Biochemistry, Genetics and Molecular Biology › Genetics

Forensic and Genetic Research

Works Count: 35839

Wikipedia

Description

This cluster of papers focuses on the genomic analysis of ancient DNA to study population history, human evolution, and forensic genetics. It covers topics such as mitochondrial DNA variation, Y chromosome diversity, population structure, and ancestry informative markers. The research includes insights into ancient human migrations, genetic admixture, and the development of methods for accurate analysis of degraded DNA.

Keywords

Ancient DNA; Genomic Analysis; Population History; Human Evolution; Forensic Genetics; Mitochondrial DNA; Y Chromosome; Admixture History; Population Structure; Ancestry Informative Markers

A Nomenclature System for the Tree of Human Y-Chromosomal Binary Haplogroups

2002-02-01

Alan J. Redd

The Y chromosome contains the largest nonrecombining block in the human genome. By virtue of its many polymorphisms, it is now the most informative haplotyping system, with applications in evolutionary … The Y chromosome contains the largest nonrecombining block in the human genome. By virtue of its many polymorphisms, it is now the most informative haplotyping system, with applications in evolutionary studies, forensics, medical genetics, and genealogical reconstruction. However, the emergence of several unrelated and nonsystematic nomenclatures for Y-chromosomal binary haplogroups is an increasing source of confusion. To resolve this issue, 245 markers were genotyped in a globally representative set of samples, 74 of which were males from the Y Chromosome Consortium cell line repository. A single most parsimonious phylogeny was constructed for the 153 binary haplogroups observed. A simple set of rules was developed to unambiguously label the different clades nested within this tree. This hierarchical nomenclature system supersedes and unifies past nomenclatures and allows the inclusion of additional mutations and haplogroups yet to be discovered. [Supplementary Table 1, available as an online supplement at www.genome.org , lists all published markers included in this survey and primer information.]

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Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA

1999-10-01

Richard M. Andrews , Iwona Kubacka , Patrick F. Chinnery +3 more

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Population genomics of Bronze Age Eurasia

2015-06-09

Morten E. Allentoft , Martin Sikora , Karl-Göran Sjögren +7 more

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The genetic legacy of the Quaternary ice ages

2000-06-22

Godfrey M. Hewitt

Genome sequence of a 45,000-year-old modern human from western Siberia

2014-10-01

Qiaomei Fu , Heng Li , Priya Moorjani +7 more

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Robust Demographic Inference from Genomic and SNP Data

2013-10-24

Laurent Excoffier , Isabelle Dupanloup , Emilia Huerta‐Sánchez +2 more

We introduce a flexible and robust simulation-based framework to infer demographic parameters from the site frequency spectrum (SFS) computed on large genomic datasets. We show that our composite-likelihood approach allows … We introduce a flexible and robust simulation-based framework to infer demographic parameters from the site frequency spectrum (SFS) computed on large genomic datasets. We show that our composite-likelihood approach allows one to study evolutionary models of arbitrary complexity, which cannot be tackled by other current likelihood-based methods. For simple scenarios, our approach compares favorably in terms of accuracy and speed with , the current reference in the field, while showing better convergence properties for complex models. We first apply our methodology to non-coding genomic SNP data from four human populations. To infer their demographic history, we compare neutral evolutionary models of increasing complexity, including unsampled populations. We further show the versatility of our framework by extending it to the inference of demographic parameters from SNP chips with known ascertainment, such as that recently released by Affymetrix to study human origins. Whereas previous ways of handling ascertained SNPs were either restricted to a single population or only allowed the inference of divergence time between a pair of populations, our framework can correctly infer parameters of more complex models including the divergence of several populations, bottlenecks and migration. We apply this approach to the reconstruction of African demography using two distinct ascertained human SNP panels studied under two evolutionary models. The two SNP panels lead to globally very similar estimates and confidence intervals, and suggest an ancient divergence (>110 Ky) between Yoruba and San populations. Our methodology appears well suited to the study of complex scenarios from large genomic data sets.

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Forensic application of DNA ‘fingerprints’

1985-12-01

Peter Gill , Alec J. Jeffreys , David J. Werrett

History and Geography of Human Genes

1994-01-01

Alberto Piazza

The genomic landscape of Neanderthal ancestry in present-day humans

2014-01-28

Sriram Sankararaman , Swapan Mallick , Michael Dannemann +5 more

Individual-specific ‘fingerprints’ of human DNA

1985-07-01

A.J. Jeffreys , Victoria Wilson , Swee Lay Thein

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Genetic variation at five trimeric and tetrameric tandem repeat loci in four human population groups

1992-02-01

Al Edwards , Holly A. Hammond , Jin Li +2 more

The complete genome sequence of a Neanderthal from the Altai Mountains

2013-12-18

Kay Prüfer , Fernando Racimo , Nick Patterson +7 more

Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments

2013-09-09

Jesse Dabney , Michael Knapp , Isabelle Glocke +7 more

Significance Outside of permafrost, no contiguous DNA sequences have been generated from material older than ∼120,000 y. By improving our ability to sequence very short DNA fragments, we have recovered … Significance Outside of permafrost, no contiguous DNA sequences have been generated from material older than ∼120,000 y. By improving our ability to sequence very short DNA fragments, we have recovered the mitochondrial genome sequence of a >300,000-y-old cave bear from Sima de los Huesos, a Spanish cave site that is famous for its rich collection of Middle Pleistocene human fossils. This finding demonstrates that DNA can survive for hundreds of thousands of years outside of permafrost and opens the prospect of making more samples from this time period accessible to genetic studies.

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Massive migration from the steppe was a source for Indo-European languages in Europe

2015-03-02

Wolfgang Haak , Iosif Lazaridis , Nick Patterson +7 more

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Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans

2013-11-19

Maanasa Raghavan , Pontus Skoglund , Kelly E. Graf +7 more

Ancient human genomes suggest three ancestral populations for present-day Europeans

2014-09-01

Iosif Lazaridis , Nick Patterson , Alissa Mittnik +7 more

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Reconstruction of human evolution: bringing together genetic, archaeological, and linguistic data.

1988-08-01

L. Luca Cavalli-Sforza , Alberto Piazza , Paolo Menozzi +1 more

The genetic information for this work came from a very large collection of gene frequencies for "classical" (non-DNA) polymorphisms of the world aborigines. The data were grouped in 42 populations … The genetic information for this work came from a very large collection of gene frequencies for "classical" (non-DNA) polymorphisms of the world aborigines. The data were grouped in 42 populations studied for 120 alleles. The reconstruction of human evolutionary history thus generated was checked with statistical techniques such as "boot-strapping". It changes some earlier conclusions and is in agreement with more recent ones, including published and unpublished DNA-marker results. The first split in the phylogenetic tree separates Africans from non-Africans, and the second separates two major clusters, one corresponding to Caucasoids, East Asians, Arctic populations, and American natives, and the other to Southeast Asians (mainland and insular), Pacific islanders, and New Guineans and Australians. Average genetic distances between the most important clusters are proportional to archaeological separation times. Linguistic families correspond to groups of populations with very few, easily understood overlaps, and their origin can be given a time frame. Linguistic superfamilies show remarkable correspondence with the two major clusters, indicating considerable parallelism between genetic and linguistic evolution. The latest step in language development may have been an important factor determining the rapid expansion that followed the appearance of modern humans and the demise of Neanderthals.

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African Populations and the Evolution of Human Mitochondrial DNA

1991-09-27

Linda Vigilant , Mark Stoneking , Henry Harpending +2 more

The proposal that all mitochondrial DNA (mtDNA) types in contemporary humans stem from a common ancestor present in an African population some 200,000 years ago has attracted much attention. To … The proposal that all mitochondrial DNA (mtDNA) types in contemporary humans stem from a common ancestor present in an African population some 200,000 years ago has attracted much attention. To study this proposal further, two hypervariable segments of mtDNA were sequenced from 189 people of diverse geographic origin, including 121 native Africans. Geographic specificity was observed in that identical mtDNA types are shared within but not between populations. A tree relating these mtDNA sequences to one another and to a chimpanzee sequence has many deep branches leading exclusively to African mtDNAs. An African origin for human mtDNA is supported by two statistical tests. With the use of the chimpanzee and human sequences to calibrate the rate of mtDNA evolution, the age of the common human mtDNA ancestor is placed between 166,000 and 249,000 years. These results thus support and extend the African origin hypothesis of human mtDNA evolution.

Ancient DNA: extraction, characterization, molecular cloning, and enzymatic amplification.

1989-03-01

Svante Pääbo

Several chemical and enzymatic properties were examined in the DNA extracted from dry remains of soft tissues that vary in age from 4 to 13,000 years and represent four species, … Several chemical and enzymatic properties were examined in the DNA extracted from dry remains of soft tissues that vary in age from 4 to 13,000 years and represent four species, including two extinct animals (the marsupial wolf and giant ground sloth). The DNA obtained was invariably of a low average molecular size and damaged by oxidative processes, which primarily manifest themselves as modifications of pyrimidines and sugar residues as well as baseless sites and intermolecular cross-links. This renders molecular cloning difficult. However, the polymerase chain reaction can be used to amplify and study short mitochondrial DNA sequences that are of anthropological and evolutionary significance. This opens up the prospect of performing diachronical studies of molecular evolutionary genetics.

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Inference of human population history from individual whole-genome sequences

2011-07-01

Heng Li , Richard Durbin

Classification of European mtDNAs From an Analysis of Three European Populations

1996-12-01

Antonio Torroni , Kirsi Huoponen , Paolo Francalacci +6 more

Mitochondrial DNA (mtDNA) sequence variation was examined in Finns, Swedes and Tuscans by PCR amplification and restriction analysis. About 99% of the mtDNAs were subsumed within 10 mtDNA haplogroups (H, … Mitochondrial DNA (mtDNA) sequence variation was examined in Finns, Swedes and Tuscans by PCR amplification and restriction analysis. About 99% of the mtDNAs were subsumed within 10 mtDNA haplogroups (H, I, J, K, M, T, U, V, W, and X) suggesting that the identified haplogroups could encompass virtually all European mtDNAs. Because both hypervariable segments of the mtDNA control region were previously sequenced in the Tuscan samples, the mtDNA haplogroups and control region sequences could be compared. Using a combination of haplogroup-specific restriction site changes and control region nucleotide substitutions, the distribution of the haplogroups was surveyed through the published restriction site polymorphism and control region sequence data of Caucasoids. This supported the conclusion that most haplogroups observed in Europe are Caucasoid-specific, and that at least some of them occur at varying frequencies in different Caucasoid populations. The classification of almost all European mtDNA variation in a number of well defined haplogroups could provide additional insights about the origin and relationships of Caucasoid populations and the process of human colonization of Europe, and is valuable for the definition of the role played by mtDNA backgrounds in the expression of pathological mtDNA mutations

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A Human Genome Diversity Cell Line Panel

2002-04-12

Howard M. Cann , Claudia de Toma , Lucien Cazes +7 more

A resource of 1064 cultured lymphoblastoid cell lines (LCLs) ([1][1]) from individuals in different world populations and corresponding milligram quantities of DNA is deposited at the Foundation Jean Dausset (CEPH) … A resource of 1064 cultured lymphoblastoid cell lines (LCLs) ([1][1]) from individuals in different world populations and corresponding milligram quantities of DNA is deposited at the Foundation Jean Dausset (CEPH) ([2][2]) in Paris. LCLs were collected from various laboratories by the Human Genome

Genetic Analyses from Ancient DNA

2004-11-02

Svante Pääbo , Hendrik N. Poinar , David Serre +7 more

▪ Abstract About 20 years ago, DNA sequences were separately described from the quagga (a type of zebra) and an ancient Egyptian individual. What made these DNA sequences exceptional was … ▪ Abstract About 20 years ago, DNA sequences were separately described from the quagga (a type of zebra) and an ancient Egyptian individual. What made these DNA sequences exceptional was that they were derived from 140- and 2400-year-old specimens. However, ancient DNA research, defined broadly as the retrieval of DNA sequences from museum specimens, archaeological finds, fossil remains, and other unusual sources of DNA, only really became feasible with the advent of techniques for the enzymatic amplification of specific DNA sequences. Today, reports of analyses of specimens hundreds, thousands, and even millions of years old are almost commonplace. But can all these results be believed? In this paper, we critically assess the state of ancient DNA research. In particular, we discuss the precautions and criteria necessary to ascertain to the greatest extent possible that results represent authentic ancient DNA sequences. We also highlight some significant results and areas of promising future research.

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Theory and Practice of Histological Techniques

1977-11-01

R N MacSween

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The phylogeography of Y chromosome binary haplotypes and the origins of modern human populations

2001-01-01

P. A. Underhill , Giuseppe Passarino , Ashleigh Lin +5 more

Although molecular genetic evidence continues to accumulate that is consistent with a recent common African ancestry of modern humans, its ability to illuminate regional histories remains incomplete. A set of … Although molecular genetic evidence continues to accumulate that is consistent with a recent common African ancestry of modern humans, its ability to illuminate regional histories remains incomplete. A set of unique event polymorphisms associated with the non‐recombining portion of the Y‐chromosome (NRY) addresses this issue by providing evidence concerning successful migrations originating from Africa, which can be interpreted as subsequent colonizations, differentiations and migrations overlaid upon previous population ranges. A total of 205 markers identified by denaturing high performance liquid chromatography (DHPLC), together with 13 taken from the literature, were used to construct a parsimonious genealogy. Ancestral allelic states were deduced from orthologous great ape sequences. A total of 131 unique haplotypes were defined which trace the microevolutionary trajectory of global modern human genetic diversification. The genealogy provides a detailed phylogeographic portrait of contemporary global population structure that is emblematic of human origins, divergence and population history that is consistent with climatic, paleoanthropological and other genetic knowledge.

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Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation

2008-10-14

Mannis van Oven , Manfred Kayser

Human mitochondrial DNA is widely used as tool in many fields including evolutionary anthropology and population history, medical genetics, genetic genealogy, and forensic science. Many applications require detailed knowledge about … Human mitochondrial DNA is widely used as tool in many fields including evolutionary anthropology and population history, medical genetics, genetic genealogy, and forensic science. Many applications require detailed knowledge about the phylogenetic relationship of mtDNA variants. Although the phylogenetic resolution of global human mtDNA diversity has greatly improved as a result of increasing sequencing efforts of complete mtDNA genomes, an updated overall mtDNA tree is currently not available. In order to facilitate a better use of known mtDNA variation, we have constructed an updated comprehensive phylogeny of global human mtDNA variation, based on both coding- and control region mutations. This complete mtDNA tree includes previously published as well as newly identified haplogroups, is easily navigable, will be continuously and regularly updated in the future, and is online available at http://www.phylotree.org.

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New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree

2008-04-02

Tatiana M. Karafet , Fernando L. Méndez , Monica B. Meilerman +3 more

Markers on the non-recombining portion of the human Y chromosome continue to have applications in many fields including evolutionary biology, forensics, medical genetics, and genealogical reconstruction. In 2002, the Y … Markers on the non-recombining portion of the human Y chromosome continue to have applications in many fields including evolutionary biology, forensics, medical genetics, and genealogical reconstruction. In 2002, the Y Chromosome Consortium published a single parsimony tree showing the relationships among 153 haplogroups based on 243 binary markers and devised a standardized nomenclature system to name lineages nested within this tree. Here we present an extensively revised Y chromosome tree containing 311 distinct haplogroups, including two new major haplogroups (S and T), and incorporating approximately 600 binary markers. We describe major changes in the topology of the parsimony tree and provide names for new and rearranged lineages within the tree following the rules presented by the Y Chromosome Consortium in 2002. Several changes in the tree topology have important implications for studies of human ancestry. We also present demography-independent age estimates for 11 of the major clades in the new Y chromosome tree.

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Mitochondrial DNA and human evolution

1987-01-01

Rebecca L. Cann , Mark Stoneking , Allan C. Wilson

Reconstructing Indian population history

2009-09-01

David Reich , Kumarasamy Thangaraj , Nick Patterson +2 more

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A Draft Sequence of the Neandertal Genome

2010-05-06

Richard E. Green , Johannes Krause , Adrian W. Briggs +7 more

Neandertals, the closest evolutionary relatives of present-day humans, lived in large parts of Europe and western Asia before disappearing 30,000 years ago. We present a draft sequence of the Neandertal … Neandertals, the closest evolutionary relatives of present-day humans, lived in large parts of Europe and western Asia before disappearing 30,000 years ago. We present a draft sequence of the Neandertal genome composed of more than 4 billion nucleotides from three individuals. Comparisons of the Neandertal genome to the genomes of five present-day humans from different parts of the world identify a number of genomic regions that may have been affected by positive selection in ancestral modern humans, including genes involved in metabolism and in cognitive and skeletal development. We show that Neandertals shared more genetic variants with present-day humans in Eurasia than with present-day humans in sub-Saharan Africa, suggesting that gene flow from Neandertals into the ancestors of non-Africans occurred before the divergence of Eurasian groups from each other.

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Tracing European Founder Lineages in the Near Eastern mtDNA Pool

2000-11-01

Martin Richards , Vincent Macaulay , Eileen Hickey +7 more

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Neandertal DNA Sequences and the Origin of Modern Humans

1997-07-01

Matthias Krings , Anne C. Stone , Ralf W. Schmitz +3 more

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Genes mirror geography within Europe

2008-08-31

John Novembre , Toby Johnson , Katarzyna Bryc +7 more

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Ancient human genome sequence of an extinct Palaeo-Eskimo

2010-02-01

Morten Rasmussen , Yingrui Li , Stinus Lindgreen +7 more

We report here the genome sequence of an ancient human. Obtained from ∼4,000-year-old permafrost-preserved hair, the genome represents a male individual from the first known culture to settle in Greenland. … We report here the genome sequence of an ancient human. Obtained from ∼4,000-year-old permafrost-preserved hair, the genome represents a male individual from the first known culture to settle in Greenland. Sequenced to an average depth of 20×, we recover 79% of the diploid genome, an amount close to the practical limit of current sequencing technologies. We identify 353,151 high-confidence single-nucleotide polymorphisms (SNPs), of which 6.8% have not been reported previously. We estimate raw read contamination to be no higher than 0.8%. We use functional SNP assessment to assign possible phenotypic characteristics of the individual that belonged to a culture whose location has yielded only trace human remains. We compare the high-confidence SNPs to those of contemporary populations to find the populations most closely related to the individual. This provides evidence for a migration from Siberia into the New World some 5,500 years ago, independent of that giving rise to the modern Native Americans and Inuit. For the first time, the sequence of a near-complete nuclear genome has been obtained from the tissue of an ancient human. It comes from permafrost-preserved hair, about 4,000 years old, of a male palaeo-Eskimo of the Saqqaq culture, the earliest known settlers in Greenland. Functional single-nucleotide polymorphism (SNP) assessment was used to assign possible phenotypic characteristics. The analysis provides evidence for a migration from Siberia into the New World some 5,500 years ago, independent of the migration that gave rise to the modern Native Americans and Inuit. Elsewhere in the issue we profile the paper's last author Eske Willerslev, who headed the project and found the lock of hair in a Copenhagen museum basement — after a fruitless search among the archaeological sites of Peary Land. The first genome sequence of an ancient human is reported. It comes from an approximately 4,000-year-old permafrost-preserved hair from a male from the first known culture to settle in Greenland. Functional single-nucleotide polymorphism (SNP) assessment is used to assign possible phenotypic characteristics and high-confidence SNPs are compared to those of contemporary populations to find those most closely related to the individual.

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mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters

2013-04-23

Hákon Jónsson , Aurélien Ginolhac , Mikkel Schubert +2 more

Abstract Motivation: Ancient DNA (aDNA) molecules in fossilized bones and teeth, coprolites, sediments, mummified specimens and museum collections represent fantastic sources of information for evolutionary biologists, revealing the agents of … Abstract Motivation: Ancient DNA (aDNA) molecules in fossilized bones and teeth, coprolites, sediments, mummified specimens and museum collections represent fantastic sources of information for evolutionary biologists, revealing the agents of past epidemics and the dynamics of past populations. However, the analysis of aDNA generally faces two major issues. Firstly, sequences consist of a mixture of endogenous and various exogenous backgrounds, mostly microbial. Secondly, high nucleotide misincorporation rates can be observed as a result of severe post-mortem DNA damage. Such misincorporation patterns are instrumental to authenticate ancient sequences versus modern contaminants. We recently developed the user-friendly mapDamage package that identifies such patterns from next-generation sequencing (NGS) sequence datasets. The absence of formal statistical modeling of the DNA damage process, however, precluded rigorous quantitative comparisons across samples. Results: Here, we describe mapDamage 2.0 that extends the original features of mapDamage by incorporating a statistical model of DNA damage. Assuming that damage events depend only on sequencing position and post-mortem deamination, our Bayesian statistical framework provides estimates of four key features of aDNA molecules: the average length of overhangs (λ), nick frequency (ν) and cytosine deamination rates in both double-stranded regions () and overhangs (). Our model enables rescaling base quality scores according to their probability of being damaged. mapDamage 2.0 handles NGS datasets with ease and is compatible with a wide range of DNA library protocols. Availability: mapDamage 2.0 is available at ginolhac.github.io/mapDamage/ as a Python package and documentation is maintained at the Centre for GeoGenetics Web site (geogenetics.ku.dk/publications/mapdamage2.0/). Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online.

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Bayesian Coalescent Inference of Past Population Dynamics from Molecular Sequences

2005-02-09

Alexei J. Drummond

We introduce the Bayesian skyline plot, a new method for estimating past population dynamics through time from a sample of molecular sequences without dependence on a prespecified parametric model of … We introduce the Bayesian skyline plot, a new method for estimating past population dynamics through time from a sample of molecular sequences without dependence on a prespecified parametric model of demographic history. We describe a Markov chain Monte Carlo sampling procedure that efficiently samples a variant of the generalized skyline plot, given sequence data, and combines these plots to generate a posterior distribution of effective population size through time. We apply the Bayesian skyline plot to simulated data sets and show that it correctly reconstructs demographic history under canonical scenarios. Finally, we compare the Bayesian skyline plot model to previous coalescent approaches by analyzing two real data sets (hepatitis C virus in Egypt and mitochondrial DNA of Beringian bison) that have been previously investigated using alternative coalescent methods. In the bison analysis, we detect a severe but previously unrecognized bottleneck, estimated to have occurred 10,000 radiocarbon years ago, which coincides with both the earliest undisputed record of large numbers of humans in Alaska and the megafaunal extinctions in North America at the beginning of the Holocene.

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Patterns of damage in genomic DNA sequences from a Neandertal

2007-08-22

Adrian W. Briggs , Udo Stenzel , Philip L. Johnson +7 more

Many waterbodies across the United States do not meet water quality standards. To help determine where and to what extent improvements should be sought, policymakers must consider the costs of … Many waterbodies across the United States do not meet water quality standards. To help determine where and to what extent improvements should be sought, policymakers must consider the costs of regulations with their monetized values. We ...Scientific knowledge related to quantifying the monetized benefits for landscape-wide water quality improvements does not meet current regulatory and benefit–cost analysis needs in the United States. In this study we addressed this knowledge gap by ...

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Chelex 100 as a Medium for Simple Extraction of DNA for PCR-Based Typing from Forensic Material

2013-03-01

P. Sean Walsh , David A. Metzger , Russell Higuchi

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 … 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.

Identifying Personal Genomes by Surname Inference

2013-01-17

Melissa Gymrek , Amy L. McGuire , David E. Golan +2 more

Sharing sequencing data sets without identifiers has become a common practice in genomics. Here, we report that surnames can be recovered from personal genomes by profiling short tandem repeats on … Sharing sequencing data sets without identifiers has become a common practice in genomics. Here, we report that surnames can be recovered from personal genomes by profiling short tandem repeats on the Y chromosome (Y-STRs) and querying recreational genetic genealogy databases. We show that a combination of a surname with other types of metadata, such as age and state, can be used to triangulate the identity of the target. A key feature of this technique is that it entirely relies on free, publicly accessible Internet resources. We quantitatively analyze the probability of identification for U.S. males. We further demonstrate the feasibility of this technique by tracing back with high probability the identities of multiple participants in public sequencing projects.

The Genetic Legacy of Paleolithic <i>Homo sapiens sapiens</i> in Extant Europeans: A Y Chromosome Perspective

2000-11-10

Ornella Semino , Giuseppe Passarino , Peter J. Oefner +7 more

A genetic perspective of human history in Europe was derived from 22 binary markers of the nonrecombining Y chromosome (NRY). Ten lineages account for >95% of the 1007 European Y … A genetic perspective of human history in Europe was derived from 22 binary markers of the nonrecombining Y chromosome (NRY). Ten lineages account for >95% of the 1007 European Y chromosomes studied. Geographic distribution and age estimates of alleles are compatible with two Paleolithic and one Neolithic migratory episode that have contributed to the modern European gene pool. A significant correlation between the NRY haplotype data and principal components based on 95 protein markers was observed, indicating the effectiveness of NRY binary polymorphisms in the characterization of human population composition and history.

Genome-wide patterns of selection in 230 ancient Eurasians

2015-11-23

Iain Mathieson , Iosif Lazaridis , Nadin Rohland +7 more

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Ancient DNA and the rewriting of human history: be sparing with Occam’s razor

2016-01-11

Marc Haber , Massimo Mezzavilla , Yali Xue +1 more

Ancient DNA research is revealing a human history far more complex than that inferred from parsimonious models based on modern DNA. Here, we review some of the key events in … Ancient DNA research is revealing a human history far more complex than that inferred from parsimonious models based on modern DNA. Here, we review some of the key events in the peopling of the world in the light of the findings of work on ancient DNA.

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The genetic history of Ice Age Europe

2016-04-29

Qiaomei Fu , Cosimo Posth , Mateja Hajdinjak +7 more

Genomic insights into the origin of farming in the ancient Near East

2016-07-25

Iosif Lazaridis , Dani Nadel , Gary O. Rollefson +7 more

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The Simons Genome Diversity Project: 300 genomes from 142 diverse populations

2016-09-20

Swapan Mallick , Heng Li , Mark Lipson +7 more

Theory and Practice of Histological Techniques

1996-01-01

Bruce A. Warren

Microsatellites: Evolution and Applications

1999-06-10

David B. Goldstein , Christian Schlötterer

Abstract Microsatellites are short stretches of repeated DNA, found in most genomes, that show exceptional variability in humans and most other species. This variability has made microsatellites the genetic marker … Abstract Microsatellites are short stretches of repeated DNA, found in most genomes, that show exceptional variability in humans and most other species. This variability has made microsatellites the genetic marker of choice for most applications, including genetic mapping and studies of the evolutionary connections between species and populations. This book brings together an international group of scientists currently working in microsatellites. Their contributions provide a detailed description of microsatellite biology, focusing on their mutation properties, generation, decay, and possible functional roles. They introduce the theoretical models that underpin the most popular methods for analysing the information that microsatellites can yield, including methods for estimating coalescent times, population divergences, and migration. Finally, the book describes the various ways in which the potential of microsatellites is being harnessed in a range of applications including medical genetics, forensics, genetic mapping, the analysis of human evolution, and conservation genetics.

Techniques of Lipidology

1973-07-01

D. N. BRINDLEY

MRBAYES: Bayesian inference of phylogeny

2001-01-01

John P. Huelsenbeck , Fredrik Ronquist

Techniques of Lipidology

1972-01-01

M. Kates

Ancient DNA reveals diverse community organizations in the 5th millennium BCE Carpathian Basin

2025-06-24

Anna Szécsényi‐Nagy , Cristian Virag , Kristóf Jakab +7 more | Nature Communications

Little is known about the genetic connection system and community organization of Late Neolithic and Early Copper Age populations of the Carpathian Basin. Here, we present a comprehensive genetic investigation … Little is known about the genetic connection system and community organization of Late Neolithic and Early Copper Age populations of the Carpathian Basin. Here, we present a comprehensive genetic investigation of these populations, leveraging whole genome data from 125 individuals. Using population genetics, kinship analyses and the study of networks of identity-by-descent haplotype segment sharing, we elucidate the social and genetic dynamics of these communities between 4800-3900 calibrated years BCE. Despite changes in settlement patterns, burial practices, and material culture, we document a high degree of genetic continuity. While one set of individuals from a large community cemetery is genetically diverse, another site is more homogenous and closed, with numerous consanguineous relationships and evidence of patrilineality and patrilocality. In this work, we document important differences in kinship systems in contemporaneous Early Copper Age communities using similar material culture and living only about 100 km apart.

Analysis of homogeneity in a historic coffin nail and screw assemblage for use in relative chronology

2025-06-20

Kayleigh Harvey , George M. Leader , Zachary D. Kline +4 more | North American Archaeologist

The historic burial ground (1722–1859) of the First Baptist Church of Philadelphia was excavated in 2016/17 as part of a development project. All human remains were reinterred in Mount Moriah … The historic burial ground (1722–1859) of the First Baptist Church of Philadelphia was excavated in 2016/17 as part of a development project. All human remains were reinterred in Mount Moriah Cemetery in 2024. The excavations recovered skeletal remains representing several hundred individuals (MNI = 354), Many of these individuals were recovered in coffins which were still in suitable condition to be documented. However, because the headstones were historically removed, dates are limited leaving artifacts and historical records to provide a time range of the sample's burial dates. Nails and screws collected from 206 of the coffins provide a unique opportunity to analyze a large sample of fasteners from a historic burial ground. This paper presents the results from a novel method of empirically driven analysis of the nails and screws in which we attempt to extract supplemental data to assist placing the coffin sample in a time range within the burial ground usage.

Should the police use genetic genealogy databases to assist in solving crime? Survey among university students

2025-06-20

Hannah Marlor , Kate Randall , Aaron Opoku Amankwaa | Forensic Science International Genetics

Genetic genealogy databases have been utilised as a novel tool by law enforcement to generate leads in difficult criminal investigations. This technique involves searching ancestry databases that contain voluntarily uploaded … Genetic genealogy databases have been utilised as a novel tool by law enforcement to generate leads in difficult criminal investigations. This technique involves searching ancestry databases that contain voluntarily uploaded DNA to identify genetic relatives of unknown suspects. The arrest of the notorious Golden State Killer using this method in 2018 brought the use of these techniques into the public eye. However, public perspectives on whether law enforcement should be granted access to this information is understudied. This study explored the attitudes towards police access to genetic genealogy amongst 373 university students through an online survey. Overall, students expressed moderate conditional support, with higher support levels for investigation of violent crimes (76 %) and crimes against children (78 %) compared to reluctant support for non-violent crimes (60 %). Women displayed greater support than men for police access (p < 0.05) in cases of violent crime (86 % vs. 75 %), crimes against children (87 % vs. 72 %), missing persons (84 % vs 76 %), and identifying human remains (88 % vs 78 %). Younger students aged 18-24 exhibited higher support for police access for violent crimes and missing persons cases than older students aged 35-50 (p < 0.05) (85 % vs. 76 %, and 86 % vs. 72 %, respectively). Qualitative findings emphasised participants' desire for oversight and protecting individual rights through warrant requirements to prevent overreach, whilst allowing societal benefits. This study provides initial evidence that educated young people recognise the potential forensic value of police access to genetic genealogy but favour strict regulations that reflect crime severity. This data can inform policy debates and legislative frameworks, balancing the utility and ethics of emerging genetic technologies. Further research across diverse populations is required to guide well informed legislations.

Revealing the range of equally likely estimates in the admixture model

2025-06-19

Carola Sophia Heinzel , Franz Baumdicker , Peter Pfaffelhuber | G3 Genes Genomes Genetics

Abstract Many ancestry inference tools, including structure and admixture, rely on the admixture model to infer both, allele frequencies p and individual admixture proportions q for a collection of individuals … Abstract Many ancestry inference tools, including structure and admixture, rely on the admixture model to infer both, allele frequencies p and individual admixture proportions q for a collection of individuals relative to a set of hypothetical ancestral populations. We show that under realistic conditions the likelihood in the admixture model is typically flat in some direction around a maximum likelihood estimate (q^,p^). In particular, the maximum likelihood estimator is non-unique and there is a complete spectrum of possible estimates. Common inference tools typically identify only a few points within this spectrum. We provide an algorithm which computes the set of equally likely (q~,p~), when starting from (q^,p^). It is analytic for K = 2 ancestral populations and numeric for K &gt; 2. We apply our algorithm to data from the 1000 genomes project, and show that inter-European estimators of q can come with a large set of equally likely possibilities. In general, markers with large allele frequency differences between populations in combination with individuals with concentrated admixture proportions lead to small areas with a flat likelihood. Our findings imply that care must be taken when interpreting results from STRUCTURE and ADMIXTURE if populations are not separated well enough.

Foren-STR: a comprehensive tool for rapid calculation of forensic parameters from autosomal STR data

2025-06-19

José Dionisio Castillo-Ortiz , Lizzette Salinas-Pineda , N. Sofía Huerta-Pacheco +1 more | International Journal of Legal Medicine

The Australian and New Zealand Forensic Science Society (ANZFSS) Western Australian Forensic Science Forum

2025-06-19

Simon W. Lewis | Australian Journal of Forensic Sciences

Comparison of Y-chromosomal STR profiles amplified using Yfiler™ Plus and Investigator Argus Y-28

2025-06-19

Penny L. Cooper , Colby M. Hymus , Marie S. Rye | Australian Journal of Forensic Sciences

A Mini Review of Short Tandem Repeat (STR) as DNA Profiling Markers in Forensic Biology

2025-06-18

Antonia Anindyanari Paramartastri Nitisara , Laurentia Henrieta Permita Sari Purba | Sainmatika Jurnal Ilmiah Matematika dan Ilmu Pengetahuan Alam

The use of forensic biology methods plays an important role in handling criminal cases such as sexual violence, murder, and assault to enhance the quality of criminal investigation. These methods … The use of forensic biology methods plays an important role in handling criminal cases such as sexual violence, murder, and assault to enhance the quality of criminal investigation. These methods use polymorphic genetic markers such as short tandem repeat (STR) or microsatellites to identify individuals based on the DNA profile of the cell nucleus left on the evidence. STR markers are considered suitable for forensic analysis due to their ability to work with degraded DNA and the high heterozygosity, providing strong discrimination capabilities. The DNA profiling process involves collecting evidence samples, DNA extraction, PCR amplification, capillary electrophoresis, and comparison with national or international DNA databases. All processes follow standards to ensure accurate results. Challenges in STR analysis include the need for skilled analysts, protocol updates, database expansion, and ethical considerations regarding genetic data. Improvements in the forensic system will enhance law enforcement effectiveness and strengthen public trust in the future of forensic science.

Application of quantitative absorption-elusion reaction for determining the group specificity of blood traces on material evidence

2025-06-18

A A Gusarov , E.P. Sabchuk , O D Yagmurov +1 more | Forensic Medical Expertise

The article shows the possibilities of improved version of quantitative absorption-elusion reaction (QAER) developed for determination of the blood traces’ group specificity on material evidence when the phenomenon of antibodies … The article shows the possibilities of improved version of quantitative absorption-elusion reaction (QAER) developed for determination of the blood traces’ group specificity on material evidence when the phenomenon of antibodies block occurs. A similar technique in the form of combination of two immunological reactions, namely absorption-elusion reaction (AER) and quantitative absorption reaction (QAR), was previously used only in the performance of forensic biological examinations of discharge traces. The conducted studies have shown the high efficiency of QAER for determining the group affiliation of blood traces: out of 197 studied objects with a negative CRA result, the presence of an antigen was established in 128 objects using quantitative accounting of the absorption phase, and in the remaining 69 objects, the truth of the negative CRA result was established — the absence of a group factor.

Utility of regional STR marker variations in Tunisian and sub-Saharan populations: insights into forensic and population genetics

2025-06-17

Asma Attaoui , Hajer Foddha , Houcemeddine Othman +2 more | Frontiers in Bioinformatics

Introduction This study investigates the genetic variability and forensic applicability of Short Tandem Repeat (STR) loci including autosomal, X and Y-STR markers, across distinct Tunisian regions and among sub-Saharan African … Introduction This study investigates the genetic variability and forensic applicability of Short Tandem Repeat (STR) loci including autosomal, X and Y-STR markers, across distinct Tunisian regions and among sub-Saharan African populations. Our objectives were to examine the regional allelic diversity of STR markers in Tunisia, and to assess the utility of these markers for forensic differentiation between Tunisian and sub-Saharan African. Methods Twenty two STRs were genotyped in 500 Tunisian individuals and 501 sub-Saharan corpses by capillary electrophoresis using commercial system kits. A Chi-square test for homogeneity was applied to assess allele distribution and Principal Component Analysis to assess geographical allele variations. Bioinformatic methods in R packages were used, such as Logistic Regression Model to predict geographic group membership and Random Forest models to evaluate the discriminative power of the analyzed STRs. Results and Discussion Statistical analyses revealed significant allelic variability between Northern, Central, and Southern Tunisia for markers such as D1S1656, D8S1179, and CSF1PO. PCA illustrated a clear genetic distinction between Tunisian and sub-Saharan populations, largely attributable to geographical and historical gene flow barriers. LRM achieved high accuracy (95.96%) in predicting geographic affiliation. RF analysis identified DYS391 as highly discriminative in population differentiation. Our findings align with prior research on Tunisian genetic diversity and extend this knowledge by illustrating allelic frequency variations in order to establish region-specific databases. Conclusion This study contributes valuable insights into the genetic structure of Tunisian and sub-Saharan populations, emphasizing tailored approaches in forensic practices.

Mitochondrial DNA HVRII (Poly-C) and HVRIII (Poly-CA) tandem repeat variation in the Koraga population

2025-06-17

Swathy Krishna , Jaison Jeevan Sequeira , Mohammed S. Mustak +1 more | Egyptian Journal of Medical Human Genetics

Abstract Background In situations where nuclear DNA samples are limited or degraded, mitochondrial DNA can be used as an alternative for forensic applications. The hypervariable (HVRIII) region located on the … Abstract Background In situations where nuclear DNA samples are limited or degraded, mitochondrial DNA can be used as an alternative for forensic applications. The hypervariable (HVRIII) region located on the D-loop of mitochondrial DNA has shown promise in forensic identification due to the presence of unique tandem repeats. In this study, we investigate the variation of Poly-C (HVRII) and Poly-CA repeats (HVRIII) in the Koraga population, a primitive tribe located along the southwestern coast of India. Findings We have identified length heteroplasmy in two specific regions (514–524 and 303–309 nucleotide positions) in the mitochondrial DNA of individuals from the Koraga tribe. Our analysis shows that the (CA)4 and C8 repeats are more frequent in the Koraga population. We have also observed that the Poly-C repeat has a higher discriminatory power (0.6499) compared to Poly-CA (0.5806). Based on the PCA results, the Koragas showed greater genetic affinity with East Asians than South Asians, with Kuntu Koragas clustering uniquely with Urali Kurumans and South Indian Muslims, Onti Koragas bridging the Soppu and Kuntu subgroups, highlighting the importance of studying each Koraga clan separately rather than as a uniform group. Conclusions Our findings suggest that the variations in the Poly-C and Poly-CA repeats in the D-loop of mitochondrial DNA can be used to complement current forensic identification methods. Additionally, our findings provide a new opportunity to investigate selection markers in mitochondrial DNA.

It’s Scarlet in the Study! Deciphering Toxic Pathologies in a Murder Mystery Party

2025-06-16

Michael DiGaetano , Colleen Donovan , Aarsh Shah +1 more | Western Journal of Emergency Medicine

Three-step forensic approach for the differentiation of human and pig fingernail-like fragments: macroscopic examination, raman spectroscopy and histogenetic analyses

2025-06-16

Marco Cummaudo , Silvia Bruni , Annalisa D’Apuzzo +6 more | International Journal of Legal Medicine

Y-mer: A k-mer based method for determining human Y chromosome haplogroups from ultra-low sequencing depth data

2025-06-16

Tarmo Puurand , Märt Möls , Lauris Kaplinski +5 more | Research Square (Research Square)

<title>Abstract</title> Determining genetic ancestry of an individual is challenging from poorly preserved or mixed samples that permit only ultra-low coverage sequence (ulcWGS) depth < 0.1x to be gained at target … <title>Abstract</title> Determining genetic ancestry of an individual is challenging from poorly preserved or mixed samples that permit only ultra-low coverage sequence (ulcWGS) depth < 0.1x to be gained at target loci. Leveraging the recent advances in telomere-to-telomere sequencing of the whole genomes with long reads we develop a new k-mer based method Y-mer and show how information from hundreds of thousands of k-mers in distance-based models enables accurate inference of chrY haplogroup from WGS sequence at depth less than 0.01x without additional PCR or capture. We test the performance of Y-mer on ancient DNA and prenatal screening data showing its potential for genetic ancestry inference for cell-free, forensic and ancient DNA research from short read WGS data.

Genetic Polymorphisms of 16 X‐STR Loci in the Yi Ethnic Minority of Chuxiong Yi Autonomous Prefecture in Yunnan Province in China

2025-06-16

Linlin Liu , Hecheng Zheng , Tiantian Zou +5 more | Annals of Human Genetics

ABSTRACT Background To study the genetic characteristics of X‐chromosome short tandem repeats (X‐STRs) in the Yunnan Yi ethnic minority. Methods We analyzed the allele frequencies and forensic parameters for 16 … ABSTRACT Background To study the genetic characteristics of X‐chromosome short tandem repeats (X‐STRs) in the Yunnan Yi ethnic minority. Methods We analyzed the allele frequencies and forensic parameters for 16 X‐STR loci in 432 unrelated Yi individuals (206 males and 226 females) in Chuxiong Yi Autonomous Prefecture, Yunnan Province. Results A total of 130 alleles were detected. Except for DXS6800, the other loci are highly polymorphic in the Yunnan Yi ethnicity. The combined values of discrimination for males (PDM) and females (PDF) were 0.999999999968561 and 0.999999999999993, respectively, which can be used for forensic medical identification and genetic studies. On the basis of the results of population comparison, there seems to be a relatively close evolutionary relationship between adjacent populations and different ethnic groups in the same region. Conclusions This study contributes to X‐chromosome genetic polymorphism data for the Yunnan Yi ethnicity and further enriches reference materials on the Chinese Yi ethnic minority.

Revolutionizing DNA Analysis: The Impact of Rapid DNA Sequencing on Modern Forensic Investigations

2025-06-12

Abubakr Muhammad | IntechOpen eBooks

This chapter explains how fast DNA sequencing is revolutionizing forensic science and making the process of criminal investigations much more accurate and efficient. The evolution of DNA analysis tools has … This chapter explains how fast DNA sequencing is revolutionizing forensic science and making the process of criminal investigations much more accurate and efficient. The evolution of DNA analysis tools has made the identification of individuals connected to crime cases significantly easier. With real-time DNA profiling, rapid sequencing cuts processing times from days to hours, making it highly useful in time-sensitive situations. Examples such as solving cold cases, identifying disaster victims, and analyzing crime scenes exemplify the revolutionary potential. The chapter also discusses the challenges in integrating rapid DNA sequencing into forensic workflows, such as data security, privacy, and ethical implications. These challenges raise the need for strong protocols and guidelines to ensure responsible use. Despite these challenges, rapid sequencing holds great promise for advancing modern criminal justice systems, offering faster and more reliable solutions to longstanding investigative challenges. This chapter underlines how bridging technology and forensic science can help shape the future of criminal investigations to foster a more effective and just legal system by bridging this gap.

Fenotipado Forense de ADN: Desafíos Jurídicos en la Investigación Criminal y su Aplicación en Europa

2025-06-10

A Boldó | Revista de Derecho y Genoma Humano Genética Biotecnología y Medicina Avanzada

El Fenotipado Forense de ADN (en adelante, FDP) es una tecnología avanzada en el ámbito de la ciencia forense que permite predecir características externamente visibles de un individuo a partir … El Fenotipado Forense de ADN (en adelante, FDP) es una tecnología avanzada en el ámbito de la ciencia forense que permite predecir características externamente visibles de un individuo a partir de perfiles genéticos obtenidos de muestras biológicas. Sistemas como Parabon Snapshot y el proyecto europeo VISAGE han demostrado la eficacia del FDP en investigaciones criminales, facilitando la identificación de sospechosos y personas desaparecidas. Sin embargo, su adopción y aplicación plantean importantes desafíos éticos y legales, especialmente en relación con el derecho a la intimidad y la protección de datos personales, conforme al Reglamento General de Protección de Datos (RGPD). En particular, se examina el artículo 9 del RGPD, que regula el tratamiento de datos personales sensibles, como aquellos que revelan el origen étnico o racial, y requiere medidas de protección reforzadas. Este artículo evalúa cómo el tratamiento de los datos genéticos mediante FDP puede ser compatible en casos de interés público esencial, siempre que se respeten los principios de proporcionalidad y necesidad para garantizar los derechos fundamentales. Además, se analiza el Reglamento Prüm II, que ha entrado en vigor recientemente y que amplía la cooperación policial en la Unión Europea mediante el intercambio automatizado de perfiles de ADN y otros datos, centrándonos especialmente en los datos biométricos. Este Reglamento plantea la posibilidad de integrar el FDP como una herramienta clave para mejorar la identificación de sospechosos y personas desaparecidas en el contexto de la investigación criminal, así como para la gestión e intercambio de datos genéticos.

Allele frequencies and forensic parameters based upon 23 Autosomal STRs loci of 406 Cambodian individuals in Thailand

2025-06-10

Nutthapicha Siripatoomrut , Tayawee Romgaew , Sunisa Aobaom | International Journal of Legal Medicine

Phase-free local ancestry inference mitigates the impact of switch errors on phase-based methods

2025-06-05

Siddharth Avadhanam , Amy L. Williams | G3 Genes Genomes Genetics

Abstract Local ancestry inference (LAI) is an indispensable component of a variety of analyses in medical and population genetics, from admixture mapping to characterizing demographic history. However, the accuracy of … Abstract Local ancestry inference (LAI) is an indispensable component of a variety of analyses in medical and population genetics, from admixture mapping to characterizing demographic history. However, the accuracy of LAI depends on a number of factors such as phase quality (for phase-based LAI methods) and time since admixture. Here we present an empirical analysis of four LAI methods using simulated individuals of mixed African and European ancestry, examining the impact of variable phase quality and a range of demographic scenarios. We find that regardless of phasing options, calls from LAI methods that operate on unphased genotypes (phase-free LAI) have 2.6-4.6% higher Pearson correlation with the ground truth than methods that operate on phased genotypes (phase-based LAI). Applying the TRACTOR phase-correction algorithm led to modest improvements in phase-based LAI, but despite this, the Pearson correlation of phase-free LAI remains 2.4-3.8% higher than phase-corrected phase-based approaches (considering the best performing methods in each category). Further, analyzing perfectly phased data yields accuracies for the phase-based LAI methods that are only slightly inferior to those of HAPMIX. Phase-free and phase-based LAI accuracy differences can dramatically impact downstream analyses: estimates of the time since admixture using phase-based LAI tracts are upwardly biased by ≈10 generations using our highest quality statistically phased data but have virtually no bias using phase-free LAI calls. This study underscores the strong dependence of phase-based LAI accuracy on phase quality and highlights the merits of LAI approaches that analyze unphased genetic data.

Ancient DNA reveals a two-clanned matrilineal community in Neolithic China

2025-06-04

Jincheng Wang , Shi Yan , Zhenguang Li +7 more | Nature

Genetic formation of Neolithic Hongshan people and demic expansion of Hongshan culture inferred from ancient human genomes

2025-06-04

Rui Wang , Liwu Zhu , Hao Ma +7 more | Molecular Biology and Evolution

Abstract The Hongshan culture, situated at the crossroads of northern and northeast China, represented one of the earliest complex societies in Neolithic East Asia. The remains of Hongshan culture have … Abstract The Hongshan culture, situated at the crossroads of northern and northeast China, represented one of the earliest complex societies in Neolithic East Asia. The remains of Hongshan culture have been found in an area stretching from today’s Inner Mongolia Autonomous Region to Liaoning Province, covering an area of over 200,000 square kilometers. However, the question of how Hongshan culture occupied such a vast geographical location, following either the demic diffusion (i.e., genetic interaction accompanied by cultural expansion) or cultural diffusion model (i.e., local groups adopting new culture without receiving genetic influence), remains unanswered due to a lack of ancient genomes. Here, we report genome-wide data from 19 individuals associated with the Hongshan culture, from the Zhengjiagou site in Hebei Province, the westernmost and southernmost Hongshan culture-related site discovered to date. We co-analyzed our newly generated Hebei Hongshan genomes with previously published 3 Hongshan culture-related genomes from the Banlashan site in Liaoning Province, located in the core region of Hongshan culture and about 473 km away from the Zhengjiagou site. Our genetic results revealed strong genetic links between the Hebei Hongshan and Liaoning Hongshan people, supporting the demic diffusion of the Hongshan culture. Both Liaoning and Hebei Hongshan people harboured Ancient Northeast Asian-related (possibly related to the local earlier Zhaobaogou culture) and Neolithic Yangshao culture-related millet farmer ancestries. Interestingly, our ancestral modelling suggested that Yangshao culture-related ancestry in the Hongshan people was more likely introduced by middle Neolithic Dawenkou culture-related farmers from Shandong, who carried about 40% of an early Neolithic Shandong hunter-gatherer-related lineage and 60% of a Yangshao culture-related lineage. Our findings highlight a complex interconnected gene pool among the West Liao River, the Central Plain, and Shandong during the middle Neolithic period.

YanHuang Paternal Genomic Resource Suggested A Weakly-Differentiated Multi-Source Admixture Model for the Formation of Han’s Founding Ancestral Lineages

2025-06-04

Zhiyong Wang , K. F. Liu , Haibing Yuan +7 more | Genomics Proteomics & Bioinformatics

Chronology of forensic bloodstain age estimation using UV–vis spectroscopy—A comprehensive review

2025-06-01

Tommy Bergmann , Dirk Labudde , Aurélien Thomas +1 more | Forensic Science International

Forensic Genomic Analysis: A Force Multiplier for Law Enforcement

2025-06-01

Gail Dutton | Genetic Engineering & Biotechnology News

Interview with Dr. Lutz Roewer, Pioneer of Y-STR DNA Analysis

2025-06-01

Nicole M.M. Novroski | Forensic Genomics

The 30-100 patrilineal nomenclature system for eastern Eurasian populations.

2025-06-01

Hui-Xin Yu , Xianpeng Zhang , Lan‐Hai Wei | PubMed

Due to the universality of human patrilineal societies, strict adherence to the patrilineal inheritance law, and a relatively fast mutation rate (about one new branch every 70 years), the non-recombining … Due to the universality of human patrilineal societies, strict adherence to the patrilineal inheritance law, and a relatively fast mutation rate (about one new branch every 70 years), the non-recombining region of the human Y-chromosome (NRY) can rapidly accumulate specific patrilineal branches that are specific to certain region, population, family, and family branch, making the Y-chromosome one of the powerful tools for studying the evolutionary history of human populations. However, early studies typically only included a limited number of SNP loci, and the classification systems in different articles varied, resulting in insufficient resolution for the evolutionary process of populations. Since 2015, with the rapid accumulation of whole-genome sequence data, the resolution of the human Y chromosome phylogenetic tree at the population level has approached its limit. In this study, we analyze the relevant research on the human Y chromosome in the past 30 years. Based on the currently highly detailed data, we identify 50 major patrilineal types or founder patrilineal types that are directly related to the origin and evolution of 16 population groups in eastern Eurasia. Furthermore, we construct a 30-100 classification system that is compatible with the diverse traditional classification systems in the past 30 years and the current most detailed phylogenies. This system takes into account both the macroscopic genetic structure of eastern Eurasian populations over a timescale of tens of thousands of years and the specific lineages directly related to the several-thousand-year history of modern ethnic groups, laying the foundation for more precise studies of the evolutionary process of ancient and modern populations in the future.

AMY2 Gene Copy Number Variation as a Marker of Genetic Diversity in Kurds

2025-06-01

Forensic applications of compound genetic markers: trends and future directions

2025-06-01

Sthabile Shabalala , Nahed Ismail , Meenu Ghai | Science & Justice

DNA forensics at forty: the way forward

2025-05-31

Hirak Ranjan Dash , Noora R. Al-Snan | International Journal of Legal Medicine

Mitochondrial ancestry from complete mitogenomes highlights a lack of characterization of indigenous haplogroups in Brazilian Amazon population

2025-05-30

Felipe Gouvêa de Souza , Gustavo Barra Matos , Cristina Santos +7 more | Communications Biology

Mitochondrial genome is an essential resource to investigate the dispersion and diversification of human populations. However, the lack of genomic data from non-European ancestry hinders demographic, anthropologic and genetic studies. … Mitochondrial genome is an essential resource to investigate the dispersion and diversification of human populations. However, the lack of genomic data from non-European ancestry hinders demographic, anthropologic and genetic studies. Indigenous people from the Brazilian Amazon are especially underrepresented among large genetic datasets, despite their significative contribution to the Brazilian genetic pool. We investigated 157 mitochondrial genomes from the Brazilian Amazon using bioinformatics tools for ancestry inference and phylogenetics. Results were compared with 2578 global mitogenomes to assess haplogroup frequencies and genetic distances. Thirteen macrohaplogroups were identified from investigated samples, including Indigenous, European and African ancestries. Despite being prominent in our sample, Indigenous haplogroup assignment confidence by prediction tools was lower and many samples lacked key-defining variants, suggesting misassignment due to low representation in reference datasets. We also identified potential new groups sharing specific variants. Thus, underrepresentation of Indigenous haplogroups contributes to phylogenetic inconsistencies and needs future investigations.

Prehistoric genomes from Yunnan reveal ancestry related to Tibetans and Austroasiatic speakers

2025-05-29

Tianyi Wang , Melinda A. Yang , Z.M. Zhu +7 more | Science

The human landscape in East and Southeast Asia is vastly complex, and successful retrieval of genome-wide data from prehistoric humans of southern East Asia is sparse. We successfully sampled 127 … The human landscape in East and Southeast Asia is vastly complex, and successful retrieval of genome-wide data from prehistoric humans of southern East Asia is sparse. We successfully sampled 127 ancient human genomes from southwestern China. A 7100-year-old female individual from central Yunnan shows a previously unsampled Basal Asian ancestry related to a ghost population that contributed to Tibetan Plateau populations. Central Yunnan populations dating to 5500 to 1400 years before present show an East Asian ancestry distinct from northern or southern East Asian ancestries that contributed to present-day East and Southeast Asians, particularly Austroasiatic speakers, and emphasizes the importance of the Red River valley for proto-Austroasiatic population history. Diverse Asian ancestries are represented in humans sampled from Yunnan, clarifying past population dynamics related to both Tibetan and Austroasiatic origins.