| 1. |
- Aktürk, Şevva, et al.
(författare)
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Benchmarking kinship estimation tools for ancient genomes using pedigree simulations
- 2024
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Ingår i: Molecular Ecology Resources. - 1755-098X .- 1755-0998.
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Tidskriftsartikel (refereegranskat)abstract
- There is growing interest in uncovering genetic kinship patterns in past societies using low-coverage palaeogenomes. Here, we benchmark four tools for kinship estimation with such data: lcMLkin, NgsRelate, KIN, and READ, which differ in their input, IBD estimation methods, and statistical approaches. We used pedigree and ancient genome sequence simulations to evaluate these tools when only a limited number (1 to 50 K, with minor allele frequency ≥0.01) of shared SNPs are available. The performance of all four tools was comparable using ≥20 K SNPs. We found that first-degree related pairs can be accurately classified even with 1 K SNPs, with 85% F1 scores using READ and 96% using NgsRelate or lcMLkin. Distinguishing third-degree relatives from unrelated pairs or second-degree relatives was also possible with high accuracy (F1 > 90%) with 5 K SNPs using NgsRelate and lcMLkin, while READ and KIN showed lower success (69 and 79% respectively). Meanwhile, noise in population allele frequencies and inbreeding (first-cousin mating) led to deviations in kinship coefficients, with different sensitivities across tools. We conclude that using multiple tools in parallel might be an effective approach to achieve robust estimates on ultra-low-coverage genomes.
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| 2. |
- Atag, Gözde, et al.
(författare)
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Population Genomic History of the Endangered Anatolian and Cyprian Mouflons in Relation to Worldwide Wild, Feral, and Domestic Sheep Lineages
- 2024
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Ingår i: Genome Biology and Evolution. - : Oxford University Press. - 1759-6653. ; 16:5
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Tidskriftsartikel (refereegranskat)abstract
- Once widespread in their homelands, the Anatolian mouflon (Ovis gmelini anatolica) and the Cyprian mouflon (Ovis gmelini ophion) were driven to near extinction during the 20th century and are currently listed as endangered populations by the International Union for Conservation of Nature. While the exact origins of these lineages remain unclear, they have been suggested to be close relatives of domestic sheep or remnants of proto-domestic sheep. Here, we study whole genome sequences of n = 5 Anatolian mouflons and n = 10 Cyprian mouflons in terms of population history and diversity, comparing them with eight other extant sheep lineages. We find reciprocal genetic affinity between Anatolian and Cyprian mouflons and domestic sheep, higher than all other studied wild sheep genomes, including the Iranian mouflon (O. gmelini). Studying diversity indices, we detect a considerable load of short runs of homozygosity blocks (<2 Mb) in both Anatolian and Cyprian mouflons, reflecting small effective population size (N-e). Meanwhile, N-e and mutation load estimates are lower in Cyprian compared with Anatolian mouflons, suggesting the purging of recessive deleterious variants in Cyprian sheep under a small long-term N-e, possibly attributable to founder effects, island isolation, introgression from domestic lineages, or differences in their bottleneck dynamics. Expanding our analyses to worldwide wild and feral Ovis genomes, we observe varying viability metrics among different lineages and a limited consistency between viability metrics and International Union for Conservation of Nature conservation status. Factors such as recent inbreeding, introgression, and unique population dynamics may have contributed to the observed disparities.
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| 3. |
- Mereu, Paolo, et al.
(författare)
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Matrilineal phylogeography of wild and feral sheep from the Mediterranean and the Middle East
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Mouflons are flagship species of the Mediterranean islands werethey persist. Once thought to be the remnants of a Europeanpopulation, archaeology suggests they were imported by humansto the islands of Cyprus in the Early Neolithic and laterto Corsica and Sardinia, and their status as wild animals hassince been disputed. To study the relationship between thisisland populations and other domestic and wild sheep fromthe Mediterranean we sequenced mitogenomes of 44 mouflonsfrom the islands, plus modern and ancient Sardinian domesticsheep and Anatolian mouflons. We used those in addition withpublicly available mitogenomes to reconstruct the phylogeny ofsheep and its closest wild relative, the Asiatic mouflon (Ovisgmelini) to describe how the free-ranging populations on theMediterranean islands fit. Our analysis highlights the structureof haplogroup B, where Sardinian mouflons form two geographicallyseparate clusters with gene flow between them and withdomestic sheep, and the isolation of the Corsican population,which appears as a basal lineage to all other sheep from thishaplogroup. While Corsican and Sardinian mouflon belong tobasal lineages of the domestic haplogroups associated with theearly European expansion, Cyprus mouflons are more relatedto Anatolian and Iranian mouflons belonging to the wild haplogroupX, which seems to be basal to the domestic C-E complex.These results highlight the unique genetic structure of thisisland populations while placing them in the wider context ofthe evolution of the Ovis genus.
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| 4. |
- Yurtman, Erinç, et al.
(författare)
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Archaeogenetic analysis of Neolithic sheep from Anatolia suggests a complex demographic history since domestication
- 2021
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 4:1
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Tidskriftsartikel (refereegranskat)abstract
- Sheep were among the first domesticated animals, but their demographic history is little understood. Here we analyzed nuclear polymorphism and mitochondrial data (mtDNA) from ancient central and west Anatolian sheep dating from Epipaleolithic to late Neolithic, comparatively with modern-day breeds and central Asian Neolithic/Bronze Age sheep (OBI). Analyzing ancient nuclear data, we found that Anatolian Neolithic sheep (ANS) are genetically closest to present-day European breeds relative to Asian breeds, a conclusion supported by mtDNA haplogroup frequencies. In contrast, OBI showed higher genetic affinity to present-day Asian breeds. These results suggest that the east-west genetic structure observed in present-day breeds had already emerged by 6000 BCE, hinting at multiple sheep domestication episodes or early wild introgression in southwest Asia. Furthermore, we found that ANS are genetically distinct from all modern breeds. Our results suggest that European and Anatolian domestic sheep gene pools have been strongly remolded since the Neolithic.
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