Imputed genomes of historical horses provide insights into modern breeding

Todd, Evelyn T.; Fromentier, Aurore; Sutcliffe, Richard F. E.; Collin, Yvette Running Horse; Perdereau, Aude; Aury, Jean‐Marc; Eché, Camille; Bouchez, Olivier; Donnadieu, Cécile; Wincker, Patrick; Kalbfleisch, Ted; Petersen, Jessica L; Orlando, Ludovic

doi:10.1016/j.isci.2023.107104

Cited by 3 publications

(4 citation statements)

References 65 publications

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“…This may also explain the relatively greater improvement in accuracy observed when restricting our analysis to transversion sites only for this sample, as transition sites, which are affected by aDNA damage, cannot be properly corrected by imputation if there is poor haplotypic representation of the relevant ancestries. Previous studies imputing ancient humans (Sousa Da Mota et al 2023), horses (Todd et al 2023) and pigs (Erven et al 2022) have shown how imputation accuracy can change depending on the ancestral composition of the reference panel. We suggest that ancestry-specific coverage cutoffs may be applied prior to imputation.…”

Section: Discussionmentioning

confidence: 99%

“…Previous studies imputing ancient humans (Sousa Da Mota et al 2023), horses (Todd et al 2023) and pigs (Erven et al 2022) have shown how imputation accuracy can change depending on the ancestral composition of the reference panel. We suggest that ancestry-specific coverage cutoffs may be applied prior to imputation.…”

Section: The First Imputed Ancient Dog and Wolf Genomesmentioning

confidence: 99%

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Imputation of ancient canid genomes reveals inbreeding history over the past 10,000 years

Bougiouri,

Charlton,

Harris

et al. 2024

Preprint

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The multi-millenia long history between dogs and humans has justly placed them at the forefront of archeological and genomic research. Despite ongoing efforts including the analysis of ancient dog and wolf genomes, many questions remain regarding their geographic and temporal origins, and the microevolutionary processes that led to the huge diversity of breeds today. Although ancient genomes provide valuable information, their use is significantly hindered by low depth of coverage and post-mortem damage, which often inhibits confident genotype calling. In the present study, we assess how genotype imputation of ancient dog and wolf genomes, utilising a large reference panel, can improve the resolution afforded by ancient genomic datasets. Imputation accuracy was evaluated by down-sampling 10 high coverage ancient and modern dog and wolf genomes to 0.05-2x coverage and comparing concordance between imputed and high coverage genotypes. We also measured the impact of imputation on principal component analyses (PCA) and runs of homozygosity (ROH). Our findings show high (R2 > 0.9) imputation accuracy for dogs with coverage as low as 0.5x and for wolves as low as 1.0x. We then imputed a worldwide dataset of 81 published ancient dog and wolf genomes, in addition to nine newly sequenced medieval and early modern period European dogs, to assess changes in inbreeding during the last 10,000 years of dog evolution. Ancient dog and wolf populations generally exhibited lower inbreeding levels than present-day individuals, though with some exceptions occurring in ancient Arctic and European dogs. Interestingly, regions with low ROH density maintained across ancient and present-day samples were significantly associated with genes related to olfaction and immune response. Our study indicates that imputing ancient canine genomes is a viable strategy that allows for the use of analytical methods previously limited to high-quality genetic data.

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Section: Discussionmentioning

confidence: 99%

Section: The First Imputed Ancient Dog and Wolf Genomesmentioning

confidence: 99%

Imputation of ancient canid genomes reveals inbreeding history over the past 10,000 years

Bougiouri,

Charlton,

Harris

et al. 2024

Preprint

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“…inference of autozygosity within, and identity by descent (IBD) between genomes. While genotype imputation is regularly used in modern livestock genetics, including cattle ( Hayes and Daetwyler 2019 ), and has been applied to ancient pigs and horses ( Erven et al 2022 ; Todd et al 2023 ), the efficacy of imputation has not been explored in ancient cattle.…”

Section: Introductionmentioning

confidence: 99%

A High-Coverage Mesolithic Aurochs Genome and Effective Leveraging of Ancient Cattle Genomes Using Whole Genome Imputation

Erven,

Scheu,

Verdugo

et al. 2024

Molecular Biology and Evolution

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Ancient genomic analyses are often restricted to utilising pseudo-haploid data due to low genome coverage. Leveraging low coverage data by imputation to calculate phased diploid genotypes that enable haplotype-based interrogation and SNP calling at unsequenced positions is highly desirable. This has not been investigated for ancient cattle genomes despite these being compelling subjects for archaeological, evolutionary and economic reasons. Here we test this approach by sequencing a Mesolithic European aurochs (18.49x; 9852-9376 calBCE), an Early Medieval European cow (18.69x; 427-580 calCE), and combine these with published individuals; two ancient and three modern. We downsample these genomes (0.25x, 0.5x, 1.0x, 2.0x) and impute diploid genotypes, utilising a reference panel of 171 published modern cattle genomes that we curated for 21.7 million (Mn) phased single-nucleotide polymorphisms (SNPs). We recover high densities of correct calls with an accuracy of >99.1% at variant sites for the lowest downsample depth of 0.25x, increasing to >99.5% for 2.0x (transversions only, minor allele frequency (MAF) ≥ 2.5%). The recovery of SNPs correlates with coverage, on average 58% of sites are recovered for 0.25x increasing to 87% for 2.0x, utilising an average of 3.5 million (Mn) transversions (MAF ≥2.5%), even in the aurochs, despite the highest temporal distance from the modern reference panel. Our imputed genomes behave similarly to directly called data in allele-frequency-based analyses; for example consistently identifying runs of homozygosity >2mb, including a long homozygous region in the Mesolithic European aurochs.

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“…Furthermore, some archaeological sites document the ritual practice of animal sacrifice, which provides excellent windows into the diversity of social norms then prescribed by the entire community. Testing why the animals sacrificed were chosen—whether as genetic kins or for special age, sexual, esthetical, behavioral, or performance phenotypes that can now be predicted genetically ( 20 ), or epigenetically ( 21 )—and their depositional patterns, holds considerable potential for deciphering past social practices and economical alliances ( 22 ). When deposited as funerary offerings, they also provide exceptional opportunities to gain insight into past systems of beliefs and social representations of the afterlife ( 18 ).…”

mentioning

confidence: 99%