Reference Database Research Articles

ITaxoTools 1.0: Improved DNA Barcode Exploration with TaxI2.

The overall availability of user-friendly software tools tailored to the analysis of DNA barcodes is limited. Several obvious functions such as detecting and visualizing the DNA barcode gap, the calculation of matrices of pairwise distances at the level of species, or the filtering and decontaminating of sets of sequences based on comparisons with reference databases can typically be carried out only by complex procedures that involve various programs and/or a substantial manual work of formatting. The iTaxoTools project aims at contributing user-friendly software solutions to improve the speed and quality of the workflow of alpha-taxonomy. In this chapter, we provide detailed protocols for the use of a substantially improved version of the tool TaxI2 for distance-based exploration of DNA barcodes. The program calculates genetic distances from prealigned data sets, or based on pairwise alignments, or with an alignment-free approach. Sequence and metadata input can be formatted as tab-delimited files and TaxI2 then computes tables, matrices and graphs of distances, and distance summary statistics within and between species and genera. TaxI2 also includes modes to compare a set of sequences against one or two reference data sets and output lists of best matches or filter data according to thresholds or reciprocal matches. Here, detailed step-by-step protocols are provided for the use of TaxI2, as well as for the interpretation of the program's output.

Comparison of traditional and molecular surveys of fish biodiversity in southern Te Wāhipounamu/Fiordland (Aotearoa/New Zealand)

AbstractEffective management of biodiversity requires regular surveillance of multiple species. Analysis of environmental DNA (eDNA) by metabarcoding holds promise to achieve this relatively easily. However, taxonomy‐focused eDNA surveys need suitable molecular reference data, which are often lacking, particularly at the species level and for remote locations. To evaluate the comparability of environmental DNA surveys and traditional surveys in a real‐life case study in a marine area of high conservation value, we conducted a biodiversity survey of the fish in remote and pristine Te Wāhipounamu/Fiordland (Aotearoa/New Zealand), incorporating multiple data sources. We compared eDNA‐derived species identifications against Baited Remote Underwater Video (BRUV) data collected at the same time and locations as eDNA. We also cross‐referenced both eDNA and BRUV data against literature and the Ocean Biodiversity Information System (OBIS), with literature and OBIS data representing a summary of multiple traditional surveying approaches. In total, we found 116 fish species in our study area. Environmental DNA detected 43 species; however, only three of those species overlap with species known from the literature, OBIS, or our BRUV analyses. A total of 61 fish species were known from the region from the literature, while OBIS listed 28 species, and our BRUV analyses picked up 26 species. BRUV data coincided more strongly than eDNA data with literature and OBIS data. Twenty of the 26 species detected by BRUV were known from literature and OBIS. We argue that limitated DNA reference databases are the main cause of this discrepancy, and our results indicate that eDNA of rare and endangered species can be detected if matching reference data were available. Environmental DNA analyses can only identify species present among reference data and with relaxed taxonomic assignment parameters may converge on relatives of detected species if the actually existing species themselves are missing among reference data. However, the high number of species detected by our eDNA analyses confirms that eDNA could be a powerful tool for biodiversity surveys if suitable investments in local reference databases were made.

Dynamic Life Cycle Assessment Framework of Cold Food Storage Facilities

The imperative of responding to anthropogenic climate change that is driving energy infrastructure managers to implement resilience enhancing policies such as hourly scale dynamic pricing concurrently drives energy intensive industries to monitor energy usage at higher fidelity. This study proposes a Dynamic Life Cycle Assessment (DLCA) framework specifically tailored for cold food storage facilities which provide essential thermodynamic resilience to the human food web and consumes a large share of the web's energy footprint. Different from the conventional LCA, which delivers a snapshot of the environmental impacts and cost statically, DLCA can accommodate temporal variations in operating conditions and energy usage. It interacts with real-time monitoring data and fluctuating energy rates to provide a more accurate and time-sensitive environment impact and cost evaluation. Key parameters from real-time sensors and reference databases are summarized to lay the foundation for DLCA of cold food storage, like operating power and hours, shipment arrival time, and transportation fuel economy. Its feasibility and reliability are validated by scenarios that simulate different operating conditions, like shift change to utilize off-peak rate and change of packaging materials. The proposed framework allows facility operators and policymakers to pinpoint bottlenecks and seize opportunities for environmental impact and cost reduction.

Comparative genomics of the Natural Killer Complex in carnivores.

The mammalian Natural Killer Complex (NKC) harbors genes and gene families encoding a variety of C-type lectin-like proteins expressed on various immune cells. The NKC is a complex genomic region well-characterized in mice, humans and domestic animals. The major limitations of automatic annotation of the NKC in non-model animals include short-read based sequencing, methods of assembling highly homologous and repetitive sequences, orthologues missing from reference databases and weak expression. In this situation, manual annotations of complex genomic regions are necessary. This study presents a manual annotation of the genomic structure of the NKC region in a high-quality reference genome of the domestic cat and compares it with other felid species and with representatives of other carnivore families. Reference genomes of Carnivora, irrespective of sequencing and assembly methods, were screened by BLAST to retrieve information on their killer cell lectin-like receptor (KLR) gene content. Phylogenetic analysis of in silico translated proteins of expanded subfamilies was carried out. The overall genomic structure of the NKC in Carnivora is rather conservative in terms of its C-type lectin receptor gene content. A novel KLRH-like gene subfamily (KLRL) was identified in all Carnivora and a novel KLRJ-like gene was annotated in the Mustelidae. In all six families studied, one subfamily (KLRC) expanded and experienced pseudogenization. The KLRH gene subfamily expanded in all carnivore families except the Canidae. The KLRL gene subfamily expanded in carnivore families except the Felidae and Canidae, and in the Canidae it eroded to fragments. Knowledge of the genomic structure and gene content of the NKC region is a prerequisite for accurate annotations of newly sequenced genomes, especially of endangered wildlife species. Identification of expressed genes, pseudogenes and gene fragments in the context of expanded gene families would allow the assessment of functionally important variability in particular species.

Mass spectrometry imaging in plants, microbes, and food: a review.

Plant health, which affects the nutritional quality and safety of derivative food products, is influenced by symbiotic interactions with microorganisms. These interactions influence the local molecular profile at the tissue level. Therefore, studying the distribution of molecules within plants, microbes, and plant-based food is crucial to assess plant health, ensure the safety and quality of the agricultural products that become part of our food supply, and plan agricultural management practices. Within this framework, the molecular distribution within plant-based samples can be visualized with mass spectrometry imaging (MSI). This review describes key MSI methodologies, highlighting the role they play in unraveling the localization of metabolites, lipids, proteins, pigments, and elemental components across plants, microbes, and food products. Furthermore, investigations that involve multimodal molecular imaging approaches combining MSI with other imaging techniques are described. The advantages and limitations of the different MSI techniques that influence their applicability in diverse agro-food studies are described to enable informed choices for tailored analyses. For example, some MSI technologies involve meticulous sample preparation while others compromise spatial resolution to gain throughput. Key parameters such as sensitivity, ionization bias and fragmentation, reference database and compound class specificity are described and discussed in this review. With the ongoing refinements in instrumentation, data analysis, and integration of complementary techniques, MSI deepens our insight into the molecular biology of the agricultural ecosystem. This in turn empowers the quest for sustainable and productive agricultural practices.

A rapid determination of wheat flours components based on near infrared spectroscopy and chemometrics

In this work, a rapid and simple analytical method for the quantitative determination of moisture, protein, wet gluten, starch and sedimentation index in the wheat flour was established by the combination of near infrared spectroscopy and chemometrics. The spectra of the 229 wheat flour samples were collected by a portable near infrared fast analyzer. The contents of these components were determined according to the relevant Chinese National Standards, and were taken as the corresponding reference database. Seven spectral pretreatment methods were employed to eliminate the optical interference from background and other noise information. The best result was obtained with FD+SG(15, 3)+MC method for moisture, protein, wet gluten and sedimentation index, FD+SG(15, 2)+MC method was more suitable for starch. The principal component numbers (PCs) were also optimized to obtain a superior model effect. Furthermore, partial least squares (PLS) and multiple linear regression (MLR) modeling methods were used to quantify the content of the components. When using FD+SG(15, 3)+MC pretreatment, all the PLS model parameters were significantly better than the MLR model. Both the predicted values and the reference values showed superior linear relationship within the calibration range. Moreover, the absolute error of the predicted values and their corresponding reference values in the PLS model were within their confidence intervals, respectively. The relative errors for moisture, protein, wet gluten and starch fluctuated little, only sedimentation index fluctuated greatly. The actual prediction correct rate of moisture, protein, wet gluten, starch and sedimentation index were 96.8%, 96.8%, 90.3%, 100.0% and 80.6%, respectively, which indicated the prediction was excellent.

Full-Length Characterization of Novel HLA-DRB1 Alleles for Reference Database Submission.

The prerequisite for successful HLA genotyping is the integrity of the large allele reference database IPD-IMGT/HLA. Consequently, it is in the laboratories' best interest that the data quality of submitted novel sequences is high. However, due to its long and variable length, the gene HLA-DRB1 presents the biggest challenge and as of today only 16% of the HLA-DRB1 alleles in the database are characterized in full length. To improve this situation, we developed a protocol for long-range PCR amplification of targeted HLA-DRB1 alleles. By subsequently combining both long-read and short-read sequencing technologies, our protocol ensures phased and error-corrected sequences of reference grade quality. This dual redundant reference sequencing (DR2S) approach is of particular importance for correctly resolving the challenging repeat regions of DRB1 intron1. Until today, we used this protocol to characterize and submit 384 full-length HLA-DRB1 sequences to IPD-IMGT/HLA.

City council help desk support system

The City Council Help Desk Support System is a comprehensive web-based software designed to assist city residents with complaints, queries, and services. This system enhances the efficiency of the City Council and improves the quality of life for citizens by addressing various issues, including fire alerts from specific locations, waste management, community grievances, interference with protected vegetation, and traffic light damage reports. Each query submitted through the portal is stored in a database for future reference. The system's AI-based chatbot provides support by offering relevant information even in the absence of staff. By leveraging digital and internet technologies, this system significantly reduces response times and automates processes across administrative, user, and staff modules. The project utilizes Agile methodology, emphasizing incremental delivery, team collaboration, continual planning, and learning to ensure value delivery at each stage. This paper explores the system's detailed functionalities, its application of Agile principles, and the results of its real-world implementation.

A rotationally-driven dynamic solid phase sodium bisulfite conversion disc for forensic epigenetic sample preparation.

The approaches to forensic human identification (HID) are largely comparative in nature, relying upon the comparison of short tandem repeat profiles to known reference materials and/or database profiles. However, many profiles are generated from evidence materials that either do not have a reference material for comparison or do not produce a database hit. As an alternative to individualizing analysis for HID, researchers of forensic DNA have demonstrated that the human epigenome can provide a wealth of information. However, epigenetic analysis requires sodium b̲is̲ulfite c̲onversion (BSC), a sample preparation method that is time-consuming, labor-intensive, prone to contamination, and characterized by DNA loss and fragmentation. To provide an alternative method for BSC that is more amenable to integration with the forensic DNA workflow, we describe a rotationally-driven, microfluidic method for dynamic solid phase-BSC (dSP-BSC) that streamlines the sample preparation process in an automated format, capable of preparing up to four samples in parallel. The method permitted decreased incubation intervals by ∼36% and was assessed for relative DNA recovery and conversion efficiency and compared to gold-standard and enzymatic approaches.

Enhancing the Value of Library through Facilities Management Understanding

Leading libraries been impacted by a number of significant technological developments and trends, as well as by the difficulties presented by outside forces like the COVID-19 pandemic. The Ministry of Higher Education Malaysia has received less money from the government since 2016. Fund allocation for libraries has also decreased concurrently. The reduction on government’s funding allocation has made it difficult for the libraries in Universiti Teknologi Malaysia particularly to manage its operations and facilities, placing restrictions on book purchases and reducing its online database. In managing every facility in the libraries such Perpustakaan Sultanah Zanariah (PSZ), Universiti Teknologi Malaysia and Perpustakaan Raja Zarith Sofea (PRZS), Universiti Teknologi Malaysia, the facility manager must use the available financial resources wisely. The goal of this study is to identify libraries facilities management expenses that the library’s management team can reduce. Content analysis and thematic analysis applied in this study in analysing the data gathered from interviews with 5 library staff. According to the findings of this study, both libraries provide a variety of facilities, including a lobby, room, discussion room, showroom, seminar room, meeting room, foyer, 24-hour study room, information search laboratory, database reference room, exhibition space, and audio visual room. Both libraries management expenses, which include library system maintenance, book repair, reference book purchases, database subscriptions, and expenses for purchasing and repairing computers and printers, have been identified and can be reduced accordingly by the management team. Overall, both libraries have to adapt to changing technological, social, and economic conditions while remaining committed to their mission of providing access to information, promoting lifelong learning, and fostering a sense of community.

Surveying lichen diversity in forests: A comparison of expert mapping and eDNA metabarcoding of bark surfaces.

Lichens are an important part of forest ecosystems, contributing to forest biodiversity, the formation of micro-niches and nutrient cycling. Assessing the diversity of lichenised fungi in complex ecosystems, such as forests, requires time and substantial skills in collecting and identifying lichens. The completeness of inventories thus largely depends on the expertise of the collector, time available for the survey and size of the studied area. Molecular methods of surveying biodiversity hold the promise to overcome these challenges. DNA barcoding of individual lichen specimens and bulk collections is already being applied; however, eDNA methods have not yet been evaluated as a tool for lichen surveys. Here, we assess which species of lichenised fungi can be detected in eDNA swabbed from bark surfaces of living trees in central European forests. We compare our findings to an expert floristic survey carried out in the same plots about a decade earlier. In total, we studied 150 plots located in three study regions across Germany. In each plot, we took one composite sample based on six trees, belonging to the species Fagussylvatica, Piceaabies and Pinussylvestris. The eDNA method yielded 123 species, the floristic survey 87. The total number of species found with both methods was 167, of which 48% were detected only in eDNA, 26% only in the floristic survey and 26% in both methods. The eDNA contained a higher diversity of inconspicuous species. Many prevalent taxa reported in the floristic survey could not be found in the eDNA due to gaps in molecular reference databases. We conclude that, currently, eDNA has merit as a complementary tool to monitor lichen biodiversity at large scales, but cannot be used on its own. We advocate for the further development of specialised and more complete databases.

Comparison of Metabarcoding Techniques for Dietary Assessment in Herbivores and Omnivores

Dietary assessment plays a crucial role in comprehending the ecological dynamics and nutritional needs of herbivores and omnivores. The metabarcoding technique has emerged as a potent tool for exploring the dietary composition of these animals. However, various metabarcoding techniques have been developed, each with its own advantages and limitations. This study aims to compare the performance of different metabarcoding techniques in herbivores and omnivores diet. We systematically reviewed 159 published manuscripts in Scopus and Google Scholar, and thematic analysis was conducted across several categories, including the marker, platform, and database utilized. Preliminary findings reveal significant variations among metabarcoding techniques across these two animal groups. The trnL gene exhibited higher taxonomic resolution for herbivorous species, whereas the combination of the 'trnL + 16s rRNA' gene exhibited superior performance for omnivorous species. The Illumina platform emerged as the most commonly used method for analyzing the diets of both herbivores and omnivores, with the primary reference database being the National Centre for Biotechnology Information (NCBI). This study offers valuable insights into the strengths and limitations of different metabarcoding techniques for dietary assessment in herbivores and omnivores and optimizing metabarcoding protocols, facilitating more precise and reliable diet analyses within these ecological groups.

Sketched reference databases for genome-based taxonomy and comparative genomics.

The analysis of curated genomic, metagenomic and proteomic data is of paramount importance in the fields of biology, medicine, education, and bioinformatics. Although this type of data is usually hosted in raw format on free international repositories, the full access requires lots of computing power and large storage disk space for the domestic user. The purpose of the study is to offer a comprehensive set of microbial genomic and proteomic reference databases in an accessible and easy-to-use form to the scientific community and demonstrate its advantages and usefulness. Also, we present a case study on the applicability of the sketched data, for the determination of overall genomic coherence between two members of the Brucellacea family, which suggests they belong to the same genomospecies that remain as discrete ecotypes. A representative set of genomes, proteomes (from type material), and metagenomes were directly collected from the NCBI Assembly database and Genome Taxonomy Database (GTDB), associated with the major groups of Bacteria, Archaea, Virus, and Fungi. Sketched databases were subsequently created and stored on handy reduced representations by using the MinHash algorithm implemented in Mash software. The obtained dataset contains more than 133 GB of space disk reduced to 883.25 MB and represents 125,110 genomics/proteomic records from eight informative contexts, which have been prefiltered to make them accessible, usable, and user-friendly with limited computational resources. Potential uses of these sketched databases are discussed, including but not limited to microbial species delimitation, estimation of genomic distances and genomic novelties, paired comparisons between proteomes, genomes, and metagenomes; phylogenetic neighbor's exploration and selection, among others.

Health risk analysis of heavy metal exposure bonded in PM2.5 at industrial area in Bandung Regency

Heavy metal contents in PM2.5 particulate dust poses potential risk to the health of human beings. This study aims to measure PM2.5 dust concentrations and characterize heavy metals bound in PM2.5 to estimate health risks in both children and adult groups. PM2.5 dust was measured in Bandung Regency in industrial land uses, located in the Dayeuhkolot sub-district. Measurement of PM2.5 concentrations using a Low Volume Air Sampler (LVAS) with PTFE filters. Sample was collected for 7 days x 24 hours. Heavy metals in PM2.5 dust were characterized using ED-XRF. Calculation of non-carcinogenic and carcinogenic health risks was only performed on metals classified as Hazardous Air Pollutants (HAPs). The average concentration of PM2.5 during the measurement period was 59,10±9,10 μg/m3, exceeding the daily ambient air quality standard based on PP No.22 of 2021 which is> 55μg/m3. The risk of non-carcinogenicity is expressed in Health Index (HI) values. The heavy metals considered in determining non-carcinogenic risk are As, Cd, Cr, Pb, Mn, Ni, Se, Fe, Zn, Si, and Sb as well as the crustal elements Si and Fe. Non-carcinogenic risk associated with exposure to heavy metals in PM2.5 showed HI<1 for both children and adults. This indicates that the exposure to heavy metals in PM2.5 around the Dayeuhkolot industrial area is at an acceptable risk level. HI value for heavy metal exposure for children was 0.34±0.17 and 0.42±0.28 for adults. In estimating the carcinogenic risk value, elements taken into account include As, Cd, Cr, Ni and Pb. Carcinogenic risk in both children and adults showed ECR>10-6 of 4.5×10-5 and 2.1×10-4, respectively. This indicates that there is an unsafe health risk that can potentially cause carcinogenic effects in the population around the Dayeuhkolot industrial area The results of this study can be used as a reference database for establishing policies related to air quality in Bandung Regency.

CHAMP delivers accurate taxonomic profiles of the prokaryotes, eukaryotes, and bacteriophages in the human microbiome.

Accurate taxonomic profiling of the human microbiome composition is crucial for linking microbial species to health outcomes. Therefore, we created the Clinical Microbiomics Human Microbiome Profiler (CHAMP), a comprehensive tool designed for the profiling of prokaryotes, eukaryotes, and viruses across all body sites. CHAMP uses a reference database derived from 30,382 human microbiome samples, covering 6,567 prokaryotic and 244 eukaryotic species, as well as 64,003 viruses. We benchmarked CHAMP against established profiling tools (MetaPhlAn 4, Bracken 2, mOTUs 3, and Phanta) using a diverse set of in silico metagenomes and DNA mock communities. CHAMP demonstrated unparalleled species recall, F1 score, and significantly reduced false positives compared to all other tools benchmarked. The false positive relative abundance (FPRA) for CHAMP was, on average, 50-fold lower than the second-best performing profiler. CHAMP also proved to be more robust than other tools at low sequencing depths, highlighting its application for low biomass samples. Taken together, this establishes CHAMP as a best-in-class human microbiome profiler of prokaryotes, eukaryotes, and viruses in diverse and complex communities across low and high biomass samples. CHAMP profiling is offered as a service by Clinical Microbiomics A/S and is available for a fee at https://cosmosidhub.com.

Speeding genomic island discovery through systematic design of reference database composition.

Genomic islands (GIs) are mobile genetic elements that integrate site-specifically into bacterial chromosomes, bearing genes that affect phenotypes such as pathogenicity and metabolism. GIs typically occur sporadically among related bacterial strains, enabling comparative genomic approaches to GI identification. For a candidate GI in a query genome, the number of reference genomes with a precise deletion of the GI serves as a support value for the GI. Our comparative software for GI identification was slowed by our original use of large reference genome databases (DBs). Here we explore smaller species-focused DBs. With increasing DB size, recovery of our reliable prophage GI calls reached a plateau, while recovery of less reliable GI calls (FPs) increased rapidly as DB sizes exceeded ~500 genomes; i.e., overlarge DBs can increase FP rates. Paradoxically, relative to prophages, FPs were both more frequently supported only by genomes outside the species and more frequently supported only by genomes inside the species; this may be due to their generally lower support values. Setting a DB size limit for our SMAll Ranked Tailored (SMART) DB design speeded runtime ~65-fold. Strictly intra-species DBs would tend to lower yields of prophages for small species (with few genomes available); simulations with large species showed that this could be partially overcome by reaching outside the species to closely related taxa, without an FP burden. Employing such taxonomic outreach in DB design generated redundancy in the DB set; as few as 2984 DBs were needed to cover all 47894 prokaryotic species. Runtime decreased dramatically with SMART DB design, with only minor losses of prophages. We also describe potential utility in other comparative genomics projects.

Optic disc morphology and interocular symmetry in children.

The purpose of the study was to obtain a pediatric reference database for optic disc parameters and interocular symmetry. To ascertain factors that modify these parameters (age, spherical equivalent [SE], and sex). This was a cross-sectional study. 90 patients aged 5-17 years fulfilled all the inclusion criteria. After a full examination including cycloplegic refraction, all patients underwent optical coherence tomography (OCT) of the papilla using the three-dimensional (3D) scan protocol of the Topcon 3D 2000 OCT device. We provide reference values for optic disc parameters in the pediatric population. We also retrieved interocular symmetry reference values for these parameters. The multivariate regression analysis did not reveal variations in any of the optic disc parameters associated with age, sex, or SE (all P ≥ 0.126). The 95th percentile limit for absolute interocular differences for the cup-to-disc area ratio was 0.24. The multivariate regression analysis revealed the absence of a correlation between asymmetry of the optic disc parameters and age, sex, and the interocular difference in SE (all P ≥ 0.105). Pediatric reference databases for optic disc parameters and ranges of normality for interocular symmetry provide key diagnostic support in diseases that affect the optic nerve.

Comparison of Allele Frequencies of Benghazi Population with Other Metapopulation

This is, to our knowledge, the first in-depth and largest study (238 samples) of genetic diversity in Y-STR haplotypes in an eastern Libyan population (recorded in Afro-Asiatic group from Metapopulation published in Y-STR Haplotype Reference Database-YHRD). Two previous studies, of a Tripoli population (West of Libya) and a Fezzan population (South Libya) analyzed a smaller number of inhabitants (63 samples and 47 samples, respectively) and (YHRD). Recently, (April 2011) YHRD recorded 47 and 82 haplotypes from Tripoli (Berber and Arabs 2011) respectively. Method: We Compare allele frequencies of Benghazi population with Y-STR Haplotype Reference Database -metapopulation. Conclusion: Benghazi population is similar to other Asian groups, such as Euro-Asian and East Asian. Hence, the Benghazi population shows genetic affinity to Asian and Middle Eastern rather than African and West North African groups.

Comparative analysis of HiSeq3000 and BGISEQ-500 sequencing platform over whole genome sequencing metagenomics data.

Recent advances in sequencing technologies and platforms have enabled to generate metagenomics sequences using different sequencing platforms. In this study, we analyzed and compared shotgun metagenomic sequences generated by HiSeq3000 and BGISEQ-500 platforms from 12 sediment samples collected across the Norwegian coast. Metagenomics DNA sequences were normalized to an equal number of bases for both platforms and further evaluated by using different taxonomic classifiers, reference databases, and assemblers. Normalized BGISEQ-500 sequences retained more reads and base counts after preprocessing, while a slightly higher fraction of HiSeq3000 sequences were taxonomically classified. Kaiju classified a higher percentage of reads relative to Kraken2 for both platforms, and comparison of reference database for taxonomic classification showed that MAR database outperformed RefSeq. Assembly using MEGAHIT produced longer assemblies and higher total contigs count in majority of HiSeq3000 samples than using metaSPAdes, but the assembly statistics notably improved with unprocessed or normalized reads. Our results indicate that both platforms perform comparably in terms of the percentage of taxonomically classified reads and assembled contig statistics for metagenomics samples. This study provides valuable insights for researchers in selecting an appropriate sequencing platform and bioinformatics pipeline for their metagenomics studies.

Identification of age at death in red deer (Cervus elaphus) through the upper dentition: Eruption pattern, wear stage and crown heights

The present research aims to determine the age at which red deer (Cervus elaphus) specimens died by examining their upper dentition. We analyzed eighty free-ranging individuals from southern Spain to establish a reference database for age calculation. The age of these individuals was identified by the mandibular teeth inferred from their known death years and the maxillary teeth were evaluated relative to them. As a result, we have provided three non-destructive methods: a description of the eruption sequence and dental replacement, a referential code for occlusal wear stages, and a regression analysis considering the height of the cusps in both upper and lower dentition. These methods offer the possibility of estimating the age at which the animals died and categorizing them into specific age groups. To evaluate the practicality of this method, we applied it to the Middle Paleolithic archaeological site of Abric Romaní. All the proposed methods allow us to approximate the age at death of red deer individuals. The most accurate results, whenever feasible, are obtained by combining these different methods. This study facilitates the inclusion of upper dentition fossils that have traditionally been omitted from the analysis in archaeological sites, allowing a better adjustment of the quantitative methods used to calculate the number of skeletal elements and the number of individuals. This, in turn, enables a more accurate construction of the anatomical and mortality profiles.