Revision and annotation of DNA barcode records for marine invertebrates: report of the 8th iBOL conference hackathon

The accuracy of specimen identification through DNA barcoding and metabarcoding relies on reference libraries containing records with reliable taxonomy and sequence quality. The considerable growth in barcode data requires stringent data curation, especially in taxonomically difficult groups such as marine invertebrates. A major effort in curating marine barcode data in the Barcode of Life Data Systems (BOLD) was undertaken during the 8th International Barcode of Life Conference (Trondheim, Norway, 2019). Major taxonomic groups (crustaceans, echinoderms, molluscs, and polychaetes) were reviewed to identify those which had disagreement between Linnaean names and Barcode Index Numbers (BINs). The records with disagreement were annotated with four tags: a) MIS-ID (misidentified, mislabeled, or contaminated records), b) AMBIG (ambiguous records unresolved with the existing data), c) COMPLEX (species names occurring in multiple BINs), and d) SHARE (barcodes shared between species). A total of 83,712 specimen records corresponding to 7,576 species were reviewed and 39% of the species were tagged (7% MIS-ID, 17% AMBIG, 14% COMPLEX, and 1% SHARE). High percentages (>50%) of AMBIG tags were recorded in gastropods, whereas COMPLEX tags dominated in crustaceans and polychaetes. The high proportion of tagged species reflects either flaws in the barcoding workflow (e.g., misidentification, cross-contamination) or taxonomic difficulties (e.g., synonyms, undescribed species). Although data curation is essential for barcode applications, such manual attempts to examine large datasets are unsustainable and automated solutions are extremely desirable.

Dinochloa Scandens (Poaceae-Bambusoideae): Distribution, Habitat Preference, and Notes on Synonymy

The distribution of Dinochloa scandens is unclear. World bamboo checklists suggest it is relatively widespread in Malesia. Here we clarify issues with herbarium specimen identification. Besides, a synonym name of D. scandens, namely D. macrocarpa collected from the Philippines, needs to be reviewed. The study aims to provide information on distribution and to review the synonym of D. scandens. The habitat preferences of D. scandens are also presented. We carried out targeted fieldwork at Gunung Halimun-Salak National Park in West Java in 2019 and extensive examination of herbarium specimens from Herbarium Bogoriense and online portals to accurately circumscribe this species. All data were analyzed descriptively. Distribution, altitude, and rainfall maps for D. scandens were produced with ArcGIS Pro. Our examination on the specimens suggests that D. scandens is indeed endemic to West Java and Banten Provinces in Indonesia. This bamboo species can be found in lowland to mountain forests with an altitude of 20-1400 m, in areas with annual rainfall between 3000-4000 mm. We support D. macrocarpa as an accepted name for a bamboo species from the Philippines and remove it from synonymy with D. scandens due to clear differences in the fruit compared to specimens of D. scandens across its range.

Authentication of garlic (Allium sativum L.) supplements using a trnLUAA mini-barcode

Garlic (Allium sativum), a widely distributed plant with great cultural and medicinal significance, is one of the most popular herbal dietary supplements in Europe and North America. Garlic supplements are consumed for a variety of reasons, including for their purported antihypertensive, antibacterial, and anticarcinogenic effects. The steady increase in the global herbal dietary supplement market paired with a global patchwork of regulatory frameworks makes the development of assays for authentication of these products increasingly important. A DNA mini-barcode assay was developed using the P6 loop of the plastid trnLUAA intron to positively identify A. sativum products. Analysis of 43 commercially available garlic herbal dietary supplements produced mini-barcode sequences for 33 supplements, all of which contained detectable amounts of A. sativum. The trnLUAA P6 mini-barcode can be highly useful for specimen identification, particularly for samples that may contain degraded DNA.

Rare specimen identification in an un-integrated taxonomy: implications of DNA sequences from a Taiwanese Philine (Mollusca, Philinidae)

Many species of the gastropod genus Philine have been named from northeastern Asia but scanty descriptions based predominantly on shells make it difficult to determine which are valid. This, plus the sporadic anatomical and genetic information available for many of these species has led to what may be described as an un-integrated taxonomy. In this situation, it is generally preferable to postpone dissection of rare and unusual specimens until relevant diagnostic characters can be established in broader studies. Micro-CT scanning and DNA sequencing were used to examine such a specimen collected recently from deep waters off northeastern Taiwan. Micro-CT examination of the morphology of the internal shell and gizzard plates suggested that, among named species, the sequenced specimen is most similar to P. otukai. It cannot, however, be definitively referred to P. otukai as that species lacks adequate anatomical description or known DNA sequences. Phylogenetic analyses of newly collected DNA sequences show the specimen to be most closely related to, but distinct from the northern Atlantic Ocean and Mediterranean species, Philine quadripartita. The sequences also confirm genetically that five or more species of Philine occur in northeast Asia, including at least three subject to considerable taxonomic uncertainty.

Morphometrical Analysis of Dry Adult Human Hip Bones by Coxal Index

Background: The hip bone is one of the most useful skeletal elements in adult skeleton for sex determination. Hip bone may be used even when fragmentary for both medico legal and archaeological purposes. The aim of the present study is to measure few morphometric parameters of various hip bones and to assess these values both side wise and gender wise. Method: The present study was conducted in department of Anatomy, Yenepoya Medical College, Mangalore. 100 adult dry human hip bones were included in the study, of which 50 were male and 50 were female hip bones. 50 bones belonged to right side and 50 to left side. The morphometrical parameters measured were length, width and weight of the hip bones. Coxal index was also calculated. Result: Range, mean, median, standard deviation and standard error of mean were determined for each parameter. Conclusions were drawn after comparing the values with series of other workers. Conclusion: The values were slightly higher on the left side compared to the bones of the right side and also the values were more in male bones compared to female bones. The study would help the forensic experts and the anthropologists in specimen identification and sex determination from skeletal remains. It would also be valuable for the anatomists and the orthopedicians in their respective fields. Keywords: Hip bone, morphometry, coxal index, sexual dimorphism, hip bone weight.

Getting science priorities straight: how to increase the reliability of specimen identification?

‘We advise the authors to find a native English speaker to proofread the manuscript’. This is a standard feedback journals give to non-native English speakers. Journals are justifiably concerned with grammar but do not show the same rigour about another step crucial to biological research: specimen identification. Surveying the author guidelines of 100 journals, we found that only 6% of them request explicitly citation of the literature used in specimen identification. Authors hamper readers from contesting specimen identification whenever vouchers, identification methods, and taxon concepts are not provided. However, unclear taxonomic procedures violate the basic scientific principle of reproducibility. The scientific community must continuously look for practical alternatives to improve taxonomic identification and taxonomic verification. We argue that voucher pictures are an accessible, cheap and time-effective alternative to mitigate (not abolish) bad taxonomy by exposing preventable misidentifications. Voucher pictures allow scientists to judge specimen identification actively, based on available data. The popularization of high-quality image devices, photo-identification technologies and computer vision algorithms yield accurate scientific photo-documentation, improving taxonomic procedures. Taxonomy is timeless, transversal and essential to most scientific disciplines in biological sciences. It is time to demand rigour in taxonomic identifications.

Automation and validation of a MALDI-TOF MS (Mass-Fix) replacement of immunofixation electrophoresis in the clinical lab

ObjectivesA matrix assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS) method (Mass-Fix) as a replacement for gel-based immunofixation (IFE) has been recently described. To utilize Mass-Fix clinically, a validated automated method was required. Our aim was to automate the pre-analytical processing, improve positive specimen identification and ergonomics, reduce paper data storage and increase resource utilization without increasing turnaround time.MethodsSerum samples were batched and loaded onto a liquid handler along with reagents and a barcoded sample plate. The pre-analytical steps included: (1) Plating immunopurification beads. (2) Adding 10 μl of serum. (3) Bead washing. (4) Eluting the immunoglobulins (Igs), and reducing to separate the heavy and light Ig chains. The resulting plate was transferred to a second low-volume liquid handler for MALDI plate spotting. MALDI-TOF mass spectra were collected. Integrated in-house developed software was utilized for sample tracking, driving data acquisition, data analysis, history tracking, and result reporting. A total of 1,029 residual serum samples were run using the automated system and results were compared to prior electrophoretic results.ResultsThe automated Mass-Fix method was capable of meeting the validation requirements of concordance with IFE, limit of detection (LOD), sample stability and reproducibility with a low repeat rate. Automation and integrated software allowed a single user to process 320 samples in an 8 h shift. Software display facilitated identification of monoclonal proteins. Additionally, the process maintains positive specimen identification, reduces manual pipetting, allows for paper free tracking, and does not significantly impact turnaround time (TAT).ConclusionsMass-Fix is ready for implementation in a high-throughput clinical laboratory.

Jenis-Jenis Tumbuhan Suku Zingiberaceae di Cagar Alam Pangi Binangga Sulawesi Tengah

(Article History: Received 14 November 2020; Revised 15 December 2020; Accepted 5 January 2021) ABSTRAKPenelitian tentang keanekaragaman jenis jahe-jahean (Zingiberaceae) di Cagar Alam Pangi Binangga telah dilakukan dari bulan Oktober 2019 - Januari 2020. Penelitian bertujuan untuk mengkaji jenis-jenis tumbuhan yang tergolong Zingiberaceae di Cagar Alam Pangi Binangga. Penelitian dilakukan secara survei di lapangan, menggunakan metoda eksplorasi (jelajah). Identifikasi spesimen dilakukan di Laboratorium Biosistematika Tumbuhan Jurusan Biologi Fakultas Matematika dan Ilmu Pengetahuan Alam Universitas Tadulako. Hasil penelitian menunjukan terdapat sebanyak 8 jenis yang terdiri atas 4 marga. Jenis yang ditemukan adalah Alpinia eremoclamis, A. rubricaulis, Alpinia sp1, Alpinia sp2, Etlingera tubilabrum, Etlingera sp., Sulettaria sp. dan Zingiber sp.Kata kunci: Cagar Alam Pangi Binangga; Sulawesi Tengah; Zingiberaceae ABSTRACTResearch on Diversity of ginger (Zingiberaceae) in the Pangi Binangga Nature Reserve has been carried out from October 2019 - January 2020. The research was aimed to determine the species of plants belong to Zingiberaceae family in the Pangi Binangga Nature Reserve. The study was conducted by survey in the field, using exploration methods (exploring). Specimen identification was carried out at the Plant Biosystematics Laboratory, Department of Biology, Faculty of Mathematics and Natural Sciences, Tadulako University. The results showed as many as 8 species consisting of 4 genera. The species found were Alpinia eremoclamis, A. rubricaulis, Alpinia sp1, Alpinia sp2, Etlingera tubilabrum, Etlingera sp., Sulettaria sp. dan Zingiber sp.Keywords: Pangi Binangga Nature Reserve; Central Sulawesi; Zingiberaceae

COI and ND1 as DNA barcodes to identify Taenia hydatigena (Cestoda: Taeniidae) from canine small intestine on Hainan Island in China

DNA barcoding based on universal gene markers is a fast, accurate, and innovative approach for the molecular discrimination of species. Some species are particularly difficult to discriminate using a traditional morphological identification method because of severely damaged morphological features. In this study, cytochrome c oxidase subunit I (COI) and NADH dehydrogenase subunit 1 (ND1) were used as barcoding markers to distinguish Taenia hydatigena in dogs on the tropical island of Hainan. Therefore, geographic differentiation based on the COI and ND1 sequences amongst the specimens and other geographic isolates in GenBank was determined by calculating the genetic distances according to the Kimura 2-parameter (K2P) model and constructing a phylogenetic tree using the neighbour-joining (NJ) method. Barcoding gap, base composition, and base saturation were tested to assess the effectiveness of the barcoding marker COI and ND1 genes for specimen identification. In addition, we analysed the barcoding gap and saturation and performed molecular evolutionary analysis of the intraspecies and interspecies diversity of Taenia.

DNA barcoding for identification of anuran species in the central region of South America

The use of COI barcodes for specimen identification and species discovery has been a useful molecular approach for the study of Anura. Here, we establish a comprehensive amphibian barcode reference database in a central area of South America, in particular for specimens collected in Mato Grosso do Sul state (Brazil), and to evaluate the applicability of the COI gene for species-level identification. Both distance- and tree-based methods were applied for assessing species boundaries and the accuracy of specimen identification was evaluated. A total of 204 mitochondrial COI barcode sequences were evaluated from 22 genera and 59 species (19 newly barcoded species). Our results indicate that morphological and molecular identifications converge for most species, however, some species may present cryptic species due to high intraspecific variation, and there is a high efficiency of specimen identification. Thus, we show that COI sequencing can be used to identify anuran species present in this region.