Cold cases and ancient trade routes
2021; Springer Nature; Volume: 22; Issue: 12 Linguagem: Inglês
10.15252/embr.202154188
ISSN1469-3178
Autores Tópico(s)Environmental DNA in Biodiversity Studies
ResumoScience & Society5 November 2021free access Cold cases and ancient trade routes DNA phenotyping and isotope analysis extend forensic science into new domains Philip Hunter Corresponding Author Philip Hunter [email protected] Freelance Journalist, London, UK Search for more papers by this author Philip Hunter Corresponding Author Philip Hunter [email protected] Freelance Journalist, London, UK Search for more papers by this author Author Information Philip Hunter *,1 1Freelance Journalist, London, UK *Corresponding author. E-mail: [email protected] EMBO Reports (2021)22:e54188https://doi.org/10.15252/embr.202154188 Philip Hunter is a freelance journalist in London, UK. PDFDownload PDF of article text and main figures. ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions Figures & Info Forensic science has always held a great and somewhat morbid fascination for many people and the application of science to solve murder mysteries has been explored in countless crime novels, movies, and series. The invention of DNA fingerprinting in 1984 further fueled this fascination as the technology’s ability to match DNA found at a crime scene with samples from suspects greatly helped to solve many current and cold cases. Since, forensic science has extended into other fields such as wildlife tracking, sourcing of commodities, and verifying the origins of food ingredients. The next great step in criminal forensics then came with DNA phenotyping as a way of gaining information about the perpetrator in cases where there is no match with suspects or a DNA-typing database. This was followed by genealogical searching, which can enable suspects to be traced in the absence of direct identification via DNA by locating relatives who are represented in DNA databases. A further variant of growing importance is genetic ancestry testing, which can also help in investigations lacking other clues. … chemistry and physics have also made huge strides in isotope analysis and it is this field in particular that has reached out well beyond the criminal domain. But it is not just biology that is hogging the limelight in forensic science: chemistry and physics have also made huge strides in isotope analysis and it is this field in particular that has reached out well beyond the criminal domain. While significant technical challenges remain in both DNA phenotyping and isotope analysis, both have already made an impact in criminal investigations, as well as research in other disciplines. DNA phenotyping These new techniques score by being complementary rather than alternatives to the longer established DNA fingerprinting or isotope analysis in general. This is particularly the case for DNA phenotyping, otherwise known as Forensic DNA Profiling (FDP). “It is not in standard DNA profiling operations yet, that is run every day, and it will never replace STR profiling,” said Susan Walsh from the Department of Biology—Forensic & Investigative Sciences Program at Indiana University-Purdue University in the United States and a pioneer in this field. “FDP is a useful intelligence tool when other avenues have not led to anything, so providing a most probable prediction of the person who left the DNA provides some new lead for law enforcement. Also, missing persons and skeletal remains benefit a lot from this technology. Cases that have no hit in the DNA database or suspect profile, or cases with very badly degraded or low amounts of DNA, are where FDP is most useful.” Cases that have no hit in the DNA database or suspect profile, or cases with very badly degraded or low amounts of DNA, are where FDP is most useful. Forensic DNA Profiling, however, is distinct from ancestry testing and genealogy searching. “Ancestry testing is a separate method and uses different DNA markers for prediction,” Walsh noted. “One should not infer an ancestry using phenotype predictions and vice versa.” DNA phenotyping, unlike fingerprinting, which is well established, is also work in progress. “Right now, simple pigmentation categories, that is blue eye or brown hair or pale skin, can be predicted with a high degree of accuracy, although of course we consistently try to improve this all the time,” Walsh commented. “Hair morphology or baldness and broad age groups looks encouraging. But facial morphology is still quite far off, as opposed to what several particular companies propose.” Although prediction of ancestry from anonymous DNA is a separate field using different DNA markers, both benefit from technical advances, especially in Massive Parallel Sequencing (MPS) spanning whole genomes. Currently, ancestry determination is fairly basic, confined to ascertaining whether a DNA sample originated from a person in one of the main continents, but this may well change. “MPS is moving towards larger multiplexes, which will allow more refined phenotype prediction, not height and BMI, but certainly common visible characteristics,” commented Christopher Phillips, Institute of Forensic Sciences, University of Santiago de Compostela in Galicia, Spain. “We have developed a 1400-plex missing persons panel in conjunction with the ICMP DNA labs in The Hague. If such levels of multiplex scale can be applied to ancestry and FDP analysis, we may be able to address the challenges of more refined ancestry, as well as expanding the traits that can be predicted (Phillips et al, 2020).” Ancestry analysis and criminal investigations Philips noted a number of other developments for ancestry determination. “Access to genome-wide variation data allows better marker selection and population reference datasets (for example the Forensic MPS AIMs Panel Reference Sets (usc.es)). There is also increased interest in microhaplotypes as a general-purpose marker type, since they have short amplicon characteristics for MPS of degraded DNA, have multiple alleles which allows mixed-DNA analysis and can provide both ID and ancestry inference capabilities,” he said. Those microhaplotypes are small genetic markers of less than 300 nucleotides, defined by 2 or more closely linked SNPs in multiple allelic combinations (Oldoni et al, 2019). They have various advantages over conventional STRs, such as lower mutation rates, which allows better differentiation between individuals. Furthermore, their value as markers has been enhanced by MPS, because it allows sequencing of both parental haplotypes at each of the many multiplexed loci. Philipps also highlighted developments in the analysis of population admixture to allow co-ancestry detection—the inheritance of given common alleles or traits from a common ancestor—which is useful in various contexts including the glut of consumer ancestry services. While several European countries have opted to allow ancestry analysis in a forensic context, others have decided against it owing to ethical considerations Phillips and colleagues have been developing new markers with the aim of refining searching abilities. “This is work in progress, but we think we have some very powerful markers, which just missed being adopted by VISAGE, as our Horizon 2020 funding finishes at the end of this year,” he said. VISAGE (VISible Attributes Through Genomics) is a EU research project, under the Horizon 2020 Framework Programme for Research, to overcome the limitation of current forensic DNA analysis by constructing composite sketches of unknown perpetrators from as many biological traces and sources as possible within current legal frameworks and ethical guidelines (https://cordis.europa.eu/project/id/740580). This last point is significant, because FTP has a controversial side effect—the risk of stigmatizing particular racial or ethnic groups if a sample suggests that suspects might have a given skin color, for example. While several European countries have opted to allow ancestry analysis in a forensic context, others have decided against it owing to ethical considerations (Phillips & Puente, 2021). Cold cases solved There have been successful applications of these techniques in criminal investigations already, particularly for resolving cold cases that had been abandoned for lack of leads or evidence. The first example of the use of DNA phenotyping occurred in 2017 when the killer of Candra Alston and her 3-year-old daughter Malaysia Boyki was identified, 6 years after the two had been found murdered in Columbia, South Carolina. At that time, DNA phenotyping was able to generate a sketch of the perpetrator, created solely from the analysis of the DNA sample found at the crime scene (Shih, 2020). An even older case was successfully revived in France in 2018 as a result of familial searching. It ended with the prosecution of the murderers of a little girl whose mutilated body had been found by a motorway in central France 31 years earlier in 1987. In this case, the parents of the murdered child, who until then had not been identified, were traced serendipitously after the DNA of their son was tested in an unrelated case and found to overlap with his dead sibling. The parents, by then aged 66 and 64, were arrested (https://www.bbc.com/news/world-europe-44479378). This field of familial searching is known formally as Forensic Genetic Genealogical DNA analysis and Searching (FGGS), or Forensic Genetic Genealogy (FGG), and combines DNA sequence analysis with traditional genealogy techniques. There have also been cold cases revived by searching genealogy databases; one of the most celebrated leading to the conviction of the Golden State Killer in California in June 2020 for 13 murders and 13 counts of kidnapping, mostly committed between the mid-1970s and mid-1980s. The killer, Joseph DeAngelo, was eventually identified after his genetic profile generated from crime scenes was uploaded to a genealogy database in 2017. An intriguing aspect of the case came when the police sought to obtain a DNA sample from the suspect to ascertain whether he was indeed the perpetrator. The authorities had him placed under surveillance to become familiar with his routines and as a result were able to obtain a tissue sample from which the DNA was extracted that matched DNA taken from the earlier crime scenes. Strontium isotope analysis Equally impressive progress has been made in the field of isotope analysis, which measures the exact amount of a wide range of isotopes in a sample. Thanks to technical advances in mass spectrometry, this can now be done from samples as small as a few nanograms and with a sensitivity of up to 10-12 isotope parts. The analysis of strontium (Sr) isotopes has proved most rewarding, but oxygen and carbon are also commonly used. As such, the 86Sr/87Sr ratio provides a valuable chemical marker for the geographic origin of a sample. Strontium is found widely in soils and rocks—as well as living organisms—since its electron configuration is similar to calcium and substitutes that element readily. The other key property is that it exists in four stable isotopes, and that the ratio between two of them, 87Sr and 86Sr, has a variable signature that depends on its geochemical origin and the age of the source rock. As such, the 86Sr/87Sr ratio provides a valuable chemical marker for the geographic origin of a sample. A key research goal, therefore, was establishing that the same ratio would appear in biological samples such as plants or pollen. “The idea is we needed confirmation of the crux assumption of using strontium isotopes to track movement, that is, that underlying isotope signatures in soil transfer without alteration to plants and herbivores,” explained Tyler Flockhart from the University of Maryland’s Centre for Environmental Science in the United States. In 2015, Flockhart eventually proved what had previously been assumed, namely that Sr ratios of herbivores and plants do correspond with minerals and bedrock in the area (Flockhart et al, 2015). Another key development was geographical mapping of Sr isotope ratios so that these could be matched with those from biological sources such as plants or insects. “This means we can collect plants to develop isoscapes and use those isoscapes to assign origins for herbivores,” said Flockart. He and his colleagues then set out to track migration of Monarch butterflies, which is not that easy since insects cannot be readily fitted with tracking beacons in the way that some mammals or birds can (Reich et al, 2021). “In the case of Monarchs this means we can determine the natal origins of the butterfly,” Flockhart added. Applications in archeology Isotope analysis in general is now proving more versatile than almost any other forensic technique and is already extending into other domains. “SIA (Strontium Isotope Analysis) can be used to provenance archaeological remains that have lost their context, such as looted Native American skull,” said Eric Bartelink from California State University, Chico. “It also is being used to aid in forensic wildlife cases, for example poaching of endangered species.” Another example lies in tracking past human migrations. One of the most noted applications of Sr isotope evidence was demonstrating the existence of a trade network between south-eastern Arabia and India during Antiquity (Ryan et al, 2021). It was already known that cotton, a plant of tropical and sub-tropical origin outside Arabia, had appeared at several sites on the Arabian Peninsula about 2000 years ago. But given its geographical location close to both Indian and African trading zones, the provenance of the cotton was unclear, as were the trading routes. It happened then that archeologists found significant botanical remains from the Late Pre-Islamic period (2nd–3rd century AD), including cotton seeds and fabrics, in a burned-down fortified building in Mleiha in the United Arab Emirates. Isotopes were isolated from the leached and charred cotton remains and their analysis indicated that the earliest cotton finds did not originate from the Oman Peninsula as some had thought but were more likely from the north-western coast of India. Confirming other indications that this trade route had developed around that time, the researchers in that study are convinced the analysis ends all doubt. “We are quite certain about this cotton trade route,” said Vladimir Dabrowski from the Muséum National d'Histoire Naturelle in France and co-author on the paper. “The strontium isotopic analysis of the cotton seeds and textiles give a similar geological signature with that of the underground in some regions of the Indian subcontinent. It would have been great to get the strontium isotopic signature of the soils from eastern Africa given that cotton comes also from this region. But cotton trade from eastern Africa is less attested than from the Indian subcontinent during this period so we are quite confident with these conclusions.” Dabrowski added that archaeobotanical evidence had also shown that the subcontinent was a cotton production center since at least the 3rd to 2nd millennium BC. Further confirmation came from pottery shards and ivory artefacts, indicating that trade between the Arab peninsula and India was well established during the Late Pre-Islamic period. “Considering all this information, importation of cotton from the Indian sub-continent to the site of Mleiha seems more than likely,” Dabrowski concluded. Several other Sr isotope studies have elucidated other ancient trading routes in and around the Middle East … Several other Sr isotope studies have elucidated other ancient trading routes in and around the Middle East, including one confirming the prominent role of the Byzantine port city of Aila, now called Aqaba, in Jordan, as a center of trade and immigration from the 1st century BC (Perry et al, 2017). In this case, strontium isotope analysis identified nonlocally-born individuals in two cemeteries from 4th to early 5th century AD. This required an accurate estimate of the “local” strontium isotope value at Aila, which was difficult to calculate because extensive food importation distorted the values from the local fauna. These, therefore, had to be combined with archaeological and historical evidence of local food production and food importation, as well as childhood dietary practices, to put the values obtained from the human remains into what was presumed to be the right context. Further developments Further advances in isotope analysis will, however, require agreement over common procedures for both sample preparation and subsequent analysis through mass spectrometry. “The lack of standardization continues to be a major issue in stable isotope forensic applications of human remains,” Bartelink commented. “The main issues have to do with firstly the need for consistency in sample prep methods, and secondly the need for standardized mass spectrometry settings. Sample prep is fairly standardized for collagen CNS isotopes of bones, tooth dentin, nails, and hair and is not really a major problem. However, oxygen isotopes of human bone and tooth enamel bioapatite are highly sensitive to sample prep method and mass spectrometry settings. This means that different researchers can get different results based on how they prep the sample, and the mass spec setting, for example acidification temperature” (Pestle et al, 2014). On the other hand, recent advances in isotope analysis have helped to promote the technology by reducing cost and complexity, while increasing speed of sample preparation and analysis. “Some of the technical advances have made running samples more automated, cheaper, and often requiring a smaller sample size,” Bartelink explained. “There are also advances with laser ablation that can be used to obtain serial sample data on tooth enamel without destroying the tooth. Compound specific amino acid analysis is becoming more routinely used and gives you isotopic data for each amino acid instead of just a bulk signature. Other advances are in geospatial mapping and use of R packages, for example, Assign R, which can help with predicting region of origin.” R is a computer programming language with associated software tools for statistical modelling, which in this case is used for geospatial analysis. … there is also some overlap in application where the two can play complementary roles, for instance, investigating past human migrations through the analysis of human remains. As DNA phenotyping and isotope analysis make further advances and find more applications in criminal investigations and research, there is also some overlap in application where the two can play complementary roles, for instance, investigating past human migrations through the analysis of human remains. Yet, while DNA phenotyping will be mostly confined to finding crime suspects, isotope analysis in combination with isoscapes seems like a much more versatile technology not just to solve current mysteries but also those from the ancient past. References Flockhart DTT, Kyser TK, Chipley D, Miller NG, Norris DR (2015) Experimental evidence shows no fractionation of strontium isotopes (87Sr/86Sr) among soil, plants, and herbivores: implications for tracking wildlife and forensic science. Isot Environ Health Stud 51: 372–381CrossrefCASPubMedWeb of Science®Google Scholar Oldoni F, Kidd KK, Podini D (2019) Microhaplotypes in forensic genetics. Forensic Sci Int Genet 38: 54–69CrossrefCASPubMedWeb of Science®Google Scholar Perry MA, Jennings C, Coleman DS (2017) Strontium isotope evidence for long-distance immigration into the Byzantine port city of Aila, modern Aqaba, Jordan. Archeol Anthropol Sci 9: 943–964CrossrefWeb of Science®Google Scholar Pestle WJ, Brooke EC, Matthew TW (2014) Quantifying inter-laboratory variability in stable isotope analysis of ancient skeletal remains. PLoS One 9: e102844CrossrefPubMedWeb of Science®Google Scholar Phillips C, Amigo J, Tillmar AO, Peck MA, de la Puente M, Ruiz-Ramírez J, Bittner F, Idrizbegović Š, Wang Y, Parsons TJ et al (2020) A compilation of tri-allelic SNPs from 1000 Genomes and use of the most polymorphic loci for a large-scale human identification panel. Forensic Sci Int Genet 46: 102232.CrossrefCASPubMedWeb of Science®Google Scholar Phillips C, de la Puente M (2021) The analysis of ancestry with small-scale forensic panels of genetic markers. Emerg Top Life Sci 5: 443–453CrossrefCASPubMedGoogle Scholar Reich MS, Flockhart DTT, Norris DR, Hu L, Bataille CP (2021) Continuous-surface geographic assignment of migratory animals using strontium isotopes: A case study with monarch butterflies. Methods Ecol Evol https://doi.org/10.1111/2041-210X.13707CrossrefGoogle Scholar Ryan SE, Dabrowski V, Dapoigny A, Gauthier C, Douville E, Tengberg M, Kerfant C, Mouton M, Desormeau X, Zazzo A et al (2021) Strontium isotope evidence for a trade network between south-eastern Arabia and India during Antiquity. Sci Rep 11: 303CrossrefCASPubMedWeb of Science®Google Scholar Shih Y (2020) DNA phenotyping: from criminal investigations to surveillance. Imperial Bioscience Review Nov 6. https://imperialbiosciencereview.com/2020/11/06/dna-phenotyping-from-criminal-investigations-to-surveillance/Google Scholar Previous ArticleNext Article Read MoreAbout the coverClose modalView large imageVolume 22,Issue 12,06 December 2021This month's cover highlights the article Regional heterogeneity of astrocyte morphogenesis dictated by the formin protein, Daam2, modifies circuit function Juyeon Jo, Hyun Kyoung Lee and colleagues. The image shows an olfactory bulb from an astrocyte‐specific Daam2 null mouse with astrocytes and neurons labeled with GFAP (red) and Thy1‐GCaMP3 (green), respectively. Loss of the formin protein Daam2 alters astrocytes morphology and calcium dynamics in a region‐specific manner, leading to alterations of synaptic activity and olfactory behavior. (Scientific image © Juyeon Jo, Baylor College of Medicine.) Volume 22Issue 126 December 2021In this issue ReferencesRelatedDetailsLoading ...
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