Recent discoveries of armyworms in Japan and their species identification using DNA barcoding

Elongating, entwining, and dragging: mechanism for adaptive locomotion of tubificine worm blobs in a confined environment

Worms often aggregate through physical connections and exhibit remarkable functions such as efficient migration, survival under environmental changes, and defense against predators. In particular, entangled blobs demonstrate versatile behaviors for their survival; they form spherical blobs and migrate collectively by flexibly changing their shape in response to the environment. In contrast to previous studies on the collective behavior of worm blobs that focused on locomotion in a flat environment, we investigated the mechanisms underlying their adaptive motion in confined environments, focusing on tubificine worm collectives. We first performed several behavioral experiments to observe the aggregation process, collective response to aversive stimuli, the motion of a few worms, and blob motion in confined spaces with and without pegs. We found the blob deformed and passed through a narrow passage using environmental heterogeneities. Based on these behavioral findings, we constructed a simple two-dimensional agent-based model wherein the flexible body of a worm was described as a cross-shaped agent that could deform, rotate, and translate. The simulations demonstrated that the behavioral findings were well-reproduced. Our findings aid in understanding how physical interactions contribute to generating adaptive collective behaviors in real-world environments as well as in designing novel swarm robotic systems consisting of soft agents.

Identification of fish species through tRNA-based primer design

BACKGROUND

The correct establishment of the barcode classification system for fish can facilitate biotaxonomists to distinguish fish species, and it can help the government to verify the authenticity of the ingredients of fish products or identify unknown fish related samples. The Cytochrome c oxidation I (COI) gene sequence in the mitochondria of each species possesses unique characteristics, which has been widely used as barcodes in identifying species in recent years. Instead of using COI gene sequences for primer design, flanking tRNA segments of COI genes from 2618 complete fish mitochondrial genomes were analyzed to discover suitable primers for fish classification at taxonomic family level. The minimal number of primer sets is designed to effectively distinguish various clustered groups of fish species for identification applications. Sequence alignment analysis and cross tRNA segment comparisons were applied to check and ensure the primers for each cluster group are exclusive.

RESULTS

Two approaches were applied to improve primer design and re-cluster fish species. The results have shown that exclusive primers for 2618 fish species were successfully discovered through in silico analysis. In addition, we applied sequence alignment analysis to confirm that each pair of primers can successfully identify all collected fish species at the taxonomic family levels.

CONCLUSIONS

This study provided a practical strategy to discover unique primers for each fishery species and a comprehensive list of exclusive primers for extracting COI barcode sequences of all known fishery species. Various applications of verification of fish products or identification of unknown fish species could be effectively achieved.

Paternal genome elimination promotes altruism in viscous populations

Population viscosity has long been thought to promote the evolution of altruism. However, in the simplest scenarios, the potential for altruism is invariant with respect to dispersal-a surprising result that holds for haploidy, diploidy, and haplodiploidy (arrhenotoky). Here, we develop a kin-selection model to investigate how population viscosity affects the potential for altruism in species with male paternal genome elimination (PGE), exploring altruism enacted by both females and males, and both juveniles and adults. We find that (1) PGE promotes altruistic behaviors relative to the other inheritance systems, and to a degree that depends on the extent of paternal genome expression. (2) Under PGE, dispersal increases the potential for altruism in juveniles and decreases it in adults. (3) The genetics of PGE can lead to striking differences in sex-specific potentials for altruism, even in the absence of any sex differences in ecology.

Multilocus DNA barcoding - Species Identification with Multilocus Data

Species identification using DNA sequences, known as DNA barcoding has been widely used in many applied fields. Current barcoding methods are usually based on a single mitochondrial locus, such as cytochrome c oxidase subunit I (COI). This type of barcoding method does not always work when applied to species separated by short divergence times or that contain introgressed genes from closely related species. Herein we introduce a more effective multi-locus barcoding framework that is based on gene capture and "next-generation" sequencing. We selected 500 independent nuclear markers for ray-finned fishes and designed a three-step pipeline for multilocus DNA barcoding. We applied our method on two exemplar datasets each containing a pair of sister fish species: Siniperca chuatsi vs. Sini. kneri and Sicydium altum vs. Sicy. adelum, where the COI barcoding approach failed. Both of our empirical and simulated results demonstrated that under limited gene flow and enough separation time, we could correctly identify species using multilocus barcoding method. We anticipate that, as the cost of DNA sequencing continues to fall that our multilocus barcoding approach will eclipse existing single-locus DNA barcoding methods as a means to better understand the diversity of the living world.

Molecular identification of dipteran pests (Diptera: Sciaroidea) from shiitake mushroom

On shiitake farms, mycophagous maggots can cause serious damage by preventing formation of the fruiting body. Recently, these pests have significantly reduced shiitake production in Korea. However, larvae and female adults cannot be identified due to their lack of morphological characteristics. Therefore, farmers and applied entomologists are unable to determine which species is the primary cause of the shiitake damage. In this study, mycophagous flies (colonized larvae) were collected from damaged shiitake farms and subsequently identified by matching identified males with the cytochrome c oxidase subunit I (COI) sequences from the larvae. Divergences of the COI sequences among the species discriminated the clusters clearly, and the mycophagous pests were identified as Camptomyia corticalis and C. heterobia. Interestingly, these two species coexisted under the bark of shiitake oak bed logs.

Molecular phylogeny of black fungus gnats (Diptera: Sciaroidea: Sciaridae) and the evolution of larval habitats

The phylogeny of the family Sciaridae is reconstructed, based on maximum likelihood, maximum parsimony, and Bayesian analyses of 4809bp from two mitochondrial (COI and 16S) and two nuclear (18S and 28S) genes for 100 taxa including the outgroup taxa. According to the present phylogenetic analyses, Sciaridae comprise three subfamilies and two genus groups: Sciarinae, Chaetosciara group, Cratyninae, and Pseudolycoriella group+Megalosphyinae. Our molecular results are largely congruent with one of the former hypotheses based on morphological data with respect to the monophyly of genera and subfamilies (Sciarinae, Megalosphyinae, and part of postulated "new subfamily"); however, the subfamily Cratyninae is shown to be polyphyletic, and the genera Bradysia, Corynoptera, Leptosciarella, Lycoriella, and Phytosciara are also recognized as non-monophyletic groups. While the ancestral larval habitat state of the family Sciaridae, based on Bayesian inference, is dead plant material (plant litter+rotten wood), the common ancestors of Phytosciara and Bradysia are inferred to living plants habitat. Therefore, shifts in larval habitats from dead plant material to living plants may have occurred within the Sciaridae at least once. Based on the results, we discuss phylogenetic relationships within the family, and present an evolutionary scenario of development of larval habitats.