Biology subjects

Llamas, B.

Publications and source records attributed to Llamas, B..

18 recordsLinked to original sources

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↗

bioRxiv2025

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

The Chonos archipelago, located in northwestern Chilean Patagonia, was historically inhabited by an Indigenous sea-faring population known to the European colonists as the "Chono". Previous research has contextualized the human occupation of this region with radiocarbon dates and ancient mitochondrial genomes, offering a partial perspective on the history of its inhabitants. Here we present a paleogenomic analysis of 20 ancient human individuals from 6 archaeological sites, dated between 1,600-50 years before present (BP). We successfully captured over 100,000 SNPs from 15 of 20 individuals and recovered 12 full mitogenomes. All individuals presented unadmixed Indigenous South American ancestry and formed a separated genetic cluster relative to other ancient and modern South American genomes, indicating a unique Chonos ancestry. This Chonos ancestry falls within a broader cluster of late-Holocene Patagonian ancestry, most similar to the Kawesqar peoples who neighbour to the south. Within the Chonos, we distinguish a northern and southern ancestry cluster. The northern Chonos cluster exhibits some genetic connections to the present-time inhabitants of the neighbouring island of Chiloe, who are connected to Huilliche Indigenous history. Our findings reveal a point of contact between southern Chonos/Patagonian ancestry to the south and Mapuche ancestry to the north, and confirm that sea-faring subsistence was a knowledge transferred between Patagonian peoples.

genomics↗

bioRxiv2025

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

Vicia sativa (common vetch, n=6) is an annual leguminous plant with high drought tolerance and high grain protein content. Historically and still today, vetches are important for nitrogen fixation to maintain cereal yields and feeding grazing livestock. In this study, we re-sequenced the genomes of 279 common vetch accessions from a wide geographic range covering western Eurasia and North Africa to construct a comprehensive nucleotide variation map. Population structure analyses indicate that the Middle Eastern region was the centre of origin of common vetch, which then entered Europe in two distinct waves. One wave propagated by humans through Turkey into the Carpathian Basin before spreading throughout Europe via "Danubian" and "Mediterranean" routes. Demographic inferences revealed a significant bottleneck for all common vetch groups initiated during the Last Glacial Maximum, followed by an expansion that coincides with the onset of the warm Holocene epoch and the Neolithic Revolution. Interestingly, we identified selective sweeps for the flowering time regulators VsSOC1 and VsFTb2 in northern latitude populations suggesting that both genes are important regulators of latitudinal adaptation. Overall, we provide valuable genomic resources for conservation and breeding programs to optimize food production in the face of population growth and reduced agricultural resources.

plant biology↗

bioRxiv2024

Epigenetic constraint of cellular genomes evolutionarily links genetic variation to function

Cellular diversity is a product of evolution acting to drive divergent regulatory programs from a common genome. Here, we use cross-cell-type epigenetic conservation to gain insight into the impact of selective constraints on genome function and phenotypic variation. By comparing chromatin accessibility across hundreds of diverse cell-types, we identify 1.4% of the human genome safeguarded by conserved domains of facultative heterochromatin, which we term regions under "cellular constraint". We calculate single-base resolution cellular constraint scores and demonstrate robust prediction of functionally important coding and non-coding loci in a cell-type-, trait-, and disease-agnostic manner. Cellular constraint annotation enhances causal variant identification, drug discovery, and clinical diagnostic predictions. Furthermore, cell-constrained sequences share paradoxical evolutionary signals of positive and negative selection, suggesting a dynamic role in driving human adaptation. Overall, this study demonstrates that evolutionary chromatin dynamics can be leveraged to inform the translation of genetic discoveries into effective biological, therapeutic, and clinical outcomes.

genetics↗

bioRxiv2024

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

BackgroundRecent ancient DNA studies uncovering large-scale demographic events in Iberia have focused primarily on Spain, with limited reports for Portugal, a country located at the westernmost edge of continental Eurasia. Here, we introduce the largest collection of ancient Portuguese genomic datasets (n = 68) to date, spanning 5,000 years, from the Neolithic to the 19th century. ResultsWe found evidence of patrilocality in Neolithic Portugal, with admixture from local hunter-gatherers and Anatolian farmers, and persistence of Upper Paleolithic Magdalenian ancestry. This genetic profile persists into the Chalcolithic, reflecting diverse local hunter- gatherer contributions. During the Bronze Age, local genetic ancestry persisted, particularly in southern Iberia, despite influences from the North Pontic Steppe and early Mediterranean contacts. The Roman period highlights Idanha-a-Velha as a hub of migration and interaction, with a notably diverse genetic profile. The Early Medieval period is marked by Central European ancestry linked to Suebi/Visigoth migrations, adding to coeval local, African, and Mediterranean influences. The Islamic and Christian Conquest periods show strong genetic continuity in northern Portugal and significant African admixture in the south, with persistent Jewish and Islamic ancestries suggesting enduring influences in the post-Islamic period. ConclusionsThis study represents the first attempt to reconstruct the genetic history of Portugal from the analysis of ancient individuals. We reveal dynamic patterns of migration and cultural exchange across millennia, but also the persistence of local ancestries. Our findings integrate genetic information with historical and archaeological data, enhancing our understanding of Iberias ancient heritage.

genomics↗

bioRxiv2024

The genetic origins and impacts of historical Papuan migrations into Wallacea

The tropical archipelago of Wallacea was first settled by anatomically modern humans (AMH) by 50 thousand years ago (kya), with descendent populations thought to have remained genetically isolated prior to the arrival of Austronesian seafarers around 3.5 kya. Modern Wallaceans exhibit a longitudinal countergradient of Papuan- and Asian-related ancestries widely considered as evidence for mixing between local populations and Austronesian seafarers, though converging multidisciplinary evidence suggests that the Papuan-related component instead comes primarily from back-migrations from New Guinea. Here, we reconstruct Wallacean population genetic history using more than 250 newly reported genomes from 12 Wallacean and three West Papuan populations and confirm that the vast majority of Papuan-related ancestry in Wallacea ([~]75-100%) comes from prehistoric migrations originating in New Guinea and only a minor fraction is attributable to the founding AMH settlers. Mixing between Papuan and local Wallacean lineages appear to have been confined to the western and central parts of the archipelago and likely occurred contemporaneously with the widespread introduction of genes from Austronesian seafarers--which now comprise between [~]40-85% of modern Wallacean ancestry--though dating historical admixture events remains challenging due to mixing continuing into the Historical Period. In conjunction with archaeological and linguistic records, our findings point to a dynamic Wallacean population history that was profoundly reshaped by the spread of Papuan genes, languages, and culture in the past 3,500 years.

evolutionary biology↗

bioRxiv2024

Benchmarking Imputed Low Coverage Genomes in a Human Population Genetics Context

Ongoing advances in population genomic methodologies have recently made it possible to study millions of loci across hundreds of genomes at a relatively low cost, by leveraging a combination of low-coverage shotgun sequencing and innovative genotype imputation methods. This approach has the potential to provide economical access to genotype information that is similar to most widely used low-cost genotyping approach - i.e. SNP panels - while avoiding potential issues related to loci being ascertained in distantly related populations. Nonetheless, adoption of imputation methods has been constrained by the lack of suitable reference panels of phased genomes, as performance degrades when panel individuals are distantly related to the target populations. Recent advances in imputation algorithms now allow genetic information from the target population to be used in the imputation process, however, potentially mitigating the lack of a suitable reference panel. Here we assess the performance of the recently released GLIMPSE imputation software on a set of 250 low coverage genomes ([~]3x) from populations from Island Southeast Asia and Near Oceania that are poorly represented in publicly available datasets, comparing the use of imputed genotypes against other common genotype calling methods for a range of standard population genomic analyses. We find that imputation performance and inference both greatly improved when genetic information from the 250 target individuals was leveraged, with comparable results to pseudo-haploid calls that trade off improved precision with reduced accuracy. Our study shows that imputed genotypes are a cost effective and robust basis for population genomic studies of groups, especially those that are poorly represented in publicly available data.

evolutionary biology↗

bioRxiv2024

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

In-solution hybridisation enrichment of genetic markers is a method of choice in paleogenomic studies, where the DNA of interest is generally heavily fragmented and contaminated with environmental DNA, and where the retrieval of genetic data comparable between individuals is challenging. Here, we benchmarked the commercial "Twist Ancient DNA" reagent from Twist Biosciences using sequencing libraries from ancestrally diverse ancient human samples with low to high endogenous DNA content (0.1-44%). For each library, we tested one and two rounds of enrichment, and assessed performance compared to deep shotgun sequencing. We find that the "Twist Ancient DNA" assay provides robust enrichment of [~]1.2M target SNPs without introducing allelic bias that may interfere with downstream population genetics analyses. Additionally, we show that pooling up to 4 sequencing libraries and performing two rounds of enrichment is both reliable and cost-effective for libraries with less than 27% endogenous DNA content. Above 38% endogenous content, a maximum of one round of enrichment is recommended for cost-effectiveness and to preserve library complexity. In conclusion, we provide researchers in the field of human paleogenomics with a comprehensive understanding of the strengths and limitations of different sequencing and enrichment strategies, and our results offer practical guidance for optimising experimental protocols.

genomics↗

bioRxiv2023

The landscape of genomic structural variation in Indigenous Australians

Indigenous Australians harbour rich and unique genomic diversity. However, Aboriginal and Torres Strait Islander ancestries are historically under-represented in genomics research and almost completely missing from reference databases. Addressing this representation gap is critical, both to advance our understanding of global human genomic diversity and as a prerequisite for ensuring equitable outcomes in genomic medicine. Here, we apply population-scale whole genome long-read sequencing to profile genomic structural variation across four remote Indigenous communities. We uncover an abundance of large indels (20-49bp; n=136,797) and structural variants (SVs; [≥]50bp; n=159,912), the majority of which are composed of tandem repeat or interspersed mobile element sequences (90%) and have not been previously annotated (73%). A large fraction of SVs appear to be exclusive to Indigenous Australians (>30%) and the majority of these are found in only a single community, underscoring the need for broad and deep sampling to achieve a comprehensive catalogue of genomic structural variation across the Australian continent. Finally, we explore short-tandem repeats (STRs) throughout the genome to characterise allelic diversity at 50 known disease loci, uncover hundreds of novel repeat expansion sites within protein-coding genes, and identify unique patterns of diversity and constraint among STR sequences. Our study sheds new light on the dimensions, diversity and evolutionary trajectories of genomic structural variation within and beyond Australia.

genomics↗

bioRxiv2023

Deep FASTQ and BAM co-compression in Genozip 15

We introduce Genozip Deep, a method for losslessly co-compressing FASTQ and BAM files. Benchmarking demonstrates improvements of 75% to 96% versus the already-compressed source files, translating to 2.3X to 6.8X better compression than current state-of-the-art algorithms that compress FASTQ and BAM separately. The Deep method is independent of the underlying FASTQ and BAM compressors, and here we present its implementation in Genozip, an established genomic data compression software.

bioinformatics↗

bioRxiv2023

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

In-solution hybridisation enrichment of genetic variation is a valuable methodology in human paleogenomics. It allows enrichment of endogenous DNA by targeting genetic markers that are comparable between sequencing libraries. Many studies have used the 1240k reagent--which enriches 1,237,207 genome-wide SNPs--since 2015, though access was restricted. In 2021, Twist Biosciences and Daicel Arbor Biosciences independently released commercial kits that enabled all researchers to perform enrichments for the same 1240k SNPs. We used the Daicel Arbor Biosciences Prime Plus kit to enrich 132 ancient samples from three continents. We identified a systematic assay bias that increases genetic similarity between enriched samples and that cannot be explained by batch effects. We present the impact of the bias on population genetics inferences (e.g., Principal Components Analysis, [f]-statistics) and genetic relatedness (READ). We compare the Prime Plus bias to that previously reported of the legacy 1240k enrichment assay. In [f]-statistics, we find that all Prime-Plus-generated data exhibit artefactual excess shared drift, such that within-continent relationships cannot be correctly determined. The bias is more subtle in READ, though interpretation of the results can still be misleading in specific contexts. We expect the bias may affect analyses we have not yet tested. Our observations support previously reported concerns for the integration of different data types in paleogenomics. We also caution that technological solutions to generate 1240k data necessitate a thorough validation process before their adoption in the paleogenomic community.

genomics↗

bioRxiv2022

Genozip 14 - advances in compression of BAM and CRAM files

SummaryGenozip performs compression of a wide range of genomic data, including widely used FASTQ, BAM and VCF file formats. Here, we introduce the latest advancement in Genozip technology, focused on compression of BAM and CRAM files. We demonstrate Genozips ability to compress data generated by a variety of study types (e.g., whole genome sequencing, DNA methylation, RNASeq), sequencing technologies and aligners, up to 2.7 times better than the current state of the art compressor, CRAM version 3.1. Availability and implementationGenozip is freely available for academic research use and has been tested for Linux, Mac and Windows. Installation instructions are available at https://genozip.com/installing.html. A user manual is available at https://genozip.com/manual.html. Supplementary informationSupplementary data are available.

bioinformatics↗

bioRxiv2022

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

We introduce Dual Coordinate VCF (DVCF), a file format that records genomic variants against two different reference genomes simultaneously and is fully compliant with the current VCF specification. As implemented in the Genozip platform, DVCF enables bioinformatics pipelines to seamlessly operate across two coordinate systems by leveraging the system most advantageous to each pipeline step, simplifying bioinformatics workflows and reducing file generation and associated data storage burden. Moreover, our benchmarking of Genozip DVCF shows that it produces more complete, less erroneous, and less biased translations across coordinate systems than two widely used alternative tools (i.e., LiftoverVcf and CrossMap). Availability and ImplementationAn open source (GPL) version of Genozip containing DVCF functionality but not compression functionality, and which includes scripts for reproducing the benchmarks presented here, is available at https://github.com/divonlan/dvcf. Documentation is available at https://genozip.com/dvcf.

bioinformatics↗

bioRxiv2021

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

Xu and colleagues (Xu et al., 2021) recently suggested a new parameterisation of BWA-mem (Li, 2013) as an alternative to the current standard BWA-aln (Li and Durbin, 2009) to process ancient DNA sequencing data. The authors tested several combinations of the -k and -r parameters to optimise BWA-mems performance with degraded and contaminated ancient DNA samples. They report that using BWA-mem with -k 19 -r 2.5 parameters results in a mapping efficiency comparable to BWA-aln with -I 1024 -n 0.03 (i.e. a derivation of the standard parameters used in ancient DNA studies; (Schubert et al., 2012)), while achieving significantly faster run times. We recently performed a systematic benchmark of four mapping software (i.e. BWA-aln, BWA-mem, NovoAlign (http://www.novocraft.com/products/novoalign), and Bowtie2 (Langmead and Salzberg, 2012) for ancient DNA sequencing data and quantified their precision, accuracy, specificity, and impact on reference bias (Oliva et al., 2021). Notably, while multiple parameterisations were tested for BWA-aln, NovoAlign, and Bowtie2, we only tested BWA-mem with default parameters. Here, we use the alignment performance metrics from Oliva et al. to directly compare the recommended BWA-mem parameterisation reported in Xu et al. with the best performing alignment methods determined in the Oliva et al. benchmarks, and we make recommendations based on the results.

bioinformatics↗

bioRxiv2019

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

Indigenous peoples have occupied the island of Puerto Rico since at least 3000 B.C. Due to the demographic shifts that occurred after European contact, the origin(s) of these ancient populations, and their genetic relationship to present-day islanders, are unclear. We use ancient DNA to characterize the population history and genetic legacies of pre-contact Indigenous communities from Puerto Rico. Bone, tooth and dental calculus samples were collected from 124 individuals from three pre-contact archaeological sites: Tibes, Punta Candelero and Paso del Indio. Despite poor DNA preservation, we used target enrichment and high-throughput sequencing to obtain complete mitochondrial genomes (mtDNA) from 45 individuals and autosomal genotypes from two individuals. We found a high proportion of Native American mtDNA haplogroups A2 and C1 in the pre-contact Puerto Rico sample (40% and 44%, respectively). This distribution, as well as the haplotypes represented, support a primarily Amazonian South American origin for these populations, and mirrors the Native American mtDNA diversity patterns found in present-day islanders. Three mtDNA haplotypes from pre-contact Puerto Rico persist among Puerto Ricans and other Caribbean islanders, indicating that present-day populations are reservoirs of pre-contact mtDNA diversity. Lastly, we find similarity in autosomal ancestry patterns between pre-contact individuals from Puerto Rico and the Bahamas, suggesting a shared component of Indigenous Caribbean ancestry with close affinity to South American populations. Our findings contribute to a more complete reconstruction of pre-contact Caribbean population history and explore the role of Indigenous peoples in shaping the biocultural diversity of present-day Puerto Ricans and other Caribbean islanders.

genomics↗

bioRxiv2018

Untangling the Evolutionary History of European Bison (Bison bonasus)

European bison (Bison bonasus) are the largest endemic vertebrates in Europe, and one of the few megafaunal species to have survived the mass megafaunal extinction during the Pleistocene/Holocene transition (12-9 thousand years ago). Untangling their evolutionary history would provide valuable information about the response of European megafauna to periods of rapid environmental change. However, a severe and recent population bottleneck obscures much of the population history that could be inferred from the genomes of modern individuals. While several studies have attempted to analyse ancient European bison populations directly using ancient DNA, their datasets were limited in temporal and geographic range. In this study we present the most comprehensive dataset of ancient European bison mitochondrial genomes to date, with 131 ancient bison samples from across the Eurasian continent covering over 50 thousand years. We reveal patterns of bison distribution and concurrent environmental changes across a broad geographical and temporal range. In particular, population expansions following periods of extensive forest reduction combined with a decrease in anthropogenic pressures suggest that European bison remain preferentially adapted to an open steppe environment through to the present day.

evolutionary biology↗

bioRxiv2018

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

The Pairwise Sequentially Markov Coalescent (PSMC), and its extension PSMC', model past population sizes from a single diploid genome. Both models have been widely applied, even to organisms with scaffold-level genome reference assemblies of limited contiguity. However it is unclear how PSMC and PSMC' perform on short scaffolds. We evaluated psmc and msmc, implementations of the PSMC and PSMC' models respectively, on simulated genomes with low contiguity, and compared results to those from fully contiguous data. Simulations with scaffolds from 100 Mb to 10 kb revealed that psmc maintains high accuracy down to lengths of 100 kb, while msmc is accurate down to 1 Mb. The discrepancy is not due to differing models, but stems from an implementation detail of msmc--homozygous tracts at the ends of scaffolds are discarded, making msmc unreliable for low contiguity genomes. We recommend excluding data that are aligned to shorter scaffolds when undertaking demographic inference.

genetics↗

bioRxiv2017

Parallel ancient genomic transects reveal complex population history of early European farmers

Ancient DNA studies have established that European Neolithic populations were descended from Anatolian migrants who received a limited amount of admixture from resident hunter-gatherers. Many open questions remain, however, about the spatial and temporal dynamics of population interactions and admixture during the Neolithic period. Using the highest-resolution genome-wide ancient DNA data set assembled to date--a total of 177 samples, 127 newly reported here, from the Neolithic and Chalcolithic of Hungary (6000-2900 BCE, n = 98), Germany (5500-3000 BCE, n = 42), and Spain (5500-2200 BCE, n = 37)--we investigate the population dynamics of Neolithization across Europe. We find that genetic diversity was shaped predominantly by local processes, with varied sources and proportions of hunter-gatherer ances try among the three regions and through time. Admixture between groups with different ancestry profiles was pervasive and resulted in observable population transformation across almost all cultural transitions. Our results shed new light on the ways that gene flow reshaped European populations throughout the Neolithic period and demonstrate the potential of time-series-based sampling and modeling approaches to elucidate multiple dimensions of historical population interactions.

genetics↗