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Davis C.,University of North Texas Health Science Center | Ge J.,University of North Texas Health Science Center | Sprecher C.,Promega Corporation | Chidambaram A.,Scientific Crime Detection Laboratory | And 6 more authors.
Forensic Science International: Genetics | Year: 2013

The Prototype PowerPlex® Y23 System (Promega Corporation, Madison, WI) is a polymerase chain reaction-based amplification kit that targets the 23 Y STR loci DYS19, DYS385a/b, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS481, DYS533, DYS549, DYS570, DYS576, DYS635, DYS643, and Y-GATA-H4. A total of 951 samples from six populations were typed to evaluate the kit and examine concordance for 17 of the loci that are in common with those that can be typed using the AmpFlSTR ® Yfiler™ kit (Life Technologies, Carlsbad, CA). A total of 16,167 loci were analyzed for each multiplex, and overall concordance was observed. Because of different kit designs, and although concordant for the genetic type, discordant calls can occur due to a deletion at the DYS448 locus. Users should take into consideration such nomenclature anomalies when comparing Y STR profiles. This new kit allows a large battery of Y STR loci to be analyzed using the same basic technologies already employed in forensic laboratories. © 2012 Elsevier Ireland Ltd. Source


Chiapella J.O.,CONICET | DeBoer V.L.,U.S. Department of Agriculture | DeBoer V.L.,Scientific Crime Detection Laboratory | Amico G.C.,CONICET | Kuhl J.C.,U.S. Department of Agriculture
American Journal of Botany | Year: 2011

Premise of the study: In the North American Arctic, the existence of one or several taxa closely related to Deschampsia cespitosa var. cespitosa has remained a puzzle for many years. Extreme morphological variation, lack of clear limits between alleged forms, and an extended geographic range often render identification keys incomplete, and raise the question of how many species this taxon represents. Methods: Morphological and molecular analysis, including multivariate statistics, ITS and the cpDNA marker trnK - rps16, was conducted on D. cespitosa var. cespitosa and related taxa using 201 herbarium specimens from northern North America (Alaska, Canada, and Greenland). Fifty-three morphological characters were recorded from all specimens, while sequences were retrieved from 167 specimens. Key results: Results show that Deschampsia cespitosa (L.) P. Beauv. var. cespitosa, D. cespitosa subsp. alpina (L.) Tzvelev, D. cespitosa subsp. beringensis (Hultén) W. E. Lawr., D. brevifolia R. Br., D. cespitosa (L.) P. Beauv. subsp. glauca (Hartm.) C. Hartm., D. mackenzieana Raup, D. cespitosa subsp. orientalis Hultén, and D. pumila (Griseb.) Ostenf. differed significantly in a few morphological variables, but molecularly are a closely related group with several sequences and haplotypes that are nearly identical. Conclusions: Overall, the evidence points to the existence of a single species, Deschampsia cespitosa. The occurrence of slightly different morphological types related to specific geographical distributions allows recognition of three additional taxa at the infraspecific level, D. cespitosa subsp. alpina, D. cespitosa subsp. beringensis, and D. brevifolia. All studied taxa showed morphological variation in a gradient, suggesting the existence of phenotypic plasticity. ©2011 Botanical Society of America. Source


Kumagai R.,Iwate Medical University | Sasaki Y.,Scientific Crime Detection Laboratory | Tokuta T.,Scientific Crime Detection Laboratory | Biwasaka H.,Scientific Crime Detection Laboratory | And 3 more authors.
Human Genetics | Year: 2010

The amelogenin gene on the Y chromosome (AMELY) is a homolog of the X chromosome amelogenin gene (AMELX), and the marker is employed for sexing in forensic casework. Deletion of the sequences in the Yp11.2 region containing the AMELY locus has been found in males from various ethnic populations. Two cases of AMELY null males found in the Japanese population had different Y haplogroups and deletion mapping. Proximal and distal breakpoints of a sample of haplogroup D2* were located in TSPYA and TSPYB arrays, respectively, suggesting that the deletion mechanism was non-allelic homologous recombination (NAHR). On the other hand, a sample of haplogroup O3a3c* had the distal breakpoint in the TSPYB array and the proximal breakpoint at position 7.94 Mb, not in the TSPYA array. The likely deletion mechanism is non-homologous end-joining. High-resolution STS mapping in the TSPYB array showed the distal breakpoints differed according to the haplogroups. The deletion length was estimated as 3.1-3.7 Mb and 1.6-1.7 Mb for the sample of haplogroup D2* and O3a3c*, respectively. These deletion events should have occurred independently. © 2010 Springer-Verlag. Source


Davis C.,University of North Texas | Ge J.,University of North Texas | Chidambaram A.,Scientific Crime Detection Laboratory | King J.,University of North Texas | And 6 more authors.
International Journal of Legal Medicine | Year: 2011

Y chromosome short tandem repeat (Y-STR) loci are important genetic markers for forensic biological evidence analyses. However, paternal inheritance, reduced effective population size, and lack of independence between loci can reduce Y-STR diversity and may yield greater population substructure effects on a locus-by-locus basis compared with the autosomal STR loci. Population studies are necessary to assess the genetic variation of forensically relevant markers so that proper inferences can be made about the rarity of DNA profiles. This study examined 16 Y-STRs in three sampled populations of Native Americans from Alaska: Inupiat, Yupik, and Athabaskan. Population genetic and statistical issues addressed were: (1) the degree of diversity at locus and haplotype levels, (2) determination of the loci that contribute more so to haplotype diversity, and (3) the effects of population substructure on forensic statistical calculations of the rarity of a Y-STR profile. All three population samples were highly polymorphic at the haplotype level for the 16 Y-STR markers; however, the Native Americans demonstrated reduced genetic diversity compared with major US populations. The degree of substructure indicated that the three populations were related and admixed in terms of paternal lineage. The examination of more polymorphic loci may be needed to increase the power of discrimination of Y-STR systems in these populations. © 2011 Springer-Verlag. Source

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