Forensic and Genetic Research

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.

Buried in two places: Lineages from elite Maya tombs also found in distant caves

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

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.

Mitotree: The Universal Human Mitochondrial Reference Phylogeny at 10x the Resolution

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

Cultural affiliation accounts for most of the spatiotemporal variation in burial rite practices

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

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.

Fast pairwise coalescence enables gene-resolution scans for recent selection in diverse human populations

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

Benchmarking of local ancestry inference with different assays and parameters

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.

Promises and limitations of local ancestry inference in imputed ancient genomes

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

First Lithic Age Caribbean genomes document pre-Ceramic genetic continuity and affinities to Central America and northern South America

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.

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.

Haplotype-based models improve sweep detection in ancient populations with complex demography

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

Fine-scale population structure within and among Malagasy societies

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

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.

ArchaicSeeker 3.0: A deep-learning framework for scalable, haplotype-resolved inference of archaic introgression

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.

South Asian Maternal Lineage haplogroup R30 Provides Phylogenetic Evidence of human dispersal across South Asia

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.

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.

Genomic history and selection in Roman and early medieval Britain

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

Whole-genome sequencing of a mid-20th-century femur from central Israel in an open missing-person case

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

Optimal Reference Panel Design in Ancient DNA Imputation from Coalescent Theory, Simulation, and Real Data Application with an Ancient Reference Panel

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.

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.

Mitochondrial genomes reveal maternal lineages of Late Iron Age sheep (Ovis aries) in Denmark

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

On the Edge of Empire: Paleogenomic Insights into Roman Dacia

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.

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.

The Origin and Migration of the Ameru Community in Kenya based on mtDNA analysis.

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: Attention-based neural networks for population genetics

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

Genome-wide genealogies reveal deep admixtures forming modern humans

This paper introduces GhostBuster, a method to detect unsampled admixture events in human history using genome-wide genealogies, revealing multiple back-to-Africa migrations and deep ancestral lineages.

{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.

Inferring hominin history with recurrent gene flow from single unphased genomes and a two-locus statistic

This paper develops a method to infer hominin demographic history using two-locus statistics from single unphased genomes, revealing two episodes of gene flow and population structure in ancient Eurasian AMH.

Genomic landscape of the medieval Hungarian elite from the Szekesfehervar royal necropolis

The paper analyzes shotgun genomes from the medieval Hungarian elite, revealing homogenization through admixture and identifying a previously unrecognized Conquest-period stratum.