Investigative genetics最新文献

{"title":"Human paternal and maternal demographic histories: insights from high-resolution Y chromosome and mtDNA sequences.","authors":"Sebastian Lippold,&nbsp;Hongyang Xu,&nbsp;Albert Ko,&nbsp;Mingkun Li,&nbsp;Gabriel Renaud,&nbsp;Anne Butthof,&nbsp;Roland Schröder,&nbsp;Mark Stoneking","doi":"10.1186/2041-2223-5-13","DOIUrl":"https://doi.org/10.1186/2041-2223-5-13","url":null,"abstract":"<p><strong>Background: </strong>Comparisons of maternally-inherited mitochondrial DNA (mtDNA) and paternally-inherited non-recombining Y chromosome (NRY) variation have provided important insights into the impact of sex-biased processes (such as migration, residence pattern, and so on) on human genetic variation. However, such comparisons have been limited by the different molecular methods typically used to assay mtDNA and NRY variation (for example, sequencing hypervariable segments of the control region for mtDNA vs. genotyping SNPs and/or STR loci for the NRY). Here, we report a simple capture array method to enrich Illumina sequencing libraries for approximately 500 kb of NRY sequence, which we use to generate NRY sequences from 623 males from 51 populations in the CEPH Human Genome Diversity Panel (HGDP). We also obtained complete mtDNA genome sequences from the same individuals, allowing us to compare maternal and paternal histories free of any ascertainment bias.</p><p><strong>Results: </strong>We identified 2,228 SNPs in the NRY sequences and 2,163 SNPs in the mtDNA sequences. Our results confirm the controversial assertion that genetic differences between human populations on a global scale are bigger for the NRY than for mtDNA, although the differences are not as large as previously suggested. More importantly, we find substantial regional variation in patterns of mtDNA versus NRY variation. Model-based simulations indicate very small ancestral effective population sizes (<100) for the out-of-Africa migration as well as for many human populations. We also find that the ratio of female effective population size to male effective population size (Nf/Nm) has been greater than one throughout the history of modern humans, and has recently increased due to faster growth in Nf than Nm.</p><p><strong>Conclusions: </strong>The NRY and mtDNA sequences provide new insights into the paternal and maternal histories of human populations, and the methods we introduce here should be widely applicable for further such studies.</p>","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"5 ","pages":"13"},"PeriodicalIF":0.0,"publicationDate":"2014-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2041-2223-5-13","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32695227","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evaluating the Y chromosomal timescale in human demographic and lineage dating.","authors":"Chuan-Chao Wang,&nbsp;M Thomas P Gilbert,&nbsp;Li Jin,&nbsp;Hui Li","doi":"10.1186/2041-2223-5-12","DOIUrl":"https://doi.org/10.1186/2041-2223-5-12","url":null,"abstract":"<p><p>Y chromosome is a superb tool for inferring human evolution and recent demographic history from a paternal perspective. However, Y chromosomal substitution rates obtained using different modes of calibration vary considerably, and have produced disparate reconstructions of human history. Here, we discuss how substitution rate and date estimates are affected by the choice of different calibration points. We argue that most Y chromosomal substitution rates calculated to date have shortcomings, including a reliance on the ambiguous human-chimpanzee divergence time, insufficient sampling of deep-rooting pedigrees, and using inappropriate founding migrations, although the rates obtained from a single pedigree or calibrated with the peopling of the Americas seem plausible. We highlight the need for using more deep-rooting pedigrees and ancient genomes with reliable dates to improve the rate estimation. </p>","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"5 ","pages":"12"},"PeriodicalIF":0.0,"publicationDate":"2014-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2041-2223-5-12","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32662770","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular genetic investigative leads to differentiate monozygotic twins.","authors":"Bruce Budowle","doi":"10.1186/2041-2223-5-11","DOIUrl":"https://doi.org/10.1186/2041-2223-5-11","url":null,"abstract":"","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"5 ","pages":"11"},"PeriodicalIF":0.0,"publicationDate":"2014-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2041-2223-5-11","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32630658","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evaluating the impacts of stressors of Pseudomonas syringae pathovar tomato on the effectiveness of multi-locus variable number tandem repeat analysis and multi-locus sequence typing in microbial forensic investigations.","authors":"Mindy James, Ulrich Melcher, Jacqueline Fletcher","doi":"10.1186/2041-2223-5-10","DOIUrl":"10.1186/2041-2223-5-10","url":null,"abstract":"<p><strong>Background: </strong>Crops in the USA are vulnerable to natural and criminal threats because of their widespread cultivation and lack of surveillance, and because of implementation of growing practices such as monoculture. To prepare for investigation and attribution of such events, forensic assays, including determination of molecular profiles, are being adapted for use with plant pathogens. The use of multi-locus variable number tandem repeat (VNTR) analysis (MLVA) and multi-locus sequence typing (MLST) in investigations involving plant pathogens may be problematic because the long lag periods between pathogen introduction and discovery of associated disease may provide enough time for evolution to occur in the regions of the genome employed in each assay. Thus, more information on the stability of the loci employed in these methods is needed.</p><p><strong>Results: </strong>The MLVA fingerprints and MLST profiles were consistent throughout the experiment, indicating that, using a specific set of primers and conditions, MLVA and MLST typing systems reliably identify P.s. tomato DC3000. This information is essential to forensic investigators in interpreting comparisons between MLVA and MLST typing profiles observed in P.s. tomato isolates.</p><p><strong>Conclusions: </strong>Our results indicate that MLVA and MLST typing systems, utilizing the specified primers and conditions, could be employed successfully in forensics investigations involving P.s. tomato. Similar experiments should be conducted in the field and with other high-consequence plant pathogens to ensure that the assays are reliable for pathogens infecting plants in their natural environment and for organisms that may display faster rates of mutation.</p>","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"5 ","pages":"10"},"PeriodicalIF":0.0,"publicationDate":"2014-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4133955/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32593994","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Validation of high throughput sequencing and microbial forensics applications.","authors":"Bruce Budowle, Nancy D Connell, Anna Bielecka-Oder, Rita R Colwell, Cindi R Corbett, Jacqueline Fletcher, Mats Forsman, Dana R Kadavy, Alemka Markotic, Stephen A Morse, Randall S Murch, Antti Sajantila, Sarah E Schmedes, Krista L Ternus, Stephen D Turner, Samuel Minot","doi":"10.1186/2041-2223-5-9","DOIUrl":"10.1186/2041-2223-5-9","url":null,"abstract":"<p><p>High throughput sequencing (HTS) generates large amounts of high quality sequence data for microbial genomics. The value of HTS for microbial forensics is the speed at which evidence can be collected and the power to characterize microbial-related evidence to solve biocrimes and bioterrorist events. As HTS technologies continue to improve, they provide increasingly powerful sets of tools to support the entire field of microbial forensics. Accurate, credible results allow analysis and interpretation, significantly influencing the course and/or focus of an investigation, and can impact the response of the government to an attack having individual, political, economic or military consequences. Interpretation of the results of microbial forensic analyses relies on understanding the performance and limitations of HTS methods, including analytical processes, assays and data interpretation. The utility of HTS must be defined carefully within established operating conditions and tolerances. Validation is essential in the development and implementation of microbial forensics methods used for formulating investigative leads attribution. HTS strategies vary, requiring guiding principles for HTS system validation. Three initial aspects of HTS, irrespective of chemistry, instrumentation or software are: 1) sample preparation, 2) sequencing, and 3) data analysis. Criteria that should be considered for HTS validation for microbial forensics are presented here. Validation should be defined in terms of specific application and the criteria described here comprise a foundation for investigators to establish, validate and implement HTS as a tool in microbial forensics, enhancing public safety and national security. </p>","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"5 ","pages":"9"},"PeriodicalIF":0.0,"publicationDate":"2014-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4123828/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32567039","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Editors' Pick: What a pain…, or not!","authors":"Manfred Kayser","doi":"10.1186/2041-2223-5-8","DOIUrl":"https://doi.org/10.1186/2041-2223-5-8","url":null,"abstract":"","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"5 ","pages":"8"},"PeriodicalIF":0.0,"publicationDate":"2014-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2041-2223-5-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32472853","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The sperm's tale.","authors":"Mark A Jobling","doi":"10.1186/2041-2223-5-6","DOIUrl":"https://doi.org/10.1186/2041-2223-5-6","url":null,"abstract":"","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"5 ","pages":"6"},"PeriodicalIF":0.0,"publicationDate":"2014-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2041-2223-5-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32437041","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Pet fur or fake fur? A forensic approach.","authors":"Elena Pilli, Rosario Casamassima, Stefania Vai, Antonino Virgili, Filippo Barni, Giancarlo D'Errico, Andrea Berti, Giampietro Lago, David Caramelli","doi":"10.1186/2041-2223-5-7","DOIUrl":"10.1186/2041-2223-5-7","url":null,"abstract":"<p><strong>Background: </strong>In forensic science there are many types of crime that involve animals. Therefore, the identification of the species has become an essential investigative tool. The exhibits obtained from such offences are very often a challenge for forensic experts. Indeed, most biological materials are traces, hair or tanned fur. With hair samples, a common forensic approach should proceed from morphological and structural microscopic examination to DNA analysis. However, the microscopy of hair requires a lot of experience and a suitable comparative database to be able to recognize with a high degree of accuracy that a sample comes from a particular species and then to determine whether it is a protected one. DNA analysis offers the best opportunity to answer the question, 'What species is this?' In our work, we analyzed different samples of fur coming from China used to make hats and collars. Initially, the samples were examined under a microscope, then the mitochondrial DNA was tested for species identification. For this purpose, the genetic markers used were the 12S and 16S ribosomal RNA, while the hypervariable segment I of the control region was analyzed afterwards, to determine whether samples belonged to the same individual.</p><p><strong>Results: </strong>Microscopic examination showed that the fibres were of animal origin, although it was difficult to determine with a high degree of confidence which species they belonged to and if they came from a protected species. Therefore, DNA analysis was essential to try to clarify the species of these fur samples.</p><p><strong>Conclusions: </strong>Macroscopic and microscopic analysis confirmed the hypothesis regarding the analyzed hair belonging to real animals, although it failed to prove with any kind of certainty which actual family it came from, therefore, the species remains unknown. Sequence data analysis and comparisons with the samples available in GenBank showed that the hair, in most cases, belonged to the Canidae family, and in one case only to Felidae.</p>","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"5 ","pages":"7"},"PeriodicalIF":0.0,"publicationDate":"2014-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4079164/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32477629","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Editors' Pick: milk sugar, migration and pastoralism in Africa.","authors":"Antti Sajantila","doi":"10.1186/2041-2223-5-5","DOIUrl":"https://doi.org/10.1186/2041-2223-5-5","url":null,"abstract":"","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"5 1","pages":"5"},"PeriodicalIF":0.0,"publicationDate":"2014-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2041-2223-5-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32222907","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular clocks ticking in the court room.","authors":"Antti Sajantila","doi":"10.1186/2041-2223-5-4","DOIUrl":"https://doi.org/10.1186/2041-2223-5-4","url":null,"abstract":"","PeriodicalId":89160,"journal":{"name":"Investigative genetics","volume":"5 1","pages":"4"},"PeriodicalIF":0.0,"publicationDate":"2014-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/2041-2223-5-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32162907","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}