Ancient DNA

First record of well-preserved canid coprolites from Eurasia: New insights into the unique ecological niche of Yuanmou Basin

This study reconstructs the Early Pleistocene paleoenvironment of the Yuanmou Basin through coproecology of the third member of the Yuanmou Formation. We examined 38 exceptionally well-preserved coprolites from a new fossil locality, and attributed the putative defecating agent to the hypercarnivorous diet canid, Sinocuon yuanmouensis through geochemical and quantitative analyses. A new ichnogenus and ichnospecies, Cuocopros yuanmouensis igen. et. isp. nov., was established based on distinctive characteristics. Multi-disciplinary analysis, including sediment palynology and lithostratigraphy, helped primarily reconstruct a significant climatic event during the early Pleistocene, coinciding with the emergence of Yuanmou Man during the fourth member of the Yuanmou Formation's deposition. The findings provide insights into coexistence between canids, hyaenas, hominoids, and other fauna, revealing a rich paleoecosystem and food chain in the region's history. This study contributes to understanding the complex ecological dynamics during this period in the Yuanmou Basin.

Changes in the level of biofilm development significantly affect the persistence of environmental DNA in flowing water

As one of the powerful tools of species biomonitoring, the utilization of environmental DNA (eDNA) technology is progressively expanding in both scope and frequency within the field of ecology. Nonetheless, the growing dissemination of this technology has brought to light a multitude of intricate issues. The complex effects of environmental factors on the persistence of eDNA in water have brought many challenges to the interpretation of eDNA information. In this study, the primary objective was to examine how variations in the presence and development of biofilms impact the persistence of grass carp eDNA under different sediment types and flow conditions. This investigation encompassed the processes of eDNA removal and resuspension in water, shedding light on the complex interactions involved. The findings reveal that with an elevated biofilm development level, the total removal rate of eDNA gradually rose, resulting in a corresponding decrease in its residence time within the mesocosms. The influence of biofilms on the persistence of grass carp eDNA is more pronounced under flowing water conditions. However, changes in bottom sediment types did not significantly interact with biofilms. Lastly, in treatments involving alternating flow conditions between flowing and still water, significant resuspension of grass carp eDNA was not observed due to interference from multiple factors, including the effect of biofilms. Our study offers preliminary insights into the biofilm-mediated mechanisms of aquatic eDNA removal, emphasizing the need for careful consideration of environmental factors in the practical application of eDNA technology for biomonitoring in natural aquatic environments.

Using eDNA to survey amphibians: Methods, applications, and challenges

In recent years, environmental DNA (eDNA) has received attention from biologists due to its sensitivity, convenience, labor and material efficiency, and lack of damage to organisms. The extensive application of eDNA has opened avenues for the monitoring and biodiversity assessment of amphibians, which are frequently small and difficult to observe in the field, in areas such as biodiversity survey assessment and detection of specific, rare and threatened, or alien invasive species. However, the accuracy of eDNA can be influenced by factors such as ambient temperature, pH, and false positives or false negatives, which makes eDNA an adjunctive tool rather than a replacement for traditional surveys. This review provides a concise overview of the eDNA method and its workflow, summarizes the differences between applying eDNA for detecting amphibians and other organisms, reviews the research progress in eDNA technology for amphibian monitoring, identifies factors influencing detection efficiency, and discusses the challenges and prospects of eDNA. It aims to serve as a reference for future research on the application of eDNA in amphibian detection.

The role of single nucleotide polymorphisms related to iron homeostasis in mesothelioma susceptibility after asbestos exposure: a genetic study on autoptic samples

Asbestos-related diseases still represent a major public health problem all over the world. Among them, malignant mesothelioma (MM) is a poor-prognosis cancer, arising from the serosal lining of the pleura, pericardium and peritoneum, triggered by asbestos exposure. Literature data suggest the key role of iron metabolism in the coating process leading to the formation of asbestos bodies, considered to be both protective and harmful. Two sample sets of individuals were taken into consideration, both residing in Broni or neighboring cities (Northwestern Italy) where an asbestos cement factory was active between 1932 and 1993. The present study aims to compare the frequency of six SNPs involved in iron trafficking, previously found to be related to protection/predisposition to MM after asbestos exposure, between 48 male subjects with documented asbestos exposure who died of MM and 48 male subjects who were exposed to asbestos but did not develop MM or other neoplastic respiratory diseases (Non-Mesothelioma Asbestos Exposed - NMAE). The same analysis was performed on 76 healthy male controls. The allelic and genotypic frequencies of a sub-group of 107 healthy Italian individuals contained in the 1000 genomes database were considered for comparison. PCR-multiplex amplification followed by SNaPshot mini-sequencing reaction was used. The findings presented in this study show that the allelic and genotypic frequencies for six SNP markers involved in iron metabolism/homeostasis and the modulation of tumor microenvironment are not significantly different between the two sample sets of MM and NMAE. Therefore, the SNPs here considered do not seem to be useful markers for individual susceptibility to mesothelioma. This finding is not in agreement with previous literature.

Exceptionally well-preserved crocodilian coprolites from the Late Eocene of Northern Vietnam: Ichnology and paleoecological significance

This study examines 55 coprolites from the Na Duong Basin to reconstruct the paleoenvironment. Coproecology sheds light on understanding the complex prey-predator relationships, trophic dynamics, and ecosystem evolution. Through quantitative and multidisciplinary analysis, the putative coprolites were attributed to crocodilian producers, leading to the establishment of a new ichnogenus and species, Crococopros naduongensis igen. et isp. nov., based on distinct characteristics and comparisons. The study provides compelling evidence of an ancient river or lake-like environment dominated by diverse crocodilian fauna, indicating a thriving food chain in the Na Duong Basin. The findings also highlight the remarkable richness of ichnofauna, fauna, flora, and the presence of a favorable climate, confirming the area as a significant fossil Lagerstätte in Southeast Asia. Overall, this study offers a unique snapshot of the past, providing valuable insights into the regional ecosystem and significantly contributing to our understanding of paleoenvironmental conditions and biotic interactions.

Diagnostic models to predict nuclear DNA and mitochondrial DNA recovery from incinerated teeth

Teeth are frequently used for human identification from burnt remains, as the structure of a tooth is resilient against heat exposure. The intricate composition of hydroxyapatite (HA) mineral and collagen in teeth favours DNA preservation compared to soft tissues. Regardless of the durability, the integrity of the DNA structure in teeth can still be disrupted when exposed to heat. Poor DNA quality can negatively affect the success of DNA analysis towards human identification. The process of isolating DNA from biological samples is arduous and costly. Thus, an informative pre-screening method that could aid in selecting samples that can potentially yield amplifiable DNA would be of excellent value. A multiple linear regression model to predict the DNA content in incinerated pig teeth was developed based on the colourimetry, HA crystallite size and quantified nuclear and mitochondrial DNA. The chromaticity a* was found to be a significant predictor of the regression model. This study outlines a method to predict the viability of extracting nuclear and mitochondrial DNA from pig teeth that were exposed to a wide range of temperatures (27 to 1000 °C) with high accuracy (99.5-99.7%).

Cranio-facial bones evaluation based on clinical CT data for sex determination in Northwest Indian population

The skull and pelvis have been the first choice of bones for determination of unknown human remains. The goal of the present study was to derive discriminant function equations by using clinical CT scan data of cranio-facial bones for sex determination in Northwest Indian population. This study was conducted at Department of Radiology, by collecting the retrospective data of CT scan of 217 samples. In the data, 106 were males and 111 were females in the age group between 20 and 80 years. The total number of parameters under investigation were 10. All the selected variables were sexually dimorphic and showed significant values. 91.7% of original grouped cases were correctly classified to their sex category. The TEM, rTEM and R were under the acceptable limits. The univariate, multivariate and stepwise discriminant function analysis recorded an accuracy of 88.9%, 91.7% and 93.6% respectively. Multivariate direct discriminant function analysis stepwise method yielded the highest level of accuracy in differentiating males and females. All the variables reflected statistically significant difference between males and females (p less than 0.001). The best single parameter with highest level of sexual dimorphic trait was length of cranial base. This study aims to provide sex assessment using clinical data of CT scan in Northwest Indian population by incorporating the BIOFB cranio-facial parameter. The morphometric measurements taken on CT scan images can be utilized by forensic experts in identification process.

Imputation of ancient human genomes

Due to postmortem DNA degradation and microbial colonization, most ancient genomes have low depth of coverage, hindering genotype calling. Genotype imputation can improve genotyping accuracy for low-coverage genomes. However, it is unknown how accurate ancient DNA imputation is and whether imputation introduces bias to downstream analyses. Here we re-sequence an ancient trio (mother, father, son) and downsample and impute a total of 43 ancient genomes, including 42 high-coverage (above 10x) genomes. We assess imputation accuracy across ancestries, time, depth of coverage, and sequencing technology. We find that ancient and modern DNA imputation accuracies are comparable. When downsampled at 1x, 36 of the 42 genomes are imputed with low error rates (below 5%) while African genomes have higher error rates. We validate imputation and phasing results using the ancient trio data and an orthogonal approach based on Mendel's rules of inheritance. We further compare the downstream analysis results between imputed and high-coverage genomes, notably principal component analysis, genetic clustering, and runs of homozygosity, observing similar results starting from 0.5x coverage, except for the African genomes. These results suggest that, for most populations and depths of coverage as low as 0.5x, imputation is a reliable method that can improve ancient DNA studies.

Revealing Joseon period People's single nucleotide polymorphism associated with lactase gene by ancient DNA analysis of human remains from archaeological sites in Korea

Lactase non-persistence (LNP), one of the causes of lactose intolerance, is related to lactase gene associated single nucleotide polymorphisms (SNPs). Since the frequency of LNP varies by ethnic group and country, the research to reveal the presence or absence of LNP for specific people has been conducted worldwide. However, in East Asia, the study of lactase gene associated SNPs have not been sufficiently examined so far using ancient human specimens from archaeological sites. In our study of Joseon period human remains (n=14), we successfully revealed genetic information of lactase gene associated SNPs (rs1679771596, rs41525747, rs4988236, rs4988235, rs41380347, rs869051967, rs145946881 and rs182549), further confirming that as for eight SNPs, the pre-modern Korean people had a lactase non-persistent genotype. Our report contributes to the establishment of LNP associated SNP analysis technique that can be useful in forthcoming studies on human bones and mummy samples from East Asian archaeological sites.

The Colorectal Cancer Microbiota Alter Their Transcriptome To Adapt to the Acidity, Reactive Oxygen Species, and Metabolite Availability of Gut Microenvironments

The gut microbiome is implicated in the pathology of colorectal cancer (CRC). However, the mechanisms by which the microbiota actively contribute to disease onset and progression remain elusive. In this pilot study, we sequenced fecal metatranscriptomes of 10 non-CRC and 10 CRC patient gut microbiomes and conducted differential gene expression analyses to assess any changed functionality in disease. We report that oxidative stress responses were the dominant activity across cohorts, an overlooked protective housekeeping role of the human gut microbiome. However, expression of hydrogen peroxide and nitric oxide-scavenging genes was diminished and augmented, respectively, positing that these regulated microbial responses have implications for CRC pathology. CRC microbes enhanced expression of genes for host colonization, biofilm formation, genetic exchange, virulence determinants, antibiotic, and acid resistances. Moreover, microbes promoted transcription of genes involved in metabolism of several beneficial metabolites, suggesting their contribution to patient metabolite deficiencies previously solely attributed to tumor cells. We showed in vitro that expression of genes involved in amino acid-dependent acid resistance mechanisms of meta-gut Escherichia coli responded differently to acid, salt, and oxidative pressures under aerobic conditions. These responses were mostly dictated by the host health status of origin of the microbiota, suggesting their exposure to fundamentally different gut conditions. These findings for the first time highlight mechanisms by which the gut microbiota can either protect against or drive colorectal cancer and provide insights into the cancerous gut environment that drives functional characteristics of the microbiome. IMPORTANCE The human gut microbiota has the genetic potential to drive colorectal cancer onset and progression; however, the expression of this genetic potential during the disease has not been investigated. We found that microbial expression of genes that detoxify DNA-damaging reactive oxygen species, which drive colorectal cancer, is compromised in cancer. We observed a greater activation of expression of genes involved in virulence, host colonization, exchange of genetic material, metabolite utilization, defense against antibiotics, and environmental pressures. Culturing gut Escherichia coli of cancerous and noncancerous metamicrobiota revealed different regulatory responses of amino acid-dependent acid resistance mechanisms in a health-dependent manner under environmental acid, oxidative, and osmotic pressures. Here, for the first time, we demonstrate that the activity of microbial genomes is regulated by the health status of the gut in vivo and in vitro and provides new insights for shifts in microbial gene expression in colorectal cancer.

Examining pathogen DNA recovery across the remains of a 14th century Italian friar (Blessed Sante) infected with Brucella melitensis

OBJECTIVE

To investigate variation in ancient DNA recovery of Brucella melitensis, the causative agent of brucellosis, from multiple tissues belonging to one individual MATERIALS: 14 samples were analyzed from the mummified remains of the Blessed Sante, a 14 ^th century Franciscan friar from central Italy, with macroscopic diagnosis of probable brucellosis.

METHODS

Shotgun sequencing data from was examined to determine the presence of Brucella DNA.

RESULTS

Three of the 14 samples contained authentic ancient DNA, identified as belonging to B. melitensis. A genome (23.81X depth coverage, 0.98 breadth coverage) was recovered from a kidney stone. Nine of the samples contained reads classified as B. melitensis (7-169), but for many the data quality was insufficient to withstand our identification and authentication criteria.

CONCLUSIONS

We identified significant variation in the preservation and abundance of B. melitensis DNA present across multiple tissues, with calcified nodules yielding the highest number of authenticated reads. This shows how greatly sample selection can impact pathogen identification.

SIGNIFICANCE

Our results demonstrate variation in the preservation and recovery of pathogen DNA across tissues. This study highlights the importance of sample selection in the reconstruction of infectious disease burden and highlights the importance of a holistic approach to identifying disease.

LIMITATIONS

Study focuses on pathogen recovery in a single individual.

SUGGESTIONS FOR FURTHER RESEARCH

Further analysis of how sampling impacts aDNA recovery will improve pathogen aDNA recovery and advance our understanding of disease in past peoples.

Memories, museum artefacts and excavations in resolving the history of maternal lineages in the Finnhorse

We used historical DNA samples to examine the history of a native horse breed, the Finnhorse. Samples were collected from private collections, museums, schools and excavations, representing the times prior to, during, and after the foundation of the breed; from the end of the 19th century and throughout the 20th century. We sequenced a fragment of mitochondrial DNA from these historical samples to study the history and evolution of maternal lineages of horses back to the early days of the breed, compared the mitochondrial DNA sequence diversity of different historical periods and modern day Finnhorses, estimated the effective population sizes, and searched for both temporal and geographic population genetic structure. We observed high maternal haplotype and nucleotide diversity at the time during the foundation of the breed, and a decrease in both measures during 1931-1970. In addition, we observed losses of some haplotypes present in the early stages of the breed. There was only slight evidence of geographical or temporal population structure. This study is, to our knowledge, the first to use such temporal sampling to reveal the history of a specific animal breed.

Using loop-primer mediated PCR to enhance the detection of poorly preserved DNA

Ancient DNA is vitally important in evolutionary research, and obtaining authentic ancient DNA sequences is critical for a proper analysis. However, it is difficult to acquire amplicons accurately and efficiently from ancient DNA templates using current techniques. Here, we established a loop-primer-mediated amplification method (L-PCR) to obtain target ancient DNA sequences with high accuracy and efficiency. The method was tested using 66 ancient samples (including 27 pig bones or teeth and 39 chicken bones) and serially diluted modern animal DNA templates. Compared to nested PCR, L-PCR was proven to be more efficient and accurate and could obtain more amplicons from both ancient pig samples and chicken bones and detect as low as 10−3 ng/μl modern pig template DNA. The efficiency was at least 100-fold that of the nested PCR. The results suggest that L-PCR is advantageous for obtaining authentic DNA sequences from poorly preserved or recalcitrant ancient specimens.

Assessing the use of environmental DNA (eDNA) as a tool in the detection of human DNA in water

Environmental DNA (eDNA) is a highly sensitive and cost-effective tool that is increasingly being applied to studies of biodiversity and species detection. This non-invasive method relies on the collection of environmental samples that contain genetic material being shed into surrounding environment by the target organism/s. While forensic science has a long history of using molecular tools for collecting DNA from the environment, the detection of human DNA from environmental water samples has been limited. This study investigated the detection and degradation rates of human eDNA in water samples under controlled laboratory conditions. Using a human-specific qPCR assay targeting the ND1 region of human mitochondrial DNA, eDNA degradation over time in water spiked with human blood was assessed. Recovery of nuclear DNA was investigated by determining if routine DNA short tandem repeat (STR) profiles of the blood source could be generated. Results demonstrated that human eDNA remains detectable for up to 11 days under laboratory conditions in environmental water and up to 35 days in distilled water. Partial STR profiles could be recovered from environmental water only up to 24 h, while, in distilled water, partial profiles continued to be recovered up to 840 h. These findings demonstrate that sampling human eDNA from aquatic samples can provide reliable human DNA detection within relatively short time windows, assisting law enforcement agencies by providing information about the potential time an individual may have been present in an area or assisting in the detection and location of a body or remains in aquatic environments.

Paleoproteomics

Paleoproteomics, the study of ancient proteins, is a rapidly growing field at the intersection of molecular biology, paleontology, archaeology, paleoecology, and history. Paleoproteomics research leverages the longevity and diversity of proteins to explore fundamental questions about the past. While its origins predate the characterization of DNA, it was only with the advent of soft ionization mass spectrometry that the study of ancient proteins became truly feasible. Technological gains over the past 20 years have allowed increasing opportunities to better understand preservation, degradation, and recovery of the rich bioarchive of ancient proteins found in the archaeological and paleontological records. Growing from a handful of studies in the 1990s on individual highly abundant ancient proteins, paleoproteomics today is an expanding field with diverse applications ranging from the taxonomic identification of highly fragmented bones and shells and the phylogenetic resolution of extinct species to the exploration of past cuisines from dental calculus and pottery food crusts and the characterization of past diseases. More broadly, these studies have opened new doors in understanding past human-animal interactions, the reconstruction of past environments and environmental changes, the expansion of the hominin fossil record through large scale screening of nondiagnostic bone fragments, and the phylogenetic resolution of the vertebrate fossil record. Even with these advances, much of the ancient proteomic record still remains unexplored. Here we provide an overview of the history of the field, a summary of the major methods and applications currently in use, and a critical evaluation of current challenges. We conclude by looking to the future, for which innovative solutions and emerging technology will play an important role in enabling us to access the still unexplored "dark" proteome, allowing for a fuller understanding of the role ancient proteins can play in the interpretation of the past.

Metagenomic Analysis Using Phylogenetic Placement-A Review of the First Decade

Phylogenetic placement refers to a family of tools and methods to analyze, visualize, and interpret the tsunami of metagenomic sequencing data generated by high-throughput sequencing. Compared to alternative (e. g., similarity-based) methods, it puts metabarcoding sequences into a phylogenetic context using a set of known reference sequences and taking evolutionary history into account. Thereby, one can increase the accuracy of metagenomic surveys and eliminate the requirement for having exact or close matches with existing sequence databases. Phylogenetic placement constitutes a valuable analysis tool per se, but also entails a plethora of downstream tools to interpret its results. A common use case is to analyze species communities obtained from metagenomic sequencing, for example via taxonomic assignment, diversity quantification, sample comparison, and identification of correlations with environmental variables. In this review, we provide an overview over the methods developed during the first 10 years. In particular, the goals of this review are 1) to motivate the usage of phylogenetic placement and illustrate some of its use cases, 2) to outline the full workflow, from raw sequences to publishable figures, including best practices, 3) to introduce the most common tools and methods and their capabilities, 4) to point out common placement pitfalls and misconceptions, 5) to showcase typical placement-based analyses, and how they can help to analyze, visualize, and interpret phylogenetic placement data.

Design considerations for advancing data storage with synthetic DNA for long-term archiving

Deoxyribonucleic acid (DNA) is increasingly emerging as a serious medium for long-term archival data storage because of its remarkable high-capacity, high-storage-density characteristics and its lasting ability to store data for thousands of years. Various encoding algorithms are generally required to store digital information in DNA and to maintain data integrity. Indeed, since DNA is the information carrier, its performance under different processing and storage conditions significantly impacts the capabilities of the data storage system. Therefore, the design of a DNA storage system must meet specific design considerations to be less error-prone, robust and reliable. In this work, we summarize the general processes and technologies employed when using synthetic DNA as a storage medium. We also share the design considerations for sustainable engineering to include viability. We expect this work to provide insight into how sustainable design can be used to develop an efficient and robust synthetic DNA-based storage system for long-term archiving.

Predicting Archaic Hominin Phenotypes from Genomic Data

Ancient DNA provides a powerful window into the biology of extant and extinct species, including humans' closest relatives: Denisovans and Neanderthals. Here, we review what is known about archaic hominin phenotypes from genomic data and how those inferences have been made. We contend that understanding the influence of variants on lower-level molecular phenotypes-such as gene expression and protein function-is a promising approach to using ancient DNA to learn about archaic hominin traits. Molecular phenotypes have simpler genetic architectures than organism-level complex phenotypes, and this approach enables moving beyond association studies by proposing hypotheses about the effects of archaic variants that are testable in model systems. The major challenge to understanding archaic hominin phenotypes is broadening our ability to accurately map genotypes to phenotypes, but ongoing advances ensure that there will be much more to learn about archaic hominin phenotypes from their genomes. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 23 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Genomics: Testing the limits of de-extinction

Resurrecting extinct species through de-extinction by genome editing requires full and unbiased information from the extinct species' genome. A new study establishes a framework to assess how much of an extinct species genome can be recovered by ancient DNA sequencing and which factors influence recovery.

Effects of Temperature on the Timeliness of eDNA/eRNA: A Case Study of Fenneropenaeus chinensis

Environmental DNA (eDNA) technology has been successfully applied to detect organisms in various aquatic ecosystems. However, eDNA has been proven to exist for a long time in environmental samples. The timeliness of eDNA detection results largely depends on the rate of molecular degradation. Environmental RNA (eRNA) is considered an excellent complementary tool because most researchers believe that RNA degrades faster than DNA in vitro, while, to the best of our knowledge, the number of published articles related to eRNA is very limited. To address an important knowledge gap, this study focused on the response mechanism of eRNA degradation to water temperature change as compared with eDNA. Changes in the concentration of eDNA and eRNA of the mitochondrial cytochrome c oxidase subunit 1 (COI) gene from Fenneropenaeuschinensis were detected at four temperatures (10, 15, 20 and 25 °C). The results showed that the degradation rate of eDNA increased with an increase in temperature. The degradation rate constants ranged from 0.011 to 0.486 h−1 and the degradation time ranged from 8 to 383 h for eDNA. The degradation rate of eRNA changed slightly with an increase in temperature. The degradation rate constants ranged from 0.190 to 0.379 h−1 and the degradation time ranged from 11 to 22 h for eRNA. eRNA showed better stability under temperature change and maintained a faster degradation rate at low temperatures. These results provide answers to the questions of whether eRNA and eDNA degradation rates are fast or slow. Furthermore, this study may suggest the potential superiority of eRNA over eDNA and promote further study of eRNA in future research.

Effects of decomposition on the recoverability of biological fluid evidence

The present research assessed how the physical and chemical changes associated with decomposition affect the detection and identification of blood and semen evidence, as well as subsequent DNA analysis. A feeder pig (postmortem interval (PMI) < 3 h) was placed within the Boston University Outdoor Research Facility for a period of 22 days. Human blood and semen were individually dispensed onto multiple areas of two cotton t-shirts; one layer of fabric was placed above and below the pig and a control. One of each sample type was collected per day for a period of 22 days from each location. It was observed that both sample types when collected from beneath the pig exhibited the greatest decline in enzymatic activity over the course of testing, followed by samples from beneath the control, which can be inferred from the increase in negative screening results compared to the other samples. Spermatozoa were observed in nearly all semen samples, even when all screening results were negative, which lead to the generation of comparable DNA profiles for nearly all semen samples typed. Genetic typing of the blood samples beneath the pig and control rarely yielded comparable data while the samples from above yielded full profiles for all but a few samples tested.

Century-Long Homogenization of Algal Communities Is Accelerated by Nutrient Enrichment and Climate Warming in Lakes and Reservoirs of the North Temperate Zone

Anthropogenic pressures can threaten lake and reservoir ecosystems, leading to harmful algal blooms that have become globally widespread. However, patterns of phytoplankton diversity change and community assembly over long-term scales remain unknown. Here, we explore biodiversity patterns in eukaryotic algal (EA) and cyanobacterial (CYA) communities over a century by sequencing DNA preserved in the sediment cores of seven lakes and reservoirs in the North Temperate Zone. Comparisons within lakes revealed temporal algal community homogenization in mesotrophic lakes, eutrophic lakes, and reservoirs over the last century but no systematic losses of α-diversity. Temporal homogenization of EA and CYA communities continued into the modern day probably due to time-lags related to historical legacies, even if lakes go through a eutrophication phase followed by a reoligotrophication phase. Further, algal community assembly in lakes and reservoirs was mediated by both deterministic and stochastic processes, while homogeneous selection played a relatively important role in recent decades due to intensified anthropogenic activities and climate warming. Overall, these results expand our understanding of global change effects on algal community diversity and succession in lakes and reservoirs that exhibit different successional trajectories while also providing a baseline framework to assess their potential responses to future environmental change.

Ancient DNA of Metagonimus yokogawai Recovered from Joseon Period Human Remains Newly Discovered at Goryeong County in South Korea

PURPOSE

Metagonimiasis, commonly seen in East Asian countries, is a parasitic disorder caused by definitive hosts' ingestion of undercooked freshwater fishes. Recently, genetic analysis has proved 28S rRNA and cytochrome c oxidase subunit I (COI) mtDNA gene to be a successful marker differentiating species of the genus Metagonimus. In the present study, using specimens from the newly discovered Joseon Dynasty human remains of Goryeong, we obtained updated genetic data on genus Metagonimus, which was also prevalent during the Joseon period.

METHODS

The ancient DNA (aDNA) was retrieved from the coprolite sample of the seventeenth century, half-mummified individual discovered at Goryeong Country, South Korea. Cloning and sequencing were performed on PCR-amplified amplicons for M. yokogawai 28S rRNA and COI mtDNA gene. The consensus sequences were used for species identification and phylogenetic analysis using NCBI/BLAST and MEGA X software.

RESULTS

Based on the COI mtDNA gene region, the Goryeong sequence was confirmed as belonging to M. yokogawai, as it was shown to form a separate cluster with other M. yokogawai taxa that are distinct also from M. takahashii and M. miyatai.

CONCLUSION

In a series of our genetic analyses on genus Metagonimus using samples retrieved from Joseon-period cases, aDNA sequences of genus Metagonimus revealed in South Korea thus far are those of M. yokogawai, but not of M. miyatai or M. takahashii yet.

Genetic analysis of mitochondrial DNA from ancient <i>Equus caballus</i> bones found at archaeological site of Joseon dynasty period capital area

Objective

To understand the domestication and spread of horses in history, genetic information is essential. However, mitogenetic traits of ancient or medieval horses have yet to be comprehensively revealed, especially for East Asia. This study thus set out to reveal the maternal lineage of skeletal horse remains retrieved from a 15th century archaeological site (Gongpyeongdong) at Old Seoul City in South Korea.

Methods

We extracted DNA from the femur of Equus caballus (SNU-A001) from Joseon period Gongpyeongdong site. Mitochondrial (mt) DNA (HRS 15128-16116) of E. caballus was amplified by polymerase chain reaction. Cloning and sequencing were conducted for the mtDNA amplicons. The sequencing results were analyzed by NCBI/BLAST and phylogenetic tool of MEGA7 software.

Results

By means of mtDNA cytochrome b and D-loop analysis, we found that the 15th century Korean horse belonged to haplogroup Q representing those horses that have historically been raised widely in East Asia.

Conclusion

The horse is unique among domesticated animals for the remarkable impact it has on human civilization in terms of transportation and trade. Utilizing the Joseon-period horse remains, we can obtain clues to reveal the genetic traits of Korean horse that existed before the introduction of Western horses.

Epigenomic Modifications in Modern and Ancient Genomes

Epigenetic changes have been identified as a major driver of fundamental metabolic pathways. More specifically, the importance of epigenetic regulatory mechanisms for biological processes like speciation and embryogenesis has been well documented and revealed the direct link between epigenetic modifications and various diseases. In this review, we focus on epigenetic changes in animals with special attention on human DNA methylation utilizing ancient and modern genomes. Acknowledging the latest developments in ancient DNA research, we further discuss paleoepigenomic approaches as the only means to infer epigenetic changes in the past. Investigating genome-wide methylation patterns of ancient humans may ultimately yield in a more comprehensive understanding of how our ancestors have adapted to the changing environment, and modified their lifestyles accordingly. We discuss the difficulties of working with ancient DNA in particular utilizing paleoepigenomic approaches, and assess new paleoepigenomic data, which might be helpful in future studies.

The Technological Advance and Application of Coprolite Analysis

Coprolites (mummified or fossilized feces), belonging to the group of ichnofossils, are fossilized remains of feces produced by animals. Various types of data from coprolites provide detailed evidence of the producer’s condition, like diet, intestinal microbiome, virus infection and parasites diseases. In addition, the palaeoenvironment information relevant to producers’ ecological niche can be drawn from taphonomy details the coprolites mirrored. At present, the phylogenetic clues of the producer’s population can be determined by advanced molecular biotechnologies. With the integration of multiple methods and techniques, coprolite has been widely accepted as an ideal material to study the diet, evolution, and palaeoenvironment of producers. In this paper, we reviewed the history of coprolite research, enumerated and interpreted the data recovered from coprolites, and explained their research value to palaeocoprology and evolutionary biology. Finally, we summarized the current directions of coprolite research and looked into its future prospects.

Discovering the Secrets of Ancient Plants: Recovery of DNA from Museum and Archaeological Plant Specimens

Plant DNA preserved in ancient specimens has recently gained importance as a tool in comparative genomics, allowing the investigation of evolutionary processes in plant genomes through time. However, recovering the genomic information contained in such specimens is challenging owing to the presence of secondary substances that limit DNA retrieval. In this chapter, we provide a DNA extraction protocol optimized for the recovery of DNA from degraded plant materials. The protocol is based on a commercially available DNA extraction kit that does not require handling of hazardous reagents.

Not dead yet: Diatom resting spores can survive in nature for several millennia

PREMISE

Understanding the adaptive capacities of species over long timescales lies in examining the revived recent and millennia-old resting spores buried in sediments. We show for the first time the revival, viability, and germination rate of resting spores of the diatom Chaetoceros deposited in sub-seafloor sediments from three ages (recent: 0 to 80 years; ancient: ~1250 (Medieval Climate Anomaly) and ~6600 (Holocene Thermal Maximum) calendar year before present.

METHODS

Recent and ancient Chaetoceros spores were revived to examine their viability and germination rate. Light and scanning electron microscopy and Sanger sequencing was done to identify the species.

RESULTS

We show that ~6600 cal. year BP old Chaetoceros resting spores are still viable and that the vegetative reproduction in recent and ancient resting spores varies. The time taken to germinate is three hours to 2 to 3 days in both recent and ancient spores, but the germination rate of the spores decreased with increasing age. The germination rate of the recent spores was ~41% while that of the ancient spores were ~31% and ~12% for the ~1250 and ~6600 cal. year BP old resting spores, respectively. Based on the morphology of the germinated vegetative cells we identified the species as Chaetoceros muelleri var. subsalsum. Sanger sequences of nuclear and chloroplast markers identified the species as Chaetoceros muelleri.

CONCLUSIONS

We identify a unique model system, Chaetoceros muelleri var. subsalsum and show that recent and ancient resting spores of the species buried in sediments in the Baltic Sea can be revived and used for long-term evolutionary studies.

Ancient Mitogenomes Reveal the Domestication and Distribution of Cattle During the Longshan Culture Period in North China

Cattle, as an important tool for agricultural production in ancient China, have a complex history of domestication and distribution in China. Although it is generally accepted that ancient Chinese taurine cattle originated from the Near East, the explanation regarding their spread through China and whether or not this spread was associated with native aurochs during ancient times are still unclear. In this study, we obtained three nearly complete mitochondrial genomes (mitogenomes) from bovine remains dating back ca. 4,000 years at the Taosi and Guchengzhai sites in North China. For the first time at the mitogenome level, phylogenetic analyses confirmed the approximately 4,000-year-old bovines from North China as taurine cattle. All ancient cattle from both sites belonged to the T3 haplogroup, suggesting their origin from the Near East. The high affinity between ancient samples and southern Chinese taurine cattle indicated that ancient Chinese cattle had a genetic contribution to the taurine cattle of South China. A rapid decrease in the female effective population size ca. 4.65 thousand years ago (kya) and a steep increase ca. 1.99 kya occurred in Chinese taurine cattle. Overall, these results provide increasing evidence of the origin of cattle in the middle Yellow River region of China.

Hydrophobic magnetic deep eutectic solvent: Synthesis, properties, and application in DNA separation

Isolating high-purity nucleic acids from complex biological samples is critical to nucleic acid analysis. In the current work, four hydrophobic magnetic deep eutectic solvents (HMDESs) were firstly designed and prepared for the extraction of DNA. The conformations of the HMDESs were simulated and H-bonding interactions in the HMDESs were investigated by density functional theory (DFT) calculation. Characterization of HMDESs' physical (magnetism, density, viscosity and hydrophobicity), and thermal (melting point and decomposition temperature) properties were conducted. Single stranded DNA (ssDNA), double stranded DNA (dsDNA) and DNA sodium salts (stDNA) that were extracted by HMDESs could be quickly collected by an external magnet. Three auxiliary extraction methods, including vortex auxiliary extraction, mechanical shaking auxiliary extraction and ultrasonic auxiliary extraction, were introduced to extract DNA with HMDESs and the extraction efficiencies were evaluated using NanoDrop. Factors that could impact the DNA extraction process, such as HMDESs volume, temperature, time, and pH, were systematically investigated via single-factor experimental analysis. The proposed extraction method can successfully extract DNA from complex matrices and E. coli cell lysate. The DNA extracted by using HMDESs are well suitable for PCR amplifications. The interaction and corresponding binding sites between HMDESs and DNA were investigated by FT-IR and DFT calculation. The extraction mechanisms were discussed: hydrophobic interaction and electrostatic interaction are two main forces driving DNA extraction by HMDESs.

Guanidinium Hydrophobic Magnetic Ionic Liquid-Based Dispersive Droplet Extraction for the Selective Extraction of DNA

Six hydrophobic magnetic guanidinium ionic liquids (HMILs) were designed and prepared for the extraction of DNA. The physical and thermal properties of the HMILs were characterized using vibrating sample magnetometry, density meter, rotational rheometer, Karl Fischer moisture, Fourier transform infrared spectrometry, and thermogravimetric analysis. Single-stranded DNA and duplex DNA extracted by HMILs can be rapidly collected by a magnet. Three assisted extraction methods, including vortex extraction, mechanical shaking extraction, and ultrasonic extraction, were introduced to extract DNA with HMILs and the extraction efficiencies were evaluated using NanoDrop. Influencing factors of the DNA extraction were comprehensively evaluated, involving the HMIL volume, extraction time, pH, and extraction temperature. The HMIL-based extraction method can well extract DNA from complex matrices and Escherichia coli cell lysates.

Forensic examination and application of areca nuts as material evidence

In this study, we aimed to explore the possibility of DNA analysis of areca nut as material evidence and the value of short tandem repeat (STR) typing of areca nut as material evidence under the condition of simulating external environment. In this study, water soaking, soil burial, sun exposure, and wet environment were used to treat areca nut residues. Chelex 100 was used to extract DNA, the PowerPlex21 kit to amplify, and the ABI PRISM^® 310 Genetic Analyzer to analyze the DNA of areca nut residues. DNA and STR typing were performed to analyze the residue after chewing. The results showed that the number of residual sites decreased with time under the conditions of water soaking, soil burial, sun exposure, and wet environment. Thus, areca nut can be used as forensic material evidence for DNA analysis and individual identification.

The effects of fossil taxa, hypothetical predicted ancestors, and a molecular scaffold on pseudoextinction analyses of extant placental orders

Pseudoextinction analyses, which simulate extinction in extant taxa, use molecular phylogenetics to assess the accuracy of morphological phylogenetics. Previous pseudoextinction analyses have shown a failure of morphological phylogenetics to place some individual placental orders in the correct superordinal clade. Recent work suggests that the inclusion of hypothetical ancestors of extant placental clades, estimated by ancestral state reconstructions of morphological characters, may increase the accuracy of morphological phylogenetic analyses. However, these studies reconstructed direct hypothetical ancestors for each extant taxon based on a well-corroborated molecular phylogeny, which is not possible for extinct taxa that lack molecular data. It remains to be determined if pseudoextinct taxa, and by proxy extinct taxa, can be accurately placed when their immediate hypothetical ancestors are unknown. To investigate this, we employed molecular scaffolds with the largest available morphological data set for placental mammals. Each placental order was sequentially treated as pseudoextinct by exempting it from the molecular scaffold and recoding soft morphological characters as missing for all its constituent species. For each pseudoextinct data set, we omitted the pseudoextinct taxon and performed a parsimony ancestral state reconstruction to obtain hypothetical predicted ancestors. Each pseudoextinct order was then evaluated in seven parsimony analyses that employed combinations of fossil taxa, hypothetical predicted ancestors, and a molecular scaffold. In treatments that included fossils, hypothetical predicted ancestors, and a molecular scaffold, only 8 of 19 pseudoextinct placental orders (42%) retained the same interordinal placement as on the molecular scaffold. In treatments that included hypothetical predicted ancestors but not fossils or a scaffold, only four placental orders (21%) were recovered in positions that are congruent with the scaffold. These results indicate that hypothetical predicted ancestors do not increase the accuracy of pseudoextinct taxon placement when the immediate hypothetical ancestor of the taxon is unknown. Hypothetical predicted ancestors are not a panacea for morphological phylogenetics.

Disentangling the complex alpha taxonomy of Andean populations of Ctenomys (Rodentia: Ctenomyidae) from northern Patagonia: the need for extensive sampling in heterogeneous landscapes

In the Andean portion of northern Patagonia, populations of Ctenomys are found from low-elevation plains to high-elevation meadows and valleys. Despite their prevalence, the taxonomy of these subterranean rodents remains poorly resolved. Using genetic and morphological data obtained from museum specimens and animals collected in the field, we examined the taxonomy of Ctenomys from southwestern Mendoza Province, Argentina. Our analyses suggest the presence of at least five species of Ctenomys within the study area. The highest, innermost portion of the Andes is occupied by C. maulinus. To the east, the mountains and foothills are inhabited by two forms associated with the “mendocinus” and the “magellanicus” lineages, respectively. The former appears to be a local variant of C. emilianus, while the latter is sister to C. pontifex. Although C. pontifex was not encountered during our field sampling, it remains a valid species that likely is restricted to the isolated Valle Hermoso in westernmost Mendoza Province. In addition, we report an undescribed form from Las Leñas Valley that is associated with the “mendocinus” lineage. This complex alpha taxonomic scenario occurs within less than one degree of latitude, thereby highlighting the need to conduct detailed field collections to improve our knowledge of the systematics of Ctenomys.

Genome-scale sequencing and analysis of human, wolf, and bison DNA from 25,000-year-old sediment

Cave sediments have been shown to preserve ancient DNA but so far have not yielded the genome-scale information of skeletal remains. We retrieved and analyzed human and mammalian nuclear and mitochondrial environmental "shotgun" genomes from a single 25,000-year-old Upper Paleolithic sediment sample from Satsurblia cave, western Georgia:first, a human environmental genome with substantial basal Eurasian ancestry, which was an ancestral component of the majority of post-Ice Age people in the Near East, North Africa, and parts of Europe; second, a wolf environmental genome that is basal to extant Eurasian wolves and dogs and represents a previously unknown, likely extinct, Caucasian lineage; and third, a European bison environmental genome that is basal to present-day populations, suggesting that population structure has been substantially reshaped since the Last Glacial Maximum. Our results provide new insights into the Late Pleistocene genetic histories of these three species and demonstrate that direct shotgun sequencing of sediment DNA, without target enrichment methods, can yield genome-wide data informative of ancestry and phylogenetic relationships.

Assessing genotyping errors in mammalian museum study skins using high-throughput genotyping-by-sequencing

The use of museum specimens held in natural history repositories for population and conservation genetic research is increasing in tandem with the use of massively parallel sequencing technologies. Short Tandem Repeats (STRs), or microsatellite loci, are commonly used genetic markers in wildlife and population genetic studies. However, they traditionally suffered from a host of issues including length homoplasy, high costs, low throughput, and difficulties in reproducibility across laboratories. Massively parallel sequencing technologies can address these problems, but the incorporation of museum specimen derived DNA suffers from significant fragmentation and exogenous DNA contamination. Combatting these issues requires extra measures of stringency in the lab and during data analysis, yet there have not been any high-throughput sequencing studies evaluating microsatellite allelic dropout from museum specimen extracted DNA. In this study, we evaluate genotyping errors derived from mammalian museum skin DNA extracts for previously characterized microsatellites across PCR replicates utilizing high-throughput sequencing. We found it useful to classify samples based on DNA concentration, which determined the rate by which genotypes were accurately recovered. Longer microsatellites performed worse in all museum specimens. Allelic dropout rates across loci were dependent on sample quantity, with high concentration museum specimens performing as well and recovering quality metrics nearly as high as the frozen tissue sample. Based on our results, we provide a set of best practices for quality assurance and incorporation of reliable genotypes from museum specimens.

Assessment of DNA Integrity From Trap-Captured Boll Weevil (Coleoptera: Curculionidae) for Use in a New PCR-Based Diagnostic Tool

The boll weevil, Anthonomus grandis grandis Boheman (Coleoptera: Curculionidae), is a major pest of commercial cotton (Gossypium hirsutum) in the southern United States and throughout Central and South America. Efforts are underway to develop a PCR-based diagnostic tool that can be used to rapidly and accurately differentiate boll weevils from other weevil species that are commonly captured in pheromone traps. However, the quantity and integrity of weevil DNA must be sufficient for a successful PCR assay. Currently, active eradication programs service traps weekly, but post-eradication programs service traps at 2- or 3-wk intervals. Consequently, captured weevils may be dead, dismembered, and exposed to environmental conditions for prolonged periods which may adversely affect the quantity and quality of weevil DNA. We documented DNA quantity and integrity in boll weevils and weevil body parts aged in traps over a 3-wk period under field conditions. The quantity of DNA extracted from whole weevils, heads, abdomens, and legs generally remained sufficient (> 1 ng/μl) for successful PCR amplification throughout the 21-d period. The integrity (fragment length) of extracted DNA declined over time but generally was sufficient (> 700 bp) for successful amplification. PCR amplification of three marker genes validated that the quality and integrity of DNA extracted from dead weevils and individual weevil body parts aged in traps up to 21 d remained at sufficient levels for the PCR-based assay. However, our data also suggested that rain events may accelerate degradation of weevil DNA.

The genomic history of the Aegean palatial civilizations

The Cycladic, the Minoan, and the Helladic (Mycenaean) cultures define the Bronze Age (BA) of Greece. Urbanism, complex social structures, craft and agricultural specialization, and the earliest forms of writing characterize this iconic period. We sequenced six Early to Middle BA whole genomes, along with 11 mitochondrial genomes, sampled from the three BA cultures of the Aegean Sea. The Early BA (EBA) genomes are homogeneous and derive most of their ancestry from Neolithic Aegeans, contrary to earlier hypotheses that the Neolithic-EBA cultural transition was due to massive population turnover. EBA Aegeans were shaped by relatively small-scale migration from East of the Aegean, as evidenced by the Caucasus-related ancestry also detected in Anatolians. In contrast, Middle BA (MBA) individuals of northern Greece differ from EBA populations in showing ∼50% Pontic-Caspian Steppe-related ancestry, dated at ca. 2,600-2,000 BCE. Such gene flow events during the MBA contributed toward shaping present-day Greek genomes.

Investigating variability in microbial community composition in replicate environmental DNA samples down lake sediment cores

Lake sediments are natural archives that accumulate information on biological communities and their surrounding catchments. Paleolimnology has traditionally focussed on identifying fossilized organisms to reconstruct past environments. In the last decade, the application of molecular methodologies has increased in paleolimnological studies, but further research investigating factors such as sample heterogeneity and DNA degradation are required. In the present study we investigated bacterial community heterogeneity (16S rRNA metabarcoding) within depth slices (1-cm width). Sediment cores were collected from three lakes with differing sediment compositions. Samples were collected from a variety of depths which represent a period of time of approximately 1,200 years. Triplicate samples were collected from each depth slice and bacterial 16S rRNA metabarcoding was undertaken on each sample. Accumulation curves demonstrated that except for the deepest (oldest) slices, the combination of three replicate samples were insufficient to characterise the entire bacterial diversity. However, shared Amplicon Sequence Variants (ASVs) accounted for the majority of the reads in each depth slice (max. shared proportional read abundance 96%, 86%, 65% in the three lakes). Replicates within a depth slice generally clustered together in the Non-metric multidimensional scaling analysis. There was high community dissimilarity in older sediment in one of the cores, which was likely due to the laminae in the sediment core not being horizontal. Given that most paleolimnology studies explore broad scale shifts in community structure rather than seeking to identify rare species, this study demonstrates that a single sample is adequate to characterise shifts in dominant bacterial ASVs.

The first record of exceptionally-preserved spiral coprolites from the Tsagan-Tsab formation (lower cretaceous), Tatal, western Mongolia

In this paper, seven coprolites from the Lower Cretaceous of Tsagan-Tsab formation have been described. Thus, producing a significant contribution to what we perceived as the first detailed study of coprolites from the Mesozoic deposits in Mongolia. The collected coprolites encompass a total of six spiral amphipolar and one scroll coprolites. We prominently identified four new coprolite ichnotaxa, such as: Hyronocoprus tsagantsabensis and Hyronocoprus hunti, to which both are ichnosp. nov.; followed by Megakalocoprus barremianensis and Scrollocoprus tatalensis, where both are ichnogen. et ichnosp. nov. Notably, CT scans revealed that all specimens showed various amounts of bony inclusions and scales, hence, deducing that the producers could have had a low acidic digestive track and were unable to dissolve bone matters. Moreover, SEM–EDS analysis concluded its carnivorous nature, thus, pointing towards piscivorous diet. The small sized Scrollocoprus is considered to be the second findings of Mesozoic era’s scroll coprolites, which contain possible plant pollens, a complete infraorbital bone, clusters of bone fragments and rhomboidal-shaped ganoid scales of the prey; and bioerosional scars have been observed on the surface. We suggest those amphipolar spiral ichnotaxa were produced by Asipenceriformes, with Pholidophoriformes as the prey, while Scrollocoprus represents fecal excrement of underived fish, possibly of sarcopterygian origins.

DNA stability: a central design consideration for DNA data storage systems

Data storage in DNA is a rapidly evolving technology that could be a transformative solution for the rising energy, materials, and space needs of modern information storage. Given that the information medium is DNA itself, its stability under different storage and processing conditions will fundamentally impact and constrain design considerations and data system capabilities. Here we analyze the storage conditions, molecular mechanisms, and stabilization strategies influencing DNA stability and pose specific design configurations and scenarios for future systems that best leverage the considerable advantages of DNA storage.

Metagonimus yokogawai Ancient DNA Recovered from 16th- to 17th-Century Korean Mummy Feces of the Joseon Dynasty

Metagonimiasis is foodborne intestinal parasitism occurring by the definitive hosts' ingestion of raw or undercooked fish, mostly commonly sweetfish. Most Metagonimus infection is caused by Metagonimus yokogawai but also rarely by Metagonimus takahashii as well as Metagonimus miyatai. Despite recent molecular work on Metagonimus spp., there are still insufficient data to reveal the genetic characteristics of ancient M. yokogawai in a wide geo-historical scope. In this study, we were successful in the analysis of M. yokogawai ancient DNA (aDNA) using coprolite samples retrieved from 16th- to 17th-century Korean mummies. In BLAST and phylogenetic analyses, M. yokogawai 28S rDNA of Korean mummies were clustered along with the 28S rDNA taxa of M. takahashii and M. miyatai in GenBank. Conversely, the cytochrome c oxidase subunit I (COI) of M. yokogawai aDNA from Korean mummies was distinctly clustered apart from M. takahashii and M. miyatai sequences. This study is the first report of its kind to identify M. yokogawai aDNA retrieved from the archaeological specimens and confirms the usefulness of COI in molecular diagnosis of M. yokogawai. Considering the rarity of reports on the genetics of genus Metagonimus spp., our study will be fundamental for the future study of M. yokogawai paleogenetics.

Teaching an Old Shell New Tricks: Extracting DNA from Current, Historical, and Ancient Mollusk Shells

The use of unconventional DNA sources has increased because the acquisition of traditional samples can be invasive, destructive, or impossible. Mollusks are one group for which novel genetic sources are crucial, but methodology remains relatively undeveloped. Many species are important ecologically and in aquaculture production. However, mollusks have the highest number of extinctions of any taxonomic group. Traditionally, mollusk shell material was used for morphological research and only recently has been used in DNA studies. In the present article, we review the studies in which shell DNA was extracted and found that effective procedures consider taxon-specific biological characteristics, environmental conditions, laboratory methods, and the study objectives. Importantly, these factors cannot be considered in isolation because of their fundamental, sometimes reciprocal, relationships and influence in the long-term preservation and recovery of shell DNA. Successful recovery of shell DNA can facilitate research on pressing ecological and evolutionary questions and inform conservation strategies to protect molluscan diversity.

The Effectiveness of Mini Primer STR CODIS in DNA Degradation as the Effect of High-Temperature Exposure

Background

More and more today, forensic identification through deoxyribonucleic acid (DNA) examination has achieved greater recognition in supporting Indonesia's law enforcement. Such examination is to determine the origin of a child, paternity cases, genealogical relation, or identifying unknown crime victims. However, along with the development of this DNA material examination, problems arise. DNA undergoes a degradation, commonly known as degraded DNA, which is one of the serious issues frequently encountered by forensic and DNA experts. Some forensic DNA experts take one of the alternatives to overcome this issue by implementing a mini primer set that is through a method to reduce the size of STR assays on DNA core locus examination.

Methods

In this study, the writers conduct research using the mini primers of CSF1PO, FGA, and D21S11 of the molar teeth exposed to 500°C temperature for 20 and 30 minutes and 750°C for the same amount of time.

Result

The findings show the DNA contents of molar teeth significantly (p < 0.05) decreased as the effect of high-temperature exposure. PCR result visualization shows CSF1PO is the only locus detected with mini primer exposed to 750°C temperature for 30 minutes (the highest exposure during this research).

Conclusions

This finding suggests that this locus is potential in examining identification through DNA analysis, especially on a degraded condition as the effect of high-temperature exposure. Besides, this could accelerate the identification process especially on mass disaster events or criminal cases.