R. John Mitchell

Y-Chromosomal Diversity in Europe Is Clinal and Influenced Primarily by Geography, Rather than by Language

Clinal patterns of autosomal genetic diversity within Europe have been interpreted in previous studies in terms of a Neolithic demic diffusion model for the spread of agriculture; in contrast, studies using mtDNA have traced many founding lineages to the Paleolithic and have not shown strongly clinal variation. We have used 11 human Y-chromosomal biallelic polymorphisms, defining 10 haplogroups, to analyze a sample of 3,616 Y chromosomes belonging to 47 European and circum-European populations. Patterns of geographic differentiation are highly nonrandom, and, when they are assessed using spatial autocorrelation analysis, they show significant clines for five of six haplogroups analyzed. Clines for two haplogroups, representing 45% of the chromosomes, are continentwide and consistent with the demic diffusion hypothesis. Clines for three other haplogroups each have different foci and are more regionally restricted and are likely to reflect distinct population movements, including one from north of the Black Sea. Principal-components analysis suggests that populations are related primarily on the basis of geography, rather than on the basis of linguistic affinity. This is confirmed in Mantel tests, which show a strong and highly significant partial correlation between genetics and geography but a low, nonsignificant partial correlation between genetics and language. Genetic-barrier analysis also indicates the primacy of geography in the shaping of patterns of variation. These patterns retain a strong signal of expansion from the Near East but also suggest that the demographic history of Europe has been complex and influenced by other major population movements, as well as by linguistic and geographic heterogeneities and the effects of drift.

The Central Siberian Origin for Native American Y Chromosomes

Y chromosomal DNA polymorphisms were used to investigate Pleistocene male migrations to the American continent. In a worldwide sample of 306 men, we obtained 32 haplotypes constructed with the variation found in 30 distinct polymorphic sites. The major Y haplotype present in most Native Americans was traced back to recent ancestors common with Siberians, namely, the Kets and Altaians from the Yenissey River Basin and Altai Mountains, respectively. Going further back, the next common ancestor gave rise also to Caucasoid Y chromosomes, probably from the central Eurasian region. This study, therefore, suggests a predominantly central Siberian origin for Native American paternal lineages for those who could have migrated to the Americas during the Upper Pleistocene.

Forensic trace DNA: a review

DNA analysis is frequently used to acquire information from biological material to aid enquiries associated with criminal offences, disaster victim identification and missing persons investigations. As the relevance and value of DNA profiling to forensic investigations has increased, so too has the desire to generate this information from smaller amounts of DNA. Trace DNA samples may be defined as any sample which falls below recommended thresholds at any stage of the analysis, from sample detection through to profile interpretation, and can not be defined by a precise picogram amount. Here we review aspects associated with the collection, DNA extraction, amplification, profiling and interpretation of trace DNA samples. Contamination and transfer issues are also briefly discussed within the context of trace DNA analysis. Whilst several methodological changes have facilitated profiling from trace samples in recent years it is also clear that many opportunities exist for further improvements.

The Genographic Project public participation mitochondrial DNA database.

The Genographic Project is studying the genetic signatures of ancient human migrations and creating an open-source research database. It allows members of the public to participate in a real-time anthropological genetics study by submitting personal samples for analysis and donating the genetic results to the database. We report our experience from the first 18 months of public participation in the Genographic Project, during which we have created the largest standardized human mitochondrial DNA (mtDNA) database ever collected, comprising 78,590 genotypes. Here, we detail our genotyping and quality assurance protocols including direct sequencing of the mtDNA HVS-I, genotyping of 22 coding-region SNPs, and a series of computational quality checks based on phylogenetic principles. This database is very informative with respect to mtDNA phylogeny and mutational dynamics, and its size allows us to develop a nearest neighbor–based methodology for mtDNA haplogroup prediction based on HVS-I motifs that is superior to classic rule-based approaches. We make available to the scientific community and general public two new resources: a periodically updated database comprising all data donated by participants, and the nearest neighbor haplogroup prediction tool.

Investigation of secondary DNA transfer of skin cells under controlled test conditions

There is a paucity of data on the relative transfer rates of deposited biological substances which could assist evaluation of the probability of given crime scene scenarios, especially for those relating to objects originally touched by hand. This investigation examines factors that may influence the secondary transfer of DNA from this source, including the freshness of the deposit, the nature of the primary and secondary substrate and the manner of contact between the surfaces. The transfer rates showed that both the primary and secondary type of substrate and the manner of contact are important factors influencing transfer of skin cells, but, unlike other biological fluids, such as blood and saliva, the freshness of the deposit in most instances is not. Skin cells deposited on a non-porous primary substrate transferred more readily to subsequent substrates than those deposited on a porous substrate. Porous secondary substrates, however, facilitated transfer more readily than non-porous secondary substrates, from both porous and non-porous surfaces. Friction as the manner of contact significantly increased the rate of transfer. The findings of this study improve our general understanding of the transfer of DNA material contained in fingerprints that is left on a surface, and assist in the evaluation of the probability of secondary and further DNA transfer under specific conditions.

Y-chromosome analysis reveals genetic divergence and new founding native lineages in Athapaskan- and Eskimoan-speaking populations

For decades, the peopling of the Americas has been explored through the analysis of uniparentally inherited genetic systems in Native American populations and the comparison of these genetic data with current linguistic groupings. In northern North America, two language families predominate: Eskimo-Aleut and Na-Dene. Although the genetic evidence from nuclear and mtDNA loci suggest that speakers of these language families share a distinct biological origin, this model has not been examined using data from paternally inherited Y chromosomes. To test this hypothesis and elucidate the migration histories of Eskimoan- and Athapaskan-speaking populations, we analyzed Y-chromosomal data from Inuvialuit, Gwich’in, and Tłįchǫ populations living in the Northwest Territories of Canada. Over 100 biallelic markers and 19 chromosome short tandem repeats (STRs) were genotyped to produce a high-resolution dataset of Y chromosomes from these groups. Among these markers is an SNP discovered in the Inuvialuit that differentiates them from other Aboriginal and Native American populations. The data suggest that Canadian Eskimoan- and Athapaskan-speaking populations are genetically distinct from one another and that the formation of these groups was the result of two population expansions that occurred after the initial movement of people into the Americas. In addition, the population history of Athapaskan speakers is complex, with the Tłįchǫ being distinct from other Athapaskan groups. The high-resolution biallelic data also make clear that Y-chromosomal diversity among the first Native Americans was greater than previously recognized.

Evaluation of tapelifting as a collection method for touch DNA

The use of tapelifting for collection of touch DNA from fabrics is routine in many jurisdictions. However, there is a paucity of data relating to the effectiveness of different types of tapes for tapelifting, the amount of tapelifting required to generate a useful profile, and whether or not tapelifting is more effective than swabbing from various substrates. This research investigates these questions by comparing two tapes of different adhesive strength currently used in forensic casework (Scotch Magic tape and Scenesafe FAST minitapes), for sampling from touch deposits on four different fabrics-cotton flannelette, cotton drill woven fabric, polyester/cotton plain woven fabric and polyester strapping. Touch DNA was deposited on four replicates of each substrate. Separate areas of each substrate replicate were sampled, either by taping with one of the two tapes or by wet/dry swabbing with cotton swabs. Tape was applied over the defined sampling area once or repeatedly for various numbers of applications. DNA was extracted, quantified and profiled from all tape and swab samples as well as the corresponding sampled substrates. Significantly more DNA was extracted, and a higher proportion of alleles detected, from Scenesafe FAST tape than from Scotch Magic tape. The amount of DNA and number of donor alleles detected generally increased as the tape was reapplied to the surface, although a threshold of collection was seen for both types of tape. For two out of four substrates, taping with Scenesafe FAST collected more DNA than swabbing and, for three substrates, generated a greater median number of donor alleles. There was no significant difference in numbers of alleles between swabbing and taping from flannelette. Based on these findings, it is recommended that a tape with stronger adhesion (such as Scenesafe FAST tapelifters) is generally preferable; that more than one application of tape is suggested (however, increasing the amount of times the area is sampled can diminish collection efficiency); and that there is an advantage using tapelifting rather than swabbing for fabrics unless, such as with flannelette, there are many loose fibres easily removed during the sampling process.

The influence of substrate on DNA transfer and extraction efficiency

The circumstances surrounding deposition of DNA profiles are increasingly becoming an issue in court proceedings, especially whether or not the deposit was made by primary transfer. In order to improve the currently problematic evaluation of transfer scenarios in court proceedings, we examined the influence a variety of nine substrate types (six varieties of fabric, plywood, tarpaulin, and plastic sheets) has on DNA transfer involving blood. DNA transfer percentages were significantly higher (p=0.03) when the primary substrate was of non-porous material (such as tarpaulin, plastic or, to a lesser degree, wood) and the secondary substrate porous (such as fabrics). These findings on transfer percentages confirm the results of previous studies. Fabric composition was also shown to have a significant (p=0.03) effect on DNA transfer; when experiments were performed with friction from a variety of fabrics to a specific weave of cotton, transfer percentages ranged from 4% (flannelette) to 94% (acetate). The propensity for the same nine substrates to impact upon the efficiency of DNA extraction procedures was also examined. Significant (p=0.03) differences were found among the extraction efficiencies from different materials. When 15μL of blood was deposited on each of the substrates, the lowest quantity of DNA was extracted from plastic (20ng) and the highest quantities extracted from calico and flannelette (650ng). Significant (p<0.05) differences also exist among the DNA extraction yield from different initial blood volumes from all substrates. Also, significantly greater (p<0.05) loss of DNA was seen during concentration of extracts with higher compared to lower initial quantities of DNA. These findings suggest that the efficiency of extraction and concentration impacts upon the final amount of DNA available for analysis and that consideration of these effects should not be ignored. The application of correction factors to adjust for any variation among extraction and concentration efficiencies among substrates is proposed.

Persistence of DNA deposited by the original user on objects after subsequent use by a second person.

There is a paucity of data regarding the persistence of DNA from prior user of an object after, its use by another person. To acquire a greater understanding of persistence we performed controlled, experiments encompassing over 179 objects that had only been used by one individual for an extended, period before used by a 2nd person for various but known duration. Our findings show that the profile, percentage contribution of the 1st user relative to the 2nd user of an object declines in a linear manner, over time. The retrieval of the profile of the initial user of the object is dependent on the type of, substrate and use of the object. When considering a hard non-porous object the 1st users profile, percentage contribution drops ∼50% immediately upon use by a 2nd person and drops to ∼15% after, 90 min. When considering a soft porous object the 1st wearers profile contribution remains, higher than that of the 2nd wearer during the first 10h of wear by the 2nd wearer and still, accounts for ∼12% after 96 h. This substrate associated difference was also observed in an, assessment of a wide range of personal objects used by 2nd users for different durations. Particular, areas of certain objects were more likely to retain a greater proportion of the 1st users DNA than other, areas. Alleles of unknown source were present on the majority of objects but rarely exceeded 10% of, the total profile. Greater knowledge of persistence will inform investigators regarding the likelihood of, detecting a profile of a particular individual based on the type of object and its history, and assist with, identifying the best areas of an object to target for DNA sampling.

MtDNA SNP multiplexes for efficient inference of matrilineal genetic ancestry within Oceania

Human mitochondrial DNA (mtDNA) is a convenient marker for tracing matrilineal bio-geographic ancestry and is widely applied in forensic, genealogical and anthropological studies. In forensic applications, DNA-based ancestry inference can be useful for finding unknown suspects by concentrating police investigations in cases where autosomal STR profiling was unable to provide a match, or can help provide clues in missing person identification. Although multiplexed mtDNA single nucleotide polymorphism (SNP) assays to infer matrilineal ancestry at a (near) continental level are already available, such tools are lacking for the Oceania region. Here, we have developed a hierarchical system of three SNaPshot multiplexes for genotyping 26 SNPs defining all major mtDNA haplogroups for Oceania (including Australia, Near Oceania and Remote Oceania). With this system, it was possible to conclusively assign 74% of Oceanian individuals to their Oceanian matrilineal ancestry in an established literature database (after correcting for obvious external admixture). Furthermore, in a set of 161 genotyped individuals collected in Australia, Papua New Guinea and Fiji, 87.6% were conclusively assigned an Oceanian matrilineal origin. For the remaining 12.4% of the genotyped samples either a Eurasian origin was detected indicating likely European admixture (1.9%), the identified haplogroups are shared between Oceania and S/SE-Asia (5%), or the SNPs applied did not allow a geographic inference to be assigned (5.6%). Sub-regional assignment within Oceania was possible for 32.9% of the individuals genotyped: 49.5% of Australians were assigned an Australian origin and 13.7% of the Papua New Guineans were assigned a Near Oceanian origin, although none of the Fijians could be assigned a specific Remote Oceanian origin. The low assignment rates of Near and Remote Oceania are explained by recent migrations from Asia via Near Oceania into Remote Oceania. Combining the mtDNA multiplexes for Oceania introduced here with those we developed earlier for all other continental regions, global matrilineal bio-geographic ancestry assignment from DNA is now achievable in a highly efficient way that is also suitable for applications with limited material such as forensic case work.