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Herded and hunted goat genomes from the dawn of domestication in the Zagros Mountains.

ABSTRACT: The Aceramic Neolithic (∼9600 to 7000 cal BC) period in the Zagros Mountains, western Iran, provides some of the earliest archaeological evidence of goat (Capra hircus) management and husbandry by circa 8200 cal BC, with detectable morphological change appearing ∼1,000 y later. To examine the genomic imprint of initial management and its implications for the goat domestication process, we analyzed 14 novel nuclear genomes (mean coverage 1.13X) and 32 mitochondrial (mtDNA) genomes (mean coverage 143X) from two such sites, Ganj Dareh and Tepe Abdul Hosein. These genomes show two distinct clusters: those with domestic affinity and a minority group with stronger wild affinity, indicating that managed goats were genetically distinct from wild goats at this early horizon. This genetic duality, the presence of long runs of homozygosity, shared ancestry with later Neolithic populations, a sex bias in archaeozoological remains, and demographic profiles from across all layers of Ganj Dareh support management of genetically domestic goat by circa 8200 cal BC, and represent the oldest to-this-date reported livestock genomes. In these sites a combination of high autosomal and mtDNA diversity, contrasting limited Y chromosomal lineage diversity, an absence of reported selection signatures for pigmentation, and the wild morphology of bone remains illustrates domestication as an extended process lacking a strong initial bottleneck, beginning with spatial control, demographic manipulation via biased male culling, captive breeding, and subsequently phenotypic and genomic selection.

SUBMITTER: Daly KG

PROVIDER: S-EPMC8237664 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundThe current extensive use of the domestic goat (Capra hircus) is the result of its medium size and high adaptability as multiple breeds. The extent to which its genetic variability was influenced by early domestication practices is largely unknown. A common standard by which to analyze maternally-inherited variability of livestock species is through complete sequencing of the entire mitogenome (mitochondrial DNA, mtDNA).ResultsWe present the first extensive survey of goat mitogenomic variability based on 84 complete sequences selected from an initial collection of 758 samples that represent 60 different breeds of C. hircus, as well as its wild sister species, bezoar (Capra aegagrus) from Iran. Our phylogenetic analyses dated the most recent common ancestor of C. hircus to ~460,000 years (ka) ago and identified five distinctive domestic haplogroups (A, B1, C1a, D1 and G). More than 90 % of goats examined were in haplogroup A. These domestic lineages are predominantly nested within C. aegagrus branches, diverged concomitantly at the interface between the Epipaleolithic and early Neolithic periods, and underwent a dramatic expansion starting from ~12-10 ka ago.ConclusionsDomestic goat mitogenomes descended from a small number of founding haplotypes that underwent domestication after surviving the last glacial maximum in the Near Eastern refuges. All modern haplotypes A probably descended from a single (or at most a few closely related) female C. aegagrus. Zooarchaelogical data indicate that domestication first occurred in Southeastern Anatolia. Goats accompanying the first Neolithic migration waves into the Mediterranean were already characterized by two ancestral A and C variants. The ancient separation of the C branch (~130 ka ago) suggests a genetically distinct population that could have been involved in a second event of domestication. The novel diagnostic mutational motifs defined here, which distinguish wild and domestic haplogroups, could be used to understand phylogenetic relationships among modern breeds and ancient remains and to evaluate whether selection differentially affected mitochondrial genome variants during the development of economically important breeds.

Project description:Abrupt changes in temperature have especially strong impacts on fragile ecosystems located in semi-arid regions. In this study, we analyzed tree-ring widths (TRW) of Mediterranean cypress (Cupressus sempervirens var. horizontalis) in the Zagros Mountains, Iran. Furthermore, we separately measured earlywood width (EWW) and latewood width (LWW) of Persian oak (Quercus brantii Lindl.) to examine if intra-annual resolution of tree-ring parameters of Q. brantii tree rings can be used as high-resolution paleoclimate proxies. Climate-growth relationships revealed that mean monthly maximum temperatures (Tmax) are a dominant factor determining radial tree growth and negatively affect both oak and cypress in the Zagros Mountains. Accordingly, we reconstructed two different seasonal windows of past Tmax variability, namely, January-March and June-August over the periods 1860-2015 and 1560-2015, respectively. Regime shift detection identified twelve warm and nine cold significant regime shifts in our summer Tmax reconstructions. The longest hot summer period occurred in the twentieth century, and two warm regime shifts occurred in 1999 and 2008. The highest values of the warm summer regime shift index occurred in 2008, which coincided with fungal pathogen attacks and insect outbreak of the oak leaf roller moth (Tortrix viridana L.) in the Zagros oak woodlands. Interestingly, we found common warm and cold periods in historic climate variability between the summer and winter Tmax reconstructions. Warm and cold regime shifts occurred simultaneously from 1955 to 2015, and significant regional warm summer and winter regime shifts have occurred between 2008 and 2015. The winter and summer Tmax reconstructions show high spatial correlations with large areas in West Asia, North Africa, and the eastern Mediterranean region. Our results strengthen initial studies on past climate variability in Iran and contribute to an enhanced understanding of past temperature variability in West Asia.

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Herded and hunted goat genomes from the dawn of domestication in the Zagros Mountains.

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