnamese Phintella spiders.

The Structure of Rice Stemborer Assemblages: A Review of Species' Distributions, Host Ranges, and Interspecific Interactions

This review describes global rice stemborer assemblages based on published species distributions, apparent host preferences, and reported shifts in assemblage composition in response to environmental factors. At least 56 moth (Lepidoptera: Crambidae, Pyralidae, Noctuidae) and fly (Diptera: Diopsidae, Chloropidae) species have been associated with rice; however, only 21 species are of potential, large-scale economic importance with a further 2 species of localized concern; most of the remaining species' associations with rice are based on dubious records without economic impacts on rice production. A list of stemborer-host associations indicates that rice stemborers are largely oligophagous on grasses (Poaceae), but a few species are polyphagous (also attacking Cyperaceae, Typhaceae, and some Eudicotyledon plants). Total stemborer abundance is determined by rice cropping patterns and management. Assemblage species richness is determined by geographical location, surrounding habitat (particularly as regards secondary and occasional species), and season. Evidence suggests that stemborer assemblage structure is largely determined through conditional interspecific competition. Regional assemblages typically include a single dominant lepidopteran species (primary species) that is largely restricted to rice and for which the climate is optimal; one or more secondary species that vary based on the age of rice attacked, rice anatomy, and the proximity to other habitats (including other crops); and occasional species that probably spill over from adjacent grasslands. The co-occurrence of lepidopteran with dipteran rice stemborers requires further research attention.

Integrative species delimitation based on COI, ITS, and morphological evidence illustrates a unique evolutionary history of the genus Paracercion (Odonata: Coenagrionidae)

Paracercion are common ‘blue and black’ colored damselflies. We explore the species boundaries of Paracercion (Odonata: Coenagrionidae) using ABGD, bPTP, GMYC and Distance-based clustering. We finally got the molecular data of all nine species of Paracercion. P. hieroglyphicum and P. melanotum were combined into one putative species based on cytochrome c oxidase I (COI). However, they were separated into two putative species based on the nuclear segment including ITS1-5.8S-ITS2 (ITS). This suggests the introgression of mtDNA in Paracercion. Paracercion barbatum and Paracercion melanotum can be separated into two species based on COI, whereas they were combined into one putative species based on ITS, which suggests a hybridization event between them. The lower interspecific divergence (COI: 0.49%) between P. barbatum and Paracercion v-nigrum indicates a recent speciation event in Paracercion. Paracercion sieboldii and P. v-nigrum can be separated into two putative species based on COI, while they were frequently merged into the same putative species based on ITS. This can be explained by incomplete lineage sorting in nDNA. Besides, P. pendulum and P. malayanum were synonymized as junior synonyms of P. melanotum. P. luzonicum was confirmed not to belong to Paracercion. The possibility of introgression, hybridization, recent speciation and incomplete lineage sorting makes species delimitation, based on molecular data, difficult and complicates understanding of the evolutionary history of Paracercion. The discordance in COI and ITS also indicates the value of using markers from different sources in species delimitation studies.

Draft nuclear genome and complete mitogenome of the Mediterranean corn borer, Sesamia nonagrioides, a major pest of maize

The Mediterranean corn borer (Sesamia nonagrioides, Noctuidae, Lepidoptera) is a major pest of maize in Europe and Africa. Here, we report an assembly of the nuclear and mitochondrial genome of a pool of inbred males and females third-instar larvae, based on short- and long-read sequencing. The complete mitochondrial genome is 15,330 bp and contains all expected 13 and 24 protein-coding and RNA genes, respectively. The nuclear assembly is 1021 Mb, composed of 2553 scaffolds and it has an N50 of 1105 kb. It is more than twice larger than that of all Noctuidae species sequenced to date, mainly due to a higher repeat content. A total of 17,230 protein-coding genes were predicted, including 15,776 with InterPro domains. We provide detailed annotation of genes involved in sex determination (doublesex, insulin-like growth factor 2 mRNA-binding protein, and P-element somatic inhibitor) and of alpha-amylase genes possibly involved in interaction with parasitoid wasps. We found no evidence of recent horizontal transfer of bracovirus genes from parasitoid wasps. These genome assemblies provide a solid molecular basis to study insect genome evolution and to further develop biocontrol strategies against S. nonagrioides.

Population genetics of the Mediterranean corn borer (Sesamia nonagrioides) differs between wild and cultivated plants

The population genetic structure of crop pest populations gives information about their spatial ecology, which helps in designing management strategies. In this paper, we investigated the genetic structure of the Mediterranean Corn Borer (MCB), Sesamia nonagrioides Lefèbvre (Lepidoptera: Noctuidae), one of the most important maize pests in the Mediterranean countries, using microsatellite markers for the first time in this species. Insects were collected in twenty-five locations in southwest and southeast France from cultivated and wild host plants (Zea mays, Sorghum halepense and Typha domingensis). Contrary to what has been reported so far in France, we found that MCB populations could be locally abundant on wild poales plants. Analysis was carried out at 11 polymorphic microsatellite markers. Molecular variance was significantly determined by geography, then by host plant, with 17% and 4%, respectively, when considered as a major effect, and with 14% and 1%, respectively, when considered as a marginal effect in permutational analysis. Multidimensional scaling (MDS) and GENELAND Bayesian clustering suggested that populations infecting wild plants (T. domingensis and S. halepense) were more structured locally than those affecting cultivated maize. In S. halepense, significant Isolation By Distance (IBD) indicated that this factor could explain genetic differentiation of the moth populations. In T. domingensis, local population differentiation was strong but did not depend on distance. The implication of this absence of population structure in maize and the heterogeneity of population genetics patterns in wild plants are discussed in the context of the population dynamics hypothesis and population management strategies.

Towards a global DNA barcode reference library for quarantine identifications of lepidopteran stemborers, with an emphasis on sugarcane pests

Lepidopteran stemborers are among the most damaging agricultural pests worldwide, able to reduce crop yields by up to 40%. Sugarcane is the world’s most prolific crop, and several stemborer species from the families Noctuidae, Tortricidae, Crambidae and Pyralidae attack sugarcane. Australia is currently free of the most damaging stemborers, but biosecurity efforts are hampered by the difficulty in morphologically distinguishing stemborer species. Here we assess the utility of DNA barcoding in identifying stemborer pest species. We review the current state of the COI barcode sequence library for sugarcane stemborers, assembling a dataset of 1297 sequences from 64 species. Sequences were from specimens collected and identified in this study, downloaded from BOLD or requested from other authors. We performed species delimitation analyses to assess species diversity and the effectiveness of barcoding in this group. Seven species exhibited <0.03 K2P interspecific diversity, indicating that diagnostic barcoding will work well in most of the studied taxa. We identified 24 instances of identification errors in the online database, which has hampered unambiguous stemborer identification using barcodes. Instances of very high within-species diversity indicate that nuclear markers (e.g. 18S, 28S) and additional morphological data (genitalia dissection of all lineages) are needed to confirm species boundaries.

Phylogeography and Population Structure of the Mediterranean Corn Borer, Sesamia nonagrioides (Lepidoptera: Noctuidae), Across Its Geographic Range

Sesamia nonagrioides (Lefèbvre) (Lepidoptera: Noctuidae), is a widespread insect pest in Africa, the Middle East, and Europe. However, its pest status varies across its distribution range. It is a major pest of maize in Europe and of sugarcane in Iran. In Africa, it is a major pest of maize in West Africa but not considered as a pest in East Africa. Recent surveys conducted in 2015 recorded S. nonagrioides to be a major pest of sugarcane in Ethiopia and reported the species for the first time in Botswana, outside its known geographic range. The genetic relationship of these records with the previously recorded population of S. nonagrioides was investigated using the cytochrome oxidase subunit I region of the mitochondrial genome. In total, 113 individuals across the geographic range of the species were analyzed and 63 haplotypes were identified. Phylogenetic analysis separated the populations into two clades with no distinct geographic distribution pattern. The genetic differentiation was also not associated with host plants and geographic distances. Results of the molecular analysis revealed the long-time establishment of S. nonagrioides population in Botswana and identified the newly recorded sugarcane population from Ethiopia as part of the wild host population in the country. The phylogeographic patterns observed among population of S. nonagrioides have probably been shaped by Pleistocene's climatic oscillations and geographic range expansions from different refugia with secondary contact and admixture. Possible reasons for the host-plant expansion by the Ethiopian population are discussed.

Opposite macroevolutionary responses to environmental changes in grasses and insects during the Neogene grassland expansion

The rise of Neogene C4 grasslands is one of the most drastic changes recently experienced by the biosphere. A central - and widely debated - hypothesis posits that Neogene grasslands acted as a major adaptive zone for herbivore lineages. We test this hypothesis with a novel model system, the Sesamiina stemborer moths and their associated host-grasses. Using a comparative phylogenetic framework integrating paleoenvironmental proxies we recover a negative correlation between the evolutionary trajectories of insects and plants. Our results show that paleoenvironmental changes generated opposing macroevolutionary dynamics in this insect-plant system and call into question the role of grasslands as a universal adaptive cradle. This study illustrates the importance of implementing environmental proxies in diversification analyses to disentangle the relative impacts of biotic and abiotic drivers of macroevolutionary dynamics.

Systematics and biology of Cotesia typhae sp. n. (Hymenoptera, Braconidae, Microgastrinae), a potential biological control agent against the noctuid Mediterranean corn borer, Sesamia nonagrioides

Many parasitoid species are subjected to strong selective pressures from their host, and their adaptive response may result in the formation of genetically differentiated populations, called host races. When environmental factors and reproduction traits prevent gene flow, host races become distinct species. Such a process has recently been documented within the Cotesiaflavipes species complex, all of which are larval parasitoids of moth species whose larvae are stem borers of Poales. A previous study on the African species C.sesamiae, incorporating molecular, ecological and biological data on various samples, showed that a particular population could be considered as a distinct species, because it was specialized at both host (Sesamianonagrioides) and plant (Typhadomingensis) levels, and reproductively isolated from other C.sesamiae. Due to its potential for the biological control of S.nonagrioides, a serious corn pest in Mediterranean countries and even in Iran, we describe here Cotesiatyphae Fernandez-Triana sp. n. The new species is characterized on the basis of morphological, molecular, ecological and geographical data, which proved to be useful for future collection and rapid identification of the species within the species complex. Fecundity traits and parasitism success on African and European S.nonagrioides populations, estimated by laboratory studies, are also included.

DNA barcoding and traditional taxonomy: an integrated approach for biodiversity conservation

Biological diversity is depleting at an alarming rate. Additionally, a vast amount of biodiversity still remains undiscovered. Taxonomy has been serving the purpose of describing, naming, and classifying species for more than 250 years. DNA taxonomy and barcoding have accelerated the rate of this process, thereby providing a tool for conservation practice. DNA barcoding and traditional taxonomy have their own inherent merits and demerits. The synergistic use of both methods, in the form of integrative taxonomy, has the potential to contribute to biodiversity conservation in a pragmatic timeframe and overcome their individual drawbacks. In this review, we discuss the basics of both these methods of biological identification (traditional taxonomy and DNA barcoding), the technical advances in integrative taxonomy, and future trends. We also present a comprehensive compilation of published examples of integrative taxonomy that refer to nine topics within biodiversity conservation. Morphological and molecular species limits were observed to be congruent in ∼41% of the 58 source studies. The majority of the studies highlighted the description of cryptic diversity through the use of molecular data, whereas research areas like endemism, biological invasion, and threatened species were less discussed in the literature.

Phylogeography of the Wheat Stem Sawfly, Cephus cinctus Norton (Hymenoptera: Cephidae): Implications for Pest Management

The wheat stem sawfly, Cephus cinctus Norton (Hymenoptera: Cephidae), is a key pest of wheat in the northern Great Plains of North America, and damage resulting from this species has recently expanded southward. Current pest management practices are inadequate and uncertainty regarding geographic origin, as well as limited data on population structure and dynamics across North America impede progress towards more informed management. We examined the genetic divergence between samples collected in North America and northeastern Asia, the assumed native range of C. cinctus using two mitochondrial regions (COI and 16S). Subsequently, we characterized the structure of genetic diversity in the main wheat producing areas in North America using a combination of mtDNA marker and microsatellites in samples collected both in wheat fields and in grasses in wildlands. The strong genetic divergence observed between North American samples and Asian congeners, in particular the synonimized C. hyalinatus, did not support the hypothesis of a recent American colonization by C. cinctus. Furthermore, the relatively high genetic diversity both with mtDNA and microsatellite markers offered additional evidence in favor of the native American origin of this pest. The genetic diversity of North American populations is structured into three genetic clusters and these are highly correlated with geography. Regarding the recent southern outbreaks in North America, the results tend to exclude the hypothesis of recent movement of damaging wheat stem sawfly populations from the northern area. The shift in host plant use by local populations appears to be the most likely scenario. Finally, the significance of these findings is discussed in the context of pest management.

Species diversity can be overestimated by a fixed empirical threshold: insights from DNA barcoding of the genus Cletus (Hemiptera: Coreidae) and the meta-analysis of COI data from previous phylogeographical studies

The use of genetic distances to identify species within the framework of DNA barcoding has to some extent improved the development of biodiversity studies. However, using a fixed empirical threshold to delimit species may lead to overestimating species diversity. In this study, we use a new data set of COI sequences for 366 specimens within the genus of Cletus as well as conduct an analysis on the same genetic data for collected morphologically defined species from previous phylogeographical studies, to test whether high intraspecific genetic divergences are common with the premises of comprehensive sampling. The results indicate C. graminis Hsiao & Cheng , is the same species with C. punctiger (Dallas, 1852) and should be synonymized and that the distributional record of C. pugnator (Fabricius, 1787) in China is correct. High intraspecific genetic differentiations (0%-4.35%) were found in C. punctiger. Furthermore, as to the mined data, the maximum intraspecific K2P distances of 186 species (48.44% of 384) exceed 3%, and 101 species (26.30%) can be divided into two or more clusters with a threshold of 3% in cluster analysis. If genetic distance is used to delimit species boundaries, the minimum interspecific K2P distance of the congeneric species should be considered rather than only using the fixed empirical value; otherwise, the species richness may be overestimated in some cases.