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.     

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.     

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.     

What would it take to describe the global diversity of parasites?

How many parasites are there on Earth? Here, we use helminth parasites to highlight how little is known about parasite diversity, and how insufficient our current approach will be to describe the full scope of life on Earth. Using the largest database of host–parasite associations and one of the world’s largest parasite collections, we estimate a global total of roughly 100 000–350 000 species of helminth endoparasites of vertebrates, of which 85–95% are unknown to science. The parasites of amphibians and reptiles remain the most poorly described, but the majority of undescribed species are probably parasites of birds and bony fish. Missing species are disproportionately likely to be smaller parasites of smaller hosts in undersampled countries. At current rates, it would take centuries to comprehensively sample, collect and name vertebrate helminths. While some have suggested that macroecology can work around existing data limitations, we argue that patterns described from a small, biased sample of diversity aren’t necessarily reliable, especially as host–parasite networks are increasingly altered by global change. In the spirit of moonshots like the Human Genome Project and the Global Virome Project, we consider the idea of a Global Parasite Project: a global effort to transform parasitology and inventory parasite diversity at an unprecedented pace.     

Andean and California condors possess dissimilar genetic composition but exhibit similar demographic histories

While genetic diversity of threatened species is a major concern of conservation biologists, historic patterns of genetic variation are often unknown. A powerful approach to assess patterns and processes of genetic erosion is via ancient DNA techniques. Herein, we analyzed mtDNA from historical samples (1800s to present) of Andean Condors (Vultur gryphus) to investigate whether contemporary low genetic variability is the result of recent human expansion and persecution, and compared this genetic history to that of California condors (Gymnogyps californianus).We then explored historic demographies for both species via coalescent simulations. We found that Andean condors have lost at least 17% of their genetic variation in the early 20th century. Unlike California condors, however, low mtDNA diversity in the Andean condor was mostly ancient, before European arrival. However, we found that both condor species shared similar demographies in that population bottlenecks were recent and co‐occurred with the introduction of livestock to the Americas and the global collapse of marine mammals. Given the combined information on genetic and demographic processes, we suggest that the protection of key habitats should be targeted for conserving extant genetic diversity and facilitate the natural recolonization of lost territories, while nuclear genomic data should be used to inform translocation plans.     

Noise does not equal bias in assessing the evolutionary history of the angiosperm flora of China: A response to Qian (2019)

In response to our paper on the evolutionary history of the Chinese flora, Qian suggests that certain features of the divergence time estimation employed might have led to biased conclusions in Lu et al (2018). Here, we consider Qian's specific criticisms, explore the extent of uncertainty in the data and demonstrate that (i) no systematic bias toward dates that are too young or too old is detected in Lu et al.; (ii) constraint of the crown age of angiosperms does not bias the generic ages estimated by Lu et al.; and (iii) ages derived from the Chinese regional phylogeny do not bias the conclusions reported by Lu et al. All these analyses confirm that the conclusions reported previously are robust. We argue that, like many large-scale biodiversity analyses, sources of noise in divergence time estimation are to be expected, but these should not be confused with bias.     

Museum specimens provide reliable SNP data for population genomic analysis of a widely distributed but threatened cockatoo species

Natural history museums harbour a plethora of biological specimens which are of potential use in population and conservation genetic studies. Although technical advancements in museum genomics have enabled genome‐wide markers to be generated from aged museum specimens, the suitability of these data for robust biological inference is not well characterized. The aim of this study was to test the utility of museum specimens in population and conservation genomics by assessing the biological and technical validity of single nucleotide polymorphism (SNP) data derived from such samples. To achieve this, we generated thousands of SNPs from 47 red‐tailed black cockatoo (Calyptorhychus banksii) traditional museum samples (i.e. samples that were not collected with the primary intent of DNA analysis) and 113 fresh tissue samples (cryopreserved liver/muscle) using a restriction site‐associated DNA marker approach (DArTseq^?). Thousands of SNPs were successfully generated from most of the traditional museum samples (with a mean age of 44 years, ranging from 5 to 123 years), although 38% did not provide useful data. These SNPs exhibited higher error rates and contained significantly more missing data compared with SNPs from fresh tissue samples, likely due to considerable DNA fragmentation. However, based on simulation results, the level of genotyping error had a negligible effect on inference of population structure in this species. We did identify a bias towards low diversity SNPs in older samples that appears to compromise temporal inferences of genetic diversity. This study demonstrates the utility of a RADseq‐based method to produce reliable genome‐wide SNP data from traditional museum specimens.     

The influence of ecological and life history factors on ectothermic temperature–size responses: Analysis of three Lycaenidae butterflies (Lepidoptera)

Body size has been shown to decrease with increasing temperature in many species, prompting the suggestion that it is a universal ecological response. However, species with complex life cycles, such as holometabolous insects, may have correspondingly complicated temperature–size responses. Recent research suggests that life history and ecological traits may be important for determining the direction and strength of temperature–size responses. Yet, these factors are rarely included in analyses. Here, we aim to determine whether the size of the bivoltine butterfly, Polyommatus bellargus, and the univoltine butterflies, Plebejus argus and Polyommatus coridon, change in response to temperature and whether these responses differ between the sexes, and for P. bellargus, between generations. Forewing length was measured using digital specimens from the Natural History Museum, London (NHM), from one locality in the UK per species. The data were initially compared to annual and seasonal temperature values, without consideration of life history factors. Sex and generation of the individuals and mean monthly temperatures, which cover the growing period for each species, were then included in analyses. When compared to annual or seasonal temperatures only, size was not related to temperature for P. bellargus and P. argus, but there was a negative relationship between size and temperature for P. coridon. When sex, generation, and monthly temperatures were included, male adult size decreased as temperature increased in the early larval stages, and increased as temperature increased during the late larval stages. Results were similar but less consistent for females, while second generation P. bellargus showed no temperature–size response. In P. coridon, size decreased as temperature increased during the pupal stage. These results highlight the importance of including life history factors, sex, and monthly temperature data when studying temperature–size responses for species with complex life cycles.     

中药博物馆数字化与科普的实践与思考

近年来,随着中医药博物馆数字化的普遍应用,馆藏文物及标本的保护能力得到了有效提高。同时,通过多媒体手段将中药馆藏及展陈标本数字化成果应用到中医药科普实践中,激发了大众对中医药传统文化的兴趣,更好地推动了中医药文化的普及。该研究以重庆市中药博物馆运用数字化开展中药科普为例,阐述了中药博物馆如何利用数字化创新中药科普工作,探讨了中药博物馆的数字化平台建设方向和数字化建设成果的科普应用方式以及中医药科普的后续方向,对促进中医药文化传播及扩大中药文化的普及力与影响力具有重要意义。该研究认为只有不断应用科技手段,逐步推动中药博物馆数字化、网络化,让中医药文化的传播不受空间和时间的限制,真正实现中药资源网络共享,才能促使中药博物馆与时俱进,充分发挥弘扬中医药文化的科普阵地作用。