Forensic and Genetic Research

Three Reagents for in-Solution Enrichment of Ancient Human DNA at More than a Million SNPs

The paper tests three reagents for in-solution enrichment of ancient human DNA and introduces a subset of SNPs that can be co-analyzed with shotgun data.

Admixture has obscured signals of historical hard sweeps in humans

The paper shows that admixture in modern European genomes has masked over 50 historic hard sweeps, suggesting underappreciation of historical selection in human evolution.

Genomic detection of a secondary family burial in a single jar coffin in early Medieval Korea

The paper uses genome-wide data to analyze the genetic relationships of six early Medieval Korean individuals buried together in a jar coffin, finding they form an extended family with no significant genetic change over 1,500 years.

KIN: A method to infer relatedness from low-coverage ancient DNA

KIN estimates relatedness from low-coverage ancient DNA by analyzing identical-by-descent segments, accurately classifying up to 3rd-degree relatives and distinguishing siblings from parent-child.

Genetic admixture history and forensic characteristics of Tibeto-Burman-speaking Qiang people explored via the newly developed Y-STR panel and genome-wide SNP data

Developmental Validation of the Illumina Infinium Assay using the Global Screening Array (GSA) on the iScan System for use in Forensic Laboratories

This study validates the Illumina Infinium assay using the Global Screening Array (GSA) for forensic applications according to SWGDAM guidelines, showing high SNP call rates and sample quality assessment methods.

sstar: A Python package for detecting archaic introgression from population genetic data with S*

sstar is a Python package that improves detection of archaic introgression in population genetic data by being robust to different demographic models.

Associations between forensic loci and neighboring gene expression levels may compromise medical privacy

The paper investigates whether forensic STRs correlate with gene expression levels, finding six significant associations that may compromise medical privacy.

A benchmarking of human Y-chromosomal haplogroup classifiers from whole-genome and whole-exome sequence data

The paper benchmarks five Y-chromosomal haplogroup classifiers using whole-genome and whole-exome sequencing data, finding YLeaf performs best for both and handles third-generation sequencing data effectively.

The genomic landscape of contemporary western Remote Oceanians

This study analyzes genome-wide data from 1,433 ni-Vanuatu individuals to trace their genetic ancestry and admixture history, revealing synchronous admixture events and social assortative mating patterns.

Comprehensive analysis of microsatellite polymorphisms in human populations

This study analyzes 8.5 million microsatellite regions across three human genome datasets, identifies polymorphic sites, and demonstrates their utility in population genetics and individual identification.

Genetic structure correlates with ethnolinguistic diversity in eastern and southern Africa

This study examines genetic structure in African populations using ethnolinguistic data, finding that language classifications better capture genetic variation than geography alone.

Fast and Accurate Kinship Estimation Using Sparse SNPs in Relatively Large Database Searches

The paper introduces a windowed kinship algorithm using sparse SNPs to estimate kinship in forensic genetics, achieving performance comparable to segment matching with fewer false associations.

Archetypal Analysis for Population Genetics

This paper introduces Archetypal Analysis for efficient genetic clustering, showing it outperforms ADMIXTURE in speed and interpretability across human and canid datasets.

ERStruct: A Python Package for Inferring the Number of Top Principal Components from Whole Genome Sequencing Data

ERStruct estimates the number of top principal components from whole-genome sequencing data using parallel computing and GPU acceleration.

Assessing human genome-wide variation in the Massim region of Papua New Guinea and implications for the Kula trading tradition

The paper analyzes genome-wide variation in the Massim region of Papua New Guinea, finding genetic patterns linked to the Kula trading tradition and suggesting genetic similarity among Kula-practicing groups.

An efficient method to identify, date and describe admixture events using haplotype information

fastGLOBETROTTER identifies, dates, and describes admixture events using haplotype information, revealing new admixture signals in European populations.

Characterization of the Y Chromosome in Newfoundland and Labrador: Evidence of a Founder Effect

The paper analyzes Y chromosome data from Newfoundland and Labrador to show genetic evidence of a founder effect, with haplotypes primarily from English and Irish sources and some contributions from Basque, French, Portuguese, and Spanish populations.

Simultaneous inference of parental admixture proportions and admixture times from unphased local ancestry calls

PAPI infers parental admixture proportions and times from unphased local ancestry data, outperforming ANCESTOR in simulations and showing assortative mating in real data.

Quantitative Evaluation of Nonlinear Methods for Population Structure Visualization & Inference

This paper evaluates nonlinear methods for visualizing and inferring population structure, finding graph-based algorithms like t-SNE and UMAP outperform PCA while neural networks perform worse.

Imputation of ancient genomes

This study evaluates the accuracy of genotype imputation for ancient genomes and finds it comparable to modern DNA, with some population-specific biases.

Estimating the timing of multiple admixture events using 3-locus Linkage Disequilibrium

The paper develops a method to estimate multiple admixture events using 3-locus linkage disequilibrium, demonstrating its accuracy on simulated data and applying it to Colombian and Mexican populations.

Hamiltonian Monte Carlo with strict convergence criteria reduces run-to-run variability in forensic DNA mixture deconvolution

This paper introduces a Hamiltonian Monte Carlo algorithm with strict convergence criteria to reduce run-to-run variability in forensic DNA mixture deconvolution without increasing runtime.

The Entwined African and Asian Genetic Roots of the Medieval Peoples of the Swahili Coast

This study analyzes ancient DNA from the Swahili coast to trace genetic admixture between African and Asian populations over time.

IBD-based estimation of X chromosome effective population size with application to sex-specific demographic history

The paper estimates X chromosome effective population size using IBD segments and applies it to infer sex-specific demographic history from UK Biobank data.

Reconstructing the genetic history of Kra-Dai speakers from Thailand

This study re-analyzes genetic data from Thailand to challenge previous conclusions about the genetic continuity between Kra-Dai speakers and Austroasiatic populations, revealing a more complex genetic history.

Genomic evidence for ancient migration routes along South America's Atlantic coast

The paper analyzes ancient genomes from Northeast Brazil and compares them to other ancient and present-day data, revealing migration routes along South America's Atlantic coast and unexpected ancestry signals.

Between fishing and farming: palaeogenomic analyses reveal cross-cultural interactions triggered by the arrival of the Neolithic in the Danube Gorges

The paper reports admixture between Neolithic farmers and Mesolithic hunter-gatherers in the Danube Gorges, supported by palaeogenomic analysis and archaeological findings.

hapCon: Estimating contamination of ancient genomes by copying from reference haplotypes

hapCon estimates contamination in ancient DNA by analyzing male X chromosomes, outperforming existing tools in low coverage regimes.

Assessing temporal and geographic contacts across the Adriatic Sea through the analysis of genome-wide data from Southern Italy

The paper analyzes genome-wide SNP data from Southern Italy and neighboring regions to assess historical contacts and genetic affinities across the Adriatic Sea.