Protein sequences bound to mineral surfaces persist into deep time

Proteins persist longer in the fossil record than DNA, but the longevity, survival mechanisms and substrates remain contested. Here, we demonstrate the role of mineral binding in preserving the protein sequence in ostrich (Struthionidae) eggshell, including from the palaeontological sites of Laetoli (3.8 Ma) and Olduvai Gorge (1.3 Ma) in Tanzania. By tracking protein diagenesis back in time we find consistent patterns of preservation, demonstrating authenticity of the surviving sequences. Molecular dynamics simulations of struthiocalcin-1 and -2, the dominant proteins within the eggshell, reveal that distinct domains bind to the mineral surface. It is the domain with the strongest calculated binding energy to the calcite surface that is selectively preserved. Thermal age calculations demonstrate that the Laetoli and Olduvai peptides are 50 times older than any previously authenticated sequence (equivalent to ~16 Ma at a constant 10°C)

Ancient goat genomes reveal mosaic domestication in the Fertile Crescent.

Current genetic data are equivocal as to whether goat domestication occurred multiple times or was a singular process. We generated genomic data from 83 ancient goats (51 with genome-wide coverage) from Paleolithic to Medieval contexts throughout the Near East. Our findings demonstrate that multiple divergent ancient wild goat sources were domesticated in a dispersed process that resulted in genetically and geographically distinct Neolithic goat populations, echoing contemporaneous human divergence across the region. These early goat populations contributed differently to modern goats in Asia, Africa, and Europe. We also detect early selection for pigmentation, stature, reproduction, milking, and response to dietary change, providing 8000-year-old evidence for human agency in molding genome variation within a partner species

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

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

Origins and genetic legacy of prehistoric dogs

Dogs were the first domestic animal, but little is known about their population history and to what extent it was linked to humans. We sequenced 27 ancient dog genomes and found that all dogs share a common ancestry distinct from present-day wolves, with limited gene flow from wolves since domestication but substantial dog-to-wolf gene flow. By 11,000 years ago, at least five major ancestry lineages had diversified, demonstrating a deep genetic history of dogs during the Paleolithic. Coanalysis with human genomes reveals aspects of dog population history that mirror humans, including Levant-related ancestry in Africa and early agricultural Europe. Other aspects differ, including the impacts of steppe pastoralist expansions in West and East Eurasia and a near-complete turnover of Neolithic European dog ancestry

The Origin of Partially Digested Bones Recovered from Archaeological Contexts in Israel

The identification, distribution and origin of partially digested bones in archaeological sites from Israel is discussed. Such finds have been cited by researchers as indicating the presence of domesticated dogs at a site. However, evidence is presented here to show that other, non-domestic carnivores may be responsible. This is based both on studies of partially digested bones from modern carnivore bone assemblages and on the presence of such bones in prehistoric deposits pre-dating the domestication of the dog.Ce travail traite de l'identification, de la distribution et de l'origine d'ossements partiellement digérés provenant de gisements archéologiques d'Israël. Certains chercheurs ont déjà souligné ce phénomène et l'expliquent par la présence de chiens domestiques. Les faits présentés dans ce travail démontrent que d'autres carnivores, non domestiques, sont peut être tout aussi responsables. Ces études ont été faites tant sur des ossements partiellement digérés de carnivores modernes que sur les mêmes ossements provenant de gisements préhistoriques antérieurs à la domestication du chien.Kolska Horwitz Liora R. The Origin of Partially Digested Bones Recovered from Archaeological Contexts in Israel. In: Paléorient, 1990, vol. 16, n°1. pp. 97-106

Temporal and Spatial Variation in Neolithic Caprine Exploitation Strategies : a Case Study of Fauna from the Site of Yiftah'el (Israel)

Three different strategies of animal exploitation appear to have co-existed during the mid-Pre-Pottery Neolithic В (PPNB) in the Southern Levant. The first, characteristic of sites in the Jordan Valley and adjacent areas was based on "incipient domestication " of goats (morphometrically identical to wild forms), a taxa which dominates the faunal assemblage. The second strategy, which is found in sites located in the western part of the Mediterranean region, was based on gazelle hunting with wild goats represented in markedly lower numbers than in the Jordan Valley sites. Here too the Capra remains are morphometrically indistinguishable from those of wild goat. A third strategy typifies sites located in the arid regions of the Sinai Peninsula, Judean and Eastern Jordanian deserts, and reflects greater continuity with Epipaleolithic hunting and gathering subsistence with only wild taxa represented. Analyses of the Neolithic faunal assemblages from the site of Yiftah'el (Lower Galilee, Israel) were carried out in order to investigate whether the observed inter-site variation in subsistence base reflects the introduction and gradual dispersion of domestic goats as opposed to their autochthonous domestication. The results from Yiftah'el show a gradual shift over time in species composition, kill-off pattern and size of goats, indicative of autochthonous domestication of Capra.Trois différentes stratégies d'exploitation animale ont coexisté durant la période du PPNB moyen dans le sud du Levant. La première caractérise les sites de la vallée du Jourdain et des régions adjacentes. Elle correspond à un proto-élevage de chèvres (morphologie identique à celle des formes sauvages) qui domine les assemblages fauniques. La seconde stratégie, qui correspond à une chasse à la gazelle ainsi qu 'une fréquence de chèvres sauvages moins élevée que dans la vallée du Jourdain, est localisée dans la partie occidentale de la région méditerranéenne. Comme dans le cas précédent, la morphologie des os de Capra ne se distingue pas de ceux des animaux sauvages. La troisième stratégie s 'observe dans les régions arides des déserts du Sinaï, de Judée et de la partie orientale de la Jordanie. Elle reflète une forte continuité des traditions épipaléolithiques de chasse et de cueillette, comprenant exclusivement des espèces sauvages. L'analyse de la faune néolithique de Yiftah'el (Basse Galilée, Israël) a été entreprise dans le but de tester si les variations des stratégies de subsistance inter-site reflètent une introduction de chèvres domestiques et leur dispersion graduelle ou, au contraire, une domestication autochtone. Les résultats montrent une évolution chronologique graduelle du spectre faunique, des âges d'abattage et de la taille des chèvres, trois facteurs qui, combinés, prouvent la domestication locale de Capra.Horwitz Liora Kolska. Temporal and Spatial Variation in Neolithic Caprine Exploitation Strategies : a Case Study of Fauna from the Site of Yiftah'el (Israel). In: Paléorient, 2003, vol. 29, n°1. pp. 19-58