Bastien Llamas

Palaeogenomics-informed inferences of European dog admixture enables scalable dingo conservation

This study uses palaeogenomes to reassess dingo ancestry, revealing consistent genetic admixture patterns and population structure over two millennia.

Exploring the Evolution of the Cariogenic Oral Pathobiont Streptococcus mutans Using Ancient DNA

This study uses ancient DNA to analyze the evolution of Streptococcus mutans over 8,000 years, showing that some virulence traits emerged with agricultural diets.

Palaeogenomics reveals 1,500 years of population history of the peoples of the Chonos Archipelago, Chile.

This study uses paleogenomics to analyze 20 ancient individuals from the Chonos Archipelago, revealing unique genetic clusters and connections to neighboring Indigenous groups.

The genetic history of Portugal over the past 5,000 years

This study analyzes 68 ancient Portuguese genomes over 5,000 years, revealing migration patterns and genetic continuity, with influences from local, African, and Mediterranean populations.

Benchmarking Imputed Low Coverage Genomes in a Human Population Genetics Context

This study benchmarks GLIMPSE imputation on low coverage genomes from underrepresented populations, showing improved performance when using target population genetic information.

Two routes from the Fertile Crescent led to the introduction of common vetch into Europe.

This study re-sequences common vetch genomes to trace two migration routes into Europe and identifies genes involved in latitudinal adaptation.

The genetic origins and impacts of historical Papuan migrations into Wallacea

This study uses genome data to show that most Papuan-related ancestry in Wallacea comes from New Guinea migrations, not from ancient human settlers.

Epigenetic constraint of cellular genomes evolutionarily links genetic variation to function

The paper identifies regions of the human genome under cellular constraint by analyzing chromatin accessibility across cell types, showing their predictive power for functional loci and applications in variant identification and drug discovery.

Optimised in-solution enrichment of over a million ancient human SNPs

This study evaluates the effectiveness of the Twist Ancient DNA reagent for enriching ancient human SNPs, finding it robust for up to 27% endogenous DNA content with two rounds of enrichment.

The landscape of genomic structural variation in Indigenous Australians

This study profiles genomic structural variation in Indigenous Australians using whole genome long-read sequencing, revealing abundant and previously unannotated variants and unique STR diversity.

Allelic bias when performing in-solution enrichment of ancient human DNA

The paper identifies a systematic bias in in-solution enrichment of ancient human DNA using the Prime Plus kit, affecting population genetics inferences and genetic relatedness.

Deep FASTQ and BAM co-compression in Genozip 15

The paper introduces Genozip Deep, a method for losslessly co-compressing FASTQ and BAM files, achieving significant compression improvements over existing methods.

Genozip 14 - advances in compression of BAM and CRAM files

Genozip 14 improves BAM and CRAM compression, achieving up to 2.7x better compression than CRAM 3.1 across various genomic data types.

Genozip Dual-Coordinate VCF format enables efficient genomic analyses and alleviates liftover limitations

The paper introduces a new VCF format that allows simultaneous representation of genomic variants against two reference genomes, improving coordinate translation accuracy and reducing data storage burden.

BWA-mem is not the best aligner for ancient DNA short reads.

The paper compares a recommended BWA-mem parameterisation for ancient DNA with other aligners using benchmark metrics from a prior study.

Ancient DNA reconstructs the genetic legacies of pre-contact Puerto Rico communities

This study uses ancient DNA to reconstruct the genetic legacies of pre-contact Puerto Rico communities, finding Native American mtDNA haplogroups and shared ancestry with the Bahamas.

Population size history from short genomic scaffolds: how short is too short?

This study evaluates the performance of PSMC and PSMC' on short genomic scaffolds and finds that psmc remains accurate down to 100 kb while msmc is only reliable for scaffolds over 1 Mb.

Parallel paleogenomic transects reveal complex genetic history of early European farmers

The paper analyzes ancient DNA data from Neolithic and Chalcolithic Europe to study population dynamics and admixture patterns across different regions and time periods.

Eight thousand years of natural selection in Europe

This study uses ancient DNA to identify genetic selection signatures in European populations over 8,000 years, finding loci related to diet, pigmentation, immunity, and height.

Iron Age and Anglo-Saxon genomes from East England reveal British migration history

The paper analyzes ancient genomes from Iron Age and Anglo-Saxon periods in East England to estimate the genetic impact of migrations on modern British populations.

Massive migration from the steppe is a source for Indo-European languages in Europe

The paper analyzes ancient DNA data from 69 Europeans to show that a massive migration from the steppe contributed to the genetic makeup of present-day Europeans and supports a steppe origin for some Indo-European languages.