Forensic and Genetic Research

Technical Report on Ancient DNA analysis of 27 African Americans from Catoctin Furnace, Maryland

This report documents the successful extraction and analysis of ancient DNA from 27 African American individuals buried at Catoctin Furnace, Maryland, as part of a study on the enslaved and free African American population there.

Ancient genomes from the last three millennia support multiple human dispersals into Wallacea

The paper analyzes ancient genomes from Wallacea to show multiple human dispersals, with southern islands showing earlier Asian contributions than previously thought.

Genomic Insights of Bruneian Malays

This study analyzes the genomes of Bruneian Malays using WGS and genotyping data, identifying novel variants and genomic sequences, and revealing genetic relationships with Filipino groups.

Kernel Local Fisher Discriminant Analysis of Principal Components (KLFDAPC) significantly improves the accuracy of predicting geographic origin of individuals

KLFDAPC improves geographic origin prediction by enhancing population separability and accuracy compared to PCA and DAPC.

Polygenic score accuracy in ancient samples: quantifying the effects of allelic turnover

This paper quantifies how allelic turnover affects polygenic score accuracy in ancient samples using theoretical models and simulations.

Tracing genetic connections of ancient Hungarians to the 6-14th century populations of the Volga-Ural region

The paper analyzes ancient genetic data to trace the genetic connections between early Hungarians and populations from the Volga-Ural region between the 6th-14th centuries, revealing long-distance mobility and genetic continuity.

Privacy-Aware Kinship Inference in Admixed Populations using Projection on Reference Panels

This paper develops a privacy-aware kinship inference method for admixed populations using reference panels and homomorphic encryption to protect genetic data.

An empirical evaluation of genotype imputation of ancient DNA

This study evaluates genotype imputation for ancient DNA using Beagle 4.0 and 1000 Genomes reference data, showing high accuracy even at low coverage and highlighting the benefits of diverse reference sets and low-coverage samples.

The Genomic Prehistory of the Indigenous People of Uruguay

This study presents the first whole genome sequences of pre-European contact Indigenous people from Uruguay, revealing connections to ancient Panama and eastern Brazil but not modern Amazonians, suggesting a distinct Atlantic coastal migration route.

Genomic analysis reveals geography rather than culture as the predominant factor shaping genetic variation in northern Kenyan human populations

This study shows that geography, not culture, mainly influences genetic variation among northern Kenyan populations.

Newfoundland and Labrador: A mosaic founder population of an Irish and British diaspora from 300 years ago.

This study analyzes the genetic structure of Newfoundland and Labrador using SNP data, revealing coastal community clustering, religious denomination associations, and a recent population bottleneck.

Disentangling signatures of selection before and after European colonization in Latin Americans

This study identifies loci under selection in Latin American admixed populations, distinguishing between pre- and post-admixture selection, and finds signals related to immunity and energy metabolism.

Properties of Two-Locus Genealogies and Linkage Disequilibrium in Temporally Structured Samples

The paper derives properties of linkage disequilibrium and haplotype patterns in temporally structured samples, providing insights for analyzing ancient and modern genetic data.

Inferring population structure in biobank-scale genomic data

SCOPE infers population structure in large genomic datasets efficiently and accurately, outperforming existing methods in speed while maintaining comparable accuracy.

Screening and selection of 21 novel microhaplotype markers for ancestry inference in ten Chinese Subpopulations

The paper identifies 21 novel microhaplotype markers for ancestry inference in ten Chinese subpopulations, showing higher accuracy than SNP-based panels.

Hunter-gatherer genomes reveal diverse demographic trajectories following the rise of farming in East Africa

The paper analyzes genomic data from the Chabu, a hunter-gatherer group in Ethiopia, revealing a population bottleneck and diverse demographic responses to agropastoralism in East Africa.

The genomic signatures of natural selection in admixed human populations

This study identifies genomic signatures of adaptive admixture in 15 admixed populations, finding evidence of beneficial mutations acquired through population mixing.

The genomic formation of Tanka people, an isolated 'Gypsies in water' in the coastal region of Southeast China

This study clarifies the genetic origin and admixture history of the Tanka people using population genomic analysis of modern and ancient Eurasian samples.

Genetic heritage of the BaPhuthi highlights an over ethnicised notion of 'Bushman' in the Maloti-Drakensberg, Southern Africa

The paper examines genetic heritage of the BaPhuthi to determine if KhoeSan ancestry reflects biological distinction or shared life-way, finding no unique eastern KhoeSan ancestry.

Relationship among evolutionary distance, variance-covariance matrix and principal component analysis

This study shows that PCA using a genetic relationship matrix is equivalent to MDS using nucleotide differences, offering a new method to predict demographic effects on genetic diversity.

A unified genealogy of modern and ancient genomes

This paper introduces a non-parametric method to infer human genealogical history from modern and ancient genomes, demonstrating its ability to reconstruct relationships and identify descendants of ancient samples.

Indian genetic heritage in Southeast Asian populations

The paper analyzes genetic data from Southeast Asian populations to identify Indian genetic heritage and its impact on local populations.

An optimized method to infer relatedness up to the 5th degree from low coverage ancient human genomes

This paper introduces a method to reliably infer relatedness up to the 4-5th degree from low coverage ancient human genomes by addressing biases in kinship analysis.

Interdisciplinary analyses of Bronze Age communities from Western Hungary reveal complex population histories

This study analyzes ancient genomes from Bronze Age Hungary, revealing complex population histories, high hunter-gatherer ancestry in some groups, and new methods for ancient DNA analysis.

Genetic population structure across Brittany and the downstream Loire basin provides new insights on the demographic history of Western Europe

The paper analyzes genetic structure in Brittany and the Loire basin to understand Western Europe's demographic history, finding increased population differentiation linked to steppe and Neolithic ancestry.

A framework for research into continental ancestry groups of the UK Biobank

The paper describes the continental ancestry and population structure of non-white British individuals in the UK Biobank using reference populations and clustering methods.

Indigenous peoples in eastern Brazil: insights from 19th century genomes and metagenomes

The paper sequences 24 ancient Brazilian genomes, including 22 Botocudos, revealing Indigenous American ancestry without external gene flow and low heterozygosity, and identifies ancient pathogen lineages.

Natural selection does not affect the estimates of effective population size based on linkage disequilibrium

This paper shows that natural selection does not affect estimates of effective population size from linkage disequilibrium, while coalescence methods are influenced by selection.

A deep learning framework for characterization of genotype data

The paper proposes a deep learning model for dimensionality reduction of genotype data, showing improved population clustering and visualization compared to PCA, t-SNE, and UMAP.

Placing ancient DNA sequences into reference phylogenies

This paper develops an automated workflow to place ancient DNA sequences into reference phylogenies, using a parsimony and likelihood-based approach, and applies it to Y-chromosomal data.