Singing from the grave: DNA from a 180 year old type specimen confirms the identity of Chrysoperla carnea (Stephens)

Phenotypic plasticity of a winter-diapause mechanism copes with the effects of summer global warming in an ectothermic predator

To adapt to changes in temperature, animals tend to invest more energy in thermal tolerance to enhance survival, which can have simultaneous costs on plastic traits. Would a decrease in genetic variability, due to global warming, affect the ability of populations with existing metabolic regulatory mechanisms to cope with extreme temperatures? To address this question, we conducted a series of experiments based on the A1B scenario of global warming, assessing within-population genetic variance in (a) morphological traits, (b) metabolic rate allometries, and (c) survival of a winter-diapausing predator ectotherm. Our study focused on the lacewing species Chrysoperla pallida, using both exogamic and endogamic artificial genetic lines. We discovered that both lines use their winter-diapausing phenotype to adapt to summer extreme temperatures caused by extreme heating conditions, but the exogamic line is prone to express phenotypic plasticity in metabolic scaling, with a trade-off between body size and mandible size, i.e. larger individuals tended to develop smaller mandibles to better survive. These findings highlight the significance of substantial phenotypic plasticity and pre-existing metabolic regulatory mechanisms in enabling ectotherms to cope with potential extreme heating occurring in global warming.

DNA Barcoding of Portuguese Lacewings (Neuroptera) and Snakeflies (Raphidioptera) (Insecta, Neuropterida)

The orders Neuroptera and Raphidioptera include the species of insects known as lacewings and snakeflies, respectively. In Portugal, these groups account for over 100 species, some of which are very difficult to identify by morphological analysis. This work is the first to sample and DNA sequence lacewings and snakeflies of Portugal. A reference collection was built with captured specimens that were identified morphologically. DNA barcode sequences of 658 bp were obtained from 243 specimens of 54 species. The results showed that most species can be successfully identified through DNA barcoding, with the exception of seven species of Chrysopidae (Neuroptera). Additionally, the first published distribution data are presented for Portugal for the neuropterans Gymnocnemiavariegata (Schneider, 1845) and Myrmecaelurus (Myrmecaelurus) trigrammus (Pallas, 1771).

New Light on Historical Specimens Reveals a New Species of Ladybird (Coleoptera: Coccinellidae): Morphological, Museomic, and Phylogenetic Analyses

Natural history collections house an important source of genetic data from yet unexplored biological diversity. Molecular data from museum specimens remain underexploited, which is mainly due to the degradation of DNA from specimens over time. However, Next-Generation Sequencing (NGS) technology can now be used to sequence "old" specimens. Indeed, many of these specimens are unique samples of nomenclatural types and can be crucial for resolving systematic or biogeographic scientific questions. Two ladybird beetle specimens from Patagonia corresponding to a new species of the genus Eriopis Mulsant were found in the collections of the Muséum national d'Histoire naturelle (MNHN), Paris. Here, we describe Eriopis patagonia Salazar, sp. nov. Total DNA of one of the two specimens was sequenced by NGS using a paired-end Illumina approach. We reconstruct and characterize the mitochondrial genome of this species (16,194 bp). Then, the protein-coding genes (PCGs) and ribosomal RNAs (rRNAs) were used to infer by maximum likelihood and Bayesian Inference the phylogenetic position of E. patagonia among 27 representatives of Coccinellidae. Phylogenetic analysis confirmed the position of Eriopis as sister group to Cycloneda Crotch. Hence, we highlight the high potential of sequencing technology for extracting molecular information from old specimens, which are used here for the systematic study of a genus, while demonstrating the importance of preserving biological collections.

Standardisation of bioacoustic terminology for insects

After reviewing the published literature on sound production in insects, a standardised terminology and controlled vocabularies have been created. This combined terminology has potential for use in automated identification systems, evolutionary studies, and other use cases where the synthesis of bioacoustic traits from the literature is required. An example implementation has been developed for the BioAcoustica platform. It is hoped that future development of controlled vocabularies will become a community effort.

Evaluation of DNA degradation and establishment of a degradation analysis model for Lepidoptera specimens

Millions of museum specimens are integral to biodiversity studies; however, DNA degradation may limit the ability to obtain DNA sequences. In this study, a degradation analysis model for Lepidoptera specimens was established. Based on this model, we revealed the characteristics of DNA fragment distribution caused by external DNA damage factors during specimen preservation. We found that the degree of DNA degradation increased over time; DNA degradation of spread and dried adult specimens was significantly higher than that in the folded and formalin-fixed larval specimens. However, the effects of folding wings on DNA degradation and the effects of the preservation method/stage (formalin-fixed larval vs air-dried adult specimens) were different for different species.

The Natural History Museum Data Portal

The Natural History Museum, London (NHM), generates and holds some of the largest global data sets relating to the biological and geological diversity of the natural world. A majority of these data were, until 2015, not widely accessible, and, even when published, were typically hard to find, poorly documented and in formats that impede discovery and integration. To better serve the bespoke needs of user communities outside and within the NHM, a dedicated data portal was developed to surface these data sets and provide a sustainable platform to encourage their citation and reuse. This paper describes the technical development of the data portal, from its inception to beta launch in December 2015, its first 2 years of operation, and future plans for the project. It outlines the development principles adopted for this prototypical project, which subsequently informed new digital project management methodologies at the NHM. The process of developing the data portal acted as a driver to implement policies necessary to encourage a culture of data sharing at the NHM.

Molecular characterization of Chrysoperla carnea (Neuroptera: Chrysopidae) from commercial insectaries in Mexico

The larvae of the Chrysoperla carnea-group (Neuroptera: Chrysopidae) are recognized among the most effective larval predators of various phytophagous arthropods. Therefore, green lacewings are commonly grown by commercial insectaries and released as biological control agents. Previous work has shown that commercial laboratories frequently supply indeterminate species of the large C. carnea cryptic species complex. In Mexico, at least 20 biological control companies have commercialized the species C. carnea, but none of the products reared by those companies have been analyzed scientifically. Thus, the goal of this work was to molecularly characterize nine C. carnea populations from Mexican insectaries using the most efficient molecular markers available: the mitochondrial genes COI, COII, ND2, and ND5. Phylogenetic analysis demonstrated a unique mitochondrial haplotype in seven commercial insectaries showing 100% similarity to the reference specimen C. plorabunda E100. In contrast, we observed two and four different mitochondrial haplotypes of the carnea-group in two commercial insectaries. More precisely, three specimens possessed the mitochondrial haplotype of the species C. zastrowi, suggesting possible natural occurrence of this haplotype in Mexico. Consequently, this study demonstrated the need for an extensive survey of the different laboratories and insectaries producing C. carnea in Mexico, including unambiguous species identification by song recordings to confirm the species identity of the observed mitochondrial haplotypes.

Mitochondrial Gene Sequence (COI) Reveals the Genetic Structure and Demographic History of Lymantria dispar (Lepidoptera: Erebidae: Lymantriinae) in and around China

The gypsy moth, Lymantria dispar, is among the most destructive quarantine pests of forests. Here, we reconstructed the genetic structure and determined the population differentiation of gypsy moths across its distribution range at different times. This information could be used to both improve the prevention and detection of gypsy moths in the field. Using 31 newly designed species-specific primers targeting fragments of 216-1102 bp, we identified 103 full-length cytochrome oxidase subunit I (COI) gene sequences from eight fresh samples and 95 L. dispar specimens collected between 1955 and 1996, mainly in China. Combining 103 full-length COI gene sequences with 146 COI gene sequences from Genbank or DNA barcode libraries, we analyzed the genetic differentiation, gene flow and haplotypes between gypsy moth populations in order to reflect the genetic structure and population dynamics of gypsy moths. We discovered 25 previously unknown haplotypes from old gypsy moth specimens. We found that the genetic diversity among gypsy moth populations (collected in the same region at different time points) was relatively high. Furthermore, the genetic structure of Chinese geographical populations (Heilongjiang, Liaoning, Beijing) in different years was distinct. Our results suggested that some gypsy moths in China showed the genetic affinity with European gypsy moths (a sub-species of gypsy moths found mainly in Europe).

Abundance and Population Decline Factors of Chrysopid Juveniles in Olive Groves and Adjacent Trees

Numerous species of the family Chrysopidae, commonly found in agroecosystems, whose larvae predate on several pests of economic importance, are regarded as biological control agents. Their abundance and diversity are influenced by vegetation cover, although little is known about the effects of semi-natural habitats on their populations. The objective of this study is to gain a better understanding of the relationship between the trees in semi-natural habitats adjacent to olive groves, juvenile stages of the family Chrysopidae and factors influencing their population decline, which is crucial for an effective habitat management program aimed at conserving these important predators. Using cardboard band traps (eight per tree), the juvenile stages were collected from 25 almond, oak, olive and pine trees over a one-year sampling period. The population decline was caused by parasitoids (26.5%), predators (5.1%) and unknown factors (13.2%). In addition, chrysopids established in olive trees showed the lowest rate of parasitism. We identified ten chrysopid species that emerged from the juveniles collected from almond, oak, olive and pine trees, with a predominance of Pseudomallada prasinus. The chrysopid–parasitoid complex was composed of five species; Baryscapus impeditus (Eulophidae), which was the most abundant, was preferentially associated with Chrysopa pallens, Chrysoperla lucasina and Chrysoperla mediterranea.

Natural enemies of armored scales (Hemiptera: Diaspididae) and soft scales (Hemiptera: Coccidae) in Chile: Molecular and morphological identification

Scale insects (Hemiptera: Sternorrhyncha: Coccomorpha) are key pests of agricultural crops and ornamental plants worldwide. Their populations are difficult to control, even with insecticides, due to their cryptic habits. Moreover, there is growing concern over the use of synthetic pesticides for their control, due to deleterious environmental effects and the emergence of resistant populations of target pests. In this context, biological control may be an effective and sustainable approach. Hymenoptera Chalcidoidea includes natural enemies of scale insects that have been successfully used in many biological control programs. However, the correct identification of pest scale species and their natural enemies is particularly challenging because these insects are very small and highly specialized. Integrative taxonomy, coupling DNA barcoding and morphological analysis, has been successfully used to characterize pests and natural enemy species. In this study, we performed a survey of parasitoids and predators of armored and soft scales in Chile, based on 28S and COI barcodes. Fifty-three populations of Diaspididae and 79 populations of Coccidae were sampled over the entire length of the country, from Arica (18°S) to Frutillar (41°S), between January 2015 and February 2016. The phylogenetic relationships obtained by Bayesian inference from multilocus haplotypes revealed 41 putative species of Chalcidoidea, five Coccinellidae and three Neuroptera. Species delimitation was confirmed using ABGD, GMYC and PTP model. In Chalcidoidea, 23 species were identified morphologically, resulting in new COI barcodes for 12 species and new 28S barcodes for 14 species. Two predator species (Rhyzobius lophantae and Coccidophilus transandinus) were identified morphologically, and two parasitoid species, Chartocerus niger and Signiphora bifasciata, were recorded for the first time in Chile.

DNA barcoding a unique avifauna: an important tool for evolution, systematics and conservation

BACKGROUND

DNA barcoding utilises a standardised region of the cytochrome c oxidase I (COI) gene to identify specimens to the species level. It has proven to be an effective tool for identification of avian samples. The unique island avifauna of New Zealand is taxonomically and evolutionarily distinct. We analysed COI sequence data in order to determine if DNA barcoding could accurately identify New Zealand birds.

RESULTS

We sequenced 928 specimens from 180 species. Additional Genbank sequences expanded the dataset to 1416 sequences from 211 of the estimated 236 New Zealand species. Furthermore, to improve the assessment of genetic variation in non-endemic species, and to assess the overall accuracy of our approach, sequences from 404 specimens collected outside of New Zealand were also included in our analyses. Of the 191 species represented by multiple sequences, 88.5% could be successfully identified by their DNA barcodes. This is likely a conservative estimate of the power of DNA barcoding in New Zealand, given our extensive geographic sampling. The majority of the 13 groups that could not be distinguished contain recently diverged taxa, indicating incomplete lineage sorting and in some cases hybridisation. In contrast, 16 species showed evidence of distinct intra-species lineages, some of these corresponding to recognised subspecies. For species identification purposes a character-based method was more successful than distance and phylogenetic tree-based methods.

CONCLUSIONS

DNA barcodes accurately identify most New Zealand bird species. However, low levels of COI sequence divergence in some recently diverged taxa limit the identification power of DNA barcoding. A small number of currently recognised species would benefit from further systematic investigations. The reference database and analysis presented will provide valuable insights into the evolution, systematics and conservation of New Zealand birds.

A DNA barcode reference library of Neuroptera (Insecta, Neuropterida) from Beijing

Neuroptera (lacewings) is one of the ancient holometabolous insect groups, but some extant species stand as important natural enemies for biological control. As the capital city of China, Beijing has a rich fauna of Neuroptera, previously with 47 species recorded and sorted in 32 genera of seven families. In this study, DNA barcoding based on sequences of COI gene fragments is used to discriminate lacewing species from Beijing. 217 DNA barcode sequences belonging to 49 species were successfully obtained. The COI barcode data worked well for identification of almost all lacewing species herein examined except Pseudomalladaprasinus (Burmeister), in which cryptic species may exist. Twenty species of Neuroptera are newly recorded from Beijing. Besides, Nothochrysinae is first recorded from Beijing. Chrysopidiaciliata (Wesmael) and Drepanepteryxalgida (Erichson) are first recorded from China.

Transfer of Cry1Ac and Cry2Ab proteins from genetically engineered Bt cotton to herbivores and predators

With the cultivation of Bt cotton, the produced insecticidal Cry proteins are ingested by herbivores and potentially transferred along the food chain to natural enemies, such as predators. In laboratory experiments with Bollgard II cotton, concentrations of Cry1Ac and Cry2Ab were measured in Lepidoptera larvae (Spodoptera littoralis, Heliothis virescens), plant bugs (Euschistus heros), aphids (Aphis gossypii), whiteflies (Bemisia tabaci), thrips (Thrips tabaci, Frankliniella occidentalis), and spider mites (Tetranychus urticae). Tritrophic experiments were conducted with caterpillars of S. littoralis as prey and larvae of ladybird beetles (Harmonia axyridis, Adalia bipunctata) and lacewings (Chrysoperla carnea) as predators. Immunological measurements (ELISA) indicated that herbivores feeding on Bt cotton contained 5%-50% of the Bt protein concentrations in leaves except whiteflies and aphids, which contained no or only traces of Bt protein, and spider mites, which contained 7 times more Cry1Ac than leaves. Similarly, predators contained 1%-30% of the Cry protein concentration in prey. For the nontarget risk assessment, this indicates that Bt protein concentrations decrease considerably from one trophic level to the next in the food web, except for spider mites that contain Bt protein concentrations higher than those measured in the leaves. Exposure of phloem sucking hemipterans is negligible.

Museums are biobanks: unlocking the genetic potential of the three billion specimens in the world's biological collections

Museums and herbaria represent vast repositories of biological material. Until recently, working with these collections has been difficult, due to the poor condition of historical DNA. However, recent advances in next-generation sequencing technology, and subsequent development of techniques for preparing and sequencing historical DNA, have recently made working with collection specimens an attractive option. Here we describe the unique technical challenges of working with collection specimens, and innovative molecular methods developed to tackle them. We also highlight possible applications of collection specimens, for taxonomy, ecology and evolution. The application of next-generation sequencing methods to museum and herbaria collections is still in its infancy. However, by giving researchers access to billions of specimens across time and space, it holds considerable promise for generating future discoveries across many fields.

Successful Recovery of Nuclear Protein-Coding Genes from Small Insects in Museums Using Illumina Sequencing

In this paper we explore high-throughput Illumina sequencing of nuclear protein-coding, ribosomal, and mitochondrial genes in small, dried insects stored in natural history collections. We sequenced one tenebrionid beetle and 12 carabid beetles ranging in size from 3.7 to 9.7 mm in length that have been stored in various museums for 4 to 84 years. Although we chose a number of old, small specimens for which we expected low sequence recovery, we successfully recovered at least some low-copy nuclear protein-coding genes from all specimens. For example, in one 56-year-old beetle, 4.4 mm in length, our de novo assembly recovered about 63% of approximately 41,900 nucleotides in a target suite of 67 nuclear protein-coding gene fragments, and 70% using a reference-based assembly. Even in the least successfully sequenced carabid specimen, reference-based assembly yielded fragments that were at least 50% of the target length for 34 of 67 nuclear protein-coding gene fragments. Exploration of alternative references for reference-based assembly revealed few signs of bias created by the reference. For all specimens we recovered almost complete copies of ribosomal and mitochondrial genes. We verified the general accuracy of the sequences through comparisons with sequences obtained from PCR and Sanger sequencing, including of conspecific, fresh specimens, and through phylogenetic analysis that tested the placement of sequences in predicted regions. A few possible inaccuracies in the sequences were detected, but these rarely affected the phylogenetic placement of the samples. Although our sample sizes are low, an exploratory regression study suggests that the dominant factor in predicting success at recovering nuclear protein-coding genes is a high number of Illumina reads, with success at PCR of COI and killing by immersion in ethanol being secondary factors; in analyses of only high-read samples, the primary significant explanatory variable was body length, with small beetles being more successfully sequenced.