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Journal Article Archive 2016-10-14T01:03:42+00:00

Journal Article Archive

Updating the African human mitochondrial DNA tree: relevance to forensic and population genetics

Journal: Forensic Science International: Genetics | Year: 2017


Analysis of human mitochondrial DNA variation plays an important role in forensic genetic investigations, especially in degraded biological samples and hair shafts. There are many issues of the mtDNA phylogeny that are of special interest to the forensic community, such as haplogroup classification or the post hoc investigation of potential errors in mtDNA datasets. We have analyzed >2200 mitogenomes of African ancestry with the aim of improving the known worldwide phylogeny. More than 300 new minor sub-clades were identified, and the Time to the Most Recent Common Ancestor (TMRCA) was estimated for each node of the phylogeny. Phylogeographic details are provided which might also be relevant in forensic genetics. The present study has special interest for forensic investigations because current analysis and interpretation of mtDNA casework rest on a solid worldwide phylogeny, as is evident from the role that phylogeny plays in popular resources in the field (e.g. Phylotree), software (e.g. Haplogrep 2), and databases (e.g. EMPOP). Apart from this forensic genetic interest, we also highlight the impact of this research in anthropological studies, such as those related to the reconstruction of the transatlantic slave trade.

Peoples: Africans | Places: Africa | Topics: TMRCA | DNA Type: mtDNA

Updating the East Asian mtDNA phylogeny: a prerequisite for the identification of pathogenic mutations

Journal: Human Molecular Genetics | Year: 2006


Peoples: | Places: | Topics: | DNA Type: mtDNA

Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans

Journal: Nature | Year: 2014


The origins of the First Americans remain contentious. Although Native Americans seem to be genetically most closely related to east Asians1, 2, 3, there is no consensus with regard to which specific Old World populations they are closest to4, 5, 6, 7, 8. Here we sequence the draft genome of an approximately 24,000-year-old individual (MA-1), from Mal’ta in south-central Siberia9, to an average depth of 1×. To our knowledge this is the oldest anatomically modern human genome reported to date. The MA-1 mitochondrial genome belongs to haplogroup U, which has also been found at high frequency among Upper Palaeolithic and Mesolithic European hunter-gatherers 10, 11, 12, and the Y chromosome of MA-1 is basal to modern-day western Eurasians and near the root of most Native American lineages 5. Similarly, we find autosomal evidence that MA-1 is basal to modern-day western Eurasians and genetically closely related to modern-day Native Americans, with no close affinity to east Asians. This suggests that populations related to contemporary western Eurasians had a more north-easterly distribution 24,000 years ago than commonly thought. Furthermore, we estimate that 14 to 38% of Native American ancestry may originate through gene flow from this ancient population. This is likely to have occurred after the divergence of Native American ancestors from east Asian ancestors, but before the diversification of Native American populations in the New World. Gene flow from the MA-1 lineage into Native American ancestors could explain why several crania from the First Americans have been reported as bearing morphological characteristics that do not resemble those of east Asians2, 13. Sequencing of another south-central Siberian, Afontova Gora-2 dating to approximately 17,000 years ago 14, revealed similar autosomal genetic signatures as MA-1, suggesting that the region was continuously occupied by humans throughout the Last Glacial Maximum. Our findings reveal that western Eurasian genetic signatures in modern-day Native Americans derive not only from post-Columbian admixture, as commonly thought, but also from a mixed ancestry of the First Americans.

Peoples: | Places: | Topics: | DNA Type: Ancient DNA, mtDNA, and Y-DNA

Using mitochondrial DNA to test the hypothesis of a European post-glacial human recolonization from the Franco-Cantabrian refuge

Journal: Heredity | Year: 2010


Peoples: | Places: | Topics: | DNA Type: mtDNA

Validation of a 17-locus Y-STR multiplex system

Journal: Forensic Science International: Genetics Supplement Series | Year: 2008


Internal validation of a commercial 17-locus Y-STR system (AmpFlSTR® Yfiler(TM), Applied Biosystems) has been performed on the ABI PRISM® 3130 Genetic Analyzer for use in forensic cases. The Yfiler(TM) kit was validated according to SWGDAM guidelines. Our results show that it is possible to obtain full profiles with as little as 30 pg of male DNA even in the presence of 20,000-fold amounts of female DNA. Reaction volume was optimized for 10 [mu]l. Male-male mixtures yielded full profiles of the minor contributor with 10-fold excess of the major contributor. Stutter values for each locus were determined from data generated for the population study which included Y-STR profiles from 156 caucasian males from the Montreal and Lac St.-Jean areas of Qu'ebec, Canada. The study recorded 141 different haplotypes of which 131 were unique with a haplotype diversity of 0.9965. A number of non-probative forensic samples from rape kit epithelial fractions and fingernail scrapings were also successfully tested.

Peoples: - | Places: - | Topics: - | DNA Type: Y-DNA

Validation of microarray-based resequencing of 93 worldwide mitochondrial genomes

Journal: Human mutation | Year: 2008


The human mitochondrial genome consists of a multicopy, circular dsDNA molecule of 16,569 base pairs. It encodes for 13 proteins, two ribosomal genes, and 22 tRNAs that are essential in the generation of cellular ATP by oxidative phosphorylation in eukaryotic cells. Germline mutations in mitochondrial DNA (mtDNA) are an important cause of maternally inherited diseases, while somatic mtDNA mutations may play important roles in aging and cancer. mtDNA polymorphisms are also widely used in population and forensic genetics. Therefore, methods that allow the rapid, inexpensive and accurate sequencing of mtDNA are of great interest. One such method is the Affymetrix GeneChip Human Mitochondrial Resequencing Array 2.0 (MitoChip v.2.0) (Santa Clara, CA). A direct comparison of 93 worldwide mitochondrial genomes sequenced by both the MitoChip and dideoxy terminator sequencing revealed an average call rate of 99.48% and an accuracy of > or =99.98% for the MitoChip. The good performance was achieved by using in-house software for the automated analysis of additional probes on the array that cover the most common haplotypes in the hypervariable regions (HVR). Failure to call a base was associated mostly with the presence of either a run of > or =4 C bases or a sequence variant within 12 bases up- or downstream of that base. A major drawback of the MitoChip is its inability to detect insertions/deletions and its low sensitivity and specificity in the detection of heteroplasmy. However, the vast majority of haplogroup defining polymorphism in the mtDNA phylogeny could be called unambiguously and more rapidly than with conventional sequencing.

Peoples: | Places: | Topics: | DNA Type: mtDNA

Variants in mitochondrial tRNAGlu, tRNAArg, and tRNAThr may influence the phenotypic manifestation of deafness-associated 12S rRNA A1555G mutation in three Han Chinese families with hearing loss

Journal: American Journal of Medical Genetics Part A | Year: 2006


Peoples: | Places: | Topics: | DNA Type: mtDNA

Variation in Short Tandem Repeats Is Deeply Structured by Genetic Background on the Human Y Chromosome

Journal: American Journal of Human Genetics | Year: 1999


Eleven biallelic polymorphisms and seven short-tandem-repeat (STR) loci mapping on the nonrecombining portion of the human Y chromosome have been typed in men from northwestern Africa. Analysis of the biallelic markers, which represent probable unique events in human evolution, allowed us to characterize the stable backgrounds or haplogroups of Y chromosomes that prevail in this geographic region. Variation in the more rapidly mutating genetic markers (STRs) has been used both to estimate the time to the most recent common ancestor for STR variability within these stable backgrounds and to explore whether STR differentiation among haplogroups still retains information about their phylogeny. When analysis of molecular variance was used to study the apportionment of STR variation among both genetic backgrounds (i.e., those defined by haplogroups) and population backgrounds, we found STR variability to be clearly structured by haplogroups. More than 80% of the genetic variance was found among haplogroups, whereas only 3.72% of the genetic variation could be attributed to differences among populations—that is, genetic variability appears to be much more structured by lineage than by population. This was confirmed when two population samples from the Iberian Peninsula were added to the analysis. The deep structure of the genetic variation in old genealogical units (haplogroups) challenges a population-based perspective in the comprehension of human genome diversity. A population may be better understood as an association of lineages from a deep and population-independent gene genealogy, rather than as a complete evolutionary unit.

Peoples: - | Places: - | Topics: - | DNA Type: Y-DNA

Vergisson 4: a left-handed Neandertal

Journal: American Journal of Physical Anthropology | Year: 2016



Handedness is an important marker for lateralization of humans in the modern and fossil record. For the most part, Neandertals and their ancestors are strongly right-handed. We describe a single tooth from a Neandertal level at Vergisson 4 (Vg 4-83). This left upper central incisor shows all the features typical of Neandertal incisors. It also exhibits a predominance of left-handed striations.


Striations on the incisor's labial surface were mapped at 20x magnification using Photoshop. Angulations of the striations were determined from their deviation from the maximum mesio-distal line and were analyzed using NIH's freeware, Image J.


Of the 60 labial surface striations, Vg 4-83 shows a strong predominance of left-handed striations (46; 76.7%), which are statistically significantly different (p < .001 with a two-tailed chi2 test) from the small number (3) of right-handed striations. Discussion

The identification of another left-handed Neandertal adds to our understanding about handedness variation in this fossil hominin. Given the high frequency of right-handed Neandertals, the 90: 10 modern ratio is still preserved in this group.

Peoples: Neandertals | Places: Vergisson 4 | Topics: Handedness and Neandertals | DNA Type: -

Vlax Roma history: what do coalescent-based methods tell us?

Journal: European Journal of Human Genetics | Year: 2004


Three coalescent-based methods allowed us to infer some aspects of the history of three Bulgarian Gypsies populations belonging to the Vlax linguistic group: the Lom, Rudari and Kalderas. We used several kinds of genetic markers: HV1 sequences of the maternally inherited mitochondrial genome and microsatellites of the paternally inherited Y chromosome and of the biparentally inherited chromosome 8. This allowed us to infer several parameters for men and women: the splitting order of the populations and the ages of the splitting events, the growth rate in each population and the migration rates between populations. Altogether, they enabled us to infer a demographic scenario that could explain the genetic diversity of Vlax Roma: recent splits occurring after the arrival in Europe, asymmetric migration flows especially for males and unequal growth rates. This represents a considerable contribution to the Vlax Roma history in comparison with the inferences from classical population genetics.

Peoples: | Places: | Topics: | DNA Type:

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