Forensic and Genetic Research

X-Chromosomal STR-based analysis of genetic diversity, structure, and phylogeny in the Sri Lankan Vedda population

This study analyzes X-chromosomal STR diversity in the Vedda population, finding significant genetic differentiation from other South Asian groups and highlighting their unique genetic heritage.

A 4,000-year genomic history of Bantu speakers from the Congo rainforest

This study uses genomic data from ancient and present-day individuals to trace the 4,000-year demographic history of Bantu speakers in the Congo rainforest, revealing early dispersals and a population crisis.

Promises and limitations of current ancient human epigenetic clocks

This study evaluates epigenetic clocks for age estimation in ancient human DNA, finding they are unreliable for continuous age-at-death but accurate for sex determination.

Ancient genomes chronicle the history of adaptive evolution in East Asia

This study uses ancient genomes to analyze adaptive evolution in East Asia, finding pre-Neolithic selection at key loci and a link between ADH1B*48His and wheat farming.

mixKIN: An ancestry-aware kinship estimation method for low coverage genomes

mixKIN improves kinship estimation from low-coverage genomes by accounting for ancestry, outperforming existing methods in admixed and heterogeneous populations.

A versatile set of computational tools for inference of genetic ancestry from human molecular data

The paper introduces RAIDS, a toolset for inferring genetic ancestry from various sequence data, including cancer and low-coverage scenarios.

Ancient Mitogenomes from Belize Provide Insights into the Mobility and Migration of Ancient Communities in Mesoamerica and the Caribbean.

The paper analyzes ancient mitogenomes from Belize to study maternal genetic continuity and mobility patterns among ancient Maya populations and their relation to present-day communities.

Recomb-Mix Cloud: a cost-efficient and scalable cloud-friendly pipeline for local ancestry inference

On the All of Us workbench, a Recomb-Mix-based cloud pipeline runs whole-genome local ancestry inference for an estimated $0.01 per sample, versus $0.43 for FLARE and $4.58 for RFMix.

Forensic likelihood ratios for shotgun sequencing data from DNA mixtures

The paper develops likelihood ratios for forensic DNA mixtures from shotgun sequencing data, showing they can be unreliable and proposing a combined evidence score to improve accuracy.

In which cases does it make sense to classify an individual into one population and what are the alternatives?

The paper evaluates methods to classify individuals into populations using ancestry informative markers, finding a naive Bayes classifier performs best in identifying out-of-reference individuals.

LoGicAl: Local ancestry and genotype calling uncertainty-aware ancestry-specific allele frequency estimation from admixed samples

LoGicAl estimates ancestry-specific allele frequencies from admixed samples by accounting for uncertainty in local ancestry and genotype calling, improving accuracy and scalability.

Migrations facilitated the cultural diffusion of megaliths in Neolithic Europe

The paper investigates whether the spread of megaliths in Neolithic Europe was due to population movements or cultural diffusion, finding that both factors interacted through trade networks.

Genetic Basis of Social Structure in the Pastoral Nomads of Central Eurasia

The paper examines the genetic basis of social structure in Kazak pastoral nomads, finding concordance between genetic and genealogical data, sex-biased admixture, and reduced runs of homozygosity linked to clan exogamy.

Stairway Plot v3: Nonparametric Demographic Inference from the Site Frequency Spectrum at Biobank Scale

Stairway Plot v3 infers nonparametric effective population size trajectories from the site frequency spectrum at biobank scale, achieving high resolution with large samples.

The DNA Legacy of Thomas Jefferson

This study uses DNA from museum hair samples to confirm Thomas Jefferson's ancestry in descendants of Sally Hemings and Martha Wayles Jefferson, supporting paternity over alternative explanations.

LAYERED GENOMIC COMPOSITION AND LINGUISTIC CONTINUITY IN GRECIA SALENTINA

The paper uses whole genome sequencing to analyze the genetic structure of a Greek-speaking community in Southern Italy, finding no strong evidence for external origins and supporting a model of continuous gene flow.

An archaic reference-free method to jointly infer Neanderthal and Denisovan introgressed segments in modern human genomes

DAIseg is a new HMM-based method that detects both Neanderthal and Denisovan introgression in modern human genomes without archaic references, outperforming existing methods in Papuan populations.

Matched full-UDG and non-UDG ancient DNA libraries reveal trade-offs in post-mortem damage correction for imputation and kinship inference

The paper compares damage correction methods for ancient DNA libraries to assess their impact on imputation and kinship inference.

Co-mutation based genetic networks to infer temporal mutation dynamics in ancient human mitochondrial genomes

The paper uses co-mutation networks to analyze ancient human mitochondrial DNA, revealing lifestyle transitions and genetic selection patterns across different ages.

DNAharvester: A Nextflow Pipeline for Analysing Highly Degraded DNA from Ancient and Historical Specimens

DNAharvester is a Nextflow pipeline designed to process highly degraded DNA from ancient specimens, improving authentic data recovery through modular workflows and contamination mitigation.

Holocene North Asian gene flow and cryptic substructure in the genome history of Nilgiri tribes

This study analyzes the genomic history of Nilgiri tribes, revealing fine-scale substructure and complex Holocene gene flow patterns.

Activity-level evaluation of DNA transfer to stockings: comparisonof HaloGen with simplified contributor-based approaches

This paper evaluates DNA transfer to stockings using HaloGen, showing its ability to distinguish active contact from social contact, while simplified methods lose important information.

SweepLink: Joint Inference of Demography and Linked~Selection from Time-series Data

SweepLink jointly infers demography and linked selection from time-series data, improving detection of selection signals compared to single-locus methods.

Joint ancestry inference reveals the landscape of archaic introgression in admixed populations

TRACTINATOR infers continental and archaic ancestry in admixed genomes using deep learning, revealing archaic introgression patterns in Latin American populations.

Recovering the pre-colonial population structure of Khoe-San descendant populations

The paper analyzes genetic ancestry in South African Coloured groups to reveal persistent Khoe-San ancestry and traces Indian Ocean slave trade signatures.

Evaluating rapid extraction methods for recovering ancient DNA from archaeological sediments

This paper evaluates rapid DNA extraction methods for ancient DNA recovery from sediments, finding that an Amicon-based method outperforms others in recovering short and modern-simulated aDNA from various sediment types.

Computing coalescence rates for complex demographies and sampling configurations

The paper introduces demestats, a software library to compute coalescence rates for demographic models, showing improved accuracy in inferring recent population history from genetic data.

Genomic impact of the second plague pandemic on three human populations

This study analyzes ancient DNA from three European sites to assess the genomic impact of the second plague pandemic, finding no strong positive selection but evidence of reduced long-range immigration post-pandemic.

The Influence of Demographic History and Genetic Architecture on Complex Traits via Runs of Homozygosity

This study investigates how population history and genetic architecture affect the association between runs of homozygosity (ROH) and complex traits using simulations.

ADVANCING GENOTYPE IMPUTATION IN ANCIENT GENOMES USING A REGION-SPECIFIC REFERENCE PANEL AND BENCHMARK GENOTYPES

This paper improves genotype imputation for ancient genomes using a region-specific reference panel and benchmark genotypes, showing enhanced accuracy and revealing genetic differentiation linked to cultural differences.