DNA capture and next-generation sequencing can recover whole mitochondrial genomes from highly degraded samples for human identification

The evolution of contemporary livestock species: Insights from mitochondrial genome

The domestication of animals marks a pivotal moment in human history, profoundly influencing our demographic and cultural progress. This process has led to significant genetic, behavioral, and physical changes in livestock species compared to their wild ancestors. Understanding the evolutionary history and genetic diversity of livestock species is crucial, and mitochondrial DNA (mtDNA) has emerged as a robust marker for investigating molecular diversity in animals. Its highly conserved gene content across animal species, minimal duplications, absence of introns, and short intergenic regions make mtDNA analysis ideal for such studies. Mitochondrial DNA analysis has uncovered distinct cattle domestication events dating back to 8000 years BC in Southwestern Asia. The sequencing of water buffalo mtDNA in 2004 provided important insights into their domestication history. Caprine mtDNA analysis identified three haplogroups, indicating varied maternal origins. Sheep, domesticated 12,000 years ago, exhibit diverse mtDNA lineages, suggesting multiple domestication events. Ovine mtDNA studies revealed clades A, B, C, and a fourth lineage, group D. The origins of domestic pigs were traced to separate European and Asian events followed by interbreeding. In camels, mtDNA elucidated the phylogeographic structure and genetic differentiation between wild and domesticated species. Horses, domesticated around 3500 BC, show significant mtDNA variability, highlighting their diverse origins. Yaks exhibit unique adaptations for high-altitude environments, with mtDNA analysis providing insights into their adaptation. Chicken mtDNA studies supported a monophyletic origin from Southeast Asia's red jungle fowl, with evidence of multiple origins. This review explores livestock evolution and diversity through mtDNA studies, focusing on cattle, water buffalo, goat, sheep, pig, camel, horse, yak and chicken. It highlights mtDNA's significance in unraveling maternal lineages, genetic diversity, and domestication histories, concluding with insights into its potential application in improving livestock production and reproduction dynamics.

Coevolution with hosts underpins speciation in brood-parasitic cuckoos

Coevolution between interacting species is thought to increase biodiversity, but evidence linking microevolutionary processes to macroevolutionary patterns is scarce. We leveraged two decades of behavioral research coupled with historical DNA analysis to reveal that coevolution with hosts underpins speciation in brood-parasitic bronze-cuckoos. At a macroevolutionary scale, we show that highly virulent brood-parasitic taxa have higher speciation rates and are more likely to speciate in sympatry than less-virulent and nonparasitic relatives. We reveal the microevolutionary process underlying speciation: Hosts reject cuckoo nestlings, which selects for mimetic cuckoo nestling morphology. Where cuckoos exploit multiple hosts, selection for mimicry drives genetic and phenotypic divergence corresponding to host preference, even in sympatry. Our work elucidates perhaps the most common, but poorly characterized, evolutionary process driving biological diversification.

Ancient and modern DNA track temporal and spatial population dynamics in the European fallow deer since the Eemian interglacial

Anthropogenic factors have impacted the diversity and evolutionary trajectory of various species. This can be through factors such as pressure on population size or range, habitat fragmentation, or extensive manipulation and translocation. Here we use time-calibrated data to better understand the pattern and processes of evolution in the heavily manipulated European fallow deer (Dama dama). During the Pleistocene, fallow deer had a broad distribution across Europe and were found as far north as Britain during the Eemian interglacial. The last glacial period saw fallow deer retreat to southern refugia and they did not disperse north afterwards. Their recolonisation was mediated by people and, from northern Europe and the British Isles, fallow deer were transported around the world. We use ancient and modern mitochondrial DNA (mtDNA) and mitogenomic data from Eemian Britain to assess the pattern of change in distribution and lineage structure across Europe over time. We find founder effects and mixed lineages in the northern populations, and stability over time for populations in southern Europe. The Eemian sample was most similar to a lineage currently in Italy, suggesting an early establishment of the relevant refuge. We consider the implications for the integration of anthropogenic and natural processes towards a better understanding of the evolution of fallow deer in Europe.

DNA Profiling in Human Identification: From Past to Present

Forensic DNA typing has been widely accepted in the courts all over the world. This is because DNA profiling is a very powerful tool to identify individuals on the basis of their unique genetic makeup. DNA evidence is capable of not only identifying the presence of specific biospecimens in a crime scene, but it is also used to exonerate suspects who are innocent of a crime. Technological advancements in DNA profiling, including the development of validated kits and statistical methods have made this tool to be more precise in forensic investigations. Therefore, validated combined DNA index system (CODIS) short tandem repeats (STRs) kits which require very small amount of DNA, coupled with real-time polymerase chain reaction (PCR) and the statistical strengths are used routinely to identify human remains, establish paternity or to match suspected crime scene biospecimens. The road to modern DNA profiling has been long, and it has taken scientists decades of work and fine tuning to develop highly accurate testing and analyses that are used today. This review will discuss the various DNA polymorphisms and their utility in human identity testing.

Development of a novel microarray data analysis tool without normalization for genotyping degraded forensic DNA

Since the arrest of the Golden State Killer in the US in April 2018, forensic geneticists have been increasingly interested in the investigative genetic genealogy (IGG) method. While this method has already been in practical use as a powerful tool for criminal investigation, we have yet to know well the limitations and potential risks. In this current study, we performed an evaluation study focusing on degraded DNA using the Affymetrix Genome-Wide Human SNP Array 6.0 platform (Thermo Fisher Scientific). We revealed one of the potential problems that occur during SNP genotype determination using a microarray-based platform. Our analysis results indicated that the SNP profiles derived from degraded DNA contained many false heterozygous SNPs. In addition, it was confirmed that the total amount of probe signal intensity on microarray chips derived from degraded DNA decreased significantly. Because the conventional analysis algorithm performs normalization during genotype determination, we concluded that noise signals could be genotype-called. To address this issue, we proposed a novel microarray data analysis method without normalization (nMAP). Although the nMAP algorithm resulted in a low call rate, it substantially improved genotyping accuracy. Finally, we confirmed the usefulness of the nMAP algorithm for kinship inferences. These findings and the nMAP algorithm will make a contribution to the advance of the IGG method.

A custom hybridisation enrichment forensic intelligence panel to infer biogeographic ancestry, hair and eye colour, and Y chromosome lineage

Massively parallel sequencing can provide genetic data for hundreds to thousands of loci in a single assay for various types of forensic testing. However, available commercial kits require an initial PCR amplification of short-to-medium sized targets which limits their application for highly degraded DNA. Development and optimisation of large PCR multiplexes also prevents creation of custom panels that target different suites of markers for identity, biogeographic ancestry, phenotype, and lineage markers (Y-chromosome and mtDNA). Hybridisation enrichment, an alternative approach for target enrichment prior to sequencing, uses biotinylated probes to bind to target DNA and has proven successful on degraded and ancient DNA. We developed a customisable hybridisation capture method, that uses individually mixed baits to allow tailored and targeted enrichment to specific forensic questions of interest. To allow collection of forensic intelligence data, we assembled and tested a custom panel of hybridisation baits to infer biogeographic ancestry, hair and eye colour, and paternal lineage (and sex) on modern male and female samples with a range of self-declared ancestries and hair/eye colour combinations. The panel correctly estimated biogeographic ancestry in 9/12 samples (75%) but detected European admixture in three individuals from regions with admixed demographic history. Hair and eye colour were predicted correctly in 83% and 92% of samples respectively, where intermediate eye colour and blond hair were problematic to predict. Analysis of Y-chromosome SNPs correctly assigned sex and paternal haplogroups, the latter complementing and supporting biogeographic ancestry predictions. Overall, we demonstrate the utility of this hybridisation enrichment approach to forensic intelligence testing using a combined suite of biogeographic ancestry, phenotype, and Y-chromosome SNPs for comprehensive biological profiling.

DNA and protein analyses of hair in forensic genetics

Hair is one of the most common pieces of biological evidence found at a crime scene and plays an essential role in forensic investigation. Hairs, especially non-follicular hairs, are usually found at various crime scenes, either by natural shedding or by forcible shedding. However, the genetic material in hairs is usually highly degraded, which makes forensic analysis difficult. As a result, the value of hair has not been fully exploited in forensic investigations and trials. In recent years, with advances in molecular biology, forensic analysis of hair has achieved remarkable strides and provided crucial clues in numerous cases. This article reviews recent developments in DNA and protein analysis of hair and attempts to provide a comprehensive solution to improve forensic hair analysis.

The Skeletal Remains of Soldiers from the Two World Wars: Between Identification, Health Research and Memorial Issues

After causing mass disasters that claimed the lives of tens of thousands of soldiers from countries around the world, the two Great Wars left some of them lost and missing. In France, these corpses reside in a legal vagueness where they belong neither to forensic anthropology nor archeology. Nevertheless, the process of identification and determining the cause of death requires the use of modern forensic anthropology by applying biological profiling and DNA analysis. New genomic methods also provide insight into the health statuses of these military populations, providing new perspectives on these periods of humanitarian crisis.

Post hoc deconvolution of human mitochondrial DNA mixtures by EMMA 2 using fine-tuned Phylotree nomenclature

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MtDNA mixtures are observed frequently and difficult to deconvolute.

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Most previous methods require raw data or quantitative information.

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EMMA 2 produces valid splittings from consensus sequences of any sequencing technology.

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EMMA 2 can deconvolute 2 and 3 person mixtures in a fast and traceable way.

In this paper we present a new algorithm for splitting (partial) human mitogenomes into components with high similarity to haplogroup motifs of Phylotree. The algorithm reads a (partial) mitogenome coded by the differences to the reference (rCRS) and outputs the estimated haplogroups of the putative components. The algorithm requires no special information on the raw data of the sequencing process and is therefore suited for the post hoc analysis of mixtures of any sequencing technology. The software EMMA 2 implementing the algorithm will be made available via the EMPOP (https://empop.online) database and extends the nine years old software EMMA for haplogrouping single mitogenomes to mixtures with at most three components.

Simultaneous Barcode Sequencing of Diverse Museum Collection Specimens Using a Mixed RNA Bait Set

A growing number of publications presenting results from sequencing natural history collection specimens reflect the importance of DNA sequence information from such samples. Ancient DNA extraction and library preparation methods in combination with target gene capture are a way of unlocking archival DNA, including from formalin-fixed wet-collection material. Here we report on an experiment, in which we used an RNA bait set containing baits from a wide taxonomic range of species for DNA hybridisation capture of nuclear and mitochondrial targets for analysing natural history collection specimens. The bait set used consists of 2,492 mitochondrial and 530 nuclear RNA baits and comprises specific barcode loci of diverse animal groups including both invertebrates and vertebrates. The baits allowed to capture DNA sequence information of target barcode loci from 84% of the 37 samples tested, with nuclear markers being captured more frequently and consensus sequences of these being more complete compared to mitochondrial markers. Samples from dry material had a higher rate of success than wet-collection specimens, although target sequence information could be captured from 50% of formalin-fixed samples. Our study illustrates how efforts to obtain barcode sequence information from natural history collection specimens may be combined and are a way of implementing barcoding inventories of scientific collection material.

The application of machine learning to predict genetic relatedness using human mtDNA hypervariable region I sequences

Human identification of unknown samples following disaster and mass casualty events is essential, especially to bring closure to family and friends of the deceased. Unfortunately, victim identification is often challenging for forensic investigators as analysis becomes complicated when biological samples are degraded or of poor quality as a result of exposure to harsh environmental factors. Mitochondrial DNA becomes the ideal option for analysis, particularly for determining the origin of the samples. In such events, the estimation of genetic parameters plays an important role in modelling and predicting genetic relatedness and is useful in assigning unknown individuals to an ethnic group. Various techniques exist for the estimation of genetic relatedness, but the use of Machine learning (ML) algorithms are novel and presently the least used in forensic genetic studies. In this study, we investigated the ability of ML algorithms to predict genetic relatedness using hypervariable region I sequences; that were retrieved from the GenBank database for three race groups, namely African, Asian and Caucasian. Four ML classification algorithms; Support vector machines (SVM), Linear discriminant analysis (LDA), Quadratic discriminant analysis (QDA) and Random Forest (RF) were hybridised with one-hot encoding, Principal component analysis (PCA) and Bags of Words (BoW), and were compared for inferring genetic relatedness. The findings from this study on WEKA showed that genetic inferences based on PCA-SVM achieved an overall accuracy of 80–90% and consistently outperformed PCA-LDA, PCA-RF and PCA-QDA, while in Python BoW-PCA-RF achieved 94.4% accuracy which outperformed BoW-PCA-SVM, BoW-PCA-LDA and BoW-PCA-QDA respectively. ML results from the use of WEKA and Python software tools displayed higher accuracies as compared to the Analysis of molecular variance results. Given the results, SVM and RF algorithms are likely to also be useful in other sequence classification applications, making it a promising tool in genetics and forensic science. The study provides evidence that ML can be utilized as a supplementary tool for forensic genetics casework analysis.

Unveiling forensically relevant biogeographic, phenotype and Y-chromosome SNP variation in Pakistani ethnic groups using a customized hybridisation enrichment forensic intelligence panel

Massively parallel sequencing following hybridisation enrichment provides new opportunities to obtain genetic data for various types of forensic testing and has proven successful on modern as well as degraded and ancient DNA. A customisable forensic intelligence panel that targeted 124 SNP markers (67 ancestry informative markers, 23 phenotype markers from the HIrisplex panel, and 35 Y-chromosome SNPs) was used to examine biogeographic ancestry, phenotype and sex and Y-lineage in samples from different ethnic populations of Pakistan including Pothwari, Gilgit, Baloach, Pathan, Kashmiri and Siraiki. Targeted sequencing and computational data analysis pipeline allowed filtering of variants across the targeted loci. Study samples showed an admixture between East Asian and European ancestry. Eye colour was predicted accurately based on the highest p-value giving overall prediction accuracy of 92.8%. Predictions were consistent with reported hair colour for all samples, using the combined highest p-value approach and step-wise model incorporating probability thresholds for light or dark shade. Y-SNPs were successfully recovered only from male samples which indicates the ability of this method to identify biological sex and allow inference of Y-haplogroup. Our results demonstrate practicality of using hybridisation enrichment and MPS to aid in human intelligence gathering and will open many insights into forensic research in South Asia.

Extended kinship analysis of historical remains using SNP capture

DNA-assisted identification of historical remains requires the genetic analysis of highly degraded DNA, along with a comparison to DNA from known relatives. This can be achieved by targeting single nucleotide polymorphisms (SNPs) using a hybridization capture and next-generation sequencing approach suitable for degraded skeletal samples. In the present study, two SNP capture panels were designed to target ~ 25,000 (25 K) and ~ 95,000 (95 K) nuclear SNPs, respectively, to enable distant kinship estimation (up to 4th degree relatives). Low-coverage SNP data were successfully recovered from 14 skeletal elements 75 years postmortem using an Illumina MiSeq benchtop sequencer. All samples contained degraded DNA but were of varying quality with mean fragment lengths ranging from 32 bp to 170 bp across the 14 samples. SNP comparison with DNA from known family references was performed in the Parabon Fx Forensic Analysis Platform, which utilizes a likelihood approach for kinship prediction that was optimized for low-coverage sequencing data with cytosine deamination. The 25 K panel produced 15,000 SNPs on average, which allowed for accurate kinship prediction with strong statistical support in 16 of the 21 pairwise comparisons. The 95 K panel increased the average SNPs to 42,000 and resulted in an additional accurate kinship prediction with strong statistical support (17 of 21 pairwise comparisons). This study demonstrates that SNP capture combined with massively parallel sequencing on a benchtop platform can yield sufficient SNP recovery from compromised samples, enabling accurate, extended kinship predictions.

Internal validation and improvement of mitochondrial genome sequencing using the Precision ID mtDNA Whole Genome Panel

With the recent advances in next-generation sequencing (NGS), mitochondrial whole-genome sequencing has begun to be applied to the field of the forensic biology as an alternative to the traditional Sanger-type sequencing (STS). However, experimental workflows, commercial solutions, and output data analysis must be strictly validated before being implemented into the forensic laboratory. In this study, we performed an internal validation for an NGS-based typing of the entire mitochondrial genome using the Precision ID mtDNA Whole Genome Panel (Thermo Fisher Scientific) on the Ion S5 sequencer (Thermo Fisher Scientific). Concordance, repeatability, reproducibility, sensitivity, and heteroplasmy detection analyses were assessed using the 2800 M and 9947A standard control DNA as well as typical casework specimens, and results were compared with conventional Sanger sequencing and another NGS sequencer in a different laboratory. We discuss the strengths and limitations of this approach, highlighting some issues regarding noise thresholds and heteroplasmy detection, and suggesting solutions to mitigate these effects and improve overall data interpretation. Results confirmed that the Precision ID Whole mtDNA Genome Panel is highly reproducible and sensitive, yielding useful full mitochondrial DNA sequences also from challenging DNA specimens, thus providing further support for its use in forensic practice.

A New Method for Sequencing the Mitochondrial Genome by Using Long Read Technology

We describe a protocol to prepare a multiplexed mtDNA library from a blood sample for performing a long read sequencing of the mitochondrial genome. All steps are carefully described to get a high enrichment of mtDNA relative to total DNA extracted from the blood sample. The obtained mutiplexed library allows the production of long sequence mtDNA reads up to 16.5 kbp with a quality enabling variant-calling by using a portable sequencer (MinION, Oxford Nanopore Technologies).

Massively parallel sequencing of human skeletal remains in Vietnam using the precision ID mtDNA control region panel on the Ion S5™ system

Mitochondrial DNA (mtDNA) analysis using Sanger sequencing has been a routine practice for the identification of human skeletal remains. However, this process is usually challenging since DNA from the remains is highly degraded and at low concentration. Recently, the advent and implementation of massively parallel sequencing (MPS) have been offered the ability to improve mtDNA sequence data for forensic analysis. To assess the utility of the Ion S5™ system - an MPS platform for mtDNA analysis in challenging samples, we sequenced the mitochondrial control region of 52 age-old skeletal remains. Using the Precision ID mtDNA Control Region Panel, 50 full and two partial control region haplotypes at relatively high mean coverage of 2494 × were achieved for variant calling. Further variant analysis at 10% threshold for point heteroplasmy showed high degradation degree in terms of DNA damage in our bone samples. A higher point heteroplasmy threshold of 20% was required to diminish most of background noise caused by the damage. The results from this study indicated the potential application of the Ion S5™ system in sequencing degraded samples in Vietnam and provided valuable data sources for forensic analyses in the future.

Progress in forensic bone DNA analysis: Lessons learned from ancient DNA

Research on ancient and forensic DNA is related in many ways, and the two fields must deal with similar obstacles. Therefore, communication between these two communities has the potential to improve results in both research fields. Here, we present the insights gained in the ancient DNA community with regard to analyzing DNA from aged skeletal material and the potential use of the developed protocols in forensic work. We discuss the various steps, from choosing samples for DNA extraction to deciding between classical PCR amplification and massively parallel sequencing approaches. Based on the progress made in ancient DNA analyses combined with the requirements of forensic work, we suggest that there is substantial potential for incorporating ancient DNA approaches into forensic protocols, a process that has already begun to a considerable extent. However, taking full advantage of the experiences gained from ancient DNA work will require comparative studies by the forensic DNA community to tailor the methods developed for ancient samples to the specific needs of forensic studies and case work. If successful, in our view, the benefits for both communities would be considerable.

Interpreting NUMTs in forensic genetics: Seeing the forest for the trees

Nuclear mitochondrial DNA (mtDNA) segments (NUMTs) were discovered shortly after sequencing the first human mitochondrial genome. They have earlier been considered to represent archaic elements of ancient insertion events, but modern sequencing technologies and growing databases of mtDNA and NUMT sequences confirm that they are abundant and some of them phylogenetically young. Here, we build upon mtDNA/NUMT review articles published in the mid 2010 s and focus on the distinction of NUMTs and other artefacts that can be observed in aligned sequence reads, such as mixtures (contamination), point heteroplasmy, sequencing error and cytosine deamination. We show practical examples of the effect of the mtDNA enrichment method on the representation of NUMTs in the mapped sequence data and discuss methods to bioinformatically filter NUMTs from mtDNA reads.

Capture enrichment and massively parallel sequencing for human identification

In the past decade, hybridization capture has gained attention within the forensic field for its possible use in human identification. One of the primary benefits to capture enrichment is its applicability to degraded DNA fragments that, due to their reduced size, are not amenable to traditional PCR enrichment techniques. Hybridization capture is typically introduced after genomic library preparation of extracted DNA templates for the subsequent enrichment of mitochondrial DNA or single nucleotide polymorphisms within the nuclear genome. The enriched molecules are then subjected to massively parallel sequencing (MPS) for sensitive and high-throughput DNA sequence generation. Bioinformatic analysis of capture product removes PCR duplicates that were introduced during the laboratory workflow in order to characterize the original DNA template molecules. In the case of aged and degraded skeletal remains, the fraction of endogenous human DNA may be very low; therefore low-coverage sequence analysis may be required. This review contains an overview of current capture methodologies and the primary literature on hybridization capture as evaluated for forensic applications.

Spatiotemporal Genetic Diversity of Lions Reveals the Influence of Habitat Fragmentation across Africa

Direct comparisons between historical and contemporary populations allow for detecting changes in genetic diversity through time and assessment of the impact of habitat fragmentation. Here, we determined the genetic architecture of both historical and modern lions to document changes in genetic diversity over the last century. We surveyed microsatellite and mitochondrial genome variation from 143 high-quality museum specimens of known provenance, allowing us to directly compare this information with data from several recently published nuclear and mitochondrial studies. Our results provide evidence for male-mediated gene flow and recent isolation of local subpopulations, likely due to habitat fragmentation. Nuclear markers showed a significant decrease in genetic diversity from the historical (HE = 0.833) to the modern (HE = 0.796) populations, whereas mitochondrial genetic diversity was maintained (Hd = 0.98 for both). Although the historical population appears to have been panmictic based on nDNA data, hierarchical structure analysis identified four tiers of genetic structure in modern populations and was able to detect most sampling locations. Mitogenome analyses identified four clusters: Southern, Mixed, Eastern, and Western and were consistent between modern and historically sampled haplotypes. Within the last century, habitat fragmentation caused lion subpopulations to become more geographically isolated as human expansion changed the African landscape. This resulted in an increase in fine-scale nuclear genetic structure and loss of genetic diversity as lion subpopulations became more differentiated, whereas mitochondrial structure and diversity were maintained over time.

Markers for genetic change

Background and aims

Wildlife conservation has focused primarily on species for the last decades. Recently, popular perception and laws have begun to recognize the central importance of genetic diversity in the conservation of biodiversity. How to incorporate genetic diversity in ongoing monitoring and management of wildlife is still an open question.

Methods

We tested a panel of multiplexed, high-throughput sequenced introns in the small mammal communities of two UNESCO World Heritage Sites on different continents to assess their viability for large-scale monitoring of genetic variability in a spectrum of diverse species. To enhance applicability across other systems, the bioinformatic pipeline for primer design was outlined.

Results

The number of loci amplified and amplification evenness decreased as phylogenetic distance increased from the reference taxa, yet several loci were still variable across multiple mammal orders.

Conclusions

Genetic variability found is informative for population genetic analyses and for addressing phylogeographic and phylogenetic questions, illustrated by small mammal examples here.

Phylogenomics of white-eyes, a 'great speciator', reveals Indonesian archipelago as the center of lineage diversity

Archipelagoes serve as important 'natural laboratories' which facilitate the study of island radiations and contribute to the understanding of evolutionary processes. The white-eye genus Zosterops is a classical example of a 'great speciator', comprising c. 100 species from across the Old World, most of them insular. We achieved an extensive geographic DNA sampling of Zosterops by using historical specimens and recently collected samples. Using over 700 genome-wide loci in conjunction with coalescent species tree methods and gene flow detection approaches, we untangled the reticulated evolutionary history of Zosterops, which comprises three main clades centered in Indo-Africa, Asia, and Australasia, respectively. Genetic introgression between species permeates the Zosterops phylogeny, regardless of how distantly related species are. Crucially, we identified the Indonesian archipelago, and specifically Borneo, as the major center of diversity and the only area where all three main clades overlap, attesting to the evolutionary importance of this region.

Mitochondrial Sequencing of Missing Persons DNA Casework by Implementing Thermo Fisher's Precision ID mtDNA Whole Genome Assay

The advent of massively parallel sequencing (MPS) in the past decade has opened the doors to mitochondrial whole-genome sequencing. Mitochondrial (mt) DNA is used in forensics due to its high copy number per cell and maternal mode of inheritance. Consequently, we have implemented the Thermo Fisher Precision ID mtDNA Whole Genome panel coupled with the Ion Chef™ and Ion S5™ for MPS analysis in the California Department of Justice, Missing Persons DNA Program. Thirty-one mostly challenging samples (degraded, inhibited, low template, or mixed) were evaluated for this study. The majority of these samples generated single source full or partial genome sequences with MPS, providing information in cases where previously there was none. The quantitative and sensitive nature of MPS analysis was beneficial, but also led to detection of low-level contaminants. In addition, we found Precision ID to be more susceptible to inhibition than our legacy Sanger assay. Overall, the success rate (full single source hypervariable regions I and II (HVI/HVII) for Sanger and control region for MPS result) for these challenging samples increased from 32.3% with Sanger sequencing to 74.2% with the Precision ID assay. Considering the increase in success rate, the simple workflow and the higher discriminating potential of whole genome data, the Precision ID platform is a significant improvement for the CA Department of Justice Missing Persons DNA Program.

Platinum-Quality Mitogenome Haplotypes from United States Populations

A total of 1327 platinum-quality mitochondrial DNA haplotypes from United States (U.S.) populations were generated using a robust, semi-automated next-generation sequencing (NGS) workflow with rigorous quality control (QC). The laboratory workflow involved long-range PCR to minimize the co-amplification of nuclear mitochondrial DNA segments (NUMTs), PCR-free library preparation to reduce amplification bias, and high-coverage Illumina MiSeq sequencing to produce an average per-sample read depth of 1000 × for low-frequency (5%) variant detection. Point heteroplasmies below 10% frequency were confirmed through replicate amplification, and length heteroplasmy was quantitatively assessed using a custom read count analysis tool. Data analysis involved a redundant, dual-analyst review to minimize errors in haplotype reporting with additional QC checks performed by EMPOP. Applying these methods, eight sample sets were processed from five U.S. metapopulations (African American, Caucasian, Hispanic, Asian American, and Native American) corresponding to self-reported identity at the time of sample collection. Population analyses (e.g., haplotype frequencies, random match probabilities, and genetic distance estimates) were performed to evaluate the eight datasets, with over 95% of haplotypes unique per dataset. The platinum-quality mitogenome haplotypes presented in this study will enable forensic statistical calculations and thereby support the usage of mitogenome sequencing in forensic laboratories.

Searching the undetected mtDNA variants in forensic MPS data

The efficiency of MPS in forensic mtDNA analysis has been thoroughly proven, although a reliable and well established data evaluation still remains a critical point. Numerous bioinformatics tools have been developed, but most of them require specific operating systems and high costs, while free open-source programs with user-friendly interfaces are few. In this study, 43 full mtGenomes were sequenced using the Ion Personal Genome Machine™ (PGM™) System and analyzed utilizing the plug-in Variant Caller (TVC) of the Ion Torrent Software Suite and the mtDNA-Server (mDS), a free web-based mitochondrial analysis tool for MPS data. The outcomes of these two different analysis tools were compared to variants noted after manual inspection of the aligned reads performed using Integrative Genomics Viewer (IGV). The comparison highlighted the presence of thirty-nine discordant variant calls, which were resolved by Sanger sequencing that confirmed the presence of all variants, except for 7 deletions. The combined adoption of IGV and Sanger type sequencing confirmatory steps, in addition of TVC and mDS analysis, resulted in a more accurate variants assignment with the detection of 32 additional true polymorphisms, which were noted in the final dataset. Regarding the heteroplasmy issue, out of a total of thirty heteroplasmic variants, twenty-eight were detected by the TVC, while the mDS detected twenty-two. Overall, none of the used bioinformatics tools were the perfect choice and a secondary analysis with an expert's opinion in complete mtGenome MPS data evaluation is still required in forensic genetic analysis.

Massive parallel sequencing in forensics: advantages, issues, technicalities, and prospects

In the last decade, next-generation sequencing (NGS) technology, alternatively massive parallel sequencing (MPS), was applied to all fields of biological research. Its introduction to the field of forensics was slower, mainly due to lack of accredited sequencers, kits, and relatively higher sequencing error rates as compared with standardized Sanger sequencing. Currently, a majority of the problematic issues have been solved, which is proven by the body of reports in the literature. Here, we discuss the utility of NGS sequencing in forensics, emphasizing the advantages, issues, the technical aspects of the experiments, commercial solutions, and the potentially interesting applications of MPS.

Ancestral mitogenome capture of the Southeast Asian banded linsang

Utilising a reconstructed ancestral mitochondrial genome of a clade to design hybridisation capture baits can provide the opportunity for recovering mitochondrial sequences from all its descendent and even sister lineages. This approach is useful for taxa with no extant close relatives, as is often the case for rare or extinct species, and is a viable approach for the analysis of historical museum specimens. Asiatic linsangs (genus Prionodon) exemplify this situation, being rare Southeast Asian carnivores for which little molecular data is available. Using ancestral capture we recover partial mitochondrial genome sequences for seven banded linsangs (P. linsang) from historical specimens, representing the first intraspecific genetic dataset for this species. We additionally assemble a high quality mitogenome for the banded linsang using shotgun sequencing for time-calibrated phylogenetic analysis. This reveals a deep divergence between the two Asiatic linsang species (P. linsang, P. pardicolor), with an estimated divergence of ~12 million years (Ma). Although our sample size precludes any robust interpretation of the population structure of the banded linsang, we recover two distinct matrilines with an estimated tMRCA of ~1 Ma. Our results can be used as a basis for further investigation of the Asiatic linsangs, and further demonstrate the utility of ancestral capture for studying divergent taxa without close relatives.

The petrous bone: Ideal substrate in legal medicine?

Over the last few years, palaeogenomic studies of the petrous bone (the densest part of the temporal bone) have shown that it is a source of DNA in both larger quantities and of better quality than other bones. This dense bone around the otic capsule has therefore been called the choice substrate in palaeogenomics. Because the practice of forensic genetics responds to different imperatives, we implemented a study aimed at (i) understanding how and why the petrous bone is an advantageous substrate in ancient DNA studies and (ii) establishing whether it is advantageous in forensic STR typing. We selected 50 individual skeletal remains and extracted DNA from one tooth and one petrous bone from each. We then amplified 24 STR markers commonly used in forensic identification and compared the quality of that amplification using the RFU intensities of the signal as read on the STR profiles. We also performed histological analyses to compare (i) the microscopic structure of a petrous bone and of a tooth and (ii) the microscopic structure of fresh petrous bone and of an archaeological or forensic sample. We show that the RFU intensities read on STR profiles are systematically higher in experiments using DNA extracted from petrous bones rather than teeth. For this reason, we were more likely to obtain a complete STR profile from petrous bone material, increasing the chance of identification in a forensic setting. Histological analyses revealed peculiar microstructural characteristics (tissue organization), unique to the petrous bone, that might explain the good preservation of DNA in that substrate. Therefore, it appears that despite the necessity of analysing longer fragments in forensic STR typing compared to NGS palaeogenomics, the use of petrous bones in forensic genetics could prove valuable, especially in cases involving infants, toothless individuals or very degraded skeletal remains.

A Guide to Carrying Out a Phylogenomic Target Sequence Capture Project

High-throughput DNA sequencing techniques enable time- and cost-effective sequencing of large portions of the genome. Instead of sequencing and annotating whole genomes, many phylogenetic studies focus sequencing effort on large sets of pre-selected loci, which further reduces costs and bioinformatic challenges while increasing coverage. One common approach that enriches loci before sequencing is often referred to as target sequence capture. This technique has been shown to be applicable to phylogenetic studies of greatly varying evolutionary depth. Moreover, it has proven to produce powerful, large multi-locus DNA sequence datasets suitable for phylogenetic analyses. However, target capture requires careful considerations, which may greatly affect the success of experiments. Here we provide a simple flowchart for designing phylogenomic target capture experiments. We discuss necessary decisions from the identification of target loci to the final bioinformatic processing of sequence data. We outline challenges and solutions related to the taxonomic scope, sample quality, and available genomic resources of target capture projects. We hope this review will serve as a useful roadmap for designing and carrying out successful phylogenetic target capture studies.

MtDNA polymorphism analyses in the Chinese Mongolian group: Efficiency evaluation and further matrilineal genetic structure exploration

BACKGROUND

Profiling of mitochondrial DNA is surely to provide valuable investigative clues for forensic cases involving highly degraded specimens or complex maternal lineage kinship determination. But traditionally used hypervariable region sequencing of mitochondrial DNA is less frequently suggested by the forensic community for insufficient informativeness. Genome-wide sequencing of mitochondrial DNA can provide considerable amount of variant information but can be high cost at the same time.

METHODS

Efficiency of the 60 mitochondrial DNA polymorphic sites dispersing across the control region and coding region of mitochondrial DNA genome was evaluated with 106 Mongolians recruited from the Xinjiang Uyghur Autonomous Region, China, and allele-specific PCR technique was employed for mitochondrial DNA typing.

RESULTS

Altogether 58 haplotypes were observed and the haplotypic diversity, discrimination power and random match probability were calculated to be 0.981, 0.972, and 0.028, respectively. Mitochondrial DNA haplogroup affiliation exhibited an exceeding percentage (12.26%) of west Eurasian lineage (H haplogroup) in the studied Mongolian group, which needed to be further verified with more samples. Furthermore, the genetic relationships between the Xinjiang Mongolian group and the comparison populations were also investigated and the genetic affinity was discovered between the Xinjiang Mongolian group and the Xinjiang Kazak group in this study.

CONCLUSION

It was indicated that the panel was potentially enough to be used as a supplementary tool for forensic applications. And the matrilineal genetic structure analyses based on mitochondrial DNA variants in the Xinjiang Mongolian group could be helpful for subsequent anthropological studies.

Mitochondrial DNA in human identification: a review

Mitochondrial DNA (mtDNA) presents several characteristics useful for forensic studies, especially related to the lack of recombination, to a high copy number, and to matrilineal inheritance. mtDNA typing based on sequences of the control region or full genomic sequences analysis is used to analyze a variety of forensic samples such as old bones, teeth and hair, as well as other biological samples where the DNA content is low. Evaluation and reporting of the results requires careful consideration of biological issues as well as other issues such as nomenclature and reference population databases. In this work we review mitochondrial DNA profiling methods used for human identification and present their use in the main cases of humanidentification focusing on the most relevant issues for forensics.

Evaluation of mitogenome sequence concordance, heteroplasmy detection, and haplogrouping in a worldwide lineage study using the Precision ID mtDNA Whole Genome Panel

The emergence of Massively Parallel Sequencing technologies enabled the analysis of full mitochondrial (mt)DNA sequences from forensically relevant samples that have, so far, only been typed in the control region or its hypervariable segments. In this study, we evaluated the performance of a commercially available multiplex-PCR-based assay, the Precision ID mtDNA Whole Genome Panel (Thermo Fisher Scientific), for the amplification and sequencing of the entire mitochondrial genome (mitogenome) from even degraded forensic specimens. For this purpose, more than 500 samples from 24 different populations were selected to cover the vast majority of established superhaplogroups. These are known to harbor different signature sequence motifs corresponding to their phylogenetic background that could have an effect on primer binding and, thus, could limit a broad application of this molecular genetic tool. The selected samples derived from various forensically relevant tissue sources and were DNA extracted using different methods. We evaluated sequence concordance and heteroplasmy detection and compared the findings to conventional Sanger sequencing as well as an orthogonal MPS platform. We discuss advantages and limitations of this approach with respect to forensic genetic workflow and analytical requirements.

SD quants-Sensitive detection tetraplex-system for nuclear and mitochondrial DNA quantification and degradation inference

Measuring the quantity of DNA present in a forensic sample is relevant in a number of ways. First, it informs the analyst about the general DNA content to adjust the volume of DNA extract used for the genotyping assay to the optimal conditions (when possible). Second, quantification values can serve as plausibility checks for the performance of the DNA extraction method used as extraction positive and negative controls demand expected values. Third and relevant to highly compromised specimens, DNA quantification can inform about the degradation state of the DNA extracted from the unknown biological sample and aid the choice of downstream genotyping assays. While there are different, commercial products for the quantification of nuclear DNA available, commercial mitochondrial DNA (mtDNA) quantification systems are rare. Even more so, the simultaneous quantification of nuclear and mtDNA that is of relevance in highly degraded forensic specimens has rarely been described. We present here a novel real-time qPCR based tetraplex system termed SD quants that targets two different-sized mtDNA and a nuclear DNA region and includes an internal positive control to monitor potential inhibition. SD quants was compared to other existing quantification systems and subjected to analysis of severely degraded DNA present in ancient DNA and aged forensic specimens. This study complies with the MIQE (Bustin et al., 2009) guidelines (when applicable).

When a lost "Petit Prince" meets Antoine de Saint Exupéry: An anthropological case report

This case study reports the anthropological analysis of bones remains discovered on Riou Island (Marseille, France) and the story of two World War II fighter pilots. The discovery of bones on "The Fountain of the Greeks" square on Riou Island occurred in the 1960's and a first anthropological study described a 35-year-old man, about 1.77 m tall, buried since an estimated period between the 13th and 16th centuries. The case was "closed" and the bones were considered as isolated archaeological remains. Few years later, near the coasts of Riou Island, parts of two planes were discovered. One was from of a German Messerschmitt Bf 109 F-4 of the Luftwaffe piloted by Prince Alexis fürst zu Bentheim und Steinfurt, and the other from a French P-38 Lightning F-5 B piloted by Antoine de Saint-Exupery. Therefore, the identification of the skeletal remains mentioned above was then thought to be perhaps one of the two World War II pilots. In this particular context we performed forensic and molecular biology analyses to resolve this identification.

Fragmented Nuclear DNA is the Predominant Genetic Material in Human Hair Shafts

While shed hairs are one of the most commonly encountered evidence types, they are among the most limited in terms of DNA quantity and quality. As a result, nuclear DNA short tandem repeat (STR) profiling is generally unsuccessful and DNA testing of shed hair is instead performed by targeting the mitochondrial DNA control region. Although the high copy number of mitochondrial DNA relative to nuclear DNA routinely permits the recovery of mitochondrial DNA (mtDNA) data in these cases, mtDNA profiles do not offer the discriminatory power of nuclear DNA profiles. In order to better understand the total content and degradation state of DNA in single shed hairs and assess the feasibility of recovering highly discriminatory nuclear DNA data from this common evidence type, high throughput shotgun sequencing was performed on both recently collected and aged (approximately 50-year-old) hair samples. The data reflect trends that have been demonstrated previously with other technologies, namely that mtDNA quantity and quality decrease along the length of the hair shaft. In addition, the shotgun data reveal that nuclear DNA is present in shed hair and surprisingly abundant relative to mitochondrial DNA, even in the most distal fragments. Nuclear DNA comprised, at minimum, 88% of the total human reads in any given sample, and generally more than 95%. Here, we characterize both the nuclear and mitochondrial DNA content of shed hairs and discuss the implications of these data for forensic investigations.

Hybrid Capture-Based Next Generation Sequencing and Its Application to Human Infectious Diseases

This review describes target-enrichment approaches followed by next generation sequencing and their recent application to the research and diagnostic field of modern and past infectious human diseases caused by viruses, bacteria, parasites and fungi.

Targeted resequencing of coding DNA sequences for SNP discovery in nonmodel species

Targeted capture coupled with high-throughput sequencing can be used to gain information about nuclear sequence variation at hundreds to thousands of loci. Divergent reference capture makes use of molecular data of one species to enrich target loci in other (related) species. This is particularly valuable for nonmodel organisms, for which often no a priori knowledge exists regarding these loci. Here, we have used targeted capture to obtain data for 809 nuclear coding DNA sequences (CDS) in a nonmodel organism, the Eurasian lynx Lynx lynx, using baits designed with the help of the published genome of a related model organism (the domestic cat Felis catus). Using this approach, we were able to survey intraspecific variation at hundreds of nuclear loci in L. lynx across the species' European range. A large set of biallelic candidate SNPs was then evaluated using a high-throughput SNP genotyping platform (Fluidigm), which we then reduced to a final 96 SNP-panel based on assay performance and reliability; validation was carried out with 100 additional Eurasian lynx samples not included in the SNP discovery phase. The 96 SNP-panel developed from CDS performed very successfully in the identification of individuals and in population genetic structure inference (including the assignment of individuals to their source population). In keeping with recent studies, our results show that genic SNPs can be valuable for genetic monitoring of wildlife species.

Evaluation of the precision ID whole MtDNA genome panel for forensic analyses

Mitochondrial DNA (mtDNA) amplification and Massively Parallel Sequencing (MPS) using an early access version of the Precision ID Whole MtDNA Genome Panel (Thermo Fisher Scientific) and the Ion Personal Genome Machine (PGM) were evaluated using 15 forensically relevant samples. Samples were selected to represent typical forensic specimens for mtDNA analysis including hairs, hair shafts, swabs and ancient solid tissue samples (bones and teeth) that were stored in the freezer for up to several years after having been typed with conventional Sanger-type Sequencing and Capillary Electrophoresis. The MPS haplotypes confirmed the earlier results in all samples and provided additional sequence information that improved discrimination power and haplogroup estimation. The results raised the appetite for further experiments to validate and apply the new technology in forensic practice.

Biological Sexing of a 4000-Year-Old Egyptian Mummy Head to Assess the Potential of Nuclear DNA Recovery from the Most Damaged and Limited Forensic Specimens

High throughput sequencing (HTS) has been used for a number of years in the field of paleogenomics to facilitate the recovery of small DNA fragments from ancient specimens. Recently, these techniques have also been applied in forensics, where they have been used for the recovery of mitochondrial DNA sequences from samples where traditional PCR-based assays fail because of the very short length of endogenous DNA molecules. Here, we describe the biological sexing of a ~4000-year-old Egyptian mummy using shotgun sequencing and two established methods of biological sex determination (R_X and R_Y), by way of mitochondrial genome analysis as a means of sequence data authentication. This particular case of historical interest increases the potential utility of HTS techniques for forensic purposes by demonstrating that data from the more discriminatory nuclear genome can be recovered from the most damaged specimens, even in cases where mitochondrial DNA cannot be recovered with current PCR-based forensic technologies. Although additional work remains to be done before nuclear DNA recovered via these methods can be used routinely in operational casework for individual identification purposes, these results indicate substantial promise for the retrieval of probative individually identifying DNA data from the most limited and degraded forensic specimens.