scholarly journals Review of the Forensic Applicability of Biostatistical Methods for Inferring Ancestry from Autosomal Genetic Markers

Genes ◽  
2022 ◽  
Vol 13 (1) ◽  
pp. 141
Author(s):  
Torben Tvedebrink
Keyword(s):  
Population Genetics ◽  
Population Structure ◽  
Genetic Markers ◽  
Forensic Genetics ◽  
Population Admixture ◽  
Region Of Origin ◽  
Missing Persons ◽  
Ancestry Inference ◽  
Forensic Genetic

The inference of ancestry has become a part of the services many forensic genetic laboratories provide. Interest in ancestry may be to provide investigative leads or identify the region of origin in cases of unidentified missing persons. There exist many biostatistical methods developed for the study of population structure in the area of population genetics. However, the challenges and questions are slightly different in the context of forensic genetics, where the origin of a specific sample is of interest compared to the understanding of population histories and genealogies. In this paper, the methodologies for modelling population admixture and inferring ancestral populations are reviewed with a focus on their strengths and weaknesses in relation to ancestry inference in the forensic context.

Overview of Forensic DNA Profiling and Database

2021 ◽  
pp. 23-29
Author(s):  
Sabreen Sabreen Aboujildah
Keyword(s):  
Genetic Markers ◽  
Tandem Repeats ◽  
Forensic Genetics ◽  
Human Leukocyte ◽  
Dna Profiling ◽  
Individual Identification ◽  
Forensic Dna ◽  
Forensic Dna Profiling ◽  
Victims Of Violence ◽  
Forensic Genetic

Deoxyribonucleic acid (DNA) profiling, has had a tremendous impact on forensic genetics. Before DNA profiling, all forensic genetic casework (e.g., Paternity testing, criminal casework, individual identification) was performed using classical serological genetic markers. Blood groups, human leukocyte antigen (HLA), and polymorphic protein and enzymes were used for solving forensic genetic casework using immunological and electrophoretic methodologies. These genetic markers were nevertheless limited when it was necessary to analyze minimal or degraded material, which is commonly involved in forensic cases. An STR is a region of human DNA containing an array of tandem repeats. Arrays range from only a 10 to about a hundred repeated units. This essay confers the basic concepts of operating of DNA in the criminal investigation. This review primarily summarizes the major tandem repeat markers used in forensic DNA profiling, that assist criminal’s conviction, exonerate the inferring individuals, and recognize victims of violence, catastrophes, and armed conflict.

scholarly journals Comprehensive genotyping of a Brazilian cassava (Manihot esculenta Crantz) germplasm bank: insights into diversification and domestication

2021 ◽  
Vol 134 (5) ◽  
pp. 1343-1362
Author(s):  
Alex C. Ogbonna ◽  
Luciano Rogerio Braatz de Andrade ◽  
Lukas A. Mueller ◽  
Eder Jorge de Oliveira ◽  
Guillaume J. Bauchet
Keyword(s):  
Population Genetics ◽  
Population Structure ◽  
Manihot Esculenta ◽  
Ex Situ ◽  
Germplasm Bank ◽  
Effective Population ◽  
Manihot Esculenta Crantz ◽  
Genetic Groups ◽  
Population Structure Analysis ◽  
Modern Breeding

Abstract Key message Brazilian cassava diversity was characterized through population genetics and clustering approaches, highlighting contrasted genetic groups and spatial genetic differentiation. Abstract Cassava (Manihot esculenta Crantz) is a major staple root crop of the tropics, originating from the Amazonian region. In this study, 3354 cassava landraces and modern breeding lines from the Embrapa Cassava Germplasm Bank (CGB) were characterized. All individuals were subjected to genotyping-by-sequencing (GBS), identifying 27,045 single-nucleotide polymorphisms (SNPs). Identity-by-state and population structure analyses revealed a unique set of 1536 individuals and 10 distinct genetic groups with heterogeneous linkage disequilibrium (LD). On this basis, a density of 1300–4700 SNP markers were selected for large-effect quantitative trait loci (QTL) detection. Identified genetic groups were further characterized for population genetics parameters including minor allele frequency (MAF), observed heterozygosity $$({H}_{o})$$ ( H o ) , effective population size estimate $$\widehat{{(N}_{e}}$$ ( N e ^ ) and polymorphism information content (PIC). Selection footprints and introgressions of M. glaziovii were detected. Spatial population structure analysis revealed five ancestral populations related to distinct Brazilian ecoregions. Estimation of historical relationships among identified populations suggests an early population split from Amazonian to Atlantic forest and Caatinga ecoregions and active gene flows. This study provides a thorough genetic characterization of ex situ germplasm resources from cassava’s center of origin, South America, with results shedding light on Brazilian cassava characteristics and its biogeographical landscape. These findings support and facilitate the use of genetic resources in modern breeding programs including implementation of association mapping and genomic selection strategies.

scholarly journals mixIndependR: a R package for statistical independence testing of loci in database of multi-locus genotypes

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Bing Song ◽  
August E. Woerner ◽  
John Planz
Keyword(s):  
Population Genetics ◽  
Linkage Disequilibrium ◽  
Genetic Markers ◽  
Software Package ◽  
Tandem Repeats ◽  
Population Data ◽  
Real Data ◽  
R Package ◽  
Nucleotide Polymorphisms ◽  
Mutual Independence

Abstract Background Multi-locus genotype data are widely used in population genetics and disease studies. In evaluating the utility of multi-locus data, the independence of markers is commonly considered in many genomic assessments. Generally, pairwise non-random associations are tested by linkage disequilibrium; however, the dependence of one panel might be triplet, quartet, or other. Therefore, a compatible and user-friendly software is necessary for testing and assessing the global linkage disequilibrium among mixed genetic data. Results This study describes a software package for testing the mutual independence of mixed genetic datasets. Mutual independence is defined as no non-random associations among all subsets of the tested panel. The new R package “mixIndependR” calculates basic genetic parameters like allele frequency, genotype frequency, heterozygosity, Hardy–Weinberg equilibrium, and linkage disequilibrium (LD) by mutual independence from population data, regardless of the type of markers, such as simple nucleotide polymorphisms, short tandem repeats, insertions and deletions, and any other genetic markers. A novel method of assessing the dependence of mixed genetic panels is developed in this study and functionally analyzed in the software package. By comparing the observed distribution of two common summary statistics (the number of heterozygous loci [K] and the number of share alleles [X]) with their expected distributions under the assumption of mutual independence, the overall independence is tested. Conclusion The package “mixIndependR” is compatible to all categories of genetic markers and detects the overall non-random associations. Compared to pairwise disequilibrium, the approach described herein tends to have higher power, especially when number of markers is large. With this package, more multi-functional or stronger genetic panels can be developed, like mixed panels with different kinds of markers. In population genetics, the package “mixIndependR” makes it possible to discover more about admixture of populations, natural selection, genetic drift, and population demographics, as a more powerful method of detecting LD. Moreover, this new approach can optimize variants selection in disease studies and contribute to panel combination for treatments in multimorbidity. Application of this approach in real data is expected in the future, and this might bring a leap in the field of genetic technology. Availability The R package mixIndependR, is available on the Comprehensive R Archive Network (CRAN) at: https://cran.r-project.org/web/packages/mixIndependR/index.html.

scholarly journals Population Admixture May Appear to Mask, Change or Reverse Genetic Effects of Genes Underlying Complex Traits

Genetics ◽  
2001 ◽  
Vol 159 (3) ◽  
pp. 1319-1323
Author(s):  
Hong-Wen Deng
Keyword(s):  
Population Genetics ◽  
False Positive ◽  
Complex Traits ◽  
Association Studies ◽  
Genetic Effects ◽  
Population Admixture ◽  
Reverse Genetic ◽  
Positive Identification ◽  
False Positive Identification

Abstract Association studies using random population samples are increasingly being applied in the identification and inference of genetic effects of genes underlying complex traits. It is well recognized that population admixture may yield false-positive identification of genetic effects for complex traits. However, it is less well appreciated that population admixture can appear to mask, change, or reverse true genetic effects for genes underlying complex traits. By employing a simple population genetics model, we explore the effects and the conditions of population admixture in masking, changing, or even reversing true genetic effects of genes underlying complex traits.

Reply to the comment by Morales et al. on “Population genetics reveal Myotis keenii (Keen’s myotis) and Myotis evotis (long-eared myotis) to be a single species”

2021 ◽  
pp. 423-432
Author(s):  
C.L. Lausen ◽  
Michael F. Proctor ◽  
David Paetkau ◽  
David W. Nagorsen ◽  
Purnima Govindarajulu ◽  
...  
Keyword(s):  
Population Genetics ◽  
Population Structure ◽  
Single Species ◽  
Distinct Species ◽  
Background Information ◽  
Distribution Data ◽  
Supporting Evidence ◽  
Post Mortem ◽  
The Impact ◽  
New Evidence

A.E. Morales et al. (2021. Can. J. Zool. 99(5): 415–422) provided no new evidence to alter the conclusions of C.L. Lausen et al. (2019. Can. J. Zool. 97(3): 267–279). We present background information, relevant comparisons, and clarification of analyses to further strengthen our conclusions. The genesis of the original “evotis–keenii” study in British Columbia (Canada) was to differentiate Myotis keenii (Merriam, 1895) (Keen’s myotis), with one of the smallest North American bat distributions, from sympatric Myotis evotis (H. Allen, 1864) (long-eared myotis), using something other than the suggested post-mortem skull size comparison, but no differentiating trait could be found, leading to the molecular genetics examination of C.L. Lausen et al. (2019). We present cumulative data that rejects the 1979 hypothesis of M. keenii as a distinct species. A.E. Morales et al. (2021) inaccurately portray C.L. Lausen et al.’s (2019) question and results; present inaccurate morphological and outdated distribution data; overstate the impact of homoplasy without supporting evidence; and misinterpret evidence of population structure.

Modern DNA and the Ancient Mediterranean

2019 ◽  
pp. 224-248
Author(s):  
Roy J. King ◽  
Peter A. Underhill
Keyword(s):  
Population Genetics ◽  
Dna Sequence ◽  
Genetic Markers ◽  
Human History ◽  
Ancient History ◽  
Dna Variation ◽  
Mutational Change

This chapter takes a look at genetics and its role in the study of ancient history. Genetics is the study of inheritance, and DNA variation is the essence of heredity. DNA sequence differences underpin genetics overall and population genetics is the study of such diversity in populations and how it changes through time. Reconstructing human history using modern DNA has been a longstanding endeavor rooted in sampling practicality. If a mutational change does not negatively affect the individual's ability to reproduce, it may be passed down to each succeeding generation, eventually becoming established in a population. Such mutations, whether beneficial, harmful, or neutral, can serve as genetic markers.

Taking Stock

2020 ◽  
pp. 268-288
Author(s):  
Dawnie Steadman ◽  
Sarah Wagner
Keyword(s):  
Human Rights ◽  
Transitional Justice ◽  
Forensic Genetics ◽  
International Committee ◽  
Red Cross ◽  
Legal Standards ◽  
Missing Persons ◽  
Post Conflict ◽  
Ethnographic Analysis

This chapter explores the evolving role of forensic genetics in human rights investigations and as a technology of postmortem identification for missing persons in ongoing conflict and post-conflict societies. How has DNA’s increasingly privileged place as a line of evidence impacted the field in terms of both medico-legal standards and heightened expectations among surviving kin and their communities? Drawing on interviews with leading figures in the field of forensic science and human rights/transitional justice (e.g., the International Commission on Missing Persons, the International Committee of the Red Cross, the Equipo Argentino de Antropología Forense, and the Colibrí Center for Human Rights), buttressed by ethnographic analysis of exhumation and identification efforts in Bosnia and Herzegovina and Uganda, the chapter provides an overview and commentary about the technology’s complicated place in unearthing truths and effecting repair.

scholarly journals Identificación de cadáveres sometidos a altas temperaturas, a partir de las características macroscópicas de sus órganos dentales y la aplicabilidad de la genética forense / Identification of Bodies Exposed to High Temperatures Based on Macroscopic...

2016 ◽  
Vol 35 (74) ◽  
Author(s):  
María Del Socorro Barraza Salcedo ◽  
Martha Leonor Rebolledo Cobos
Keyword(s):  
High Temperatures ◽  
Dental Pulp ◽  
Literature Search ◽  
Forensic Genetics ◽  
Forensic Odontology ◽  
Genetic Identification ◽  
Dental Tissues ◽  
Relationship Of ◽  
The Relationship ◽  
Forensic Genetic

<p><strong>ABSTRACT. </strong><em><strong>Background:</strong></em> Forensic dentistry in cases of incineration provides scientific elements that allow the identification of bodies, by analyzing dental organs, through the isolation of DNA obtained from the pulp as an alternative to confirm the identity of the victim. When the degree of temperature is highly elevated, dental tissues are vulnerable and therefore the DNA pulp is not salvageable, wasting resources and time by lack of standards to identify macroscopic characteristics that indicate this situation reliably. <em><strong>Objective:</strong></em> To describe the main features of teeth subjected to high temperatures and the relationship of these to the viability of their DNA, as a contribution to forensic genetic identification. <em><strong>Methods:</strong></em> A literature search for three databases were used; Pubmed, EBSCO and Google academician, 50 articles were selected in several languages, which made regarding the descriptors "cremated teeth; violence; Forensic Odontology; ID; DNA samples; dental pulp". <em><strong>Results:</strong></em> Most authors reported the resistance of dental tissues when subjected to high temperatures and others showed the success of the identification through dental comparisons. <em><strong>Conclusions:</strong></em> A successful identification evidenced by DNA extracted from bone and dental remains. The literature reviewed suggests that up to certain temperatures, can be carried out identification by forensic genetics of cremated victims by DNA contained in dental pulp. Strict national referencing was observed in the physical characteristics or incinerated dental macroscopic bodies.</p>

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