Forensic and Genetic Research

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.

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.

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.

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.

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.

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.

Cold adaptation in Upper Paleolithic hunter-gatherers of eastern Eurasia

This study analyzes 42 genomes from Jomon hunter-gatherers to show they adapted to cold environments through positive selection during the Last Glacial Maximum.

High Resolution Ancestry Deconvolution for Next Generation Genomic Data

This paper introduces Gnomix, a high-resolution ancestry deconvolution method for next-generation genomic data, achieving higher accuracy and faster performance than existing methods.

Paleogenomic Evidence for Genetic Heterogeneity and Prior Admixture in Gothic-Associated Communities of Late Antique Bulgaria

The paper analyzes ancient DNA from Gothic-associated communities in Late Antique Bulgaria, finding genetic heterogeneity and admixture between northern and southern ancestry components.

Ancestry, admixture, and pathogens in contemporaneous Neolithic farmers and foragers on the Island of Gotland

The paper analyzes ancestry, admixture, and pathogens in Neolithic farmers and foragers from Gotland, finding recent gene flow and widespread Yersinia pestis strains.

Faster inference of complex demographic models from large allele frequency spectra

The paper introduces a new method for inferring complex demographic models from genetic variation data, achieving significant speedups over existing methods.

Severe bottleneck of ancient Homo populations: Insights from computational modeling and fossil evidence

The paper uses computational modeling and fossil evidence to show a severe population bottleneck in ancient Homo around 930,000 years ago, linked to hominin dispersals and brain size increase.

A Transparent and Generalizable Deep Learning Framework for Genomic Ancestry Prediction

This paper develops a deep learning framework for genomic ancestry prediction that is generalizable across diverse populations and interpretable using attribution techniques.

ADAMIXTURE: Adaptive First-Order Optimization for Biobank-Scale Genetic Clustering

ADAMIXTURE improves genetic clustering for large datasets by combining EM with Adam optimization, achieving faster runtime and scalability without sacrificing accuracy.

ARGformer: learning on ancestral recombination graphs with transformers

ARGformer uses transformers to learn embeddings from ancestral recombination graphs, enabling population structure analysis and ancestry inference without genotype data.

Likelihood Ratios Given Activity-Level Propositions for DNA Transfer Evidence: Theoretical Foundations of the HaloGen Framework (Part I)

This paper establishes the theoretical basis of HaloGen, a hierarchical Bayesian framework for evaluating DNA evidence under competing activity-level propositions using likelihood ratios.

Likelihood Ratios Given Activity-Level Propositions for DNA Transfer Evidence: Practical Implementation and Simulation Studies Using the HaloGen Engine (Part II)

This paper implements and evaluates the HaloGen framework for calculating activity-level likelihood ratios in DNA transfer evidence, showing how case context affects results.

Faroese Whole Genomes Provide Insight into Ancestry and Recent Selection

This study analyzes whole genome sequencing data from the Faroe Islands to explore ancestry, genetic diversity, and signals of recent selection in a North Atlantic founder population.

Enhancement of hidden Markov model analyses for improved inference of archaic introgression in modern humans

This paper improves HMM analyses for inferring archaic introgression in modern humans by introducing sampling methods and hybrid decoding, showing better accuracy in admixture estimates.

Are genetically defined "metapopulations" self-evident in YHRD?

The paper investigates whether YHRD's metapopulations are self-evident by analyzing genetic structure using cluster analysis and finds weak genetic structure that does not support clear subgrouping.

CHARON: Estimating the drift time and the number of individuals in environmental DNA with diploid individuals

CHARON estimates the number of individuals and drift time in eDNA samples using statistical methods, validated with simulations and synthetic data.

Layers in the sand: The genetic imprint of migration, culture, and Indus craft in the Thar desert

This study analyzes genetic diversity in Thar Desert communities, revealing migration, cultural influences, and admixture shaping their genetic landscape.

Fault-tolerant pedigree reconstruction from pairwise kinship relations

This paper introduces repare, a software method to automatically reconstruct pedigrees from ancient genomes using pairwise kinship relations, showing improved flexibility and accuracy over manual methods.

Rapid and robust sex determination from ancient enamel proteomes using protSexInferer

Using the share of AMELY-specific among all sex-specific amelogenin peptides (RAMELY), enamel proteomes are sexed consistently across four search engines, tolerating false-positive AMELY hits without manual checks.

The persistence and loss of hard selective sweeps amid admixture in ancient Eurasians

This study uses a domain-adaptive neural network to detect selective sweeps in ancient Eurasian genomes, finding that hard sweeps at loci related to neuronal, reproductive, pigmentation, and signaling traits persisted despite admixture.

{micro}CT Scanning Effects on DNA and a Multi-Step Workflow for Archaeological Petrous Bones

Fifty micro-CT-scanned archaeological petrous bones from Argentina did not differ significantly from 43 unscanned ones on six ancient DNA metrics, motivating a multi-step workflow that scans bones before destructive sampling.

From bones to sediments: ancient human DNA from open-air archaeological sites

This study retrieves ancient human mitochondrial DNA from sediments around bones at archaeological sites, confirming its reliability and offering a non-destructive alternative for ancient DNA research.

Analytical expectations for ancestry junction accumulation in admixed genomes

The paper develops a model to predict ancestry switches in admixed genomes and validates it against simulations and empirical data.

Fine-scale structure of a whole regional population through genetics and genealogies

This study reveals fine-scale genetic structure in the Saguenay-Lac-Saint-Jean region using genotype data and genealogies, showing a genetic gradient and historical migration patterns.