Archaeogenetic analysis of Neolithic sheep from Anatolia suggests a complex demographic history since domestication

The Population History of Domestic Sheep Revealed by Paleogenomes

Sheep was one of the first domesticated animals in Neolithic West Eurasia. The zooarchaeological record suggests that domestication first took place in Southwest Asia, although much remains unresolved about the precise location(s) and timing(s) of earliest domestication, or the post-domestication history of sheep. Here, we present 24 new partial sheep paleogenomes, including a 13,000-year-old Epipaleolithic Central Anatolian wild sheep, as well as 14 domestic sheep from Neolithic Anatolia, two from Neolithic Iran, two from Neolithic Iberia, three from Neolithic France, and one each from Late Neolithic/Bronze Age Baltic and South Russia, in addition to five present-day Central Anatolian Mouflons and two present-day Cyprian Mouflons. We find that Neolithic European, as well as domestic sheep breeds, are genetically closer to the Anatolian Epipaleolithic sheep and the present-day Anatolian and Cyprian Mouflon than to the Iranian Mouflon. This supports a Central Anatolian source for domestication, presenting strong evidence for a domestication event in SW Asia outside the Fertile Crescent, although we cannot rule out multiple domestication events also within the Neolithic Fertile Crescent. We further find evidence for multiple admixture and replacement events, including one that parallels the Pontic Steppe-related ancestry expansion in Europe, as well as a post-Bronze Age event that appears to have further spread Asia-related alleles across global sheep breeds. Our findings mark the dynamism of past domestic sheep populations in their potential for dispersal and admixture, sometimes being paralleled by their shepherds and in other cases not.

Ancient Sheep Genomes Reveal Four Millennia of North European Short-Tailed Sheep in the Baltic Sea Region

Sheep are among the earliest domesticated livestock species, with a wide variety of breeds present today. However, it remains unclear how far back this diversity goes, with formal documentation only dating back a few centuries. North European short-tailed (NEST) breeds are often assumed to be among the oldest domestic sheep populations, even thought to represent relicts of the earliest sheep expansions during the Neolithic period reaching Scandinavia <6,000 years ago. This study sequenced the genomes (up to 11.6X) of five sheep remains from the Baltic islands of Gotland and Åland, dating from the Late Neolithic (∼4,100 cal BP) to historical times (∼1,600 CE). Our findings indicate that these ancient sheep largely possessed the genetic characteristics of modern NEST breeds, suggesting a substantial degree of long-term continuity of this sheep type in the Baltic Sea region. Despite the wide temporal spread, population genetic analyses show high levels of affinity between the ancient genomes and they also exhibit relatively high genetic diversity when compared to modern NEST breeds, implying a loss of diversity in most breeds during the last centuries associated with breed formation and recent bottlenecks. Our results shed light on the development of breeds in Northern Europe specifically as well as the development of genetic diversity in sheep breeds, and their expansion from the domestication center in general.

Population Genomic History of the Endangered Anatolian and Cyprian Mouflons in Relation to Worldwide Wild, Feral, and Domestic Sheep Lineages

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 (Ne). Meanwhile, Ne 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 Ne, 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.

Ancient mitogenomes from Pre-Pottery Neolithic Central Anatolia and the effects of a Late Neolithic bottleneck in sheep (Ovis aries)

Occupied between ~10,300 and 9300 years ago, the Pre-Pottery Neolithic site of Aşıklı Höyük in Central Anatolia went through early phases of sheep domestication. Analysis of 629 mitochondrial genomes from this and numerous sites in Anatolia, southwest Asia, Europe, and Africa produced a phylogenetic tree with excessive coalescences (nodes) around the Neolithic, a potential signature of a domestication bottleneck. This is consistent with archeological evidence of sheep management at Aşıklı Höyük which transitioned from residential stabling to open pasturing over a millennium of site occupation. However, unexpectedly, we detected high genetic diversity throughout Aşıklı Höyük's occupation rather than a bottleneck. Instead, we detected a tenfold demographic bottleneck later in the Neolithic, which caused the fixation of mitochondrial haplogroup B in southwestern Anatolia. The mitochondrial genetic makeup that emerged was carried from the core region of early Neolithic sheep management into Europe and dominates the matrilineal diversity of both its ancient and the billion-strong modern sheep populations.

Phenotype transition from wild mouflon to domestic sheep

The domestication of animals started around 12,000 years ago in the Near East region. This "endless process" is characterized by the gradual accumulation of changes that progressively marked the genetic, phenotypic and physiological differences between wild and domesticated species. The main distinctive phenotypic characteristics are not all directly attributable to the human-mediated selection of more productive traits. In the last decades, two main hypotheses have been proposed to clarify the emergence of such a set of phenotypic traits across a variety of domestic species. The first hypothesis relates the phenotype of the domesticated species to an altered thyroid hormone-based signaling, whereas the second one relates it to changes in the neural crest cells induced by selection of animals for tameness. These two hypotheses are not necessarily mutually exclusive since they may have contributed differently to the process over time and space. The adaptation model induced by domestication can be adopted to clarify some aspects (that are still controversial and debated) of the long-term evolutionary process leading from the wild Neolithic mouflon to the current domestic sheep. Indeed, sheep are among the earliest animals to have been domesticated by humans, around 12,000 years ago, and since then, they have represented a crucial resource in human history. The aim of this review is to shed light on the molecular mechanisms and the specific genomic variants that underlie the phenotypic variability between sheep and mouflon. In this regard, we carried out a critical review of the most recent studies on the molecular mechanisms that are most accredited to be responsible for coat color and phenotype, tail size and presence of horns. We also highlight that, in such a complicate context, sheep/mouflon hybrids represent a powerful and innovative model for studying the mechanism by which the phenotypic traits related to the phenotypic responses to domestication are inherited. Knowledge of these mechanisms could have a significant impact on the selection of more productive breeds. In fact, as in a journey back in time of animal domestication, the genetic traits of today's domestic species are being progressively and deliberately shaped according to human needs, in a direction opposite to that followed during domestication.

Ancient mitochondrial genome depicts sheep maternal dispersal and migration in Eastern Asia

Sheep have been one of the most important groups of animals since ancient times. However, the knowledge of their migration routes and genetic relationships is still poorly understood. To investigate sheep maternal migration histories alongside Eurasian communications routes, in this study, we obtain mitochondrial genomes (mitogenomes) from 17 sheep remains in 6 Chinese sites and 1 Uzbekistan site dated 4429-3100 years before present (BP). By obtaining the mitogenomes from the sheep (4429-3556 BP) found in the Tongtian Cave site in Xinjiang, Altai region of northwest China, our results support the emergence of haplogroup C sheep in Xinjiang as early as 4429-3556 BP. The combined phylogenetic analyses with extant ancient and modern sheep mitogenomes suggest that the Uzbekistan-Altai region may have been a migration hub for early sheep in eastern Asia. At least two migration events have taken place for sheep crossing Eurasia to China, one passing by Uzbekistan and Northwest China to the middle and lower reaches of the Yellow River at approximately 4000 BP and another following the Altai region to middle Inner Mongolia from 4429 BP to 2500 BP. Overall, this study provides further evidence for early sheep utilization and migration patterns in Eastern Asia.

The time and place of origin of South Caucasian languages: insights into past human societies, ecosystems and human population genetics

This study re-examines the linguistic phylogeny of the South Caucasian linguistic family (aka the Kartvelian linguistic family) and attempts to identify its Urheimat. We apply Bayesian phylogenetics to infer a dated phylogeny of the South Caucasian languages. We infer the Urheimat and the reasons for the split of the Kartvelian languages by taking into consideration (1) the past distribution ranges of wildlife elements whose names can be traced back to proto-Kartvelian roots, (2) the distribution ranges of past cultures and (3) the genetic variations of past and extant human populations. Our best-fit Bayesian phylogenetic model is in agreement with the widely accepted topology suggested by previous studies. However, in contrast to these studies, our model suggests earlier mean split dates, according to which the divergence between Svan and Karto-Zan occurred in the early Copper Age, while Georgian and Zan diverged in the early Iron Age. The split of Zan into Megrelian and Laz is widely attributed to the spread of Georgian and/or Georgian speakers in the seventh-eighth centuries CE. Our analyses place the Kartvelian Urheimat in an area that largely intersects the Colchis glacial refugium in the South Caucasus. The divergence of Kartvelian languages is strongly associated with differences in the rate of technological expansions in relation to landscape heterogeneity, as well as the emergence of state-run communities. Neolithic societies could not colonize dense forests, whereas Copper Age societies made limited progress in this regard, but not to the same degree of success achieved by Bronze and Iron Age societies. The paper also discusses the importance of glacial refugia in laying the foundation for linguistic families and where Indo-European languages might have originated.

Demographic reconstruction of the Western sheep expansion from whole-genome sequences

As one of the earliest livestock, sheep (Ovis aries) were domesticated in the Fertile Crescent about 12,000-10,000 years ago and have a nearly worldwide distribution today. Most of our knowledge about the timing of their expansions stems from archaeological data but it is unclear how the genetic diversity of modern sheep fits with these dates. We used whole-genome sequencing data of 63 domestic breeds and their wild relatives, the Asiatic mouflon (O. gmelini, previously known as O. orientalis), to explore the demographic history of sheep. On the global scale, our analysis revealed geographic structuring among breeds with unidirectional recent gene flow from domestics into Asiatic mouflons. We then selected 4 representative breeds from Spain, Morocco, the United Kingdom, and Iran to build a comprehensive demographic model of the Western sheep expansion. We inferred a single domestication event around 11,000 years ago. The subsequent westward expansion is dated to approximately 7,000 years ago, later than the original Neolithic expansion of sheep and slightly predating the Secondary Product Revolution associated with wooly sheep. We see some signals of recent gene flow from an ancestral population into Southern European breeds which could reflect admixture with feral European mouflon. Furthermore, our results indicate that many breeds experienced a reduction of their effective population size during the last centuries, probably associated with modern breed development. Our study provides insights into the complex demographic history of Western Eurasian sheep, highlighting interactions between breeds and their wild counterparts.

MTaxi: A comparative tool for taxon identification of ultra low coverage ancient genomes

A major challenge in zooarchaeology is to morphologically distinguish closely related species' remains, especially using small bone fragments. Shotgun sequencing aDNA from archeological remains and comparative alignment to the candidate species' reference genomes will only apply when reference nuclear genomes of comparable quality are available, and may still fail when coverages are low. Here, we propose an alternative method, MTaxi, that uses highly accessible mitochondrial DNA (mtDNA) to distinguish between pairs of closely related species from ancient DNA sequences. MTaxi utilises mtDNA transversion-type substitutions between pairs of candidate species, assigns reads to either species, and performs a binomial test to determine the sample taxon. We tested MTaxi on sheep/goat and horse/donkey data, between which zooarchaeological classification can be challenging in ways that epitomise our case. The method performed efficiently on simulated ancient genomes down to 0.3x mitochondrial coverage for both sheep/goat and horse/donkey, with no false positives. Trials on n=18 ancient sheep/goat samples and n=10 horse/donkey samples of known species identity also yielded 100% accuracy. Overall, MTaxi provides a straightforward approach to classify closely related species that are difficult to distinguish through zooarchaeological methods using low coverage aDNA data, especially when similar quality reference genomes are unavailable. MTaxi is freely available at https://github.com/goztag/MTaxi.

Genomic perspectives on human dispersals during the Holocene

Nearly 20 y ago, Jared Diamond and Peter Bellwood reviewed the evidence for the associated spread of farming and large language families by the demographic expansions of farmers. Since then, advances in obtaining and analyzing genomic data from modern and ancient populations have transformed our knowledge of human dispersals during the Holocene. Here, we provide an overview of Holocene dispersals in the light of genomic evidence and conclude that they have a complex history. Even when there is a demonstrated connection between a demographic expansion of people, the spread of agriculture, and the spread of a particular language family, the outcome in the results of contact between expanding and resident groups is highly variable. Further research is needed to identify the factors and social circumstances that have influenced this variation and complex history.

Fine-mapping and identification of candidate causal genes for tail length in the Merinolandschaf breed

Docking the tails of lambs in long-tailed sheep breeds is a common practice worldwide. But this practice is associated with pain. Breeding for a shorter tail could offer an alternative. Therefore, this study aimed to analyze the natural tail length variation in the Merinolandschaf and to identify causal alleles for the short tail phenotype segregating within long-tailed breeds. We used SNP-based association analysis and haplotype-based mapping in 362 genotyped (Illumina OvineSNP50) and phenotyped Merinolandschaf lambs. Genome-wide significant regions were capture sequenced in 48 lambs and comparatively analyzed in various long and short-tailed sheep breeds and wild sheep subspecies. Here we show a SNP located in the first exon of HOXB13 and a SINE element located in the promotor of HOXB13 as promising candidates. These results enable more precise breeding towards shorter tails, improve animal welfare by amplification of ancestral alleles and contribute to a better understanding of differential embryonic development.

An endemic pathway to sheep and goat domestication at Aşıklı Höyük (Central Anatolia, Turkey)

Sheep and goats (caprines) were domesticated in Southwest Asia in the early Holocene, but how and in how many places remain open questions. This study investigates the initial conditions and trajectory of caprine domestication at Aşıklı Höyük, which preserves an unusually high-resolution record of the first 1,000 y of Neolithic existence in Central Anatolia. Our comparative analysis of caprine age and sex structures and related evidence reveals a local domestication process that began around 8400 cal BC. Caprine management at Aşıklı segued through three viable systems. The earliest mode was embedded within a broad-spectrum foraging economy and directed to live meat storage on a small scale. This was essentially a "catch-and-grow" strategy that involved seasonal capture of wild lambs and kids from the surrounding highlands and raising them several months prior to slaughter within the settlement. The second mode paired modest levels of caprine reproduction on site with continued recruitment of wild infants. The third mode shows the hallmarks of a large-scale herding economy based on a large, reproductively viable captive population but oddly directed to harvesting adult animals, contra to most later Neolithic practices. Wild infant capture likely continued at a low level. The transitions were gradual but, with time, gave rise to early domesticated forms and monumental differences in human labor organization, settlement layout, and waste accumulation. Aşıklı was an independent center of caprine domestication and thus supports the multiple origins evolutionary model.