The impact of sequencing depth and relatedness of the reference genome in population genomic studies: A case study with two caddisfly species (Trichoptera, Rhyacophilidae, Himalopsyche).

Whole genome sequencing for generating SNP data is increasingly used in population genetic studies. However, obtaining genomes for massive numbers of samples is still not within the budgets of many researchers. It is thus imperative to select an appropriate reference genome and sequencing depth to ensure the accuracy of the results for a specific research question, while balancing cost and feasibility. To evaluate the effect of the choice of the reference genome and sequencing depth on downstream analyses, we used five confamilial reference genomes of variable relatedness and three levels of sequencing depth (3.5×, 7.5× and 12×) in a population genomic study on two caddisfly species: Himalopsyche digitata and H. tibetana. Using these 30 datasets (five reference genomes × three depths × two target species), we estimated population genetic indices (inbreeding coefficient, nucleotide diversity, pairwise F ST, and genome-wide distribution of F ST) based on variants and population structure (PCA and admixture) based on genotype likelihood estimates. The results showed that both distantly related reference genomes and lower sequencing depth lead to degradation of resolution. In addition, choosing a more closely related reference genome may significantly remedy the defects caused by low depth. Therefore, we conclude that population genetic studies would benefit from closely related reference genomes, especially as the costs of obtaining a high-quality reference genome continue to decrease. However, to determine a cost-efficient strategy for a specific population genomic study, a trade-off between reference genome relatedness and sequencing depth can be considered.

Gene Flow and Diversification in Himalopsyche martynovi Species Complex (Trichoptera: Rhyacophilidae) in the Hengduan Mountains.

The Hengduan Mountains are one of the most species-rich mountainous areas in the world. The origin and evolution of such a remarkable biodiversity are likely to be associated with geological or climatic dynamics, as well as taxon-specific biotic processes (e.g., hybridization, polyploidization, etc.). Here, we investigate the mechanisms fostering the diversification of the endemic Himalopsyche martynovi complex, a poorly known group of aquatic insects. We used multiple allelic datasets generated from 691 AHE loci to reconstruct species and RaxML phylogenetic trees. We selected the most reliable phylogenetic tree to perform network and gene flow analyses. The phylogenetic reconstructions and network analysis identified three clades, including H. epikur, H. martynovi sensu stricto and H. cf. martynovi. Himalopsyche martynovi sensu stricto and H. cf. martynovi present an intermediate morphology between H. epikur and H. viteceki, the closest known relative to the H. martynovi-complex. The gene flow analysis revealed extensive gene flow among these lineages. Our results suggest that H. viteceki and H. epikur are likely to have contributed to the evolution of H. martynovi sensu stricto and H. cf. martynovi via gene flow, and thus, our study provides insights in the diversification process of a lesser-known ecological group, and hints at the potential role of gene flow in the emergence of biological novelty in the Hengduan Mountains.

Geographical range evolution of the genus Polypedates (Anura: Rhacophoridae) from the Oligocene to present.

Currently, the genus Polypedates comprises 26 species distributed in South, Southeast, and East Asia. Because of their relatively low dispersal capability and intolerance to seawater, this genus is ideal for the study of terrestrial range evolution that extends into the island archipelagos of southeastern Asia. In this study, based on data compiled for Polypedatesfrom previous studies and partial mitochondrial and nuclear genes collected in this study, we performed systematic biogeographical analysis. We confirmed a Sundaland origin for the extant genus and showed northward dispersal into mainland Southeast Asia and Asia, which coincided with the timing of paleoclimatic change from the Oligocene to Middle Miocene. Climate fluctuations had a profound impact on species diversification within the genus Polypedates. Furthermore, the Red River did not mediate species exchange between Southeast Asia and mainland Asia until the end of the Miocene, with the sudden onset of northward dispersal in several clades independently at that time. Alternatively, the lineage of widespread insular P. leucomystaxstrongly supports the hypothesis of terrestrial connection between island archipelagos of Southeast Asia during the Mid-Pleistocene paleoclimate fluctuations. Our biogeographical analysis also supports the recent introduction of P. leucomystax to the Philippines and Ryukyus, as previously suggested.

Anti-complementary constituents of Anchusa italica.

Activity-guided fractionation for complement inhibitors led to the isolation of 24 known compounds from Anchusa italica. Chemical types include eight megastigmane compounds, five triterpenoid compounds, five lignan compounds, three flavonoid compounds, two alkaloid compounds and one phenthyl alcohol compound. Among which, a lignan (medioresinol), an alkaloid (5-hydroxypyrrolidin-2-one) and a flavonoid (5-hydroxyl-3', 4', 6, 7-tetramethoxy flavone) exhibited better anticomplementary effects with CH50 values ranging from 0.07 to 0.82 mM, which are plausible candidates for developing potent anticomplementary agents.

Crystallographic snapshots of the interplay between reactive guest and host molecules in a porous coordination polymer: stereochemical coupling and feedback mechanism of three photoactive centers triggered by UV-induced isomerization, dimerization, and polymerization reactions.

We carried out photopolymerization by [2 + 2] dimerization of a photoreactive guest molecule in the channels of a photoreactive porous coordination polymer. The photoreactions of the guest and two host ligands were monitored by single-crystal X-ray crystallography, providing snapshots of the interplay between the reactive centers. By correlating the structures of these three photocenters, a strong synergism was discovered among three reaction (quasi)equilibria and three types of photochemical reactions (isomerization, dimerization, and polymerization). This result indicates a strong coupling and feedback mechanism among the photocenters moderated by the coordination backbone.

[Synthesis of diethyl N-[p-(methylamino)benzoyl]-L-glutamate].

OBJECTIVE: To find a best synthesis method of diethyl N-[p-(methylamino)benzoyl]-L-glutamate(1). METHODS: Using diethyl N-(p- aminobenzoyl)-L-glutamate (2) as a starting material via a one-pot process of benzylation and methylation, the diethyl N-[p-(methylamino)benzoyl ]-L-glutamate (3) is prepared in high yield. Then compound 1 was conveniently obtained from debenzylation of compound 3 by Pd/C. RESULTS: The target compound was obtained through 2-step reaction in 88% overall yield in only 6 h, and its structure was identified by 1HNMR and MS. CONCLUSION: It is a convenient and efficient method of preparation of diethyl N-[p-(methylamino)benzoyl]-L-glutamate.