Biology subjects

Bergström, A.

Publications and source records attributed to Bergström, A..

4 recordsLinked to original sources

bioRxiv2026

Joint dog and wolf genealogies reveal the evolution of the canine genome

Dogs and their closest extant relative, the grey wolf, diverged around 30k years ago, but have since experienced complex histories of gene flow involving other canids, adaptive pressures due to close association with humans, and changing climates. We infer joint genealogies of dogs, grey wolves, and a coyote using available whole genomes to reconstruct the evolutionary forces shaping the dog genome. These genealogies reveal multiple strong mutation-rate pulses unique to dogs, including signals detectable across ancient dogs from the past 10,000 years. We further detect pervasive genealogical signatures of purifying selection and find that GC-biased gene conversion is a major driver of diversity patterns around gene promoters in dogs. We introduce a new genealogy-based selection scan, TwigScan, that computes time-stratified differentiation, increasing power over traditional FST-based approaches. Applying this framework, alongside a second single-population test for detecting more recent selection within dogs, we identify multiple known and novel loci with signatures of positive selection. Among these, the region surrounding the amylase 2B locus shows evidence of introgression from a deeply divergent, unsampled canid lineage with divergence comparable to that of dholes. AMY2B duplications appear to occur exclusively on this introgressed haplotype which increased in frequency approximately 7,000-8,000 years ago, coinciding with increased reliance on starch-rich diets in human populations. Together, these results show how mutation-rate variation, gene conversion, selection, and inter-species gene flow have jointly shaped the dog genome, highlighting the power of genealogical approaches for resolving complex evolutionary histories.

evolutionary biology↗

bioRxiv2026

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

Dingoes, mainland Australias sole terrestrial apex mammal for over 3,000 years, are important components of many ecosystems and Indigenous cultural heritage. Yet conflicts with farmers over livestock predation following European colonisation led to widespread lethal control. These measures are further reinforced by perceptions of hybrid ancestry with European dogs. Accurate estimation of European dog ancestry is therefore essential for effective conservation, but existing tests yield highly conflicting results. Leveraging pre-colonial dingo palaeogenomes and a robust ancestry modelling framework, we reassess the genetic ancestry of contemporary populations. Our approach corrects limitations and biases in existing methods, producing consistent estimates even with as few as 10,000 genome-wide transversion genetic markers. Accounting for admixture uncovers population structure that has persisted for over two millennia and reveals patterns of genetic admixture coinciding with human activity during the colonial era. This study underscores the value of palaeogenomes as a vital conservation tool, offering insights unattainable from modern DNA alone. By clarifying ancestry and population structure, our study offers a robust foundation for effective regionally informed dingo management across Australia.

genomics↗

bioRxiv2023

Improving data archiving practices in ancient genomics

The sequencing of ancient DNA from preserved biological remains is producing a rich record of past genetic diversity in humans and other species. However, unless the primary data is made available in public archives in an appropriate fashion, its long-term value will not be fully realised. I surveyed publicly archived data from 42 recent ancient genomics studies. I found that half of the studies archived incomplete subsets of the generated genomic data, preventing accurate replication and representing a loss of data of potential use for future research. None of the studies met all archiving criteria that could be considered best practice. Based on these results, I make six recommendations for data producers: 1) archive all sequencing reads, not just those that can be aligned to a reference genome, 2) archive read alignments as well, but as secondary analysis files linked to the underlying raw read files, 3) provide correct experiment metadata on how samples, libraries and sequencing runs relate to each other, 4) provide informative sample metadata in the public archives, 5) publish and archive data from screening, low-coverage, poorly performing and negative experiments, and 6) document data archiving choices in papers, and review these as part of peer review processes. Given the reliance on destructive sampling of finite material, I argue that ancient genomics studies have a particularly strong responsibility to ensure the longevity and reusability of generated data.

genomics↗

bioRxiv2019

Insights into human genetic variation and population history from 929 diverse genomes

Genome sequences from diverse human groups are needed to understand the structure of genetic variation in our species and the history of, and relationships between, different populations. We present 929 high-coverage genome sequences from 54 diverse human populations, 26 of which are physically phased using linked-read sequencing. Analyses of these genomes reveal an excess of previously undocumented private genetic variation in southern and central Africa and in Oceania and the Americas, but an absence of fixed, private variants between major geographical regions. We also find deep and gradual population separations within Africa, contrasting population size histories between hunter-gatherer and agriculturalist groups in the last 10,000 years, a potentially major population growth episode after the peopling of the Americas, and a contrast between single Neanderthal but multiple Denisovan source populations contributing to present-day human populations. We also demonstrate benefits to the study of population relationships of genome sequences over ascertained array genotypes. These genome sequences are freely available as a resource with no access or analysis restrictions.

genomics↗