基于高密度单核苷酸多态性的共祖远亲缘关系预测算法准确性研究

目的 研究构建基于共祖（identity-by-descent，IBD）片段算法预测远亲缘关系分析流程并评估预测准确性。方法 采用高密度单核苷酸多态性（single nucleotide polymorphism，SNP）芯片对253份家系样本进行检测，研究基于IBD片段算法的分析流程进行两两个体间亲缘关系预测，评估预测准确性。随机减少SNP位点，评估位点数对算法预测准确性的影响。结果 IBD片段算法预测1~7级亲缘关系平均置信区间准确率为94.72%，预测可信度为99.77%，6级及以上亲缘关系预测时出现假阴性。随着SNP数量减少，预测准确性会出现一定程度的下降。结论 IBD片段算法可用于7级以内亲缘关系的预测，该算法在群体遗传学、法医遗传学等领域有重要应用价值。     

亲缘关系预测系统

报道了一个基于全基因组数据的亲缘关系预测系统(Kinship Prediction System Version 1.0, KPSv1.0),其旨在给定一个自定义群体中所有个体的全基因组数据文件,通过亲缘关系预测算法,计算出群体中所有存在的亲缘关系对,并将结果可视化为家谱图,进而搜寻某个未知个体与多个已知个体的复杂亲缘关系,为物证鉴定提供强有力的线索。系统不仅将以往复杂的预测流程变得简单化、自动化,而且将预测结果进行了界面化,并和用户建立了更好的交互性,大大地提升了运算效率,在人类遗传学、法医遗传学等领域有重要的应用价值。     

对未知关系个体进行系谱推断的自动分析系统

基于短串联重复序列(short tandem repeat, STR)和单核苷酸多态性(single nucleotide polymorphism, SNP)的亲缘关系推断在群体遗传学、法医学等领域应用广泛,但目前没有成熟的系统可以实现针对STR数据和SNP数据的自动批量化处理。为弥补这一空白,项目组开发了一款基于STR数据和SNP数据的DNA系谱推断系统(DNA Genealogy Analyzer Version 1.0, DGA v1.0),该系统可运用STR和SNP亲缘关系预测算法计算未知亲缘关系群体中的所有亲缘关系。系统核心算法部分基于Python语言实现,前端部分采用HTML和CSS语言编写,整体采用Python的Flask框架开发。该系统与已有分析方法相比,结果一致性为100%,运算效率提高了800%以上,在群体遗传学等领域有重要应用价值。     

蚂蚁(膜翅目 :蚁科)的同巢识别与亲缘识别行为及机理概述(英文)

蚂蚁属真社会性昆虫。真社会性最主要的特性是在一个社会集团内个体间有生殖上的分工。即多数个体 (如工蚁 ,兵蚁等 )自身不行生殖 ,而一生“竭力”“帮助”少数个体 (如蚁后和雄蚁 )繁殖后代。蚂蚁生活的基本单位是社群 (colony)。一个单独的个体 (除创建蚁后 )是没有意义的。“典型”的社群由一个创建蚁后和其后代组成 (即单母 :monogyny)。单母社群内个体间亲缘关系密切。在自然界 ,多母社群 (polygyny)亦普遍存在。在多母社群里 ,如蚁后间亲缘关系密切 (如姐妹 ) ,社群内遗传关系同质性亦较高 ,个体间的平均遗传相关也密切。但如蚁后间亲缘关系疏远或无亲缘关系 ,那么社群内遗传异质性很高 ,个体间平均遗传相关也随之降低。和其它复杂的社会群体一样 ,蚂蚁社会拥有高度发达的通讯系统。社群不仅需要在内部个体间相互沟通以确保社群的平衡和协调性 ,而且必需和社群外各种息息相关的有机体间交流信息 ,以便有效利用有用的资源并避开各种危险。如果说信息素是蚂蚁通讯最重要的物质基础 ,那么对周围各类生物的识别便是蚂蚁通讯最为基本的环节。蚂蚁的识别行为及其机理是多样的 ,其生物学功能亦随被识别的对象不同而异。如 :为了确保社会群体的安全 ,蚂蚁必须准确识别“敌”、“我”和“朋友”。为了使得     

基于分块主成分分析的太行山猕猴面部相似性

2012 年4 ～8 月,在太行山猕猴国家级自然保护区济源管理局天坛山管护区(北纬35°05′ ～ 35°15′,东经112°12′ ～ 112°22′),对太行山猕猴王屋1 群(WW - 1)内的3 个母系单元(matrilineal unit) 中大于(等于)3 岁龄的26 只个体进行面部拍照,获取其面部特写照片,进而利用分块主成分分析(modular principal component analysis,MPCA)法,对个体进行面部识别分析,旨在探讨个体间面部相似度与亲缘关系的相关性。结果表明:(1)太行山猕猴个体间的面部相似度与亲缘类型有关,母亲与大于3 岁龄子代间的面部相似度为0.93 ±0. 00,显著高于单元内(0. 89 ± 0. 00)和单元间(0.84 ±0.01)的面部相似度;(2)太行山猕猴个体的面部特征随年龄增长而变化,4 岁(含4 岁)龄以上个体与母亲间的面部相似度较高(0.88 ～ 0. 95),依此值可准确地识别母子关系。本研究采用量化方法对非人灵长类个体间面部相似度进行分析,发现太行山猕猴个体间的面部相似度与亲缘关系密切相关;研究结果可为非人灵长类的个体识别提供较为客观的手段和方法。     

基于亲权鉴定的千岛湖社鼠家群遗传结构与亲缘关系特征研究

于2009年7月至2010年11月,对浙江千岛湖两个岛屿上的社鼠(Niviventer confucianus)种群进行标志重捕,并采用8个高多态性的微卫星位点,对两个岛屿的社鼠种群进行家群分析和亲权鉴定,探讨了社鼠家群的亲缘关系特征。结果显示,8个微卫星位点能可靠地对两个岛屿社鼠种群进行亲权鉴定,A岛已确定亲缘关系的71只社鼠分为12个家群,家群中的个体数最多达到19个,B岛已确定的49只社鼠个体共分为11个家群,家群中的个体数最多达到14个。家群内部成员之间的亲缘关系表现为配对繁殖的个体对间亲缘系数最小,揭示了社鼠倾向于选择亲缘关系较远的异性作为配偶。家群中雄性后代个体之间与雌性个体之间的亲缘关系相比,两岛表现情况相反,该结果暗示两岛屿上社鼠扩散行为可能有所不同。通过计算与同一雄性(或同一雌性)交配的个体间的亲缘系数,发现两个岛屿上的社鼠在与不同异性交配时也存在选择性,即避免选择亲缘关系较近的异性作为混交的对象。     

人类Y染色体36个新STR位点的筛选与鉴定

通过对NCBI数据库中的Y-STR位点和生物信息学预测的新Y-STR位点的分析,选取了133个位点在48个全球分布的样本中进行检测验证,获得41个可靠的高频位点,其中36个为首次发现验证的新Y-STR位点。利用这41个Y-STR位点,在200个上海随机男性样本中共发现200种单倍型,实现了人群内个体间100%区分,并通过对浙江江山一姜氏聚集地的9个5代以内无血缘关系的姜氏个体和7个上海随机人群的姜氏个体的单倍型的分析,发现6个江山姜氏个体具较近的亲缘关系(彼此差异位点在2～4个之间)。这41个Y-STR位点具备较高的信息度,能有效区分群体内不同家族来源的个体,这将有助于群体内个体间近代亲缘关系研究,并有望在法医学法医个体识别、亲权鉴定,人类起源、迁徙等研究中发挥重大作用。     

六种石磺科贝类超氧化物歧化酶和酯酶同工酶分析

采用聚丙烯酰胺垂直板凝胶电泳分离技术对中国东南沿海的石磺科6种石磺的腹足、肝胰脏两种组织的超氧化物歧化酶和酯酶同工酶进行分析.明确了其酶谱的特征及分布,并利用聚类分析方法对种间的亲缘关系进行了研究.同工酶聚类分析显示,紫色疣石磺(Peronia verruculata)和小紫疣石磺(Peronia sp.)的亲缘关系最近;里氏拟石磺(Paraoncidium reevesii)和白底拟石磺(Paraoncidium sp.)聚为一类;平疣桑椹石磺(Platevindex mortoni)和瘤背石磺(Onchidium struma)聚为一类.种间的个体酶谱表型有差异,同属的种间差异小于不同属的种间差异.酶谱的差异程度与形态分类学中的亲缘关系相近.利用超氧化物歧化酶同工酶和酯酶同工酶酶谱表型也可以作为一种蛋白分子标记应用于石磺科属种的分类鉴定.     

近缘物种的遗传多样性及其亲缘关系的取样策略研究

取样策略的问题目前大多停留于对单一物种的种质资源研究.然而,对野生近缘植物取样策略的研究,不仅有利于准确快捷地阐明物种间的系统发育关系,而且对于了解遗传多样性分布状况,制定野外考察、材料收集取样及保护策略均有重要的理论指导意义.以巴山松及其近缘种为例,利用cpSSR(叶绿体微卫星)和AFLP2种分子标记对其取样策略和统计方法进行分析,揭示居群取样个体数和基因位点数与遗传多样性的关系以及基因(引物)和系统树构建方法对亲缘关系确定的影响.研究表明:(1)居群取样个体数和基因位点数差异对遗传多样性影响并不显著,但当居群取样个体数为30个左右,单引物基因位点数为60个以上,总位点数为480个以上时,所得遗传多样性及亲缘关系较为准确可靠.(2)较多数目的基因(引物)对于得到较为准确可靠的亲缘关系分析是十分必要的.(3)系统树构建方法对近缘种亲缘关系的确定有一定的影响.     

我国6个地方绵羊品种微卫星DNA多态性研究

利用聚丙烯酰胺凝胶电泳技术研究了我国蒙古羊、乌珠穆沁羊、哈萨克羊、阿勒泰羊、滩羊和藏绵羊 6个地方绵羊品种 17个微卫星标记的多态性 ,以探讨其遗传多样性、起源分化及群体间的遗传亲缘关系。结果表明微卫星标记不同位点间遗传多样性差异极显著 (P <0 0 1) ,群体间多态信息含量 (PIC)、近交程度 (Fis)和观察杂合度 (Obs .Het)差异不显著 ,但基因多样性 (genediversity)和期望杂合度 (Exp .Het)差异显著 (P <0 0 5 )。所研究的我国 6个地方绵羊品种与欧洲品种具有相似的遗传多样性 ,但具有较高的近交系数。个体和群体的聚类分析结果提示我国地方绵羊品种可能起源于两类祖先。群体间的聚类分析结果还表明 ,蒙古羊与乌珠穆沁羊分化不明显且具有较近的遗传亲缘关系 ,蒙古羊与藏绵羊间分化明显且具有较远的遗传亲缘关系。滩羊、阿勒泰羊以及藏绵羊间也具有较近的遗传亲缘关系。所研究的我国 6个地方绵羊品种的遗传分化 (Fst)与西班牙绵羊品种接近 ,但明显小于欧洲其他绵羊品种     

Diptera and Coleoptera of potential forensic importance in southeastern Brazil: relative abundance and seasonality

Abstract. To determine the species of Diptera and Coleoptera that visit and breed in carrion, four experiments, one for each season, were conducted from November 1992 to October 1993 in the vicinity of Campinas city, Southeastern Brazil. For each experiment two pigs weighing c. 10 kg were killed with a blow to the head with a blunt metallic object and immediately exposed, one in the shade and the other under sunlight. Adult insects and larvae leaving the carcass to pupate were collected daily. In addition, female blowflies were dissected in order to determine the stage of ovarian development. Five species of Calliphoridae: Chrysomya albiceps, C.megacephala, C.putoria, Phaenicia eximia and Hemilucilia segmentaria; three of Sarcophagidae: Pattonella intermutans, Liopygia ruficornis and Adiscochaeta ingens , and three of beetles: Dermestes maculatus, D. peruvianus (Dermestidae) and Necrobia rufipes (Cleridae), were considered of potential forensic importance, for they were able to breed in carrion exposed to natural environmental conditions. In addition, several fly species showed a definite seasonal pattern, with the Calliphoridae breeding more frequently during the warmer months of the year, and the Sarcophagidae preferring the cooler periods.     

Statistical basis for positive identification in forensic anthropology

Forensic scientists are often expected to present the likelihood of DNA identifications in US courts based on comparative population data, yet forensic anthropologists tend not to quantify the strength of an osteological identification. Because forensic anthropologists are trained first and foremost as physical anthropologists, they emphasize estimation problems at the expense of evidentiary problems, but this approach must be reexamined. In this paper, the statistical bases for presenting osteological and dental evidence are outlined, using a forensic case as a motivating example. A brief overview of Bayesian statistics is provided, and methods to calculate likelihood ratios for five aspects of the biological profile are demonstrated. This paper emphasizes the definition of appropriate reference samples and of the "population at large," and points out the conceptual differences between them. Several databases are introduced for both reference information and to characterize the "population at large," and new data are compiled to calculate the frequency of specific characters, such as age or fractures, within the "population at large." Despite small individual likelihood ratios for age, sex, and stature in the case example, the power of this approach is that, assuming each likelihood ratio is independent, the product rule can be applied. In this particular example, it is over three million times more likely to obtain the observed osteological and dental data if the identification is correct than if the identification is incorrect. This likelihood ratio is a convincing statistic that can support the forensic anthropologist's opinion on personal identity in court.     

Fungal microbiota dynamics as a postmortem investigation tool: focus on Aspergillus,Penicillium and Candida species

Aims: To investigate the presence of fungi during three human decomposition stages: bloated, putrefaction and skeletonization. Methods and Results: The samples were gathered in the city of Fortaleza, Ceará, Brazil, from the public morgue and cemeteries. The material was submitted to conventional mycological procedures by direct examination and macro/micro morphological and biochemical analyses. The main fungi isolated were Aspergillus spp., Penicillium spp. and Candida spp. in the bloated stage (n = 34 cadavers) and in the putrefaction stage (n = 6 cadavers), while in the skeletonization stage (n = 20 cadavers), the main fungi were Aspergillus spp., Penicillium spp. and Mucor sp. Conclusions: Aspergillus, Penicillium and Candida species were associated with decomposed human cadavers. Significance and Impact of the Study: These findings enable tracing out the profile of fungal communities of human cadavers for the first time. However, much more research will be necessary to develop this new segment of mycology and to enable its routine use in forensic science.     

The macromorphoscopic databank

The development of identification standards in forensic anthropology requires large and appropriate reference samples comprising individuals with modern birth years. Recent advances in macromorphoscopic trait data collection and analysis have created a need for reference data for classification models and biological distance analyses. The Macromorphoscopic Databank (N ～ 7,397) serves that function, making publicly available trait scores for a large sample (n = 2,363) of modern American populations and world‐wide groups of various geographic origins (n = 1,790). In addition, the MaMD stores reference data for a large sample (n = 3,244) of pre‐, proto‐ and historic Amerindian data, useful for biodistance studies and finer‐levels of analysis during NAGPRA‐related investigations and repatriations. In developing this database, particular attention was given to the level of classification needed during the estimation of ancestry in a forensic context. To fill the knowledge gap that currently exists in the analysis of these data, the following overview outlines many of the issues and their potential solutions. Developing valuable tools that are useful to other practitioners is the purpose of growing a databank. As the Macromorphoscopic Databank develops through data collection efforts and contributions from the field, its utility as a research and teaching tool will also mature, in turn creating a vital resource for forensic anthropologists for future generations.     

Data on morphometric analysis of anterior teeth from Hazaribag College of Dental Sciences and Hospital,jharkhand

It is of interest to document data on morphometric (measurement of external form) analysis of maxillary and mandibular anterior teeth collected from a dental set up using mesio-distal (MD) dimension. The mesiodistal dimensions of all permanent anterior teeth (central incisor, lateral incisor and canine) of 25 males and 25 females patients were recorded using digital vernier calipers. Data were charted and statistical analysis was done using Mann Whitney U test. Data shows sexual dimorphism for every tooth between males and females. However, dimorphism was exhibited only in maxillary and mandibular canine, mandibular central incisors, and lateral incisor. Hence,odontometric parameters offer simple, reliable and cost-effective in forensic investigation for recording gender discrimination.     

Incorporating Argumentation through Forensic Science

This article outlines how to incorporate argumentation into a forensic science unit using a mock trial. Practical details of the mock trial include: (1) a method of scaffolding students’ development of their argument for the trial, (2) a clearly outlined set of expectations for students during the planning and implementation of the mock trial, and (3) an example of how to use questioning to guide students through the planning of the mock trial. While a general forensic science unit is provided in the article, a teacher can use the details of the mock trial with any forensic science unit for either middle school or secondary science students.     

Analysis of quantitative methods for rib seriation using the Spitalfields documented skeletal collection

Accurate rib seriation is essential in forensic anthropology and bioarchaeology for determination of minimum numbers of individuals, sequencing trauma patterns to the chest, and identification of central ribs for use in age estimation. We investigate quantitative methods for rib seriation based on three metric variables: superior (anterior) costo-transverse crest height (SCTCH), articular facet of the tubercle-to-angle length (AFTAL), and head-to-articular facet length (HAFL). The sample consists of complete but unseriated sets of ribs from 133 individuals from the documented (known age and sex) and undocumented skeletal collections of Christ Church Spitalfields, London. This research confirms the results of an earlier study (Hoppa and Saunders [1998] J. Forensic. Sci. 43:174-177) and extends it with the application of two new metric traits and further analyses of sex differences. Analyses of variance showed that SCTCH and AFTAL are significantly associated (P < 0.001) with rib number. Tukey tests of pairwise rib comparisons revealed that for two dimensions (SCTCH and AFTAL), the central ribs (3rd-6th) are significantly distinct from each other (P < 0.05). Using simple ranking of either the SCTCH or AFTAL traits, the proportion of correctly identified ribs within +/-1 position was 80%, compared to initial seriation using morphological methods (Dudar [1993] J. Forensic. Sci. 28:788-797; Mann [1993] J. Forensic. Sci. 28:151-155). Significant sex dimorphism was also identified for these two traits. Analysis of the HAFL trait produced somewhat equivocal results, suggesting that this variable is not reliable for rib seriation. The variable SCTCH proves to be the most useful dimension for seriation, and shows that all but the 7th-9th ribs can be distinguished from others in the sequence, with important results for the 4th rib, where ranking allowed identification in 86% of cases, consistent with morphological methods for intact ribs.     

Technical note: A report on the Forensic Anthropology Database for Assessing Methods Accuracy

We report on the functionality, available support, and research capability of the Forensic Anthropology Database for Assessing Methods Accuracy (FADAMA; DOJ DUBX0213). FADAMA is an online repository for case data from identified forensic skeletal cases. The goal of FADAMA is to address the lack of adequate measures for assessing accuracy and reliability of forensic anthropology methods. FADAMA requires users to apply for access with their university or organization credentials. Verified users may upload and download anonymized case data via the user interface, after signing a terms of service agreement outlining ethical behavior. Case data uploads require information about the actual biological profile of the decedent and the forensic anthropology estimations. Uploading case data takes approximately 15–25 min. FADAMA users currently have 85 methods to select from when entering case data, with the capability to add new methods as they are developed. Access to the database is free, and online video tutorials are available for users covering database functionality. Currently, the database houses anonymized case data for over 350 identified cases from across the U.S. Funding has been allocated for a database technician to assist offices with large caseloads to upload cases. As it stands, the database is easy to use, and maintains thoughtful tools to assist users. The power of the database to identify trends in both method accuracy and usage is apparent, and will continue to grow as more cases are added.