Zhiyong Yuan

Universal COI primers for DNA barcoding amphibians

DNA barcoding is a proven tool for the rapid and unambiguous identification of species, which is essential for many activities including the vouchering tissue samples in the genome 10K initiative, genealogical reconstructions, forensics and biodiversity surveys, among many other applications. A large‐scale effort is underway to barcode all amphibian species using the universally sequenced DNA region, a partial fragment of mitochondrial cytochrome oxidase subunit I COI. This fragment is desirable because it appears to be superior to 16S for barcoding, at least for some groups of salamanders. The barcoding of amphibians is essential in part because many species are now endangered. Unfortunately, existing primers for COI often fail to achieve this goal. Herein, we report two new pairs of primers (➀, ➁) that in combination serve to universally amplify and sequence all three orders of Chinese amphibians as represented by 36 genera. This taxonomic diversity, which includes caecilians, salamanders and frogs, suggests that the new primer pairs will universally amplify COI for the vast majority species of amphibians.

Geological events play a larger role than Pleistocene climatic fluctuations in driving the genetic structure of Quasipaa boulengeri (Anura: Dicroglossidae)

Paleoclimatic and paleogeological events have been identified as being the two main drivers of genetic structuring in extant organisms. We used a montane stream‐dwelling frog, Quasipaa boulengeri, to explore the relative roles played by these drivers on species in southern China, a region needing thorough studies. We detected four major matrilines, and no broadly distributed haplotypes occurred. The complex orogenesis of south‐western China drove matrilineal divergence in Q. boulengeri into highly structured geographical units. These matrilines subsequently persisted in situ with stable populations rather than undergoing expansions during glacial cycling. The unification of the upper and middle Yangtze River in the Three Gorges mountain region mediated downstream colonization of this frog. Analyses identified geological events as playing a larger role than climatic fluctuations in driving the population history of Q. boulengeri. Nuclear allele analyses indicated gene flow; this maintained genetic cohesion of the species. South‐eastern Sichuan Basin was identified as the area of secondary contact for several matrilines, and this area deserves further study and special protection.

Synthesis and characterization of boron-containing MCM-48 cubic mesoporous molecular sieves

Boron-containing MCM-48 cubic mesoporous molecular sieves with different boron contents were synthesized and characterized by XRD, N-2 adsorption, TEM, and NMR spectroscopy. All BMCM-48 samples possess high porosities with a relatively narrow pore size distribution, and the pore structure of BMCM-48 is relatively uniform. In the as-synthesized form boron is tetrahedrally coordinated. Most of the boron is not removable by calcination and/or rehydration treatments

Vanadium- and chromium-containing mesoporous MCM-41 molecular sieves with hierarchical structure

The structures and properties of materials are profoundly altered under high pressure due to a large change of atom spacing, chemical bonding and Gibbs free energies. Therefore, materials with novel structures and properties call be created via a process known as pressure-induced phase transition. Here we report the investigations of pressure effects on the elastic properties and the glass transition of Zr-, Pd-based bulk metallic glasses (BMGs), The elastic constants and the Debye temperatures, of a Zr41Ti14Cu12.5Ni10Be22.5C1 and a Pd39Ni10Cu30P21 BMGs are measured by using an ultrasonic technique, and their pressure dependence is exhibited. The equations of state (EOS) of the two BMGs are established. The acoustic attenuation behaviors are also monitored with various pressure in the two BMGs, and a marked difference between the two BMGs is revealed, The effects of pressure-induced structural relaxation on the glass transition of the Pd39Ni10Cu30P21 BMG are investigated by a temperature-modulated differential scanning calorimetry technique. The pressure dependence of the reversible and irreversible glass transition is explained.

Comprehensive characterization of iron oxide containing mesoporous molecular sieve MCM-41

We have synthesized iron oxide-containing mesoporous silica MCM-41 by a direct route. This material has a significant microporousity, which might be related with the loading of iron oxide in the MCM-41 mesopores, though no crystalline phases of iron oxide were detected by XRD. Intensity deviations and extra bright intensity within the pores, as well as local superstructural phases within a large area, were observed in the TEM images. The position and area of such a crystalline phase could change during the successive electron beam exposure and resulted in a formation of a cycle. These phenomena imply the possible existence of small Fe2O3 nanocrystals loaded in the mesoporous silica materials with regular and oriented arrangement. EELS spectrum of the sample proves the existence of iron, but the chemical environment of iron in the MCM-41 silica should be different from that of bulk amorphous porous iron oxide. The small iron oxide crystals in the MCM-41 sample might be linked with silica wall through oxygen. Another possibility is that iron oxide reacts with silica during synthesis, causing the partial crystallization of the MCM-41 framework. In other words, microcrystals of iron oxide may exist in the silica matrix.

A novel multilocus phylogenetic estimation reveals unrecognized diversity in Asian horned toads, genus Megophrys sensu lato (Anura: Megophryidae)

The horned toad assemblage, genus Megophrys sensu lato, currently includes three groups previously recognized as the genera Atympanophrys, Xenophrys and Megophrys sensu stricto. The taxonomic status and species composition of the three groups remain controversial due to conflicting phenotypic analyses and insufficient phylogenetic reconstruction; likewise, the position of the monotypic Borneophrys remains uncertain with respect to the horned toads. Further, the diversity of the horned toads remains poorly understood, especially for widespread species. Herein, we evaluate species-level diversity based on 45 of the 57 described species from throughout southern China, Southeast Asia and the Himalayas using Bayesian inference trees and the Generalized Mixed Yule Coalescent (GMYC) approach. We estimate the phylogeny using both mitochondrial and nuclear DNA data. Analyses reveal statistically significant mito-nuclear discordance. All analyses resolve paraphyly for horned toads involving multiple strongly supported clades. These clades correspond with geography. We resurrect the genera Atympanophrys and Xenophrys from the synonymy of Megophrys to eliminate paraphyly of Megophrys s.l. and to account for the morphological, molecular and biogeographic differences among these groups, but we also provide an alternative option. Our study suggests that Borneophrys is junior synonym of Megophrys sensu stricto. We provide an estimation of timeframe for the horned toads. The mitochondrial and nuclear trees indicate the presence of many putative undescribed species. Widespread species, such as Xenophrys major and X. minor, likely have dramatically underestimated diversity. The integration of morphological and molecular evidence can validate this discovery. Montane forest dynamics appear to play a significant role in driving diversification of horned toads.

Red River barrier and Pleistocene climatic fluctuations shaped the genetic structure of Microhyla fissipes complex (Anura: Microhylidae) in southern China and Indochina

South China and Indochina host striking species diversity and endemism. Complex tectonic and climatic evolutions appear to be the main drivers of the biogeographic patterns. In this study, based on the geologic history of this region, we test 2 hypotheses using the evolutionary history of Microhyla fissipes species complex. Using DNA sequence data from both mitochondrial and nuclear genes, we first test the hypothesis that the Red River is a barrier to gene flow and dispersal. Second, we test the hypothesis that Pleistocene climatic cycling affected the genetic structure and population history of these frogs. We detect 2 major genetic splits that associate with the Red River. Time estimation suggests that late Miocene tectonic movement associated with the Red River drove their diversification. Species distribution modeling (SDM) resolves significant ecological differences between sides of the Red River. Thus, ecological divergence also probably promoted and maintained the diversification. Genogeography, historical demography, and SDM associate patterns in southern China with climate changes of the last glacial maximum (LGM), but not Indochina. Differences in geography and climate between the 2 areas best explain the discovery. Responses to the Pleistocene glacial–interglacial cycling vary among species and regions.

A missing geographic link in the distribution of the genus Echinotriton (Caudata: Salamandridae) with description of a new species from southern China

Disjunct geographic distribution of a species or a group of species is the product of long-term interaction between organisms and the environment. Filling the distributional gap by discovery of a new population or a species has significant biogeographic implications, because it suggests a much wider past distribution and provides evidence for the route of range expansion/contraction. The salamandrid genus Echinotriton (commonly known as spiny salamanders, spiny newts, or crocodile newts) has two species that are restricted to two widely separated areas, one in eastern Zhejiang province, China and the other in the Ryukyu Archipelago of Japan. It has been hypothesized that Echinotriton was once continuously distributed between the two areas through a historical land bridge that connected mainland China, Taiwan, and the archipelago. Finding fossils or relic populations along the postulated distribution are strong evidence for the hypothesis. Hundred-twenty-two years after the description of E. andersoni and eight-one years after that of E. chinhaiensis, we discover a third species of Echinotriton in southern China, which fills the distributional gap of the former two species. Species status of the new species is confirmed through molecular phylogenetic analysis and morphological comparison. Mitochondrial DNA indicates that the new species is sister to E. chinhaiensis, while nuclear DNA does not support this relationship. The new species has a very large quadrate projection, a single line of lateral warts pierced by distal rib extremities, normally developed 5th toes, and conical skin tubercles. Our discovery supports the hypothesis that there was a continuous distribution of Echinotriton from eastern coastal China to the Ryukyu Archipelago. We suggest that other species of this genus may also be found in Taiwan. Due to the rarity of this new species, we urge all hobbyists to refrain themselves from collecting this salamander or leaking locality information if encountered, and boycott any trading.

06-P-09 - Controlled synthesis of microporous and mesoporous silica-based molecular sieves in the presence of dodecyldimethylbenzylammonium chloride

Publisher Summary This chapter discusses a controlled synthesis of microporous and mesoporous silica-based molecular sieves in the presence of dodecyldimethylbenzylammonium chloride (DDBAC). Microporous silicas with the pore size of 12.2 A are prepared by either S + X - I + or S + I - pathways at room temperature using DDBAC surfactant. The pore size of the synthesized materials could be tuned from microporous to mesoporous range by the crystalline temperature or using the mixed surfactants of DDBAC and cetylpyridinium chloride. The pore structure can transfer from disordered tubular array to ordered hexagonal phase by the increase of the molar ratio of cetylpyridium chloride (CPCl) to DDBAC.

The Chinese giant salamander exemplifies the hidden extinction of cryptic species

Overexploitation, habitat destruction, human-driven climate change and disease spread are resulting in the extinction of innumerable species, with amphibians being hit harder than most other groups [1]. Few species of amphibians are widespread, and those that are often represent complexes of multiple cryptic species. This is especially true for range-restricted salamanders [2]. Here, we used the widespread and critically endangered Chinese giant salamander (Andrias davidianus) to show how genetically uninformed management efforts can negatively affect species conservation. We find that this salamander consists of at least five species-level lineages. However, the extensive recent translocation of individuals between farms, where the vast majority of extant salamanders now live, has resulted in genetic homogenization. Mitochondrial DNA (mtDNA) haplotypes from northern China now predominate in farms. Unfortunately, hybrid offspring are being released back into the wild under well-intentioned, but misguided, conservation management. Our findings emphasize the necessity of genetic assessments for seemingly well-known, widespread species in conservation initiatives. Species serve as the primary unit for protection and management in conservation actions [3], so determining the taxonomic status of threatened species is a major concern, especially for amphibians. The level of threat to amphibians may be underestimated, and existing conservation strategies may be inadvertently harmful if conducted without genetic assessment.