Raymond Tobler

Seasonal fluctuations in fitness result in severe reductions in effective population size

The paper simulates seasonally fluctuating selection in Drosophila populations and shows it reduces genome-wide effective population size by ~50%.

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.

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.

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.

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.

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.

Admixture has obscured signals of historical hard sweeps in humans

The paper shows that admixture in modern European genomes has masked over 50 historic hard sweeps, suggesting underappreciation of historical selection in human evolution.

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.

Unsupervized Quantification of Demographic Structure for Single-copy Alignments

The paper introduces a method to quantify demographic structure in single-copy sequence alignments by analyzing relationships between individuals and genomic positions, and demonstrates its application with empirical data.