Hitomi Hongo

Mitochondrial DNA analysis shows a Near Eastern Neolithic origin for domestic cattle and no indication of domestication of European aurochs.

The extinct aurochs (Bos primigenius primigenius) was a large type of cattle that ranged over almost the whole Eurasian continent. The aurochs is the wild progenitor of modern cattle, but it is unclear whether European aurochs contributed to this process. To provide new insights into the demographic history of aurochs and domestic cattle, we have generated high-confidence mitochondrial DNA sequences from 59 archaeological skeletal finds, which were attributed to wild European cattle populations based on their chronological date and/or morphology. All pre-Neolithic aurochs belonged to the previously designated P haplogroup, indicating that this represents the Late Glacial Central European signature. We also report one new and highly divergent haplotype in a Neolithic aurochs sample from Germany, which points to greater variability during the Pleistocene. Furthermore, the Neolithic and Bronze Age samples that were classified with confidence as European aurochs using morphological criteria all carry P haplotype mitochondrial DNA, suggesting continuity of Late Glacial and Early Holocene aurochs populations in Europe. Bayesian analysis indicates that recent population growth gives a significantly better fit to our data than a constant-sized population, an observation consistent with a postglacial expansion scenario, possibly from a single European refugial population. Previous work has shown that most ancient and modern European domestic cattle carry haplotypes previously designated T. This, in combination with our new finding of a T haplotype in a very Early Neolithic site in Syria, lends persuasive support to a scenario whereby gracile Near Eastern domestic populations, carrying predominantly T haplotypes, replaced P haplotype-carrying robust autochthonous aurochs populations in Europe, from the Early Neolithic onward. During the period of coexistence, it appears that domestic cattle were kept separate from wild aurochs and introgression was extremely rare.

Pig Domestication and Human-Mediated Dispersal in Western Eurasia Revealed through Ancient DNA and Geometric Morphometrics

Zooarcheological evidence suggests that pigs were domesticated in Southwest Asia ∼8,500 BC. They then spread across the Middle and Near East and westward into Europe alongside early agriculturalists. European pigs were either domesticated independently or more likely appeared so as a result of admixture between introduced pigs and European wild boar. As a result, European wild boar mtDNA lineages replaced Near Eastern/Anatolian mtDNA signatures in Europe and subsequently replaced indigenous domestic pig lineages in Anatolia. The specific details of these processes, however, remain unknown. To address questions related to early pig domestication, dispersal, and turnover in the Near East, we analyzed ancient mitochondrial DNA and dental geometric morphometric variation in 393 ancient pig specimens representing 48 archeological sites (from the Pre-Pottery Neolithic to the Medieval period) from Armenia, Cyprus, Georgia, Iran, Syria, and Turkey. Our results reveal the first genetic signatures of early domestic pigs in the Near Eastern Neolithic core zone. We also demonstrate that these early pigs differed genetically from those in western Anatolia that were introduced to Europe during the Neolithic expansion. In addition, we present a significantly more refined chronology for the introduction of European domestic pigs into Asia Minor that took place during the Bronze Age, at least 900 years earlier than previously detected. By the 5th century AD, European signatures completely replaced the endemic lineages possibly coinciding with the widespread demographic and societal changes that occurred during the Anatolian Bronze and Iron Ages.

Ancient Mitochondrial DNA Reveals the Origin of Sus scrofa from Rebun Island, Japan

Abstract. The Kabukai A site (5 to 8C A.D.) of the Okhotsk cultural area is on Rebun Island, a small island near the coast, north–northwest of Hokkaido, Japan. Specimens of Sus scrofa, called the Sakhalin pig, were discovered in five cultural layers at the Kabukai A site. Ancient DNA was extracted from the remains of 42 Sakhalin pig bones. Thirty-nine nucleotide sequences of the 574-bp mitochondrial DNA control region, estimated to have originated from at least 21 individuals, were amplified and analyzed phylogenetically. Nine distinct haplotypes (A1, A2, A3, B1, B2, C1, C2, D1, and D2) from this site were classified into four haplotype groups (A, B, C, and D) by parsimonious network analysis. Phylogenetic analysis of 9 ancient and 55 modern haplotypes indicated that the population of Sakhalin pigs at the Kabukai A site belonged to two distinct clusters; haplotype groups A and B formed a cluster comprised only of themselves, and haplotype groups C and D belonged to the cluster of one of the two genetic groups of Japanese wild boars uniquely distributed in the western part of Japan, including one northeast Mongolian wild boar. Analysis of the haplotype distribution among three archaeological sites and their historical transitions among the five layers reflecting the cultural periods at the Kabukai A site suggests that the Sakhalin pig populations were introduced from Sakhalin island and the Amur River basin in the northeastern Eurasian continent together with some cultural influences.

Variation in Mitochondrial DNA of Vietnamese Pigs: Relationships with Asian Domestic Pigs and Ryukyu Wild Boars

Abstract Mitochondrial DNA (mtDNA) sequences (574 bp) of 30 Vietnamese pigs (large and small) were examined and compared with those of 61 haplotypes from wild boars and domestic pigs from various locations in Asia. The large Vietnamese pigs had genetic links to Ryukyu wild boars in southern Japan. The small Vietnamese pigs were closely related to other East Asian domestic pigs. These results indicate that Vietnamese pigs are genetically diverse and may be descendents of wild and domestic pigs from other regions of Asia.

Prehistoric introduction of domestic pigs onto the Okinawa Islands: Ancient mitochondrial DNA evidence

Abstract. Ancient DNAs of Sus scrofa specimens excavated from archaeological sites on the Okinawa islands were examined to clarify the genetic relationships among prehistoric Sus scrofa, modern wild boars and domestic pigs inhabiting the Ryukyu archipelago, the Japanese islands, and the Asian continent. We extracted remain DNA from 161 bone specimens excavated from 12 archaeological sites on the Okinawa islands and successfully amplified mitochondrial DNA control region fragments from 33 of 161 specimens. Pairwise difference between prehistoric and modern S. scrofa nucleotide sequences showed that haplotypes of the East Asian domestic pig lineage were found from archaeological specimens together with Ryukyu wild boars native to the Ryukyu archipelago. Phylogenetic analysis of 14 ancient sequences (11 haplotypes; 574 bp) indicated that S. scrofa specimens from two Yayoi-Heian sites (Kitahara and Ara shellmiddens) and two Recent Times sites (Wakuta Kiln and Kiyuna sites) are grouped with modern East Asian domestic pigs. Sus scrofa specimens from Shimizu shellmidden (Yayoi-Heian Period) were very closely related to modern Sus scrofa riukiuanus but had a unique nucleotide insertion, indicating that the population is genetically distinct from the lineage of modern Ryukyu wild boars. This genetic evidence suggests that domestic pigs from the Asian continent were introduced to the Okinawa islands in the early Yayoi-Heian period (1700–2000 BP), or earlier.

The Process of Ungulate Domestication at Çayönü, Southeastern Turkey: A Multidisciplinary Approach focusing on Bos sp. and Cervus elaphus

Hongo H., Pearson J., Öksüz B. & Igezdi G. 2009. — The Process of Ungulate Domestication at Çayönü, Southeastern Turkey: A Multidisciplinary Approach focusing on Bos sp. and Cervus elaphus. Anthropozoologica 44(1): 63-78. ABSTRACT Bos and Cervus remains from Prepottery and Pottery Neolithic levels at Çayönü Tepesi are examined employing a multidisciplinary approach, combining the analysis of morphology, age profiles, and stable isotopes in bone collagen. The results show that the process of cattle domestication started at about the same time as three other ungulate taxa (sheep, goats and pigs), by the Channelled Building Subphase (end of Early PPNB/ beginning of Middle PPNB). Two stages are evident in the process of domestication: the initial appearance of domestic animals could be detected in the faunal remains by the appearance of some small-sized individuals and subtle changes in the kill-off patterns, as well as in the changes in stable isotope ratios of carbon and nitrogen. While hunting of wild progenitors continued, there was an overall decrease in the proportion of miscellaneous wild taxa in the assemblage. The second stage of the domestication process begins in the late-final PPNB, suggested by marked size reduction and demographic change, namely the increase of females in the assemblage, as well as dramatic increase in sheep and goats.

Food and social complexity at Çayönü Tepesi, southeastern Anatolia: Stable isotope evidence of differentiation in diet according to burial practice and sex in the early Neolithic

Highlights ► People from secondary burials (Skull Building) had different diets to those buried beneath houses. ► In the later Cell Plan sub-phase of occupation males and females had different diets. ► Dietary variation resulted from different types and/or amounts of meat and plant protein. ► The isotope results follow sex and burial practice suggesting food reinforced social behaviours.

Prehistoric Sado Island Populations of Sus scrofa Distinguished from Contemporary Japanese Wild Boar by Ancient Mitochondrial DNA

Ancient mitochondrial DNA (mtDNA) mainly from Jomon Period Sus scrofa bone specimens (6,100–1,700 years old) was examined to clarify the genetic relationships between prehistoric and contemporary S. scrofa on Hokkaido, Honshu, Sado, and Izu islands of the Japanese Archipelago. Phylogenetic analysis of the mtDNA control region (574 bp) and analysis of pairwise nucleotide differences between prehistoric and contemporary S. scrofa sequences showed the following relationships between these groups: (1) a group genetically similar to contemporary Japanese wild boars was found mainly on Honshu Island, Hokkaido Island, and the Izu Islands, and (2) a monophyletic group distinct from contemporary Japanese wild boars was found on Sado Island. These results suggest that prehistoric people introduced S. scrofa from Honshu Island to Hokkaido Island and the Izu Islands. The estimated divergence times between the prehistoric Sado group and the other prehistoric S. scrofa is approximately congruent with the geological isolation of Sado Island from Honshu Island. Our results suggest that this extinct S. scrofa population was present on Sado Island as recently as around 2,000 years ago.

Science in Archaeology: A Review

Author(s): Patrick E. McGovern, Thomas L. Sever, J. Wilson Myers, Eleanor Emlen Myers, Bruce Bevan, Naomi F. Miller, S. Bottema, Hitomi Hongo, Richard H. Meadow, Peter Ian Kuniholm, S. G. E. Bowman, M. N. Leese, R. E. M. Hedges, Frederick R. Matson, Ian C. Freestone, Sarah J. Vaughan, Julian Henderson, Pamela B. Vandiver, Charles S. Tumosa, Curt W. Beck, Patricia Smith, A. M. Child, A. M. Pollard, Ingolf Thuesen, Catherine Sease Source: American Journal of Archaeology, Vol. 99, No. 1 (Jan., 1995), pp. 79-142 Published by: Archaeological Institute of America Stable URL: http://www.jstor.org/stable/506880 Accessed: 16/07/2009 14:57

mtDNA variation in Vietnamese pigs, with particular emphasis on the genetic relationship between wild boars from Vietnam and the Ryukyu Islands

ABSTRACT To examine the genetic origin of Ryukyu wild boar, we sequenced mitochondrial DNA (mtDNA: 574-bp) from Vietnamese wild boar and Vietnamese indigenous domestic pigs and compared these sequences with the mtDNA of Ryukyu wild boar by phylogenetic analysis. Numerous Vietnamese wild boars were genetically related to Ryukyu wild boar, suggesting that descendants of the ancestors of Ryukyu wild boar still inhabit Vietnam. The mtDNA sequences of Vietnamese indigenous domestic pigs are extremely diverse and are thought to have contributed to the diversity of mtDNA among East Asian domestic pigs.