Identification of Species by Combining Molecular and Morphological Data Using Convolutional Neural Networks.

Integrative taxonomy is central to modern taxonomy and systematic biology, including behavior, niche preference, distribution, morphological analysis, and DNA barcoding. However, decades of use demonstrate that these methods can face challenges when used in isolation, for instance, potential misidentifications due to phenotypic plasticity for morphological methods, and incorrect identifications because of introgression, incomplete lineage sorting, and horizontal gene transfer for DNA barcoding. Although researchers have advocated the use of integrative taxonomy, few detailed algorithms have been proposed. Here, we develop a convolutional neural network method (morphology-molecule network [MMNet]) that integrates morphological and molecular data for species identification. The newly proposed method (MMNet) worked better than four currently available alternative methods when tested with 10 independent data sets representing varying genetic diversity from different taxa. High accuracies were achieved for all groups, including beetles (98.1% of 123 species), butterflies (98.8% of 24 species), fishes (96.3% of 214 species), and moths (96.4% of 150 total species). Further, MMNet demonstrated a high degree of accuracy ($>$98%) in four data sets including closely related species from the same genus. The average accuracy of two modest subgenomic (single nucleotide polymorphism) data sets, comprising eight putative subspecies respectively, is 90%. Additional tests show that the success rate of species identification under this method most strongly depends on the amount of training data, and is robust to sequence length and image size. Analyses on the contribution of different data types (image vs. gene) indicate that both morphological and genetic data are important to the model, and that genetic data contribute slightly more. The approaches developed here serve as a foundation for the future integration of multimodal information for integrative taxonomy, such as image, audio, video, 3D scanning, and biosensor data, to characterize organisms more comprehensively as a basis for improved investigation, monitoring, and conservation of biodiversity. [Convolutional neural network; deep learning; integrative taxonomy; single nucleotide polymorphism; species identification.].

Characterization and Phylogenetic Analysis of the Complete Mitochondrial Genome of Laelia suffusa (Lepidoptera: Erebidae, Lymantriinae).

In this study, the complete mitochondrial genome of a white tussock moth, Laelia suffusa (Walker, 1855) (Lepidoptera: Erebidae, Lymantriinae), was sequenced and annotated. The genome sequence was 15,502 bp in length and comprised 13 PCGs, 2 rRNAs, 22 tRNAs, and a single noncoding control region (CR). The nucleotide composition of the genome was highly A + T biased, accounting for 79.04% of the whole genome and with a slightly positive AT skewness (0.015). Comparing the gene order with the basal species of Lepidoptera, a typical trnM rearrangement was detected in the mitogenome of L. suffusa. Besides, the trnM rearrangement was found at the head of trnI and trnQ, rather than at the back. The 13 PCGs used ATN as their start codons, except for the cox1 which used CGA. Out of the 22 tRNAs, only 1 tRNA (trnS1) failed to fold in a typical cloverleaf secondary structure. The conserved motif 'ATAGA + poly-T' was detected at the start of the control region which was similar to other Lepidoptera species. In total, 10 overlapping regions and 19 intergenic spacers were identified, ranging from 1 to 41 and 2 to 73 bp, respectively. Phylogenetic analysis showed that Lymantriinae was a monophyletic group with a high support value and L. suffusa was closely related to tribe Orgyiini (Erebidae, Lymantriinae). Moreover, the phylogenetic relationship of Noctuoidea (Lepidoptera) species was reconstructed using two datasets (13 PCGs and 37 genes) and these supported the topology of (Notodontidae + (Erebidae + (Nolidae + (Euteliidae + Noctuidae)))).

Efficient COI barcoding using high throughput single-end 400 bp sequencing.

BACKGROUND: Over the last decade, the rapid development of high-throughput sequencing platforms has accelerated species description and assisted morphological classification through DNA barcoding. However, the current high-throughput DNA barcoding methods cannot obtain full-length barcode sequences due to read length limitations (e.g. a maximum read length of 300 bp for the Illumina's MiSeq system), or are hindered by a relatively high cost or low sequencing output (e.g. a maximum number of eight million reads per cell for the PacBio's SEQUEL II system). RESULTS: Pooled cytochrome c oxidase subunit I (COI) barcodes from individual specimens were sequenced on the MGISEQ-2000 platform using the single-end 400 bp (SE400) module. We present a bioinformatic pipeline, HIFI-SE, that takes reads generated from the 5' and 3' ends of the COI barcode region and assembles them into full-length barcodes. HIFI-SE is written in Python and includes four function modules of filter, assign, assembly and taxonomy. We applied the HIFI-SE to a set of 845 samples (30 marine invertebrates, 815 insects) and delivered a total of 747 fully assembled COI barcodes as well as 70 Wolbachia and fungi symbionts. Compared to their corresponding Sanger sequences (72 sequences available), nearly all samples (71/72) were correctly and accurately assembled, including 46 samples that had a similarity score of 100% and 25 of ca. 99%. CONCLUSIONS: The HIFI-SE pipeline represents an efficient way to produce standard full-length barcodes, while the reasonable cost and high sensitivity of our method can contribute considerably more DNA barcodes under the same budget. Our method thereby advances DNA-based species identification from diverse ecosystems and increases the number of relevant applications.

Regional assemblages shaped by historical and contemporary factors: Evidence from a species-rich insect group.

Understanding diversity patterns requires accounting for the roles of both historical and contemporary factors in the assembly of communities. Here, we compared diversity patterns of two moth assemblages sampled from Taihang and Yanshan mountains in Northern China and performed ancestral range reconstructions using the Multi-State Speciation and Extinction model, to track the origins of these patterns. Further, we estimated diversification rates of the two moth assemblages and explored the effects of contemporary ecological factors. From 7,788 specimens we identified 835 species belonging to 23 families, using both DNA barcode analysis and morphology. Moths in Yanshan mountains showed higher species diversity than in Taihang mountains. Ancestral range analysis indicated Yanshan as the origin, with significant historical dispersals from Yanshan to Taihang. Asymmetrical diversification, population expansion, along with frequent and considerable gene flow were detected between communities. Moreover, dispersal limitation or the joint effect of environment filtering and dispersal limitation were inferred as main driving forces shaping current diversity patterns. In summary, we demonstrate that a multiscale (community, population and species level) analysis incorporating both historical and contemporary factors can be useful in delineating factors contributing to community assembly and patterning in diversity.

Phylogenetic analyses with four new Cretaceous bristletails reveal inter-relationships of Archaeognatha and Gondwana origin of Meinertellidae.

Based on fifteen Archaeognatha (=Microcoryphia) specimens from Myanmar (Burmese) amber, including males, females and immatures, two new genera and four species, Cretaceomachilis longa sp.n., Unimeinertellus abundus gen. et sp.n., U. bellus sp.n. and Nullmeinertellus wenxuani gen. et sp.n., are described. Phylogenetic analyses of taxa in Archaeognatha were conducted using Maximum parsimony and Bayesian inference based on morphological characters and DNA sequence data. Our results confirm the phylogenetic position of the new genera, clarify the monophyly of Meinertellidae and indicate that the 'paleo-types' excluding Ditrigoniophthalmus are nested within the Machilidae group, but suggest that the three subfamilies within Machilidae may be artificial. The diversity of meinertellids with derived characters found from the Cretaceous indicate that the divergence time of Machilidae and Meinertellidae is much earlier than the Cretaceous. We propose the possibility that Meinertellidae might have originated on Gondwana.

Multiplex sequencing of pooled mitochondrial genomes-a crucial step toward biodiversity analysis using mito-metagenomics.

The advent in high-throughput-sequencing (HTS) technologies has revolutionized conventional biodiversity research by enabling parallel capture of DNA sequences possessing species-level diagnosis. However, polymerase chain reaction (PCR)-based implementation is biased by the efficiency of primer binding across lineages of organisms. A PCR-free HTS approach will alleviate this artefact and significantly improve upon the multi-locus method utilizing full mitogenomes. Here we developed a novel multiplex sequencing and assembly pipeline allowing for simultaneous acquisition of full mitogenomes from pooled animals without DNA enrichment or amplification. By concatenating assemblies from three de novo assemblers, we obtained high-quality mitogenomes for all 49 pooled taxa, with 36 species >15 kb and the remaining >10 kb, including 20 complete mitogenomes and nearly all protein coding genes (99.6%). The assembly quality was carefully validated with Sanger sequences, reference genomes and conservativeness of protein coding genes across taxa. The new method was effective even for closely related taxa, e.g. three Drosophila spp., demonstrating its broad utility for biodiversity research and mito-phylogenomics. Finally, the in silico simulation showed that by recruiting multiple mito-loci, taxon detection was improved at a fixed sequencing depth. Combined, these results demonstrate the plausibility of a multi-locus mito-metagenomics approach as the next phase of the current single-locus metabarcoding method.

Mitochondrial phylogenomics and genetic relationships of closely related pine moth (Lasiocampidae: Dendrolimus) species in China, using whole mitochondrial genomes.

BACKGROUND: Pine moths (Lepidoptera; Bombycoidea; Lasiocampidae: Dendrolimus spp.) are among the most serious insect pests of forests, especially in southern China. Although COI barcodes (a standardized portion of the mitochondrial cytochrome c oxidase subunit I gene) can distinguish some members of this genus, the evolutionary relationships of the three morphospecies Dendrolimus punctatus, D. tabulaeformis and D. spectabilis have remained largely unresolved. We sequenced whole mitochondrial genomes of eight specimens, including D. punctatus wenshanensis. This is an unambiguous subspecies of D. punctatus, and was used as a reference for inferring the relationships of the other two morphospecies of the D. punctatus complex. We constructed phylogenetic trees from this data, including twelve published mitochondrial genomes of other Bombycoidea species, and examined the relationships of the Dendrolimus taxa using these trees and the genomic features of the mitochondrial genome. RESULTS: The eight fully sequenced mitochondrial genomes from the three morphospecies displayed similar genome structures as other Bombycoidea species in terms of gene content, base composition, level of overall AT-bias and codon usage. However, the Dendrolimus genomes possess a unique feature in the large ribosomal 16S RNA subunits (rrnL), which are more than 60 bp longer than other members of the superfamily and have a higher AC proportion. The eight mitochondrial genomes of Dendrolimus were highly conservative in many aspects, for example with identical stop codons and overlapping regions. But there were many differences in start codons, intergenic spacers, and numbers of mismatched base pairs of tRNA (transfer RNA genes). Our results, based on phylogenetic trees, genetic distances, species delimitation and genomic features (such as intergenic spacers) of the mitochondrial genome, indicated that D. tabulaeformis is as close to D. punctatus as is D. punctatus wenshanensis, whereas D. spectabilis evolved independently from D. tabulaeformis and D. punctatus. Whole mitochondrial DNA phylogenies showed that D. spectabilis formed a well-supported monophyletic clade, with a clear species boundary separating it from the other congeners examined here. However, D. tabulaeformis often clustered with D. punctatus and with the subspecies D. punctatus wenshanensis. Genetic distance analyses showed that the distance between D. tabulaeformis and D. punctatus is generally less than the intraspecific distance of D. punctatus and its subspecies D. punctatus wenshanensis. In the species delimitation analysis of Poisson Tree Processes (PTP), D. tabulaeformis, D. punctatus and D. punctatus wenshanensis clustered into a putative species separated from D. spectabilis. In comparison with D. spectabilis, D. tabulaeformis and D. punctatus also exhibit a similar structure in intergenic spacer characterization. These different types of evidence suggest that D. tabulaeformis is very close to D. punctatus and its subspecies D. punctatus wenshanensis, and is likely to be another subspecies of D. punctatus. CONCLUSIONS: Whole mitochondrial genomes possess relatively rich genetic information compared with the traditional use of single or multiple genes for phylogenetic purposes. They can be used to better infer phylogenetic relationships and degrees of relatedness of taxonomic groups, at least from the aspect of maternal lineage: caution should be taken due to the maternal-only inheritance of this genome. Our results indicate that D. spectabilis is an independent lineage, while D. tabulaeformis shows an extremely close relationship to D. punctatus.

Predicting habitat suitability for the soybean pod borer Leguminivora glycinivorella (Matsumura) using optimized MaxEnt models with multiple variables.

The soybean pod borer Leguminivora glycinivorella (Matsumura) is one of the most important soybean pests and often causes serious damage to Glycine max (L.) Merr., a leading source of dietary protein and oil in animal feed. However, the potential distribution patterns of this economically important pest and its driving factors require further investigation. Here, we used the optimized MaxEnt model to predict the potential distribution of this pest with multiple variables associated with climate, land use, and host plant, at its recorded range and a globe scale. Based on 4 variable combinations, the results show that the current suitable habitats of L. glycinivorella are primarily distributed in most of China, the Korean Peninsula, and Japan. Whereas no suitable area is present in other continents. In future projections, the suitable region shows a slight northward expansion compared with the result predicted with current climatic conditions, and the suitable areas of almost all future projections were stable in size. Among the 9 bioclimatic factors, BIO03 (isothermality) consistently highly contributes to the predictions, indicating that temperature may be a key factor influencing the habitat distribution of L. glycinivorella. Comparative analyses of projections further show that non-climatic factors are informative in the modeling as routinely used bioclimate variables. The spatio-temporal distribution patterns of suitable habitats and the regulatory factors predicted in this study could provide important guidance for L. glycinivorella management.

Ecological niche shift and suitable area expansion of a globally invasive species Phthorimaea operculella.

Phthorimaea operculella is a major potato pest of global importance, early warning and detection of which are of significance. In this study, we analyzed the climate niche conservation of P. operculella during its invasion by comparing the overall climate niche from three dimensions, including the differences between native range (South America) and entire invaded region (excluding South America), the differences bwtween native range (South America) and five invaded continents (North America, Oceania, Asia, Africa, and Europe), as well as the differences between native region (South America) and an invaded region (China). We constructed ecological niche models for its native range (South America) and invaded region (China). The results showed that the climatic niche of the pest has expanded to varying degrees in different regions, indicating that the pest could well adapt to new environments during the invasion. Almost all areas of South America are suitable for P. operculella. In China, its suitable area is mainly concentrated in Shandong, Hebei, Tianjin, Beijing, Henan, Hubei, Yunnan, Guizhou, Sichuan, Hainan, northern Guangxi, southern Hunan, Anhui, Guangdong, Jiangsu, southern Shanxi, and southern Shaanxi. With increasing greenhouse gas emissions and global temperature, its suitable area will decrease at low latitude and increase gradually at high latitude. Specifically, the northern boundary will extend to Liaoning, Jilin, and the southeastern region of Inner Mongolia, while the western boundary extends to Sichuan and the southeast Qinghai-Tibet Plateau. The suitable area in the southeast Yunnan-Guizhou Plateau, Hainan Island, and the south of Yangtze River, will gradually decrease. The total suitable habitat area for P. operculella in China is projected to increase under future climate condition. From 2081 to 2100, under the three greenhouse gas emissions scenarios of ssp126, ssp370, and ssp585, the suitable area is expected to increase by 27.78, 165.54, and 140.41 hm2, respectively. Therefore, it is crucial to strengtehen vigilance and implement strict measures to prevent the further expansion of P. operculella.

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.

Pre-Columbian origins of Native American dog breeds, with only limited replacement by European dogs, confirmed by mtDNA analysis.

Dogs were present in pre-Columbian America, presumably brought by early human migrants from Asia. Studies of free-ranging village/street dogs have indicated almost total replacement of these original dogs by European dogs, but the extent to which Arctic, North and South American breeds are descendants of the original population remains to be assessed. Using a comprehensive phylogeographic analysis, we traced the origin of the mitochondrial DNA lineages for Inuit, Eskimo and Greenland dogs, Alaskan Malamute, Chihuahua, xoloitzcuintli and perro sín pelo del Peru, by comparing to extensive samples of East Asian (n = 984) and European dogs (n = 639), and previously published pre-Columbian sequences. Evidence for a pre-Columbian origin was found for all these breeds, except Alaskan Malamute for which results were ambigous. No European influence was indicated for the Arctic breeds Inuit, Eskimo and Greenland dog, and North/South American breeds had at most 30% European female lineages, suggesting marginal replacement by European dogs. Genetic continuity through time was shown by the sharing of a unique haplotype between the Mexican breed Chihuahua and ancient Mexican samples. We also analysed free-ranging dogs, confirming limited pre-Columbian ancestry overall, but also identifying pockets of remaining populations with high proportion of indigenous ancestry, and we provide the first DNA-based evidence that the Carolina dog, a free-ranging population in the USA, may have an ancient Asian origin.

'Junk' that matters: the role of transposable elements in bumblebee genome evolution.

Transposable elements (TEs) are mobile DNA sequences that are widely distributed in eukaryotic genomes, where they are known to serve as a major force in genome evolution. The phenotypic impacts of TEs, while less well-studied, have also been discovered. Bumblebees are globally important pollinators in natural ecosystems and agriculture. Although TEs comprise a small fraction of bumblebee genomes, emerging evidence suggests that TEs are the major contributor of genome size variation across species and are involved in the formation of new coding and regulatory sequences. We review recent discoveries related to TEs in bumblebees, as well as outlining three key questions for the future of the field. In the future, we argue long-read sequencing technologies and genome editing techniques will help us identify TEs in bumblebees, unveil mechanisms that could account for their silencing and limited abundance, and uncover their contributions to phenotypic diversification, ecological adaptation, and speciation.

The complete mitochondrial genome of a satin moth: Leucoma chrysoscela (Lepidoptera: Erebidae, Lymantriinae).

We describe the mitogenome sequence of Leucoma chrysoscela (Collenette, 1934) collected in the Longtan National Forest Park, which is located in the southeast of China. The assembled mitogenome is 15,508 bp in length and consists 13 protein coding genes, 22 transfer-RNA genes, 2 ribosomal-RNA genes, and one A + T rich region. The most common start codon for 13 PCGs is ATT and the most common termination codon is TAA. The overall G + C content was only 20.45% in the heavy strand. The result of phylogenetic analysis shows that the relationship of L. chrysoscela is close to the species in the same subfamily Lymantriinae.

Robust Impact Effect and Super-Lyophobic Reduced Galinstan on Polymers Applied for Energy Harvester.

In this paper, we present a novel reduced Galinstan-based microfluidic energy harvester, which can converse kinetic energy to electricity from an arbitrary vibration source. Firstly, the wetting behaviors of reduced Galinstan are performed, which shows a robust impact effect on polymer substrates. Moreover, the electric circuit model of the reduced Galinstan-based energy harvester is made and discussed by the use of the EDLCs (electrical double layer capacitors). After modeling, the microfluidic energy harvester with coplanar microfluidic channels is designed and fabricated. Finally, the performance of the microfluidic energy harvester is investigated, which can harvest multi-direction vibration energy. The experiment results demonstrate that the novel reduced Galinstan-based microfluidic energy harvester is suitably and uniquely applied in a complex vibration environment.

An intercontinental comparison of insect seed predation between introduced and native oaks.

Novel interactions between introduced oaks and their natural enemies across different continents provide an opportunity to test the enemy release hypothesis (ERH) at local and global scales. Based on the ERH, we assessed the impacts of native seed-feeding insects on introduced and native oaks within and among continents. We combined a common-garden experiment in China and biogeographic literature surveys to measure seed predation by insects and the proportion of acorn embryos surviving after insect infestation among 4 oak species with different geographical origins: Quercus mongolica origin from China, Q. robur and Q. petraea from Europe, and Q. rubra from North America. Mostly supporting the ERH, oaks in introduced continents escaped seed predation compared to those in native continents and compared to other native oaks in introduced continents. Common-garden comparisons showed that total acorn infestation rate of introduced Q. rubra (section Lobatae) was considerably lower than that of native oaks (section Quercus) in China and Europe, likely because of the differences in seed traits associated with different oak sections. Literature surveys showed that seed predation of introduced oaks was lower in the introduced continent than in the native continent. Embryo survival was higher in introduced Q. rubra than native oaks in China and Poland. However, insect seed predation of recently introduced Q. rubra in China was similar to that in Europe, which is not consistent with the ERH. Our results suggest that reduced acorn attack by native insects and higher embryo survival after acorn damage could increase the establishment success or invasion risk of introduced oaks in non-native continents.

Insights into the structure and composition of mineralized hard cocoons constructed by the oriental moth, Monema (Cnidocampa) flavescens Walker.

Animals widely use minerals and organic components to construct biomaterials with excellent properties, such as teeth, bones, molluscan shells and eggshells. The larvae of the oriental moth, Monema (Cnidocampa) flavescens Walker, secrete silk proteins that combine closely with calcareous minerals to construct a hard cocoon, which is completely different from the mineral-free Bombyx mori cocoon. The cocoons of oriental moths are likely to be the hardest among the cocoons constructed by insect species. The cocoons of oriental moths were found to be mainly composed of calcium oxalates and Asx/Ser/Gly-rich cocoon proteins, but the types of calcium oxalates and cocoon proteins remain to be elucidated. In this study, we provide an in-depth explanation of the inorganic and organic components in the oriental moth cocoon. Microscopy and imaging technologies revealed that the cocoon is composed of mineral crystals, silk fibers and other organic matter. X-ray diffraction and infrared spectral analyses showed that the mineral crystals in the oriental moth cocoon were mainly CaC2H2O4·H2O. ICP-OES analysis suggested that the mineral crystals in the cocoons were mainly CaC2H2O4·H2O. LC-MS/MS-based proteomics allowed us to identify 467 proteins from the oriental moth cocoon, including 252 uncharacterized proteins, 87 enzymes, 36 small molecule binding proteins, and 5 silk proteins. Among the uncharacterized proteins, 25 of which were Asn-rich proteins because they contained a high proportion of Asn residues (19.1%-41.4%). Among the top 20 cocoon proteins with the highest abundance, 9 of which were Asn-rich proteins. The qPCR was used to investigate the expression patterns of the major cocoon protein-coding genes. Three fibroins and three Asn-rich proteins were expressed only in the silk gland but not in other tissues. The expression of Asn-rich proteins in the silk gland gradually increased from the anterior silk gland to the posterior silk gland. These findings provide important references for understanding the formation mechanism and mechanical properties of mineralized hard cocoons constructed by oriental moths.

Potential efficacy of mitochondrial genes for animal DNA barcoding: a case study using eutherian mammals.

BACKGROUND: A well-informed choice of genetic locus is central to the efficacy of DNA barcoding. Current DNA barcoding in animals involves the use of the 5' half of the mitochondrial cytochrome oxidase 1 gene (CO1) to diagnose and delimit species. However, there is no compelling a priori reason for the exclusive focus on this region, and it has been shown that it performs poorly for certain animal groups. To explore alternative mitochondrial barcoding regions, we compared the efficacy of the universal CO1 barcoding region with the other mitochondrial protein-coding genes in eutherian mammals. Four criteria were used for this comparison: the number of recovered species, sequence variability within and between species, resolution to taxonomic levels above that of species, and the degree of mutational saturation. RESULTS: Based on 1,179 mitochondrial genomes of eutherians, we found that the universal CO1 barcoding region is a good representative of mitochondrial genes as a whole because the high species-recovery rate (> 90%) was similar to that of other mitochondrial genes, and there were no significant differences in intra- or interspecific variability among genes. However, an overlap between intra- and interspecific variability was still problematic for all mitochondrial genes. Our results also demonstrated that any choice of mitochondrial gene for DNA barcoding failed to offer significant resolution at higher taxonomic levels. CONCLUSIONS: We suggest that the CO1 barcoding region, the universal DNA barcode, is preferred among the mitochondrial protein-coding genes as a molecular diagnostic at least for eutherian species identification. Nevertheless, DNA barcoding with this marker may still be problematic for certain eutherian taxa and our approach can be used to test potential barcoding loci for such groups.

The First Mitogenomes of the Subfamily Odontiinae (Lepidoptera, Crambidae) and Phylogenetic Analysis of Pyraloidea.

The complete mitochondrial genomes of three species of Odontiinae were newly sequenced: Dausara latiterminalis Yoshiyasu, Heortia vitessoides (Moore), and Pseudonoorda nigropunctalis (Hampson). These circular and double-stranded mitogenomes vary from 15,084 bp to 15,237 bp in size, including 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), and 22 transfer RNA genes (tRNAs) and an A + T-rich region. The nucleotide composition indicated a strong A/T bias. Most PCGs are initiated with an ATN codon and terminated by a codon of TAR. All tRNAs could be folded into the clover-leaf structure with the exception of trnS1 (AGN), in which the dihydrouridine (DHU) arm formed a simple loop, and the motif 'ATAG' and 'ATTTA' in the A + T-rich region was also founded. The phylogenomic analyses covering Odontiinae + 11 subfamilies of Pyraloidea were conducted. Similar topologies were generated from both Bayesian inference (BI) and maximum likelihood (ML) analyses based on the nucleotide and amino acid sequence data. There was some discrepancy in the sister-group relationship of Odontiinae and Glaphyriinae, and the relationships among the subfamilies in the 'CAMMSS clade' of the Crambidae. The results of this study suggest that mitogenomic data are useful for resolving the deep-level relationships of Pyraloidea and the topologies generated from amino acid data might be more realistic and reliable. Moreover, more mitogenomic taxon sampling and larger scale analyses with more genes or a combination of mitogenomic and nuclear genes are needed to reconstruct a comprehensive framework of the pyraloid phylogeny.

High-Efficiency Large-Area Printed Multilayer Liquid Metal Wires for Stretchable Biomedical Sensors with Recyclability.

Stretchable conductors are essential for soft robots, wearable on-skin electronic technologies, and bioelectronics. The utilization of sophisticated stretchable conductors requires a new, simple, rapid, and large-scale printing process whose features include high stretchability, high precision, multilayers, and recyclability simultaneously for commercial wearable electronics. To address this need, an LM (liquid metal) wire was developed using a simple, rapid, and large-scale soft stamper-based printing process and employed to realize LM wire-based conductors and capacitors, which simultaneously offer high stretchability (>380%), high precision past 50 µm, and electromechanical response stability after stretching for up to an hour. Based on the excellent electromechanical responses, the LM wire-based capacitors, as strain sensors, attached to finger joints resulted in precise gesture detection. Meanwhile, a simple transparent wearable e-skin consisting of a 6 × 6 LM wire-based capacitor array without rigid parts successfully monitored a multi-point touch. At last, a portable noninvasive stretchable multilayer LM wire-based pulse sensor with recyclability is fabricated to monitor the patient's heartbeats. The experimental results reveal that the stretchable biomedical sensors have the potential to help patients to improve their life in healthcare, including replacement prosthetic devices, daily and sports activity tracking, continuous health monitoring, and others.

Plant-herbivorous insect networks: who is eating what revealed by long barcodes using high-throughput sequencing and Trinity assembly.

Interactions between plants and insects are among the most important life functions for all organism at a particular natural community. Usually a large number of samples are required to identify insect diets in food web studies. Previously, Sanger sequencing and next generation sequencing (NGS) with short DNA barcodes were used, resulting in low species-level identification; meanwhile the costs of Sanger sequencing are expensive for metabarcoding together with more samples. Here, we present a fast and effective sequencing strategy to identify larvae of Lepidoptera and their diets at the same time without increasing the cost on Illumina platform in a single HiSeq run, with long-multiplex-metabarcoding (COI for insects, rbcL, matK, ITS and trnL for plants) obtained by Trinity assembly (SHMMT). Meanwhile, Sanger sequencing (for single individuals) and NGS (for polyphagous) were used to verify the reliability of the SHMMT approach. Furthermore, we show that SHMMT approach is fast and reliable, with most high-quality sequences of five DNA barcodes of 63 larvae individuals (54 species) recovered (full length of 100% of the COI gene and 98.3% of plant DNA barcodes) using Trinity assembly (up-sized to 1015 bp). For larvae diets identification, 95% are reliable; the other 5% failed because their guts were empty. The diets identified by SHMMT approach are 100% consistent with the host plants that the larvae were feeding on during our collection. Our study demonstrates that SHMMT approach is reliable and cost-effective for insect-plants network studies. This will facilitate insect-host plant studies that generally contain a huge number of samples.