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Michael Hofreiter - One of the best experts on this subject based on the ideXlab platform.
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progress in forensic bone DNA analysis lessons learned from Ancient DNA
Forensic Science International-genetics, 2021Co-Authors: Michael Hofreiter, Jiri Sneberger, Martin Pospisek, Daniel VanekAbstract: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.
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the future of Ancient DNA technical advances and conceptual shifts
BioEssays, 2015Co-Authors: Michael Hofreiter, Johanna L A Paijmans, Helen Goodchild, Camilla Speller, Axel Barlow, Gloria G Fortes, Jessica A Thomas, Arne Ludwig, Matthew J CollinsAbstract:Technological innovations such as next generation sequencing and DNA hybridisation enrichment have resulted in multi-fold increases in both the quantity of Ancient DNA sequence data and the time depth for DNA retrieval. To date, over 30 Ancient genomes have been sequenced, moving from 0.7× coverage (mammoth) in 2008 to more than 50× coverage (Neanderthal) in 2014. Studies of rapid evolutionary changes, such as the evolution and spread of pathogens and the genetic responses of hosts, or the genetics of domestication and climatic adaptation, are developing swiftly and the importance of palaeogenomics for investigating evolutionary processes during the last million years is likely to increase considerably. However, these new datasets require new methods of data processing and analysis, as well as conceptual changes in interpreting the results. In this review we highlight important areas of future technical and conceptual progress and discuss research topics in the rapidly growing field of palaeogenomics.
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a paleogenomic perspective on evolution and gene function new insights from Ancient DNA
Science, 2014Co-Authors: Beth Shapiro, Michael HofreiterAbstract:The publication of partial and complete paleogenomes within the last few years has reinvigorated research in Ancient DNA. No longer limited to short fragments of mitochondrial DNA, inference of evolutionary processes through time can now be investigated from genome-wide data sampled as far back as 700,000 years. Tremendous insights have been made, in particular regarding the hominin lineage. With rare exception, however, a paleogenomic perspective has been mired by the quality and quantity of recoverable DNA. Though conceptually simple, extracting Ancient DNA remains challenging, and sequencing Ancient genomes to high coverage remains prohibitively expensive for most laboratories. Still, with improvements in DNA isolation and declining sequencing costs, the taxonomic and geographic purview of paleogenomics is expanding at a rapid pace. With improved capacity to screen large numbers of samples for those with high proportions of endogenous Ancient DNA, paleogenomics is poised to become a key technology to better understand recent evolutionary events.
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a rapid column based Ancient DNA extraction method for increased sample throughput
Molecular Ecology Resources, 2010Co-Authors: Nadin Rohland, Heike Siedel, Michael HofreiterAbstract:Genetic analyses using museum specimens and Ancient DNA from fossil samples are becoming increasingly important in phylogenetic and especially population genetic studies. Recent progress in Ancient DNA sequencing technologies has substantially increased DNA sequence yields and, in combination with barcoding methods, has enabled large-scale studies using any type of DNA. Moreover, more and more studies now use nuclear DNA sequences in addition to mitochondrial ones. Unfortunately, nuclear DNA is, due to its much lower copy number in living cells compared to mitochondrial DNA, much more difficult to obtain from low-quality samples. Therefore, a DNA extraction method that optimizes DNA yields from low-quality samples and at the same time allows processing many samples within a short time frame is immediately required. In fact, the major bottleneck in the analysis process using samples containing low amounts of degraded DNA now lies in the extraction of samples, as column-based methods using commercial kits are fast but have proven to give very low yields, while more efficient methods are generally very time-consuming. Here, we present a method that combines the high DNA yield of batch-based silica extraction with the time-efficiency of column-based methods. Our results on Pleistocene cave bear samples show that DNA yields are quantitatively comparable, and in fact even slightly better than with silica batch extraction, while at the same time the number of samples that can conveniently be processed in parallel increases and both bench time and costs decrease using this method. Thus, this method is suited for harvesting the power of high-throughput sequencing using the DNA preserved in the millions of paleontological and museums specimens.
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is amino acid racemization a useful tool for screening for Ancient DNA in bone
Proceedings of The Royal Society B: Biological Sciences, 2009Co-Authors: Matthew J Collins, Nadin Rohland, Beth Shapiro, Kirsty Penkman, Reimer C Dobberstein, Stefanie Ritztimme, Michael HofreiterAbstract:Many rare and valuable Ancient specimens now carry the scars of Ancient DNA research, as questions of population genetics and phylogeography require larger sample sets. This fuels the demand for reliable techniques to screen for DNA preservation prior to destructive sampling. Only one such technique has been widely adopted: the extent of aspartic acid racemization (AAR). The kinetics of AAR are believed to be similar to the rate of DNA depurination and therefore a good measure of the likelihood of DNA survival. Moreover, AAR analysis is only minimally destructive. We report the first comprehensive test of AAR using 91 bone and teeth samples from temperate and high-latitude sites that were analysed for DNA. While the AAR range of all specimens was low (0.02–0.17), no correlation was found between the extent of AAR and DNA amplification success. Additional heating experiments and surveys of the literature indicated that d/l Asx is low in bones until almost all the collagen is lost. This is because aspartic acid is retained in the bone within the constrained environment of the collagen triple helix, where it cannot racemize for steric reasons. Only if the helix denatures to soluble gelatin can Asx racemize readily, but this soluble gelatine is readily lost in most burial environments. We conclude that Asx d/l is not a useful screening technique for Ancient DNA from bone.
Nadin Rohland - One of the best experts on this subject based on the ideXlab platform.
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Human auditory ossicles as an alternative optimal source of Ancient DNA.
Genome research, 2020Co-Authors: Kendra Sirak, Nadin Rohland, Eadaoin Harney, Swapan Mallick, Daniel Fernandes, Olivia Cheronet, Matthew Mah, Nicole Adamski, Nasreen Broomandkhoshbacht, Kimberly CallanAbstract:DNA recovery from Ancient human remains has revolutionized our ability to reconstruct the genetic landscape of the past. Ancient DNA research has benefited from the identification of skeletal elements, such as the cochlear part of the osseous inner ear, that provides optimal contexts for DNA preservation; however, the rich genetic information obtained from the cochlea must be counterbalanced against the loss of morphological information caused by its sampling. Motivated by similarities in developmental processes and histological properties between the cochlea and auditory ossicles, we evaluate the ossicles as an alternative source of Ancient DNA. We show that ossicles perform comparably to the cochlea in terms of DNA recovery, finding no substantial reduction in data quantity and minimal differences in data quality across preservation conditions. Ossicles can be sampled from intact skulls or disarticulated petrous bones without damage to surrounding bone, and we argue that they should be used when available to reduce damage to human remains. Our results identify another optimal skeletal element for Ancient DNA analysis and add to a growing toolkit of sampling methods that help to better preserve skeletal remains for future research while maximizing the likelihood that Ancient DNA analysis will produce useable results.
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Human Auditory Ossicles as an Alternative Optimal Source of Ancient DNA
2019Co-Authors: Kendra Sirak, Nadin Rohland, Eadaoin Harney, Swapan Mallick, Daniel Fernandes, Olivia Cheronet, Matthew Mah, Nicole Adamski, Nasreen Broomandkhoshbacht, Kimberly CallanAbstract:ABSTRACT DNA recovery from Ancient human remains has revolutionized our ability to reconstruct the genetic landscape of the past. Ancient DNA research has benefited from the identification of skeletal elements, such as the cochlear part of the osseous inner ear, that provide optimal contexts for DNA preservation; however, the rich genetic information obtained from the cochlea must be counterbalanced against the loss of valuable morphological information caused by its sampling. Motivated by similarities in developmental processes and histological properties between the cochlea and auditory ossicles, we evaluated the efficacy of ossicles as an alternative source of Ancient DNA. We demonstrate that ossicles perform comparably to the cochlea in terms of DNA recovery, finding no substantial reduction in data quality, quantity, or authenticity across a range of preservation conditions. Ossicles can be sampled from intact skulls or disarticulated petrous bones without damage to surrounding bone, and we argue that, when available, they should be selected over the cochlea to reduce damage to skeletal integrity. These results identify a second optimal skeletal element for Ancient DNA analysis and add to a growing toolkit of sampling methods that help to better preserve skeletal remains for future research while maximizing the likelihood that Ancient DNA analysis will produce useable results.
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Partial uracil-DNA-glycosylase treatment for screening of Ancient DNA.
Philosophical transactions of the Royal Society of London. Series B Biological sciences, 2015Co-Authors: Nadin Rohland, Eadaoin Harney, Swapan Mallick, Susanne Nordenfelt, David ReichAbstract:The challenge of sequencing Ancient DNA has led to the development of specialized laboratory protocols that have focused on reducing contamination and maximizing the number of molecules that are extracted from Ancient remains. Despite the fact that success in Ancient DNA studies is typically obtained by screening many samples to identify a promising subset, Ancient DNA protocols have not, in general, focused on reducing the time required to screen samples. We present an adaptation of a popular Ancient library preparation method that makes screening more efficient. First, the DNA extract is treated using a protocol that causes characteristic Ancient DNA damage to be restricted to the terminal nucleotides, while nearly eliminating it in the interior of the DNA molecules, allowing a single library to be used both to test for Ancient DNA authenticity and to carry out population genetic analysis. Second, the DNA molecules are ligated to a unique pair of barcodes, which eliminates undetected cross-contamination from this step onwards. Third, the barcoded library molecules include incomplete adapters of short length that can increase the specificity of hybridization-based genomic target enrichment. The adapters are completed just before sequencing, so the same DNA library can be used in multiple experiments, and the sequences distinguished. We demonstrate this protocol on 60 Ancient human samples.
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a rapid column based Ancient DNA extraction method for increased sample throughput
Molecular Ecology Resources, 2010Co-Authors: Nadin Rohland, Heike Siedel, Michael HofreiterAbstract:Genetic analyses using museum specimens and Ancient DNA from fossil samples are becoming increasingly important in phylogenetic and especially population genetic studies. Recent progress in Ancient DNA sequencing technologies has substantially increased DNA sequence yields and, in combination with barcoding methods, has enabled large-scale studies using any type of DNA. Moreover, more and more studies now use nuclear DNA sequences in addition to mitochondrial ones. Unfortunately, nuclear DNA is, due to its much lower copy number in living cells compared to mitochondrial DNA, much more difficult to obtain from low-quality samples. Therefore, a DNA extraction method that optimizes DNA yields from low-quality samples and at the same time allows processing many samples within a short time frame is immediately required. In fact, the major bottleneck in the analysis process using samples containing low amounts of degraded DNA now lies in the extraction of samples, as column-based methods using commercial kits are fast but have proven to give very low yields, while more efficient methods are generally very time-consuming. Here, we present a method that combines the high DNA yield of batch-based silica extraction with the time-efficiency of column-based methods. Our results on Pleistocene cave bear samples show that DNA yields are quantitatively comparable, and in fact even slightly better than with silica batch extraction, while at the same time the number of samples that can conveniently be processed in parallel increases and both bench time and costs decrease using this method. Thus, this method is suited for harvesting the power of high-throughput sequencing using the DNA preserved in the millions of paleontological and museums specimens.
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is amino acid racemization a useful tool for screening for Ancient DNA in bone
Proceedings of The Royal Society B: Biological Sciences, 2009Co-Authors: Matthew J Collins, Nadin Rohland, Beth Shapiro, Kirsty Penkman, Reimer C Dobberstein, Stefanie Ritztimme, Michael HofreiterAbstract:Many rare and valuable Ancient specimens now carry the scars of Ancient DNA research, as questions of population genetics and phylogeography require larger sample sets. This fuels the demand for reliable techniques to screen for DNA preservation prior to destructive sampling. Only one such technique has been widely adopted: the extent of aspartic acid racemization (AAR). The kinetics of AAR are believed to be similar to the rate of DNA depurination and therefore a good measure of the likelihood of DNA survival. Moreover, AAR analysis is only minimally destructive. We report the first comprehensive test of AAR using 91 bone and teeth samples from temperate and high-latitude sites that were analysed for DNA. While the AAR range of all specimens was low (0.02–0.17), no correlation was found between the extent of AAR and DNA amplification success. Additional heating experiments and surveys of the literature indicated that d/l Asx is low in bones until almost all the collagen is lost. This is because aspartic acid is retained in the bone within the constrained environment of the collagen triple helix, where it cannot racemize for steric reasons. Only if the helix denatures to soluble gelatin can Asx racemize readily, but this soluble gelatine is readily lost in most burial environments. We conclude that Asx d/l is not a useful screening technique for Ancient DNA from bone.
Matthew J Collins - One of the best experts on this subject based on the ideXlab platform.
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a new model for Ancient DNA decay based on paleogenomic meta analysis
Nucleic Acids Research, 2017Co-Authors: Roselyn Ware, Logan Kistler, Oliver Smith, Matthew J Collins, Robin G. AllabyAbstract:The persistence of DNA over archaeological and paleontological timescales in diverse environments has led to a revolutionary body of paleogenomic research, yet the dynamics of DNA degradation are still poorly understood. We analyzed 185 paleogenomic datasets and compared DNA survival with environmental variables and sample ages. We find cytosine deamination follows a conventional thermal age model, but we find no correlation between DNA fragmentation and sample age over the timespans analyzed, even when controlling for environmental variables. We propose a model for Ancient DNA decay wherein fragmentation rapidly reaches a threshold, then subsequently slows. The observed loss of DNA over time may be due to a bulk diffusion process in many cases, highlighting the importance of tissues and environments creating effectively closed systems for DNA preservation. This model of DNA degradation is largely based on mammal bone samples due to published genomic dataset availability. Continued refinement to the model to reflect diverse biological systems and tissue types will further improve our understanding of Ancient DNA breakdown dynamics.
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a new model for Ancient DNA decay based on paleogenomic meta analysis
bioRxiv, 2017Co-Authors: Logan Kistler, Roselyn Ware, Oliver Smith, Matthew J Collins, Robin G. AllabyAbstract:The persistence of DNA over archaeological and paleontological timescales in diverse environments has led to revolutionary body of paleogenomic research, yet the dynamics of DNA degradation are still poorly understood. We analyzed 185 paleogenomic datasets and compared DNA survival with environmental variables and sample ages. We find cytosine deamination follows a conventional thermal age model, but we find no correlation between DNA fragmentation and sample age over the timespans analyzed, even when controlling for environmental variables. We propose a model for Ancient DNA decay wherein fragmentation rapidly reaches a threshold, then subsequently slows. The observed loss of DNA over time is likely due to a bulk diffusion process, highlighting the importance of tissues and environments creating effectively closed systems for DNA preservation.
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the future of Ancient DNA technical advances and conceptual shifts
BioEssays, 2015Co-Authors: Michael Hofreiter, Johanna L A Paijmans, Helen Goodchild, Camilla Speller, Axel Barlow, Gloria G Fortes, Jessica A Thomas, Arne Ludwig, Matthew J CollinsAbstract:Technological innovations such as next generation sequencing and DNA hybridisation enrichment have resulted in multi-fold increases in both the quantity of Ancient DNA sequence data and the time depth for DNA retrieval. To date, over 30 Ancient genomes have been sequenced, moving from 0.7× coverage (mammoth) in 2008 to more than 50× coverage (Neanderthal) in 2014. Studies of rapid evolutionary changes, such as the evolution and spread of pathogens and the genetic responses of hosts, or the genetics of domestication and climatic adaptation, are developing swiftly and the importance of palaeogenomics for investigating evolutionary processes during the last million years is likely to increase considerably. However, these new datasets require new methods of data processing and analysis, as well as conceptual changes in interpreting the results. In this review we highlight important areas of future technical and conceptual progress and discuss research topics in the rapidly growing field of palaeogenomics.
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is amino acid racemization a useful tool for screening for Ancient DNA in bone
Proceedings of The Royal Society B: Biological Sciences, 2009Co-Authors: Matthew J Collins, Nadin Rohland, Beth Shapiro, Kirsty Penkman, Reimer C Dobberstein, Stefanie Ritztimme, Michael HofreiterAbstract:Many rare and valuable Ancient specimens now carry the scars of Ancient DNA research, as questions of population genetics and phylogeography require larger sample sets. This fuels the demand for reliable techniques to screen for DNA preservation prior to destructive sampling. Only one such technique has been widely adopted: the extent of aspartic acid racemization (AAR). The kinetics of AAR are believed to be similar to the rate of DNA depurination and therefore a good measure of the likelihood of DNA survival. Moreover, AAR analysis is only minimally destructive. We report the first comprehensive test of AAR using 91 bone and teeth samples from temperate and high-latitude sites that were analysed for DNA. While the AAR range of all specimens was low (0.02–0.17), no correlation was found between the extent of AAR and DNA amplification success. Additional heating experiments and surveys of the literature indicated that d/l Asx is low in bones until almost all the collagen is lost. This is because aspartic acid is retained in the bone within the constrained environment of the collagen triple helix, where it cannot racemize for steric reasons. Only if the helix denatures to soluble gelatin can Asx racemize readily, but this soluble gelatine is readily lost in most burial environments. We conclude that Asx d/l is not a useful screening technique for Ancient DNA from bone.
Kay Prufer - One of the best experts on this subject based on the ideXlab platform.
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present day DNA contamination in Ancient DNA datasets
BioEssays, 2020Co-Authors: Stephane Peyregne, Kay PruferAbstract:Present-day contamination can lead to false conclusions in Ancient DNA studies. A number of methods are available to estimate contamination, which use a variety of signals and are appropriate for different types of data. Here an overview of currently available methods highlighting their strengths and weaknesses is provided, and a classification based on the signals used to estimate contamination is proposed. This overview aims at enabling researchers to choose the most appropriate methods for their dataset. Based on this classification, potential avenues for the further development of methods are discussed.
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snpad an Ancient DNA genotype caller
Bioinformatics, 2018Co-Authors: Kay PruferAbstract:Motivation The study of Ancient genomes can elucidate the evolutionary past. However, analyses are complicated by base-modifications in Ancient DNA molecules that result in errors in DNA sequences. These errors are particularly common near the ends of sequences and pose a challenge for genotype calling. Results I describe an iterative method that estimates genotype frequencies and errors along sequences to allow for accurate genotype calling from Ancient sequences. The implementation of this method, called snpAD, performs well on high-coverage Ancient data, as shown by simulations and by subsampling the data of a high-coverage Neandertal genome. Although estimates for low-coverage genomes are less accurate, I am able to derive approximate estimates of heterozygosity from several low-coverage Neandertals. These estimates show that low heterozygosity, compared to modern humans, was common among Neandertals. Availability and implementation The C++ code of snpAD is freely available at http://bioinf.eva.mpg.de/snpAD/. Supplementary information Supplementary data are available at Bioinformatics online.
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quantifying and reducing spurious alignments for the analysis of ultra short Ancient DNA sequences
BMC Biology, 2018Co-Authors: Cesare De Filippo, Matthias Meyer, Kay PruferAbstract:The study of Ancient DNA is hampered by degradation, resulting in short DNA fragments. Advances in laboratory methods have made it possible to retrieve short DNA fragments, thereby improving access to DNA preserved in highly degraded, Ancient material. However, such material contains large amounts of microbial contamination in addition to DNA fragments from the Ancient organism. The resulting mixture of sequences constitutes a challenge for computational analysis, since microbial sequences are hard to distinguish from the Ancient sequences of interest, especially when they are short. Here, we develop a method to quantify spurious alignments based on the presence or absence of rare variants. We find that spurious alignments are enriched for mismatches and insertion/deletion differences and lack substitution patterns typical of Ancient DNA. The impact of spurious alignments can be reduced by filtering on these features and by imposing a sample-specific minimum length cutoff. We apply this approach to sequences from four ~ 430,000-year-old Sima de los Huesos hominin remains, which contain particularly short DNA fragments, and increase the amount of usable sequence data by 17–150%. This allows us to place a third specimen from the site on the Neandertal lineage. Our method maximizes the sequence data amenable to genetic analysis from highly degraded Ancient material and avoids pitfalls that are associated with the analysis of ultra-short DNA sequences.
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harvesting information from ultra short Ancient DNA sequences
bioRxiv, 2018Co-Authors: Cesare De Filippo, Matthias Meyer, Kay PruferAbstract:The study of Ancient DNA is hampered by degradation, resulting in short DNA fragments. Advances in laboratory methods have made it possible to retrieve short DNA fragments, thereby improving access to DNA preserved in highly degraded, Ancient material. However, such material contains large amounts of microbial contamination in addition to DNA fragments from the Ancient organism. The resulting mixture of sequences constitute a challenge for computational analysis, since microbial sequences are hard to distinguish from the Ancient sequences of interest, especially when they are short. Here, we develop a method to quantify spurious alignments based on the presence or absence of rare variants. We find that spurious alignments are enriched for mismatches and insertion/deletion differences and lack substitution patterns typical of Ancient DNA. The impact of spurious alignments can be reduced by filtering on these features and by imposing a sample-specific minimum length cutoff. We apply this approach to sequences from the ~430,000 year-old Sima de los Huesos hominin remains, which contain particularly short DNA fragments, and increase the amount of usable sequence data by 17-150%. This allows us to place a third specimen from the site on the Neandertal lineage. Our method maximizes the sequence data amenable to genetic analysis from highly degraded Ancient material and avoids pitfalls that are associated with the analysis of ultra-short DNA sequences.
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snpad an Ancient DNA genotype caller
bioRxiv, 2018Co-Authors: Kay PruferAbstract:Motivation: The study of Ancient genomes can elucidate the evolutionary past. However, analyses are complicated by base-modifications in Ancient DNA molecules that result in errors in DNA sequences. These errors are particularly common near the ends of sequences and pose a challenge for genotype calling. Results: I describe an iterative method that estimates genotype frequencies and errors along sequences to allow for accurate genotype calling from Ancient sequences. The implementation of this method, called snpAD, performs well on high-coverage Ancient data, as shown by simulations and by subsampling the data of a high-coverage Neandertal genome. Although estimates for low-coverage genomes are less accurate, I am able to derive approximate estimates of heterozygosity from several low-coverage Neandertals. These estimates show that low heterozygosity, compared to modern humans, was common among Neandertals.
Daniel Fernandes - One of the best experts on this subject based on the ideXlab platform.
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Ancient DNA reveals monozygotic newborn twins from the upper palaeolithic
Communications Biology, 2020Co-Authors: Maria Teschlernicola, Daniel Fernandes, Marc Handel, Thomas Einwogerer, Ulrich Simon, Christine Neugebauermaresch, Stefan Tangl, Patrick Heimel, Toni Dobsak, Anika RetzmannAbstract:The Upper Palaeolithic double burial of newborns and the single burial of a ca. 3-month-old infant uncovered at the Gravettian site of Krems-Wachtberg, Austria, are of paramount importance given the rarity of immature human remains from this time. Genome-wide Ancient DNA shows that the male infants of the double grave are the earliest reported case of monozygotic twins, while the single grave´s individual was their 3rd-degree male relative. We assessed the individuals´ age at death by applying histological and µCT inspection of the maxillary second incisors (i2) in conjunction with C- and N-isotope ratios and Barium (Ba) intake as biomarker for breastfeeding. The results show that the twins were full-term newborns, and that while individual 2 died at birth, individual 1 survived for about 50 days. The findings show that Gravettian mortuary behaviour also included re-opening of a grave and manipulation of its layout and content. Maria Teschler-Nicola et al. use Ancient DNA sequencing to report the earliest known case of human monozygotic twins found in a previously discovered Upper Palaeolithic burial site. Using bioanthropological and archaeological techniques, they also find that the twins were full-term newborns and that Ancient mortuary behavior included re-opening of grave sites to bury related individuals together.
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Ancient DNA reveals monozygotic newborn twins from the upper palaeolithic
Communications Biology, 2020Co-Authors: Maria Teschlernicola, Daniel Fernandes, Marc Handel, Thomas Einwogerer, Ulrich Simon, Christine Neugebauermaresch, Stefan Tangl, Patrick Heimel, Toni Dobsak, Anika RetzmannAbstract:The Upper Palaeolithic double burial of newborns and the single burial of a ca. 3-month-old infant uncovered at the Gravettian site of Krems-Wachtberg, Austria, are of paramount importance given the rarity of immature human remains from this time. Genome-wide Ancient DNA shows that the male infants of the double grave are the earliest reported case of monozygotic twins, while the single grave´s individual was their 3rd-degree male relative. We assessed the individuals´ age at death by applying histological and µCT inspection of the maxillary second incisors (i2) in conjunction with C- and N-isotope ratios and Barium (Ba) intake as biomarker for breastfeeding. The results show that the twins were full-term newborns, and that while individual 2 died at birth, individual 1 survived for about 50 days. The findings show that Gravettian mortuary behaviour also included re-opening of a grave and manipulation of its layout and content.
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Human auditory ossicles as an alternative optimal source of Ancient DNA.
Genome research, 2020Co-Authors: Kendra Sirak, Nadin Rohland, Eadaoin Harney, Swapan Mallick, Daniel Fernandes, Olivia Cheronet, Matthew Mah, Nicole Adamski, Nasreen Broomandkhoshbacht, Kimberly CallanAbstract:DNA recovery from Ancient human remains has revolutionized our ability to reconstruct the genetic landscape of the past. Ancient DNA research has benefited from the identification of skeletal elements, such as the cochlear part of the osseous inner ear, that provides optimal contexts for DNA preservation; however, the rich genetic information obtained from the cochlea must be counterbalanced against the loss of morphological information caused by its sampling. Motivated by similarities in developmental processes and histological properties between the cochlea and auditory ossicles, we evaluate the ossicles as an alternative source of Ancient DNA. We show that ossicles perform comparably to the cochlea in terms of DNA recovery, finding no substantial reduction in data quantity and minimal differences in data quality across preservation conditions. Ossicles can be sampled from intact skulls or disarticulated petrous bones without damage to surrounding bone, and we argue that they should be used when available to reduce damage to human remains. Our results identify another optimal skeletal element for Ancient DNA analysis and add to a growing toolkit of sampling methods that help to better preserve skeletal remains for future research while maximizing the likelihood that Ancient DNA analysis will produce useable results.
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Human Auditory Ossicles as an Alternative Optimal Source of Ancient DNA
2019Co-Authors: Kendra Sirak, Nadin Rohland, Eadaoin Harney, Swapan Mallick, Daniel Fernandes, Olivia Cheronet, Matthew Mah, Nicole Adamski, Nasreen Broomandkhoshbacht, Kimberly CallanAbstract:ABSTRACT DNA recovery from Ancient human remains has revolutionized our ability to reconstruct the genetic landscape of the past. Ancient DNA research has benefited from the identification of skeletal elements, such as the cochlear part of the osseous inner ear, that provide optimal contexts for DNA preservation; however, the rich genetic information obtained from the cochlea must be counterbalanced against the loss of valuable morphological information caused by its sampling. Motivated by similarities in developmental processes and histological properties between the cochlea and auditory ossicles, we evaluated the efficacy of ossicles as an alternative source of Ancient DNA. We demonstrate that ossicles perform comparably to the cochlea in terms of DNA recovery, finding no substantial reduction in data quality, quantity, or authenticity across a range of preservation conditions. Ossicles can be sampled from intact skulls or disarticulated petrous bones without damage to surrounding bone, and we argue that, when available, they should be selected over the cochlea to reduce damage to skeletal integrity. These results identify a second optimal skeletal element for Ancient DNA analysis and add to a growing toolkit of sampling methods that help to better preserve skeletal remains for future research while maximizing the likelihood that Ancient DNA analysis will produce useable results.
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isolating the human cochlea to generate bone powder for Ancient DNA analysis
Nature Protocols, 2019Co-Authors: Ron Pinhasi, Kendra Sirak, Daniel Fernandes, Olivia CheronetAbstract:The cortical bone that forms the structure of the cochlea, part of the osseous labyrinth of the inner ear, is now one of the most frequently used skeletal elements in analyses of human Ancient DNA. However, there is currently no published, standardized method for its sampling. This protocol describes the preparation of bone powder from the cochlea of fragmented skulls in which the petrous pyramid of the temporal bone is accessible. Using a systematic process of bone removal based on distinct anatomical landmarks and the identification of relevant morphological features, a petrous pyramid is cleaned with a sandblaster, and the cochlea is located, isolated, and reduced to a homogeneous bone powder. All steps are carried out in dedicated Ancient DNA facilities, thus reducing the introduction of contamination. This protocol requires an understanding of Ancient DNA clean-room procedures and basic knowledge of petrous pyramid anatomy. In 50-65 min, it results in bone powder with endogenous DNA yields that can exceed those from teeth and other bones by up to two orders of magnitude. Compared with drilling methods, this method facilitates a more precise targeting of the cochlea, allows the user to visually inspect the cochlea and remove any residual sediment before the generation of bone powder, and confines the damage to the inner ear region and surface of the petrous portion of fragmentary crania.