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      Inner and inter population structure construction of Chinese Jiangsu Han population based on Y23 STR system

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          Abstract

          In this study, we analyzed the genetic polymorphisms of 23 Y-STR loci from PowerPlex ® Y23 system in 916 unrelated healthy male individuals from Chinese Jiangsu Han, and observed 912 different haplotypes including 908 unique haplotypes and 4 duplicate haplotypes. The haplotype diversity reached 0.99999 and the discrimination capacity and match probability were 0.9956 and 0.0011, respectively. The gene diversity values ranged from 0.3942 at DYS438 to 0.9607 at DYS385a/b. Population differentiation within 10 Jiangsu Han subpopulations were evaluated by R ST values and visualized in Neighbor-Joining trees and Multi-Dimensional Scaling plots as well as population relationships between the Jiangsu Han population and other 18 Eastern Asian populations. Such results indicated that the 23 Y-STR loci were highly polymorphic in Jiangsu Han population and played crucial roles in forensic application as well as population genetics. For the first time, we reported the genetic diversity of male lineages in Jiangsu Han population at a high-resolution level of 23 Y-STR set and consequently contributed to familial searching, offender tracking, and anthropology analysis of Jiangsu Han population.

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          Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material.

          Procedures utilizing Chelex 100 chelating resin have been developed for extracting DNA from forensic-type samples for use with the PCR. The procedures are simple, rapid, involve no organic solvents and do not require multiple tube transfers for most types of samples. The extraction of DNA from semen and very small bloodstains using Chelex 100 is as efficient or more efficient than using proteinase K and phenol-chloroform extraction. DNA extracted from bloodstains seems less prone to contain PCR inhibitors when prepared by this method. The Chelex method has been used with amplification and typing at the HLA DQ alpha locus to obtain the DQ alpha genotypes of many different types of samples, including whole blood, bloodstains, seminal stains, buccal swabs, hair and post-coital samples. The results of a concordance study are presented in which the DQ alpha genotypes of 84 samples prepared using Chelex or using conventional phenol-chloroform extraction are compared. The genotypes obtained using the two different extraction methods were identical for all samples tested.
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            Abundant gene conversion between arms of palindromes in human and ape Y chromosomes.

            Eight palindromes comprise one-quarter of the euchromatic DNA of the male-specific region of the human Y chromosome, the MSY. They contain many testis-specific genes and typically exhibit 99.97% intra-palindromic (arm-to-arm) sequence identity. This high degree of identity could be interpreted as evidence that the palindromes arose through duplication events that occurred about 100,000 years ago. Using comparative sequencing in great apes, we demonstrate here that at least six of these MSY palindromes predate the divergence of the human and chimpanzee lineages, which occurred about 5 million years ago. The arms of these palindromes must have subsequently engaged in gene conversion, driving the paired arms to evolve in concert. Indeed, analysis of MSY palindrome sequence variation in existing human populations provides evidence of recurrent arm-to-arm gene conversion in our species. We conclude that during recent evolution, an average of approximately 600 nucleotides per newborn male have undergone Y-Y gene conversion, which has had an important role in the evolution of multi-copy testis gene families in the MSY.
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              Y chromosome sequence variation and the history of human populations.

              Binary polymorphisms associated with the non-recombining region of the human Y chromosome (NRY) preserve the paternal genetic legacy of our species that has persisted to the present, permitting inference of human evolution, population affinity and demographic history. We used denaturing high-performance liquid chromatography (DHPLC; ref. 2) to identify 160 of the 166 bi-allelic and 1 tri-allelic site that formed a parsimonious genealogy of 116 haplotypes, several of which display distinct population affinities based on the analysis of 1062 globally representative individuals. A minority of contemporary East Africans and Khoisan represent the descendants of the most ancestral patrilineages of anatomically modern humans that left Africa between 35,000 and 89,000 years ago.
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                Author and article information

                Contributors
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Investigation
                Role: Data curationRole: Resources
                Role: MethodologyRole: Supervision
                Role: Formal analysis
                Role: Funding acquisitionRole: Writing – original draftRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                13 July 2017
                2017
                : 12
                : 7
                : e0180921
                Affiliations
                [1 ] Zhongshan City People's Hospital, Zhongshan, Guangdong, P. R., China
                [2 ] DNA Laboratory, Public Security Bureau of Changzhou, Changzhou, Jiangsu, P. R., China
                [3 ] Department of Psychiatry, Psychiatry Center of Chinese People’s Liberation Army, No. 102 Hospital of People’s Liberation Army, Changzhou, Jiangsu, P. R., China
                [4 ] DNA Laboratory, Public Security Bureau of Yangzhou, Yangzhou, Jiangsu, P. R., China
                [5 ] School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, P. R., China
                National Cheng Kung University, TAIWAN
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                ‡ These authors are co-first authors on this work.

                Author information
                http://orcid.org/0000-0001-6365-7032
                Article
                PONE-D-17-19528
                10.1371/journal.pone.0180921
                5509181
                28704439
                3bd37f4e-8ee5-4040-b393-3da30871da37
                © 2017 Wang et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 23 May 2017
                : 25 June 2017
                Page count
                Figures: 6, Tables: 2, Pages: 15
                Funding
                Funded by: the Natural Science Foundation of Guangdong Province, China
                Award ID: No. 2015A030310080
                Award Recipient :
                This project was supported by the Natural Science Foundation of Guangdong Province, China (NSF of Guangdong Province, No. 2015A030310080).
                Categories
                Research Article
                People and places
                Population groupings
                Ethnicities
                Han Chinese
                Biology and Life Sciences
                Evolutionary Biology
                Population Genetics
                Biology and Life Sciences
                Genetics
                Population Genetics
                Biology and Life Sciences
                Population Biology
                Population Genetics
                Biology and Life Sciences
                Genetics
                Heredity
                Genetic Mapping
                Haplotypes
                People and Places
                Geographical Locations
                Asia
                Singapore
                Biology and Life Sciences
                Genetics
                Genetic Loci
                Medicine and Health Sciences
                Diagnostic Medicine
                Clinical Laboratory Sciences
                Forensics
                Social Sciences
                Law and Legal Sciences
                Forensics
                Biology and Life Sciences
                Evolutionary Biology
                Evolutionary Systematics
                Phylogenetics
                Phylogenetic Analysis
                Biology and Life Sciences
                Taxonomy
                Evolutionary Systematics
                Phylogenetics
                Phylogenetic Analysis
                Computer and Information Sciences
                Data Management
                Taxonomy
                Evolutionary Systematics
                Phylogenetics
                Phylogenetic Analysis
                Biology and Life Sciences
                Cell Biology
                Chromosome Biology
                Chromosomes
                Sex Chromosomes
                Y Chromosomes
                Custom metadata
                All relevant data are available from figshare at: https://doi.org/10.6084/m9.figshare.5150128.

                Uncategorized
                Uncategorized

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