Specimen Vouchers Research Articles

Vascular Plant Communities and Flora of the Seven Lakes Nature Preserve in Michigan's Eastern Upper Peninsula

The Seven Lakes Nature Preserve comprises nearly 2,400 hectares of aquatic, wetland, and upland habitats in southeastern Alger and northeastern Schoolcraft counties in the eastern Upper Peninsula of Michigan. The preserve was obtained and protected by the J.A. Woollam Foundation and has undergone several expansions. In an area of Michigan with relatively limited development and few roads, the natural communities of Seven Lakes are highly intact, and many of its habitats have recovered since the historic logging era. Botanical surveys were conducted in 2016, 2017, 2020, 2021, and 2022 with the goals of describing the natural communities and ecosystem processes and of producing a comprehensive floristic inventory. The post-glacial natural history of the region and a description of climate and soils are provided. A floristic quality assessment was performed, yielding a Total Floristic Quality Index of 99.9, a Total Mean C of 4.5 and a Native Mean C of 5.3. Within the upland forests, shrubby and forested wetlands, and open wetlands, eleven plant communities are described following the classification system proposed by the Michigan Natural Features Inventory. The floristic affinities of rare or otherwise noteworthy taxa are discussed, as are potential threats to the ecosystem. Four-hundred ninety-three species and four hybrids were observed during our surveys, 147 species are represented by specimen vouchers and 440 are recorded as photo vouchers on iNaturalist. Sixteen new species records for Alger County are reported.

Oxytoxaceae are prorocentralean rather than peridinialean dinophytes and taxonomic clarification of heterotrophic Oxytoxum lohmannii (≡ “Amphidinium” crassum) by epitypification

During evolution of Dinophyceae, size reduction of the episome has occurred in several lineages (including unarmoured Amphidiniales and armoured Prorocentrales). One such species is Amphidinium crassum, whose taxonomic identity is elusive though showing morphological similarities with Oxytoxaceae (currently placed in armoured Peridiniales). Plankton samples were taken at the type locality of A. crassum in Kiel Bight (Baltic Sea) in order to establish monoclonal strains. The protist material was examined in detail using light and electron microscopy, and a long (2984 bp) ribosomal RNA sequence gained was part of a taxon sample comprising 206 specimen vouchers and representing the known molecular diversity of Dinophyceae. Cells of A. crassum were ovoid and exhibited a plate pattern po, 4′, 1a, 6′′, 5c, 4s, 5′′′, 1′′′′. In the molecular phylogeny, the species seemed to belong neither to Amphidiniales nor to Peridiniales but to Prorocentrales and clustered with other representatives of Oxytoxaceae. The morphological diversity of Prorocentrales appears thus expanded, and the group may include a number of previously unrecognised representatives unusually having five postcingular and only a single antapical plate. The taxonomic identity of A. crassum is clarified by epitypification, and the species notably exhibits both an apical pore and an additional epithecal pore.

Noteworthy new angiosperm plant distribution records for New Mexico and Colorado, U.S.A.

Eleven angiosperm plant species are added to the flora of New Mexico that were revealed through herbarium curation associated with a project to digitize and unify the two herbaria of New Mexico State University (NMC & NMCR) and through ongoing field work. One, Dimorphocarpa candicans, is restored to the state’s flora, after it was earlier placed into synonymy with D. wislizeni, a close but morphologically distinct relative. The current IUCN Redlist conservation status of endangered (EN) for Gossypium thurberi should be revisited given its newly discovered range extension into southwestern New Mexico. New county-level distribution records are provided for a total of 16 taxa. Crepis tectorum, one of the species added to the flora of New Mexico, is likewise documented for Colorado, where it occurs in three counties. All of the plants added to the floras pertain to species that are either native or introduced with the potential to spread and become naturalized in the landscape. A putative introgressive population is also reported for New Mexico between Quercus turbinella and Q. laceyi, the latter otherwise unknown in the state. For all new records, full citations of specimen vouchers are provided to document the extended distributional ranges.

Annotated checklist of the primarily freshwater fishes of Guyana

Guyana, located in northern South America north of Brazil between Venezuela and Suriname, includes portions of the Orinoco, Amazon, and Courantyne river basins, a majority of the Essequibo River Basin, and all of the Berbice and Demerara river basins. Partly as a consequence of historical and contemporary drainage complexity, Guyana has a remarkably diverse freshwater fish fauna. Here, we compile the first comprehensive list of Guyana's freshwater fishes, totaling some 657 species-level taxa (97 first records, 117 endemics and at least three introduced species), based on photographic records, published reports, and over 145,000 type and non-type specimens in 29 museum collections. The IUCN conservation status for each species is provided. We separately list an additional 151 undocumented species that are possibly or likely present in Guyana based on their adjacent distributions in either the Orinoco River Delta in Venezuela or the Courantyne River in Suriname. The largest holdings of fish specimen vouchers and frozen fish tissues from Guyana are housed at the Royal Ontario Museum, Toronto (ROM), Auburn University Museum, Auburn (AUM), University of Michigan Museum of Zoology, Ann Arbor (UMMZ), and the Academy of Natural Sciences of Drexel University, Philadelphia (ANSP). Additional important collections of Guyanese fishes are deposited at the Centre for Study of Biological Diversity, Georgetown, Guyana (CSBD), Field Museum of Natural History, Chicago (FMNH), Illinois Natural History Survey, Champaign (INHS), The Natural History Museum, London (NHMUK, formerly BMNH), Oregon State University, Corvallis (OS), and the US National Museum, Washington (USNM). Despite the many collections that have been made in Guyana, many species still lack vouchered specimens or tissues, and many more species require formal description.

Specimen Identifiers: Linking tissues, DNA samples, and sequence data to voucher specimens in publicly accessible databases

Nearly all disciplines of biology now have some form of molecular genetic analyses incorporated into areas of their research, from systematics, ecology, and behavior, to physiology and conservation. In order for science to be transparent, the source and provenance of the genetic material used must be easily identifiable and traceable, following the FAIR principles of being Findable Accessible, Interoperable, and Reusable (Wilkinson et al. 2016). Natural history collections are ever-increasingly facilitating the use of genetic components from collection objects, and in some cases increasing the number and types of collection objects under their care (i.e., tissue/DNA-only, e.g., blood, feather, skin- fin-clips, environmental samples). Most natural history collections are now making their holdings available online, either on their own platforms or via aggregate search engines like the Global Biodiversity Information Facility (GBIF) and the Global Genome Biodiversity Network (GGBN). Many natural history collections are also now using digital management systems, where digital identifiers such as Digital Object Identifiers (DOIs) and Uniform Resource Identifiers (URIs) are assigned to objects in collections (Güntsch et al. 2017), including multiple objects derived from the same individual organism (e.g., voucher specimen, images, and genomic samples). Associated objects may receive different digital identifiers in order to be uniquely identifiable in the digital management system, but sharing this information on third-party platforms (e.g., GBIF, GGBN) is challenging, especially in avoiding duplicate entries. Furthermore, genetic materials are often sought out by researchers external to the holding collection institution, and molecular sequence data are then generated and deposited in third-party public repositories, such as GenBank and the Barcode of Life Database (BOLD). Making genomic material digitally discoverable to researchers, and linking them and data generated from these samples back to the associated voucher specimens is another challenge. Fortunately, there is a current international initiative to collate the different forms of data surrounding a voucher specimen, as a Digital Extended Specimen (DES), across multiple institutions worldwide (Hardisty et al. 2022). The National Center for Biotechnology Information (NCBI), which hosts GenBank, has created a BioCollections Database to curate metadata for natural history collections and linking sequence data to voucher specimens (Sharma et al. 2018). Institution codes, collection codes, and catalog numbers are linked to create a “structured voucher” annotation (following the Darwin Core Triplet) to standardize usage across interconnected databases (e.g., GenBank, European Nucleotide Archive, and the DNA Databank of Japan). However, duplicate institution codes can make this complicated, and collection institutions that use digital identifiers instead of traditional catalog numbers make this even more challenging. The NCBI BioCollections Database curators have resolved the duplicate institution codes problem, by adding the three-letter country code (or state code, within the same country). However, this database is used only for sequence data, in GenBank, and related databases (e.g., ENA, DDBJ), which raises the question, is there a need for a more universal biocollection codes database? Additionally, as museums move towards using digital identifiers, in the place of catalog numbers, confusion can arise when multiple digital identifiers are assigned to parts of the same “specimen” (e.g., specimen voucher, tissue, DNA, images, etc.). For instance, if a given specimen has unique URIs for the voucher specimen, the DNA, and an image, a researcher borrowing the DNA, might use the DNA URI as an identifier for the genetic database. A different researcher, at a later date, might see that specimen (or image) in the museum’s collection, and think it is a different specimen of that species, when in fact it is the same specimen. This could result in a second researcher borrowing the sample and publishing it as a “new” sequence. Researchers already have difficulties in submitting sequences to GenBank, as several have confused field numbers for catalog numbers from the National Museum of Natural History, Smithsonian Institution (Mulcahy et al. 2022). Some museums, using modifiable codes, can append a primary code (from the specimen voucher) for additional “parts” of that specimen. For example, if the primary code for an insect specimen ends in “…6d15ce”, a leg taken for DNA extraction could be modified as “…6d15ce_leg” and “…6d15ce_dna” for the extract. This minimizes the chances for mistaking these as being from different specimens. However, if completely different codes are assigned to different parts of the same specimen, the chance increases for mistaking two objects from the same specimen as being from different specimens. Collections staff must carefully consider the hierarchical relationships of objects in their collections, and how they are assigned URIs, especially when considering long-term operability in current and future aggregate database structures (e.g., GBIF, GGBN, NCBI, and the DES). In this presentation, these issues are raised and the difficulties in linking specimens, genomic resources, and associated data in aggregate databases and data repositories are discussed.

Which mammals can be identified from camera traps and crowdsourced photographs?

Abstract While museum voucher specimens continue to be the standard for species identifications, biodiversity data are increasingly represented by photographic records from camera traps and amateur naturalists. Some species are easily recognized in these pictures, others are impossible to distinguish. Here we quantify the extent to which 335 terrestrial nonvolant North American mammals can be identified in typical photographs, with and without considering species range maps. We evaluated all pairwise comparisons of species and judged, based on professional opinion, whether they are visually distinguishable in typical pictures from camera traps or the iNaturalist crowdsourced platform on a 4-point scale: (1) always, (2) usually, (3) rarely, or (4) never. Most (96.5%) of the 55,944 pairwise comparisons were ranked as always or usually distinguishable in a photograph, leaving exactly 2,000 pairs of species that can rarely or never be distinguished from typical pictures, primarily within clades such as shrews and small-bodied rodents. Accounting for a species geographic range eliminates many problematic comparisons, such that the average number of difficult or impossible-to-distinguish species pairs from any location was 7.3 when considering all species, or 0.37 when considering only those typically surveyed with camera traps. The greatest diversity of difficult-to-distinguish species was in Arizona and New Mexico, with 57 difficult pairs of species, suggesting the problem scales with overall species diversity. Our results show which species are most readily differentiated by photographic data and which taxa should be identified only to higher taxonomic levels (e.g., genus). Our results are relevant to ecologists, as well as those using artificial intelligence to identify species in photographs, but also serve as a reminder that continued study of mammals through museum vouchers is critical since it is the only way to accurately identify many smaller species, provides a wealth of data unattainable from photographs, and constrains photographic records via accurate range maps. Ongoing specimen voucher collection, in addition to photographs, will become even more important as species ranges change, and photographic evidence alone will not be sufficient to document these dynamics for many species.

The mycological collection of G. C. Girgensohn from the middle of the 19th century

Since 1844, vouchers of mycological specimens collected from the territory of the historic Baltic provinces of the Russian Empire have been preserved in Estonian natural history collections. A pedagogue and an amateur bryologist, Gustav Carl Girgensohn (1786–1872) compiled a collection of 109 specimens of fungi and myxomycetes sampled from the Livonian Governorate, mostly from the vicinity of Tartu, in years 1844–1859. Girgensohn’s collection, which is kept in the fungarium of the Estonian University of Life Sciences, is introduced here for the first time. Among his specimens there are two notable ascomycetes—coprophilous Poronia punctata (Xylariaceae, Sordariomycetes), recently evaluated in Estonia as Critically Endangered according to IUCN criteria, and Microstoma protractum (Sarcoscyphaceae, Pezizomycetes), recently evaluated as Endangered. The collection’s eleven quite well-preserved specimens of myxomycetes represent six species, the least common of which is Diderma radiatum. In addition, the article introduces nine lichen specimens and one fungal specimen from Girgensohn’s bryophyte collection at the Natural History Museum of the University of Tartu. The most remarkable species among this collection is Lobaria pulmonaria (Lobariaceae, Lecanoromycetes), red-listed and protected in many countries.

Phytochemical and antibacterial properties of root extracts from Portulaca oleracea Linn. (Purslane) utilised in the management of diseases in Nigeria

Background: Bacteria as etiological agents have been reported to cause many diseases and have increased the rate of mortality globally. Their resistance to conventional medicine has made medicinal plants a credible alternative in the management of diseases caused by bacterial infection. In the recent times many research efforts have been directed towards the exploration of phytoconstituents with antibacterial potentials. Medicinal plants are widely used as antibacterial agents because of their high therapeutic performance, low toxicity, and affordability. Aim: This work was designed to identify secondary metabolites present in root extracts of ethno-medicinally utilised Portulaca oleracea L. and evaluate their antibacterial activities. Setting: The roots of P. oleracea L. were obtained from the Forest Research Institute of Nigeria (FRIN), Ibadan, Nigeria and authenticated in the Forest Research Herbarium, where voucher samples were deposited with specimen voucher number FIH-112030. Methods: Phytochemical screening was carried out using standard qualitative tests and the antibacterial activity of extracts was evaluated using agar well diffusion method whilst the minimum inhibitory concentration (MIC) was evaluated by micro-dilution method. The screening was assessed against Bacillus subtilis, Candida albicans, Enterobacter cloacae, Escherichia coli, Klebsiella pneumoniae, Micrococcus luteus, Pseudomonas aeruginosa, Salmonella typhi, Shigella dysenteriae, Staphylococcus aureus and Streptococcus agalactiae , which are responsible for the transmission of common diseases in Nigeria. Statistical analysis was performed by one-way analysis of variance (ANOVA) with GraphPad Prism 8.0 and results were expressed as mean ± s.d. Duncan’s New Multiple range test were applied at 0.05 level of significance ( p < 0.05). Results: Phytochemical screening of P. oleracea L. showed the presence of carbohydrates, steroids, triterpenes, cardiac glycosides, and saponins. All extracts showed a high level of minimum inhibition concentration against the pathogens except K. pneumoniae, M. luteus and P. aeruginosa. Generally the antibacterial activity of extracts increased with decrease in polarity as compared with ciprofloxacin. The mean (± s.d.) values were significantly different by Duncan’s multiple range tests with p < 0.05. Conclusion: Portulaca oleracea L. has been identified for the first time as a good antibacterial agent, which corroborates the ethno-medicinal uses of the plant.

The Genomic Resources Collection Policy of the Finnish Museum of Natural History

The Genomic Resources Collection is a separate, independently managed part of the natural history collections of the Finnish Museum of Natural History Luomus specifically intended for consumptive research. The GRC policy deals with the materials that are archived for the very purpose of enabling the study of biological diversity at the genome level, DNA extractions of animal, fungal and plant specimens, and animal tissue samples stored deep-frozen for purposes of future DNA extraction. The GRC policy defines the purpose of the collections, the objectives and content of the procedures and activities related to them, the distribution of responsibilities for collection management and maintenance in Luomus, and the principles of collection accumulation, preservation and accessibility. The aim of the GRC is to store and loan genomic samples for research purposes. In taxonomic coverage the collection overlaps with all the taxonomically delimited specimen collections managed by the Zoology and Botany Units, but is distinguished as being directed to preserve the genomic (DNA) information irrespective of the phenotypic variation that are the focus of specimen collections. The GRC includes both Finnish and foreign samples, all legally and ethically obtained, mostly linked to a specimen voucher in the taxonomic collections. The GRC samples are documented and trackable in Luomus collections management system. In accordance with the Universities Act, the GRC belongs to the national natural science collections of Luomus. For their part, the GRC collection implement the mission of Luomus, which is to be “responsible for the preservation, accumulation and exhibition of the national natural history collections and for research and education relating to them”.

Progress Out of a Pandemic: Global collections, data sharing, and changing standards of practice

The COVID-19 pandemic has disrupted all aspects of our lives, but has also spawned new opportunities. Months of multidisciplinary, global collaboration have explored the connections between natural history collections and COVID-19. Museums have unrivalled (and still largely untapped) potential to contribute data, methods, and expertise to prediction, mitigation, and prevention efforts related to zoonotic disease outbreaks (DiEuliis et al. 2016, Dunnum et al. 2017), and there is a clear need for ongoing collaboration across (at least) microbiology, disease ecology, and natural history collections. In addition, we note that the roadblocks to effective data access and integration related to microbes and their hosts are a microcosm of the larger data landscape; solving these issues in the context of COVID-19—from liberating data from publications to ensuring digital connections between voucher specimens and all derived viral genetic sequences—will improve biodiversity data access and use more broadly. Efforts since March 2020 have promoted collaboration across disciplines, international boundaries, and continents. At iDigBio, staff updated information about genetic/genomic resources available in US mammal collections; 24 records were added and information enhanced (Cortez and Soltis 2020). The Distributed System of Scientific Collections (DiSSCo) and the Consortium of European Taxonomic Facilities (CETAF) formed a worldwide COVID-19 Task Force (TaF). A US-led group formed the ViralMuse Task Force, working in concert with the TaF. Activities of the TaF centered on four areas: building a hub to coalesce knowledge from this group in a central location – including mining mammals-of-the-world literature, improving the metadata shared when publishing sequence data, encouraging virologists to voucher in museum collections, and gathering critical research questions around zoonotic disease from the scientific community. Through an online public event, this TaF shared work to date and critical next steps. Ongoing efforts include further refinement of metadata requirements for deposition of viral genetic data to include host specimen voucher identifiers, development of methods for better integration of bat and pathogen data from the literature and databases, analysis of community surveys, and development of webinars, symposia, and publications to report the work of the TaF. Members of the ViralMuse group worked to raise awareness of the critical value of and need for museum experts, collections data, and samples in any analyses of zoonotic events. ViralMuse members (Cook et al. 2020) stressed the need for collaborative action to: develop guidelines for keeping samples of both pathogens and hosts. develop and implement metadata requirements for physical specimens and samples. expand investment in infrastructure, both cyber and physical, to support archives of biological materials. increase communication and development of new channels of dialogue and collaboration among museum scientists, microbiologists, bioinformaticians, biomedical professionals, and disease ecologists. enhance financial support and realize strong leadership from federal agencies, international partners, and private foundations to develop proactive, multi-disciplinary approaches to future pandemics (see also da Silva et al. 2020). develop guidelines for keeping samples of both pathogens and hosts. develop and implement metadata requirements for physical specimens and samples. expand investment in infrastructure, both cyber and physical, to support archives of biological materials. increase communication and development of new channels of dialogue and collaboration among museum scientists, microbiologists, bioinformaticians, biomedical professionals, and disease ecologists. enhance financial support and realize strong leadership from federal agencies, international partners, and private foundations to develop proactive, multi-disciplinary approaches to future pandemics (see also da Silva et al. 2020). ViralMuse continues to advance these goals. To reach a broader audience, we published an article in The Conversation (Soltis et al. 2020). A new project, funded by the US National Science Foundation (NSF), is aimed at enhancing existing published museum specimen data relevant to one potential reservoir of SARS-CoV-2, horseshoe bats (Mast and Paul 2020). NSF has also provided support to foster continued collaboration, infrastructure development, and integration of communities of practice concerning zoonotic diseases (Soltis and Paul 2020). From a TDWG perspective, issues relating to data access, data standards, and data integration require attention. Methods to liberate data from publications need to be expanded, and proposed metadata requirements for viral genetic sequences need to be implemented by international databases and adopted by the community. A summit on collections management software could help align efforts to both store and share the necessary host-pathogen information in standards-compliant formats that support discovery, access, and citation/attribution. A new and effective communication strategy is needed to develop an integrated research community (comprising the biodiversity, collections, data science, disease ecology, microbiology, and One Health communities) and to support needed changes in standards of practice (emphasizing vouchering, data standards, and data integration).

Preliminary Study on Tree Species Composition, Diversity and Biomass of Dipterocarpus and Hopea genera of Bukit Bakar Forest Eco Park, Machang, Kelantan

A study on species composition, diversity and biomass of genera Dipterocarpus and Hopea at Bukit Bakar Forest Eco Park, Machang, Kelantan was conducted. A total of 5 ecological plots with measurement of 20 m x 20 m were established. All trees with diameter at breast height (dbh) less than 5.0 cm were tagged, measured and collected for specimen identifications and voucher specimen’s preparations. The floristic composition of Bukit Bakar Eco Park consists of 135 individuals represented by 1 family, 2 genera and 17 species. The most abundance species recorded was Dipterocarpus crinitus Dyer with 23 individuals were recorded. Dipterocarpus crinitus (Dipterocarpaceae) was the most important species according to Important Value index (IVi) calculated at IVi = 17.73%. Dipterocarpaceae was the most high species diversity according to Shannon Wiener Index, H’=2.02 (H’ max =2.30) for Dipterocarpus spp. and H’=1.90 (H’ max =1.94) for Hopea spp. and Simpson’s Index of Diversity for Dipterocarpus spp. is 0.85 and 0.86 for Hopea spp.. Whilst Hopea had a slightly higher Species Evenness Index (EH=0.98) compared to Dipterocarpus (EH=0.87). Total tree biomass estimation in the study area was at 145.18 t/ha.

Fishes collected during the 2017 MarineGEO assessment of Kāne‘ohe Bay, O‘ahu, Hawai‘i

AbstractWe report the results of a survey of the fishes of Kāne‘ohe Bay, O‘ahu, conducted in 2017 as part of the Smithsonian Institution MarineGEO Hawaii bioassessment. We recorded 109 species in 43 families. The most speciose families were Acanthuridae (11 species), Gobiidae (11 species), Pomacentridae (10) and Chaetodontidae (9 species). Nine of the species that we collected are known or suspected to be introduced to the Hawaiian Islands. Specimens were identified, measured and photographed. All specimen vouchers were fixed in formalin and ultimately transferred to 75% ethanol for long-term storage. For nearly all species, we took multiple tissue samples from specimen vouchers prior to formalin-fixation; we preserved tissues in 95% ethanol and then stored them at −80°C. The 5′-end of the mitochondrial cytochrome oxidase I gene (mtCOI) was sequenced for 94 species to confirm their taxonomic identification. Using these barcode sequences, we also measured genetic distances between collected individuals and their conspecifics from other localities outside Hawaii to verify the hypothesis that Hawaiian populations of species broadly distributed throughout the Indo-Pacific may be genetically distinct. We present select case studies to demonstrate the potential for undiscovered endemism in the Hawaiian fish biota.

A PRELIMINARY CHECKLIST OF Ficus L. SPECIES IN KUANTAN, PAHANG

Ficus is the largest genus in the Moraceae family, with more than 700 species worldwide. It was classified into a distinct genus based on the unique nature of its inflorescence. Until recently, there was no official record of the Ficus checklist in Kuantan, Pahang. Therefore, this study aims to develop the preliminary checklist of Ficus species in Kuantan Pahang. Plant samples were collected from selected areas of Kuantan. Plant samples were pressed, dried and mounted on a herbarium board and processed as specimen vouchers. Based on this study, 14 species of Ficus were recorded. The list of Ficus presented in this study could be used for future research and as a reference source for conservation activities.

Current situation of DNA Barcoding data in biodiversity and genomics databases and data integration for museomics

The museomics activity regards museum-preserved specimens as rich resources for DNA studies by extracting and analyzing DNA from these specimens in conjunction with their biodiversity information. Also in biodiversity field, DNA sequence data such as DNA barcoding has become essential as evidence for species identification and phylogenetic analysis as well as occurrence and morphological information. To accelerate biodiversity informatics, it is important to utilize both biodiversity occurrence and morphology data, and bioinformatics sequencing data. There are many databases for biodiversity domain such as GBIF (The Global Biodiversity Information Facility) for species occurrence records, EoL (The Encyclopedia of Life) as a knowledge base of all species, and BOLD (The Barcode of Life Data) for DNA barcoding data. In genomics science, molecular data involving DNA and protein sequences have been captured by the DNA Data Bank in Japan (DDBJ), the European Bioinformatics Institute (EBI, UK), and the National Center for Biotechnology Information (NCBI, US) under the International Nucleotide Sequence Database Collaboration (INSDC) for more than 30 years. Recently, NCBI launched a new database called BioCollections, including 7,930 culture collections, museums, herbaria, and other natural history collections. In addition, we can submit biodiversity information such as specimen voucher IDs, BOLD IDs, and latitude/longitude with DNA sequences. To find out the current situation, I downloaded GenBank (Nucleotide) files (updated at 22 Feb 2019) from the NCBI FTP (file transfer protocol) site and extracted biodiversity features including specimen voucher IDs and BOLD IDs. For Insecta, there are 2,427,343 sequence entries with specimen voucher ID and 1,766,142 entries with BOLD ID of 3,389,495 total entries. The most abundant species with voucher IDs is “Cecidomyiidae sp. BOLD−2016” (Diptera) (35,861 sequence entries). The most frequently referred voucher ID is “USNMENT00921257” (1510 sequence entries), indicating Stenamma megamanni (Hymenoptera, Formicidae, Myrmicinae). For flowering plants (Magnoliophyta), of 3,094,140 total entries, 1,109,420 sequence entries are assigned with voucher IDs and 73,409 entries with BOLD IDs. Additionally, 79,891 matK entries and 63,821 rbcL entries are submitted with voucher IDs, without BOLD IDs. I also retrieved BOLD data for Insecta and flowering plants. The 2,368,801 GenBank entries are referred from 4,176,481 BOLD total entries for Insecta, and the 259,245 GenBank entries from 345,706 BOLD entries for flowering plants. Some DNA barcoding data exist redundantly in BOLD database because BOLD imports sequences from NCBI submitted as DNA barcoding data in BOLD. These entries have different BOLD IDs but same BIN_URL is assigned. Recently, high-throughput sequencing technology, also called next-generation sequencing technology (NGS), has made a great impact in genomic science. Biodiversity researchers became to perform not only DNA barcoding but also RNA-Seq with NGS. NGS also accelerates museomics activity. NGS data are archived to the Sequence Read Archive (SRA) database, and sample information is described in BioSample database in INSDC. To utilize NGS data for biodiversity field, we will need to integrate such databases and other biodiversity databases. We, Database Center for Life Science, tackle to integrate life science data with Semantic Web technology. We held annual meetings to integrate life science data, called BioHackathons, in which researchers from all over the world participated. We began to RDFize BioSample data, but we should import existing schemes used in the biodiversity field including Darwin Core.

Application of matrix-assisted laser desorption/ionization mass spectrometry to identify species of Neotropical Anopheles vectors of malaria

BackgroundMalaria control in Panama is problematic due to the high diversity of morphologically similar Anopheles mosquito species, which makes identification of vectors of human Plasmodium challenging. Strategies by Panamanian health authorities to bring malaria under control targeting Anopheles vectors could be ineffective if they tackle a misidentified species.MethodsA rapid mass spectrometry identification procedure was developed to accurately and timely sort out field-collected Neotropical Anopheles mosquitoes into vector and non-vector species. Matrix-assisted laser desorption/ionization (MALDI) mass spectra of highly-abundant proteins were generated from laboratory-reared mosquitoes using different extraction protocols, body parts, and sexes to minimize the amount of material from specimen vouchers needed and optimize the protocol for taxonomic identification. Subsequently, the mass spectra of field-collected Neotropical Anopheles mosquito species were classified using a combination of custom-made unsupervised (i.e., Principal component analysis—PCA) and supervised (i.e., Linear discriminant analysis—LDA) classification algorithms.ResultsRegardless of the protocol used or the mosquito species and sex, the legs contained the least intra-specific variability with enough well-preserved proteins to differentiate among distinct biological species, consistent with previous literature. After minimizing the amount of material needed from the voucher, one leg was enough to produce reliable spectra between specimens. Further, both PCA and LDA were able to classify up to 12 mosquito species, from different subgenera and seven geographically spread localities across Panama using mass spectra from one leg pair. LDA demonstrated high discriminatory power and consistency, with validation and cross-validation positive identification rates above 93% at the species level.ConclusionThe selected sample processing procedure can be used to identify field-collected Anopheles species, including vectors of Plasmodium, in a short period of time, with a minimal amount of tissue and without the need of an expert mosquito taxonomist. This strategy to analyse protein spectra overcomes the drawbacks of working without a reference library to classify unknown samples. Finally, this MALDI approach can aid ongoing malaria eradication efforts in Panama and other countries with large number of mosquito’s species by improving vector surveillance in epidemic-prone sites such as indigenous Comarcas.

<b>Appearances are deceptive: molecular phylogeny recovers the Scaly Gecko <I>Hemidactylus scabriceps</I> (Reptilia: Squamata: Gekkonidae) as a member of a scansorial and rupicolous clade</b>

We reassess the systematics of Hemidactylus scabriceps, a recently rediscovered and poorly known gecko, and elucidate its phylogenetic position using molecular data for the first time. Contrary to previous speculations prompted by its morphological resemblance to other terrestrial Hemidactylus, our phylogenetic analyses recovered H. scabriceps to be a part of a clade consisting of the large-bodied, rock-dwelling Hemidactylus – the H. prashadi group. Hemidactylus scabriceps also shows high levels of intraspecific genetic divergence, indicative of cryptic diversity. We also confirm the synonymy of the monotypic genus Lophopholis (erected for H. scabriceps) with Hemidactylus. We elaborate on the morphology of the type specimen and other recent voucher specimens, and compare it with sister species and other ground-dwelling Hemidactylus in peninsular India. Species distribution of this ‘outlier’ clade member has been modeled using MaxEnt. These exercises confirm that it is primarily a smooth-scaled, plain-dwelling, terrestrial species unlike other members in its clade. This unexpected pattern of genetic alliance and contrasting body form plus habitat associations further underscores the unstudied complexity of peninsular India’s geological history. Historical denudation of rock formations could have driven evolution of some of these otherwise rupicolous, scansorial gekkonids into smaller terrestrial lizards.

Pseudanthias emma new species, with notes on a collection of anthiadine serranid fishes from off Myanmar (eastern Indian Ocean).

Recent exploratory trawling off the coast of Myanmar by the R/V Dr Fridtjof Nansen has resulted in the collection of six species of anthiadine serranid fishes. Four of the species are represented by specimen vouchers: Pseudanthias emma sp. nov., P. gibbosus (Klunzinger), Odontanthias rhodopeplus (Günther) and Plectranthias sp. 1. The remaining two species are represented only by photographs: Plectranthias sp. 2 and Sacura sanguinea Motomura, Yoshida Vilasri. Pseudanthias emma is described from the 107 mm SL holotype. It is distinguished from congeners in having the following combination of characters: dorsal rays X,16; pectoral rays 18; lateral-line scales 42; third dorsal-fin spine longest, prolonged; no papillae on posterior margin of orbit; soft part of dorsal with low scaly sheath; subopercle and interopercle indistinctly serrated; caudal fin weakly concave centrally, with elongate filaments extending from second to uppermost and second to lowermost branched rays. Plectranthias sp. 1 is a probable new species closely allied to P. sagamiensis (Katayama), from which it appears to differ in having fewer segmented dorsal rays and fewer rows of cheek scales. Plectranthias sp. 2 is a probable new species closely allied to P. alcocki Bineesh, Akhilesh, Gopalakrishnan Jena, from which it appears to differ in lacking a large black spot on the operculum and dusky ventral spot on the abdomen. New character, habitat and distribution information is provided for all six species. Pseudanthias vizagensis Krishna, Rao Venu is suggested as a probable junior synonym of P. pillai Heemstra Akhilesh.

VIRMISCO – The Virtual Microscope Slide Collection

Digitisation allows scientists rapid access to research objects. For transparent to semi-transparent three-dimensional microscopic objects, such as microinvertebrates or small body parts of organisms, available databases are scarce. Most mounting media used for permanent microscope slides deteriorate after some years or decades, eventually leading to total damage and loss of the object. However, restoration is labour-intensive, and often the composition of the mounting media is not known. A digital preservation of important material, especially types, is important and an urgent need. The Virtual Microscope Slide Collection – VIRMISCO project has developed recommendations for taking microscopic image stacks of three-dimensional objects, depositing and presenting such series of digital image files or z-stacks as an online platform. The core of VIRMISCO is an online viewer, which enables the user to virtually focus through an object online as if using a real microscope. Additionally, VIRMISCO offers features such as search, rotating, zooming, measuring, changing brightness or contrast, taking snapshots, leaving feedback as well as downloading complete z-stacks as jpeg files or video file. The open source system can be installed by any institution and can be linked to common database or images can be sent to the Senckenberg Museum of Natural History Görlitz. The benefits of VIRMISCO are the preservation of important or fragile material, to avoid loan, to act as a digital archive for image files and to allow determination by experts from the distance, as well as providing reference libraries for taxonomic research or education and providing image series as online supplementary material for publications or digital vouchers of specimens of molecular investigations are relevant applications for VIRMISCO.

The NCBI BioCollections Database.

The rapidly growing set of GenBank submissions includes sequences that are derived from vouchered specimens. These are associated with culture collections, museums, herbaria and other natural history collections, both living and preserved. Correct identification of the specimens studied, along with a method to associate the sample with its institution, is critical to the outcome of related studies and analyses. The National Center for Biotechnology Information BioCollections Database was established to allow the association of specimen vouchers and related sequence records to their home institutions. This process also allows cross-linking from the home institution for quick identification of all records originating from each collection. Database URL: https://www.ncbi.nlm.nih.gov/biocollections

English

The objective of this study is to conduct an ethnobotanical survey of medicinal plants used in management of depression among Hausa tribes in order to establish an informational data base. An ethnobotanical survey was conducted in December 2015 in Zaria, Kaduna State, Nigeria. Data were collected based on an oral interview with the aid of semi structured questionnaire. Only data from willing respondents were obtained and documented. Plant specimens were collected along the line, they were subsequently dried and mounted. It was then taken for identification and authentication in the Herbarium Section of Biological Sciences, Ahmadu Bello University, Zaria where specimen voucher numbers were deposited. Information on sources, safety, methods of preparation and administrations, identity, local and botanical names of medicinal plants used in the management of depression among Hausa tribe of Kaduna State was obtained. An informational database was established and specimen with voucher numbers was deposited in the herbarium. Key words: Ethnobotanical survey, depression, botanical names, medicinal plants, safety.