Forensic and Genetic Research

ORIAN is a deep learning framework for local ancestry inference that works with and without reference panels, achieving high accuracy in both settings.

The paper uses ancient DNA to show matrilineal kinship structures and recurrent unions between dominant maternal groups in Iron Age Britain.

The paper evaluates local ancestry inference methods across varying FST values, finding a feasibility threshold and showing that input quality, not architecture, limits performance.

The paper investigates the sex bias in admixture between Jomon hunter-gatherers and continental farmers in modern Japanese genomes, finding a female-biased contribution from continental farmers.

This study examines the genomic makeup of modern Italian Alpine valleys, showing they retain ancient Neolithic ancestry and show microgeographic genetic subclusters shaped by isolation and drift.

This study uses ancient whole-genome data to show geographically structured selection during the Neolithic transition in Western Eurasia, involving both farmer and hunter-gatherer alleles.

The paper analyzes genome-wide genealogies to detect ancient gene flow from a super-archaic lineage using integer partition distributions.

This study benchmarks Nanopore sequencing for STR profiling using R10.4.1 flowcells and basecalling models, showing improved genotyping accuracy with newer models.

This study applies a modified natural vector method to mitochondrial genome data from the 1000 Genomes Project to evaluate population genetic characteristics beyond pairwise comparisons.

The paper develops DEEP, an ARG-free method to detect Denisovan-mediated superarchaic introgression, finding 0.4-0.6% of genomic windows with evidence of such ancestry in Oceanians, Tibetans, and Han Chinese.

This paper evaluates the impact of retaining close relatives on demographic inference using IBD-based methods and finds that retaining relatives reduces bias in Ne estimates.

This paper introduces a friction-based model to improve the accuracy of tracing human genetic ancestry by incorporating geographic migration costs, showing better performance in estimating origins and genetic flux in simulated and real-world scenarios.

The paper analyzes genetic data from Maya tombs and caves to show that elite lineages extended their ancestral connections across distant locations.

Mitotree constructs the largest human mitochondrial phylogeny with higher resolution, identifying new branches and improving accuracy over previous references.

The paper analyzes the relationship between spatiotemporal cultural variation and genomic data to determine how cultural affiliation influences burial practices.

This paper introduces a GPU-accelerated method to compute pairwise coalescence times at gene resolution, identifying recent selection signals in diverse human populations.

This study benchmarks local ancestry inference across different genotyping assays and parameters, showing that ultra low-pass WGS with GLIMPSE2 achieves high accuracy, while SNP microarrays perform poorly.

This study evaluates the reliability of local ancestry inference methods for imputed ancient genomes across various demographic and sampling scenarios.

This paper generates genome-wide data from pre-Ceramic Caribbean individuals, showing genetic continuity with Central America and northern South America and small, locally structured communities.

This study shows haplotype-based models are more effective than SFS methods for detecting selective sweeps in ancient populations with complex demographics.

This study identifies fine-scale population structure within Madagascar using genome-wide data, revealing distinct subpopulations and historical migration patterns.

ArchaicSeeker 3.0 detects archaic introgression using deep learning, outperforming existing methods in precision, recall, and F1 score across diverse genomic contexts and population sizes.

The paper analyzes haplogroup R30 in South Asia to trace human dispersal, finding it originated in the Indian subcontinent ~50 kya and shows evidence of multiple migrations.

This study analyzes ancient genomes from Roman and early medieval Britain to uncover population history, ancestry shifts, and selection patterns shaping modern genetic diversity.

The paper reports whole-genome sequencing of a mid-20th-century femur from Israel, revealing Arab ancestry instead of the proposed Ashkenazi Jewish origin.

This paper evaluates optimal reference panels for ancient DNA imputation using coalescent theory, simulations, and a real dataset, finding that including ancient samples improves imputation accuracy for rare variants.

This study analyzes mitochondrial genomes from Late Iron Age sheep in Denmark, finding high haplotype diversity and genetic links to modern European populations.

This study uses genomic data from Roman Dacia to show sex-biased ancestry patterns, indicating male-mediated gene flow and complex demographic interactions in Roman frontier communities.

This study uses mtDNA analysis of the Ameru community in Kenya to trace maternal origins and migration patterns, revealing diverse haplogroups with links to West, Central, and East Africa, as well as Eurasia.

Attentive-SPIDNA uses attention mechanisms to infer population size history from genomic data, outperforming existing methods and handling varying haplotype numbers.