A catalog of bird specimens associated with Prince Maximilian of Wied-Neuwied and potential type material in the natural history collection in Wiesbaden

Bird specimens collected by 19^th century explorer and ornithologist Prince Maximilian of Wied-Neuwied form one of the foundation collections of the American Museum of Natural History in New York. However, parts of his collection remained in Germany and came to the Museum Wiesbaden. Since Wied described numerous new species without designating types, some of these specimens might be type material. Here we present a catalog of the 30 Wiesbaden specimens associated with him and discuss their potential type status. We conclude that 17 individuals in 11 species are potential type specimens that should be considered in future taxonomic work.     

云南省(虫齿)目二新种和灰背蛇(虫齿)的记述((虫齿)目:厚(虫齿)科、叉(虫齿)科、围(虫齿)科)

本文记述了云南省(虫齿)目二新种,Tapinella bannana sp.n.和Peripsocus plurimaculatus sp.n.及一新种记录种Ophiodopelma semicets Lee and Thornton,其雄虫为首次记载。     

The Linnaean fish collection in the Zoological Museum of the University of Uppsala

Specimens of fishes preserved in the Zoological Museum, University of Uppsala, which are believed to have been examined by Linnaeus, are listed. Most of these were originally given to the University in several donations by benefactors of the Academy and were described by Linnaeus in dissertations defended by students. Some specimens, however, are believed to have originated from Linnaeus's own collection. Many of the specimens have type status and this is discussed together with notes on other surviving Linnaean fish specimens.     

Trends in plant carbon concentration and plant demand for N throughout this century

 Atmospheric CO₂ concentration has increased by 25% over the preindustrial level. A parallel increase in C concentration and decreases in N concentration and δ¹³C of plants grown throughout this century have been observed in plant specimens stored in herbaria. We tested our previous results in a study of 12 more species collected in the western Mediterranean throughout this century (1920–1930, 1945–1955, and 1985–1990) and tree rings of Quercus pubescens from the same area. These changes were accompanied by apparent increases in condensed tannin concentration. A decreasing trend in δ¹⁵N both in herbarium material and tree rings was also found, indicating that ecosystems might cope with higher plant N demand by decreasing N losses and increasing N fixation and mineralization. These results may contribute to a better understanding of the effects of global change on carbon and nitrogen cycling. Received: 12 November 1995 / Accepted: 17 May 1996     

Trace elements in hair of blackfoot disease

Blackfoot disease is a peripheral vascular disease resulting in gangrene of the lower extremities. Though extensive epidemiological study has implicated that high arsenic content in artesian well water of the endemic area, bears some important connection with the disease, the etiology of the disease is still unknown. In this study, attention is paid to multielement determination in order to find out whether the trace elements in hair of Blackfoot disease patients are different from those of the controls. Experimental results indicate that the concentrations of As and Se in hair of patients are significantly higher than those of the controls, but Ca and Zn are significantly lower than those of the controls. The possible connection of these elements with the etiology of the disease is discussed.     

An effective method for isolating DNA from historical specimens of baleen

DNA was isolated from an early twentieth century museum specimen of northern right whale baleen. A system of stringent controls and a novel set of cetacean specific primers eliminated contamination from external sources and ensured the authenticity of the results. Sequence analysis revealed that there were informative nucleotide positions between the museum specimen and extant members of the population and closely related species. The results indicate that museum specimens of baleen can be used to assess historical genetic population structure of the great whales.     

Hirticrusta gen. nov. segregated from Neofomitella in Polyporaceae (Polyporales)

Taxonomic studies including morphological observations and phylogenetic analyses were conducted on Japanese “uragin-take”, an unidentified species from Amazonia, Brazil and their allies. Phylogenetic analyses using ITS, nrLSU and RPB2 regions revealed that “uragin-take”, Neofomitella polyzonata and the unidentified species formed a monophyletic clade separate from the clade including the other four Neofomitella spp. and that “uragin-take” is conspecific with N. polyzonata. Morphological investigations on authentic specimens revealed that Polyporus subradiatus is a prior name for N. polyzonata. We propose Hirticrusta gen. nov. typified by H. subradiata segregated from Neofomitella, and we erected H. amazonica sp. nov. for the unidentified species. Hirticrusta is characterized by annual to biennial and sessile basidiocarps, semicircular to dimidiate pileus, velutinous to tomentose hairs on pileus surface, buff to brown context with a crustose layer indicated by a dark brown line forming a longitudinal section below the superficial hairs, a trimitic hyphal system, crustose layer composed of parallel and densely arranged brown hyphae and cylindrical basidiospores. The new species, H. amazonica is distinguishable from other polypores by downy and long tomentum on the pileus surface (up to 20 mm thick), brown context with a dark brown layer below the tomentum and round pores (5–7/mm).     

A method to generate multilocus barcodes of pinned insect specimens using MiSeq

For molecular insect identification, amplicon sequencing methods are recommended because they offer a cost‐effective approach for targeting small sets of informative genes from multiple samples. In this context, high‐throughput multilocus amplicon sequencing has been achieved using the MiSeq Illumina sequencing platform. However, this approach generates short gene fragments of <500 bp, which then have to be overlapped using bioinformatics to achieve longer sequence lengths. This increases the risk of generating chimeric sequences or leads to the formation of incomplete loci. Here, we propose a modified nested amplicon sequencing method for targeting multiple loci from pinned insect specimens using the MiSeq Illumina platform. The modification exists in using a three‐step nested PCR approach targeting near full‐length loci in the initial PCR and subsequently amplifying short fragments of between 300 and 350 bp for high‐throughput sequencing using Illumina chemistry. Using this method, we generated 407 sequences of three loci from 86% of all the specimens sequenced. Out of 103 pinned bee specimens of replicated species, 71% passed the 95% sequence similarity threshold between species replicates. This method worked best for pinned specimens aged between 0 and 5 years, with a limit of 10 years for pinned and 14 years for ethanol‐preserved specimens. Hence, our method overcomes some of the challenges of amplicon sequencing using short read next generation sequencing and improves the possibility of creating high‐quality multilocus barcodes from insect collections.     

Index hopping on the Illumina HiseqX platform and its consequences for ancient DNA studies

The high‐throughput capacities of the Illumina sequencing platforms and the possibility to label samples individually have encouraged wide use of sample multiplexing. However, this practice results in read misassignment (usually <1%) across samples sequenced on the same lane. Alarmingly high rates of read misassignment of up to 10% were reported for lllumina sequencing machines with exclusion amplification chemistry. This may make use of these platforms prohibitive, particularly in studies that rely on low‐quantity and low‐quality samples, such as historical and archaeological specimens. Here, we use barcodes, short sequences that are ligated to both ends of the DNA insert, to directly quantify the rate of index hopping in 100‐year old museum‐preserved gorilla (Gorilla beringei) samples. Correcting for multiple sources of noise, we identify on average 0.470% of reads containing a hopped index. We show that sample‐specific quantity of misassigned reads depends on the number of reads that any given sample contributes to the total sequencing pool, so that samples with few sequenced reads receive the greatest proportion of misassigned reads. This particularly affects ancient DNA samples, as these frequently differ in their DNA quantity and endogenous content. Through simulations we show that even low rates of index hopping, as reported here, can lead to biases in ancient DNA studies when multiplexing samples with vastly different quantities of endogenous material.