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Proceedings of the 9th Conference of the International Councilof Archaeozoology, Durham, August 2002Series Editors: Keith Dobney, Peter Rowley-Conwy and Umberto Albarella

Edited byJ.-D. Vigne, J. Peters and D. Helmer

First Steps ofAnimal Domestication

New archaeozoological approaches

© Oxbow Books 2005

ISBN 1 84217 121 6

Contents

Preface .............................................................................................................................................................................. vii Keith Dobney, Peter Rowley-Conwy and Umberto Albarella

1. New archaeological approaches to trace the first steps of animal domestication:general presentation, reflections and proposals ......................................................................................................... 1Jean-Denis Vigne, Daniel Helmer and Joris Peters

Principles and concepts2. Experimental animal domestication and its application to the study of animal exploitation in prehistory ............... 18

Benjamin S. Arbuckle

3. The domestication of the wolf – the inevitable first? ............................................................................................... 34Werner Müller

4. Breaking the mold: a consideration of variation in the evolution of animal domestication ..................................... 41Richard W. Redding

New techniques and their application5. Assessing the origin and diffusion of domestic goats using ancient DNA ............................................................ 50

Helena Fernández, Pierre Taberlet, Marjan Mashkour, Jean-Denis Vigne and Gordon Luikart

6. Kernel smoothing and mixture analyses for the determination of the sex ratios at death,at the beginning of domestication of ungulates ....................................................................................................... 55Hervé Monchot, Marjan Mashkour and Jean-Denis Vigne

7. Two novel methods for the study of dental morphological variation in Sus scrofa,in order to identify separate breeding groups within archaeological assemblages ................................................. 61Sylvia Warman

Animal domestication in West Asia8. Pig exploitation at Hagoshrim; a prehistoric site in the Southern Levant ................................................................ 80

Annat Haber, Tamar Dayan and Nimrod Getz

9. Identifying early domestic cattle from Pre-Pottery Neolithic sites on the Middle Euphratesusing sexual dimorphism ........................................................................................................................................... 86Daniel Helmer, Lionel Gourichon, Hervé Monchot, Joris Peters and Maria Saña Segui

10. The upper Euphrates-Tigris basin: cradle of agro-pastoralism? ............................................................................. 96Joris Peters, Angela von den Dreisch and Daniel Helmer

11. A View from the Zagros: new perspectives on livestock domestication in the Fertile Crescent .......................... 125Melinda A. Zeder

Animal domestication in East Asia12. Wild pig? Or domesticated boar? An archaeological view on the domestication of Sus scrofa in Japan .............. 148

Akira Matsui, Naotaka Ishiguro, Hitomi Hongo and Masao Minagawa

13. Wild boar remains from the Neolithic (Jomon Period) sites on the Izu Islandsand in Hokkaido Island, Japan ................................................................................................................................. 160Kyomi Yamazaki, Osamu Takahashi, Hiroki Sugawara, Naitaka Ishiguro and Hideki Endo

148 Akira Matsui, Naotaka Ishiguro, Hitomi Hongo and Masao Minagawa

12. Wild pig? Or domesticated boar? An archaeologicalview on the domestication of Sus scrofa in Japan

Akira Matsui, Naotaka Ishiguro, Hitomi Hongo and Masao Minagawa

9th ICAZ Conference, Durham 2002The First Steps of Animal Domestication (eds J.-D. Vigne, J. Peters and D. Helmer) pp. 148–159

Introduction

The wild boar (Sus scrofa) is distributed from temperateand tropical Eurasia to northern Africa. It has been saidthat the wild boar was domesticated in Western Asia asearly as or slightly later than sheep and goats (Hongo &Meadow 1998, 2000; Peters et al. 1999; Ervynck et al.2001).

The Japanese wild boar (Sus scrofa leucomystax) isdistributed on Honshu, Shikoku and Kyushu islands butnot in Hokkaido (Fig. 1). In the southern islands, theRyukyu wild boar (Sus scrofa riukiuanus) is distributedacross Okinawa, Amami and Yaeyama islands. TheRyukyu wild boar was thought to be a subspecies of theJapanese wild boar, and their small size considered an

adaptation to life on a small island. DNA analysis byIshiguro suggested the possibility that they originated insoutheastern Asia, because the mtDNA of the large sizewild boar in Vietnam is similar to that of the Ryukyuwild boar (Hongo et al. 2002)

Before World War II, the paleontologist H. Matsumoto(1930) theorized that, during the Jomon Period (10,000to 3000 BP), the wild boar in Northeastern Japan was arelic of the Pleistocene because of its extremely largesize. Thus, he stated that it should be separated from themodern Japanese wild boar and renamed the Nippon wildboar (Sus nipponicus). The Asian wild boar was alsoclassified as Sus scrofa vittatus due to its shorterlachrymal bone (Clutton-Brook 1981, p. 72). In the past

The domestic pig, Sus scrofa, is one of the hallmark species representing the global manipulation of wild animalsby humans. It is now clear that unraveling the zoological nomenclature of the genus Sus in Europe and Asia (thereare currently 15 subspecies designations) requires more than the use of traditional methods detailing cranialmorphological criteria. One of the fundamentally important issues in zooarchaeology in East Asia and Japan,including the Ryukyu (Okinawa) archipelago, has been the timing and nature of the domestication of the pig fromits wild cousin, the wild boar; research on this problem in Japan dates to before the 1930’s. Therefore, we appliedmtDNA and stable carbon and nitrogen isotope analysis in order to separate the domestic pigs from the wild boarsin bone samples recovered from the Japanese mainland, Ryukyu archipelago, Korea, and Vietnam. The resultsdemonstrate that the domestic pig and wild boar can be distinguished by these methods. Carbon and nitrogenisotope analysis shows that two feeding patterns developed during domestication, one based on consumption ofhuman leftovers and human excrements (high 15N content) and the other utilizing cultivated C4 plants. We concludethat the isotopic signatures of Sus remains from archaeological sites in East Asia form three clusters. Two clustersreflect two different methods of raising pigs in Korea. In addition, wild boars consuming solely natural C3 plantsshow features similar to sika deer. Genetic relationships were examined using 574–bp mitochondrial DNA controlregion sequences for prehistoric Sus bones on the Ryukyu islands, domestic pigs on the Ryukyu archipelago and theAsian continent, and modern wild boars. Some of the Sus samples from Yayoi sites (ca. 2,000 cal. BP) andpremodern sites (ca. 16–19th c. AD) clustered phylogenetically with East Asian domesticated pigs. This indicatesthat domestic pigs were bred on Okinawa during the Yayoi Period, 2000 years ago. Furthermore, it is apparent thatthe Sus sp., although we may not call them domestic pigs, that had been bred appeared by at least 7000 BP onOkinawa.

149Wild pig? Or domesticated boar?

few decades, however, various subspecies of wild boarhave been integrated into one species as Sus scrofa,including S. s. vittatus and S. s. riukiuanus.

The revision by Fujita et al. (2000) concludes that S.nipponicus belongs to S. scrofa, basing on skull and teethcharacteristics. This designation includes wild boarremains from the Middle Pleistocene in Honshu. Thegeneral revision by Groves (1981) is the most currentstudy on the taxonomy and phylogeny of the genus Sus.He lists 15 subspecies of S. scrofa, basing on morph-ological characteristics of the skull and teeth. S. scrofa iswidespread in the northern Africa, Eurasia and its alliedislands, and has a wide range of morphological variationrelative to its surrounding ranges. This variation makesit difficult to establish taxonomy and phylogeny for Susscrofa. However, in Japan two subspecies, S. s. leuco-mystax and S. s. riukiuanus, can be clearly recognized bysize and teeth morphology.

General issues of pig domestication in Japan

In general, strong indication for the domestication of thepig have been determined using the following criteria:

1) The appearance of one species at archaeological sitesbeyond its original distribution,

2) A decrease in body size compared to its wildancestors,

3) An imbalance in age and sex ratios.

In Japan, the first criterion is the most effective foraddressing the domestication issue.

Wild boar remains were found in prehistoric sites,from the Jomon and Yayoi periods, even on small isolatedislands where large wild mammals have never survivednaturally. The earliest known wild boar remains fromremote islands were found at the Shimotakabora site onOshima Island, one of the Izu islands in Tokyo Prefecture.The site is dated to the Initial Jomon period, 6–7,000years BP. Boar remains have also been found at archaeo-logical sites in other Izu Islands from the Jomon periodto the Kofun period (around the 7th century AD). K.Yamazaki (2001) found that they were smaller than wild

Figure 1. Map of Okinawa and adjoining area with archaeological sites cited in the text.


boars in Honshu Island and theorized that they weresemi-domesticated by the Jomon inhabitants of thesesmall islands.

Boar bones are also found on Sado Island in NiigataPrefecture at Jomon and Yayoi sites. We selected a sampleof the Sus remains recovered from the Fujizuka shellmidden, dating to the Middle Jomon (ca. 4,500 BP) foranalysis. In addition, we found that they are almost aslarge as the Honshu population, and that their DNA issomewhat different from the Japanese wild boar. Weconcluded that they are a relic population of their Pleisto-cene wild ancestors (Morii et al. 2002).

In the late 1980’s, Nishimoto (1989) reported that thedomesticated pigs were introduced into the Japanesearchipelago from Korea or China at the beginning of theYayoi Period, ca. 3–500 BP. His arguments were basedon morphological and palaeopathologial indicators.Nishimoto (1991) also proposed the existence of manyYayoi pigs included in the Sus remains recovered frompreviously excavated Yayoi sites. The idea of the existenceof domesticated pigs in the Yayoi period has becomewidely accepted by many Japanese archaeologists.Nishimoto also argued for the presence of a small numberof domesticated pigs from the Sus bones recovered fromthe Torihama shell midden in Fukui Prefecture duringthe Early Jomon period (ca. 6,000 BP). His idea of pigdomestication from as early as the Early Jomon wascriticized archaeologically by M. Watanabe (2000), andon molecular biological grounds by T. Ozawa (2000).Ozawa couldn’t identify domesticated pigs mtDNA inhis sample and thus denied the existence of domesticatedpigs during the Jomon and Yayoi periods. Ozawa’smethod of analysis, however, was simpler and his samplewas smaller than those used by Ishiguro. In short, theexistence of Yayoi pigs has remained controversial topicin Japan over the past several years.

Application of ancient mtDNA analysis to thequestion for the origin of pig domestication

Archaeological issues and materials

Matsui (1997) reported on the faunal remains from theGushibaru shell midden on Iejima island, adjacent toOkinawa (Fig. 1). This shell midden yielded indigenouspottery with a small amount of Yayoi pottery that ischaracteristic of Kyushu island. Although the Yayoiperiod is characterized as the first agricultural societybetween ca. 500 cal. BC and early 3rd AD , it is not clearthat the contemporaneous Okinawa culture had adoptedagriculture and some archeologists refer to it as theOkinawan Later Shell Midden period. Matsui (1997)pointed out that Sus remains of unusually large size wereincluded among the small Ryukyu wild boar remains. Healso suggested that the large individuals in the assemblagewere imported and kept from Kyushu because of their

association with Yayoi pottery, and that they might bedomesticated pigs.

The Gushibaru Sus specimens were broken into smallfragments and in most cases, the articular ends of longbones were missing. Thus, it was not possible tostatistically compare the size of the Sus bones from thesite with Yayoi boar remains or with the modern Japanesewild boar. It was also difficult to separate the samplesinto two populations by observations of morphologicalnon-metric traits, since there were no clear boundariesbetween the large or small bone samples. However, heshowed that about 10 percent of the fragments werederived from large sized boar. He also measured thelength and width of the lower third molar excavated fromvarious sites in Okinawa and made it clear that they hadbecome larger from 6000 BP (the Early Jomon times,based on samples from the Noguni B site) to 2500 BP(the Early Yayoi period, based on samples from theGushibaru midden and other shell middens; see Fig. 2).In order to verify the initial observation that the largesized bones represented domesticated pigs, the Sussamples from the Gushibaru shell midden, as well asboth modern and ancient Ryukyu wild boar specimenswere subjected to mtDNA analysis.

DNA method

As the preservation of ancient DNA in archaeologicalspecimens is often poor and too fragmentary for amp-lification, it is difficult to construct a genealogical chartof the Japanese and Ryukyu wild boar groups (Okumuraet al. 1996). The following procedure was adopted toamplify the ancient DNA.

Three primer sets, A, B, and C, designed within thepig mtDNA control region were used in the analysis.Primers mitL76(5'-AATATGCGACCCCAAAAATrTAACCATT130)and mitH62 (5'-CCTOCCAAOCGGGTrocTGG351)for set A,primers mitL119(5'-CAGTCAACATGCGTATCACC301) and mitH124(5'-ATGOCT-GAGTCCAAOCATCC567) for set B,and primers mitL104(5'-TGGA-CTAGTGACTAATCAGCCCAT518) andmitH106 (5'-ACGT-GTACGCACGTGTACGC704) forset C amplify 258–, 305–, and 229–bp fragments,respectively (Watanobe et al. 2001).The numbers on the upper right of the primers denote thecorresponding nucleotide positions of the 3' -terminalnucleotide of the primers (Okumura et al. l996). L and Hdesignate light and heavy strands respectively.

PCRs were made using the following conditions: onecycle of DNA denaturation and AmpliTaq Gold (PerkinElmer) activation at 95ºC for 10 minutes, annealing at57ºC (60ºC for primer set A) for 1 minute, and extensionat 72ºC for 1 minute were followed by 50 cycles ofdenaturation at 94ºC for 30 s, annealing at 57ºC (60ºC)


for 30s, and extension at 72ºC for 1 minutes. When fewor no PCR products were detected, a semi-nested PCRstrategy was used. Semi-nested PCR amplifications werecarried out with primers mitL76 and mitH61 (5'-CTGGTTTCACGCG-GCATGG336) for set A, primersmitL120 (5'-ACCGCCATTAGAT-CACGAOC318) andmitH124 for set B, and primers mitL105 (5'-CCATOCTCACACATAACTGAGGTT537) and mitH106 for set C, with 1 micro of the first PCR product for30 cycles as described above. To ensure the reliability ofthe results, we repeated the amplifications at least twicefor each sample, and blank extracts were amplified inparallel with the samples.

PCR products were purified using a Centricon 100micro-concentrator (Amicon) for use as sequencingtemplates. Nucleotide sequences of both strands weredetermined using an Applied Biosystems 377 DNAsequencer with a BigDye Terminator Cycle SequencingKit (Applied Biosystems). When nucleotide sequencesobtained from two independent PCR products differedfrom each other, a third PCR amplification and sub-sequent direct sequencing were carried out to verify thesequence. Moreover, the nucleotide sequences wereindependently verified in a second laboratory. A 574 bpsequence was obtained by connecting the three DNAfragments amplified by primer sets A, B, and C(Watanobe et al. 2002, 224).

Results of mtDNA analysis

The results of the analysis (Tab. 1, 2, 3) yielded aneighbor-joining tree for Sus scrofa related to ancientmtDNA and modern specimens (Fig. 3).

At first, the results of mtDNA analysis were not clearenough to identify the nature of the Sus bones from theGushibaru shell midden. Most of the samples of the site

were identified as being native Ryukyu wild boar inorigin. A large mature male mandible might indicatethat the prehistoric people at Gushibaru shell middenkept only male pigs for breeding purposes. If they keptmale domestic pigs and used females from the indigenousRyukyu wild boar population for crossbreeding, intro-duced males had no influence on the mtDNA due to theirmaternal genetic inheritance.

The most interesting result is witnessed in the speci-mens from Kume Island, one of the remote islands ofOkinawa island group. We detected a peculiar nucleotideinsertion (A at position 138 in table 2) in all haplotypes(A7 to A11) for the specimens from the Shimizu shellmidden on Kume Island (Watanobe et al. 2002).Interestingly, no wild boars inhabit Kume Island today,as the island appears to be too small (59 km²) to sustaina wild boar population. Therefore, wild boar were prob-ably introduced to Kume Island from other islands of theRyukyu archipelago. The unique genetic characteristicsof this Shimizu boar group (cluster IIa), however, havenot been found in samples from other areas of the Ryukyuarchipelago (Okumura et al. 1996; Watanobe et al. 2002).The ancestor of the Shimizu boar group should then befound somewhere on the Asian continent. Recently, wesequenced and analyzed the same region of mtDNA fromVietnamese native pigs and Korean wild boars (Hongo etal. 2002). The results indicated that Vietnamese nativepigs contained nucleotide variations closely related tothe Ryukyu wild boar, including the Shimizu boar group.The insertion of nucleotide A at position 138 in theShimizu boar group is also found in the Korean wildboar and the domesticated Hampshire pig breed fromEngland (Okumura et al. 1996; Watanobe et al. 2001).These results suggest that the genetic characteristics ofthe Shimizu boar group may have been derived fromancestors on the Asian continent.

Size of lower third mollar of suids in Okinawa sites

8

9

10

11

12

13

14

15

16

15 17 19 21 23 25 27 29 31 33 35

Lenght (mm)

Noguni B,(7130-4330 BP)

Gushibaru (2-3 AD)

Ara (1 AD/BP)

Nagarabaru West (4-5 AD)

Figure 2. Size of lower 3rd molar of the suids in Okinawa sites.


As mentioned above, Ozawa (2000) made claims forthe existence of the domestic pig during the Yayoi period.He claimed that Sus specimens excavated from sites fromthe Late Jomon through to Yayoi period were geneticallyidentical to Japanese wild boars based on his analysis ofpartial 255–bp. nucleotide sequences of the mtDNAcontrol region. While modern Japanese wild boars couldbe distinguished from continental Asian Sus scrofa by

only one nucleotide substitution (nucleotide positionnumber 15,936) in his results, we could not replicate thatdistinction based on the network of fragment B with onesubstitution at position 15,936. The difference betweenOzawa’s results and ours may be due not only to thelength of the sequences used but also to the total numberof modern haplotypes used in the analysis. A sufficientnumber of reference haplotypes is required to resolve the

Archaeological PCR resultsa PCR

b

Site Specimen Period ID fA fB fC Ordinary Seminested

Noguni B shellmidden Radius early Jomon 81 +++ - - +++ fA, fC

Mandible 130 + - - - - ++ fA, fC

Kogachibaru shellmidden Mandible late Jomon 143 ++ - - ++ fA, fC

Mandible 144 +++ - - ++ fA, fC

Mandible 146 ++ ++ - - fA, fB

Chiarabaru site Mandible late Jomon 150 ++ - - + - - fA, fC

Mandible 151 ++ - - - - fA

Kitahara shellmidden Maxilla early Yayoi-Heian 87 +++ ++ ++ fC fA, fB

Shimizu shellmidden Mandible early Yayoi-Heian 102 +++ - - +++ fA, fC

Mandible 104 + - - ++ ++ fA fB, fC

Mandible 105 +++ ++ ++ fA, fC fB

Mandible 107 +++ + - - ++ fA fB, fC

Mandible 108 +++ - - +++ fA, fC

Mandible 109 +++ ++ +++ fA, fB, fC

Humerus 110 ++ + - - - - fB fA

Femur 111 +++ - - ++ fA, fC

Ulna 152 ++ ++ ++ fA, fB, fC

Ulna 155 ++ ++ ++ fA, fB, fC

Ulna 156 +++ ++ ++ fA, fB, fC

Nagarabaru Nishi shellmidden Teeth early Yayoi-Heian 5 ++ ++ ++ fA, fB, fC

Teeth 13 ++ ++ ++ fA, fB, fC

Gushibaru shellmidden Mandible early Yayoi-Heian 17 ++ ++ ++ fA, fB, fC

Mandible 20 ++ ++ ++ fC fA, fB

Ara shellmidden Maxilla early Yayoi-Heian 115 ++ +++ ++ fA, fB fC

Mandible 119 +++ - - - - fA

Mandible 120 +++ ++ +++ fA, fB fC

Mandible 123 + - - - - +++ fA fC

Mandible 124 ++ - - + - - fA, fC

Humerus 157 ++ - - ++ fA, fC

Wakuta Kiln site Mandible Recent Times 125 ++ ++ +++ fA, fB, fC

Mandible 126 + - - - - ++ fA fC

Kyuna site Mandible Recent Times 127 +++ ++ ++ fA, fB, fC

Mandible 128 ++ ++ ++ fA, fB, fC

a: The fA, fB and fC show the DNA fragment amplified by the A, B and C set primers, respectively. -, not amplified; +, once amplified;

++, twice amplified independently; +++, amplified three times.

b: Ordinary or seminested PCR were done to amplify the ancient DNA.

Table 1. Characteristics of archaeological specimens and their DNA amplification.


Nuc

leot

ide

posi

tions

a

fA

fB

fC

Arc

haeo

logi

cal

111111111222222222233333*3333333344444444455*555666666667

333455688134466788900002*3447889900456799903*467134566990

Si

te

Sour

ce /

ID

168649126572919709512374*2399891267432602921*316180839033

Hap

loty

peb

Clu

ster

c

Mei

shan

pig

A--TTGCCTTCCACCTTAGCCATT*CCCCAATCTTACGCCCCAC*ATGTGACCATGG

M23

I

Japa

nese

wild

boa

r •--•••••C••TG•••••••••••*•••••••••••T•••••G•*•C••••••••AA

M13

I

Ryu

kyu

wild

boa

r •--••••T•••TG•••••••••C•*••••G•••••G••••••••*•C••••••••••

M16

II

E

urop

ean

wil

d bo

ar

GC-C••TT•••TG•••••••••C•*••••••C•••G••••••••*AC•G••••GCA•

M54

II

I

Lan

drac

e GC-CCA•T•••TG•••C•A•••CC*••••••C••••••••••••*••A•••••••••

M40

IV

Nog

uni B

she

llmid

den

81

•--••••••••TG•T•C•••••••*********************•C•••G••••••

ND

130

*********************************************•C••••••••••

ND

Kog

achi

baru

she

llmid

den

143

•--•••••••••••••••••••••*********************•C••••••••••

ND

144

•--••••T••TT••••••••••C•*********************•C•••••••CA•

ND

146

•--•••••••••••••••••••••*•••••••••••••••••••***********

ND

Chi

arab

aru

site

15

0 •--••••••••T••••••••••••*******************************

ND

151

•--•••••••••••••C•••••••*******************************

ND

Kit

ahar

a sh

ellm

idde

n 87

•--••••••••T••••••••••••*•••••••••••••••••••*••••••••••••

A1

(M33

) I

Shim

izu

shel

lmid

den

102

•-A••••••••T••••••••••C•*********************•C•••••••CA•

ND

104

•-A••••••••T••••••••••C•*••••G•••••G••••T•••*•C•••••••CA•

A7

IIa

105

•-A••••••••T••••••••••C•*•••TG••T••G••••••••*•C•••••••CA•

A8

IIa

107

•-A••••••••T••••••••••C•*********************•C•••••••CA•

ND

108

•-A••••••••T••••••••••C•*********************•C•••••••CA•

ND

109

•-A••••••••T••••••••••C•*••T•G•••••G•••••T•T*•C•••••••CA•

A9

IIa

110

•-A••••••••T••••••••••C•*******************************

ND

111

•-A•••TT•••T••••••••••C•*********************•C•••••••CA•

ND

152

•-A••••••••T••••••••••C•*••••G•••••G••••••••*•C•••••••CA•

A10

II

a

15

5 •-A••••••••T••••••••••C•*••••G•••••G••••••••*•C•••••••CA•

A10

II

a

15

6 •-A••••••••T••••••••••C•*T•••G•••••GT••T••••*•C•••••••CA•

A11

II

a N

agar

abar

u N

ishi

she

llmid

den

5 •--••••T•••T••••••••••••*••••G•C•••GT•••••••*•C•••••••CA•

A5

II

13

•--••••T•••T••••••••••C•*•T••G•C•••GT•••••••*•C•••••••CA•

A6

II

Gus

hiba

ru s

hellm

idde

n 17

*********************************************•C•••••••CA•

ND

20

*********************************************•C•••••••CA•

ND

Ara

she

llmid

den

115

•--•••••••••••••••••••••*••••••••C••T•••••••*••••••••••••

A2

(M31

) I

119

•--•••••••••••••••••••••*••••••••C••T•••••••***********

ND

120

•--•••••••••••••••••••••*••••••••C••T•••••••*••••••••••••

A2

(M31

) I

123

*********************************************•C•••••••CA•

ND

124

•--••••T•••T••••••••••C•*******************************

ND

157

•--••••T•••T••••••••••C•*********************•C•••••••CA•

ND

Wak

uta

Kil

n si

te

125

•--•••••••••••••C•••••••*•••••••••••T•••••••*••••••••••••

A3

I

12

6 *********************************************••••••••••••

ND

Kiy

una

site

12

7 •--••••••••T••••••••••••*•••••••••••••••••••*••••••••••••

A1

(M33

) I

128

•--••••••••T••••C•••T•••*•••••••••••••T•••••*•C••••••••••

A4

I a:

Nuc

leot

ide

posi

tion

1 co

rres

pond

s to

the

firs

t pos

ition

of

the

com

plet

e D

NA

seq

uenc

es o

f co

ntro

l reg

ions

des

crib

ed b

y O

kum

ura

et a

l. (1

996)

.

A d

ot (

•) d

enot

es n

ucle

otid

e id

enti

ty w

ith

the

Mei

shan

pig

seq

uenc

e, a

das

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problem of the existence Sus specimens from archaeo-logical sites in Japan (Morii et al. 2002).

Stable isotope analysis of Sus bones

The potential of stable isotope analysis

Stable carbon and nitrogen isotopes of human bones fromarchaeological sites have been used to reconstruct ancienthuman diets. We applied this method to discriminate adomesticated Sus population from the wild populations,assuming that the diet of domesticated pigs may bedifferent from that of a wild population. Domestic pigscan be fed on leftovers as well as human excrement–this

was a popular method to feeding pigs in Okinawa beforethe World War II. On the other hand, the wild boars inthe Japanese archipelago generally depend on plant roots,acorns, and small animals like lizards and snakes. Thesedifferences might result in a change in the 13C content oftheir dietary carbon and nitrogen. For instance, if boarssolely eat natural plants, their bone collagen should fallwithin almost the same range as that of a typical herbi-vorous animal, such as deer. Nitrogen isotope ratio, areknown to be useful indicator of trophic levels in anecosystem, and might reveal how often wild boars includeanimals in their diet. This can be used to detect if boarwere fed a human-like diet including marine resourcesor animal protein.

Table 3. Pairwise nucleotide differences between ancient and modern partial control region sequences of Sus scrofa.

Archaeological Pairwise nucleotide difference (%)b

Site ID Regiona East Asian pigs Japanese wild boars Ryukyu wild boars Sus scrofa group

c

Noguni B shellmidden 81 fA+fC 1.2 ± 0.3 1.6 ± 0.4 2.0 ± 0.4 (Unique)

130 fC 0.5 ± 0.3 1.5 ± 0.7 0.7 ± 0.7 East Asian pig, Ryukyu wild boar

Kogachibaru shellmidden 143 fA+fC 0.6 ± 0.2 1.5 ± 0.4 1.4 ± 0.4 (Unique)

144 fA+fC 1.9 ± 0.2 2.0 ± 0.3 0.8 ± 0.3 (Unique)

146 fA+fB 0.6 ± 0.4 1.2 ± 0.3 1.4 ± 0.2 East Asian pig

Chiarabaru site 150 fA 0.7 ± 0.5 0.9 ± 0.5 1.4 ± 0.4 East Asian pig, Japanese wild boar

151 fA 0.7 ± 0.4 1.1 ± 0.4 2.5 ± 0.4 (Unique)

Kitahara shellmidden 87 fA+fB+fC 0.5 ± 0.3 1.1 ± 0.2 1.2 ± 0.3 East Asian pig

Shimizu shellmidden 102 fA+fC 1.7 ± 0.3 1.7 ± 0.3 1.1 ± 0.3 (Unique)

104 fA+fB+fC 1.7 ± 0.2 1.9 ± 0.2 0.9 ± 0.2 (Unique)

105 fA+fB+fC 1.9 ± 0.2 2.1 ± 0.2 1.1 ± 0.2 (Unique)

107 fA+fC 1.7 ± 0.3 1.7 ± 0.3 1.1 ± 0.3 (Unique)

108 fA+fC 1.7 ± 0.3 1.7 ± 0.3 1.1 ± 0.3 (Unique)

109 fA+fB+fC 2.1 ± 0.2 2.3 ± 0.2 1.2 ± 0.2 (Unique)

110 fA 1.8 ± 0.5 1.7 ± 0.4 1.7 ± 0.7 (Unique)

111 fA+fC 2.1 ± 0.5 2.2 ± 0.3 1.1 ± 0.3 (Unique)

152 fA+fB+fC 1.5 ± 0.2 1.7 ± 0.2 0.7 ± 0.2 (Unique)

155 fA+fB+fC 1.5 ± 0.2 1.7 ± 0.2 0.7 ± 0.2 (Unique)

156 fA+fB+fC 1.9 ± 0.3 1.9 ± 0.2 1.2 ± 0.2 (Unique)

Nagarabaru Nishi shellmidden 5 fA+fB+fC 1.5 ± 0.2 1.6 ± 0.2 0.8 ± 0.2 (Unique)

13 fA+fB+fC 1.8 ± 0.2 1.9 ± 0.2 0.9 ± 0.2 (Unique)

Gushibaru shellmidden 17 fC 1.6 ± 0.4 1.8 ± 0.5 0.5 ± 0.7 Ryukyu wild boar

20 fC 1.6 ± 0.4 1.8 ± 0.5 0.5 ± 0.7 Ryukyu wild boar

Ara shellmidden 115 fA+fB+fC 0.6 ± 0.3 1.2 ± 0.2 1.9 ± 0.3 East Asian pig

119 fA+fB 0.8 ± 0.3 1.1 ± 0.2 2.2 ± 0.2 East Asian pig

120 fA+fB+fC 0.6 ± 0.3 1.2 ± 0.2 1.9 ± 0.3 East Asian pig

123 fC 1.6 ± 0.4 1.8 ± 0.5 0.5 ± 0.7 Ryukyu wild boar

124 fA 1.6 ± 0.4 1.7 ± 0.4 0.6 ± 0.7 Ryukyu wild boar

157 fA+fC 1.6 ± 0.2 1.7 ± 0.3 0.6 ± 0.3 Ryukyu wild boar

Wakuta Kiln site 125 fA+fB+fC 0.5 ± 0.2 1.0 ± 0.2 1.8 ± 0.3 (Unique)

126 fC 0.2 ± 0.4 1.5 ± 0.7 1.3 ± 0.7 East Asian pig

Kiyuna site 127 fA+fB+fC 0.5 ± 0.3 1.1 ± 0.2 1.2 ± 0.3 East Asian pig

128 fA+fB+fC 0.9 ± 0.2 1.3 ± 0.2 1.4 ± 0.2 (Unique)

a: fA, fB and fC show the DNA fragment amplified by A, B and C set primers, respectively.

b: Mean values ± standard deviations are pairwise nucleotide differences (%) between an ancient and all distinct sequences detected in

each Sus scrofa group.

c: Sus scrofa groups with a detected sequence idnetical with each ancient sequence are listed.


M30M39

A1(M33)M38M25

M26M23M32

M24M35

M28M29

M27M37

A2(M31)A3

A4M34

M36M21

M22M3

M5M6

M2M4

M7M1

M11M10

M9M8

M12M15

M14M13

M16M17

M18M19

M20A5

A6A7

A8A9

A10A11

M54M55

M40M47M49

M52M42

M45M53

M51M46

M48M44

M43M50

M41

European Dom

esticPigs

European Wild Boar

M40-53

M54,55

M16-20Ryukyu Wild Boar

M1-15

JapaneseWi ld

Boar

NortheasternWild BoarM21,22

East Asian Domestic PigsM23-39 I

II

III

IV

IIa

0.0050

A:AncientM:Modern

Figure 3. Phylogenetic tree constructed from 57 modern and 10 ancient sequences (574–bp) of the mtDNA controlregion using the neighbor-joining (NJ) method. The sequences obtained from archaeological specimens in this studyare indicated by large print. Bootstrap resampling was done 1,000 times, and probabilities greater than 50% are shownon the corresponding branches (Morii et al. 2002).


Archaeological samples

In addition to the Sus specimens from archaeologicalsites in Okinawa, the main islands of the Japanesearchipelago, and Korean sites were also analyzed. Wehave analyzed 102 Sus and 5 cattle (Bos taurus) fromvarious Okinawa Island sites. Bones from the Jomon siteson the main Japanese islands, including Hokkaido and52 Sus, 3 Cervus sp., one dog and one human bone fromfive sites in Korea were also analyzed.

We can show the results of two of Korean sites wherethe reports have been published (Fig. 4). One is Kuang-mong-dong site, located at the northeastern coast ofRepublic of Korea and excavated by Gonryo University(in press). This site is dated to approximately the 1st c.AD, and the bones were preserved in good condition inwaterlogged sediments. We have analyzed seven bonespecimens of Sus and one of sika-deer (Crevus sp.).

The other site is Kimhae-Phaechong Shell Middennear Pusan city, dated between 1st and 5th AD approx-imately. This was excavated by Japanese archaeologistsin 1920 and 1934–5, (Hamada and Umehara 1923) .The

Pusan National University excavated the same locationsin 1998 in order to observe the stratigraphy (PusanNational University 2002) and subsequently reported thefaunal remains (Cheng et al. 2003).

Results of stable isotope analysis

The results (Fig. 5) clearly revealed two groups ofanomalies in the archaeological specimens, with respectto a vegetarian diet: one with a high 15N content, theother with a high 13C content. The former may indicatefeeding on human leftovers or a marine diet, while thelatter is likely to indicate C4 type plants. The formergroup includes many specimens from Okinawa and theKimhae shell midden in Korea (Minagawa and Matsui2002). The latter isotopic signature can be seen in twospecimens from the Gushibaru shell midden and Osato-Gusuku as well as Kuang-mong-dong. As the modernRyukyu wild boars show the range of a typical herbivorousratio, these two archaeological groups seem to be derivedfrom domesticated pigs.

Fig. 4. Map of Japan and Korea with archaeological sites cited in the text.

25°N

30°

35°

40°

45°

125°E 130° 135° 140° 145°

Equidistant conic projection

500250

Km

0


There are some edible C4 plants in East Asia, in-cluding foxtail millet (Setaria italica ssp. italica), barn-yard millet (Echinochloa utilis), Chinese millet (Panicummiliaceum) and sorghum (Sorghum bicolor). They wereall popular cereals in Northeastern Asia especially in theHwang Ho River (the Yellow River) basin. Therefore,since these plants predominant in this area, the lattergroup was probably fed with cultivated millet.

Sus remains recovered from the Noguni B shell middenshowed relatively higher 15N content, suggesting that theyprobably ate fish and other marine resources as well ashuman leftovers and excrement. This result supports theview that some animals were kept and fed by people.There are also specimens that fall within the high d15Nrange for the typical wild boar of Honshu. The isotopicfeatures of 13C and 15N of these populations also overlapswith the range of sika deer (Cervus nippon) recoveredfrom Jomon and Yayoi sites on the main islands. This isa strong indication that pigs were most likely to havebeen fed on natural C3 plants.

At the Kangmung Dong site in Korea, dated approx-imately to the 1st century AD., the d13C and d15N of Susbones are almost the same as those of the two specimensfrom the Gushibaru shell midden (Minagawa and Matsuiin press). These samples are also similar to most of thecattle specimens from Osato castle in Okinawa, dated tothe 15th century AD, in that they show significantconsumption of C4 plants. Millet was very common as astaple food in some regions of Korea, thus, it is likelythat people used surplus millet for feeding pigs. Indeed,a famous Japanese folk song titled Hietsuki-bushi notes

that the amount of grain produced by threshing foxtailmillet is only 30 % of the weight of original spikelets.This indicates that millet was an important grain at thistime.

The consumption of C4 plants estimated from the Susremains at these sites is unique since the same result hasnot been observed in specimens from the other islands ofthe Japanese archipelago. We believe that these indiv-iduals were brought from Korea or Mainland China eitheras livestock or as meat. Other archaeological evidencefor indirect trade with China has been found includingChinese coins. However, evidence for this contact is notstrong in the Yayoi or Later Okinawa Shell Midden Periodand only became more common during the Gushuku(Castle) period, ca. 15–16th c. AD.

Based on these results, we conclude that the isotopicsignatures of Sus remains from archaeological sites inEast Asia tend to form three clusters (see fig. 5). Two ofthese groups reflect two different methods of pig-raisingin Korea. In the first group, Sus was fed mainly on humanleftovers or marine resources characterized by higher 15Ncontent. In the second group, the population was quitelikely fed on C4 millet leftovers indicated by a high 13Ccontent. In addition to these domesticated populations,wild boars that consumed solely natural C3 plants showanother distinctive features similar to those of sika deer(Fig. 5).

��

��

Domestication patterns identified by dietary analysis of

Sus scrofa from Japan and Korea

0

5

10

15

-25 -20 -15 -10 -513

15

N

Sus in Gusibaru Ie Is

Sus in Nagarabaru Ie Is.

Sus in Noguni Okinawa Is.

Susin Iki Is.

Sus in Shimizu Kume Is.

Sus in Ara Ie Is., Okinawa

Cervus in Iki Is

Modern wild boar Ishigaki Is.

Sus in Osato in Okinawa

Sus in Kangmug Dong(AD1C)

Sus in Kimhae

��

��

Herbivorous Ratio

C4 Plant

High 15Nitrogen

0

Figure 5. Result of the stable isotopic analysis in Japan and Korea.


Discussion and conclusion

Although it is still difficult to distinguish wild specimensfrom domesticated ones by means of bone morphology,we have clearly demonstrated that the use of multipleanalytic methods such as mtDNA and stable isotopeanalysis does make it possible to distinguish betweenthem.

Genetic relationships were examined using 574–bp.mitochondrial DNA (mtDNA) control region sequencesfor prehistoric Sus bones on Okinawan islands, domes-ticated pigs inhabiting the Ryukyu archipelago and theAsian continent, and modern wild boars. Out of 161samples collected from 12 archaeological sites on theOkinawan islands, 33 samples were successfully amp-lified and sequenced. Pairwise difference analysis betweenprehistoric and modern Sus sequences showed that someEast Asian domesticated pigs and modern Ryukyu wildboar haplotypes were found among the archaeologicalsamples. The boars from Shimizu shell midden on Kumeisland, Okinawa (Yayoi Period) were related to Ryukyuwild boars, but were clearly differentiated by a uniquesingle base pair insertion, that is also observed in theVietnamese wild boar group. This may suggest that theywere brought from southern China and southeast Asia(i.e. Cambodia) to Kume Island as domesticated pigs.The 14 Sus samples from two Yayoi (Kitahara and Arashell middens, ca. 2,000 BP) and the Premodern (ca. 16–19th c. AD) Wakuta Kiln and Kiyuna sites clusteredwith East Asian domesticated pigs in the phylogeneticanalysis. This indicates that domesticated pigs were kepton Kume Island during the Yayoi Period.

The second method we used to differentiate wild boarfrom domestic pig is stable isotope analysis. The hypo-thesis we are operating under is that the diet of the wildboar may change from natural foods to the leftovers andexcrements of the human diet during the initial stages ofdomestication. We applied this method to Sus bones fromthe Ryukyu Islands, the main islands of the Japanesearchipelago and the Korean Peninsula. Carbon andnitrogen isotope compositions in prehistoric boar boneshowed a similar range to that of deer in central Japan,suggesting that the natural herbivores fed mainly on C3plants. However, from the Early Jomon period, boars inRyukyu showed an unusual enrichment of 15N, althoughno change occurred in 13C, suggesting significant con-sumption of animals in the boar diets. In contrast, someboars from historic sites and pigs from Ryukyu showedsignificant enrichment of 13C, indicating the consumptionof C4 plants or marine foods. We conclude that twofeeding patterns were developed during the domesticationprocess: one pattern mainly based on the consumption ofhuman leftovers and excrements, characterized by high15N, and the other, a system utilizing cultivated C4 plants,although their contribution to the diet was variable.

Based on mtDNA and stable isotope analyses ofarchaeological Sus remains, we suggest that the boarsfound in early sites in the Ryukyu Islands that show the

first pattern of the isotope results were probably tradeimports, while later sites showing the second dietarypattern reflect the spread of domesticates to the RyukyuIslands.

Ie Island is located to the north of the Okinawa Islandgroup (fig. 1). It has a sheltered beach with no reef but isprotected from typhoons and other seasonal strong windsby the mountains behind. Taking advantage of thisenvironmental setting, the prehistoric Okinawa peopleprobably used this location as a trading post on the wayto Kyushu. For example, several deposits of special coneshells, Conidae spp. were unearthed in the dunes withinthe Gushibaru shell midden. These cone shells couldhave been obtained in the sea of southern Japan and werewidely traded for use as material for making braceletsduring the Jomon, Yayoi, and Kofun periods throughoutJapan. Therefore the site most likely flourished as atrading port between the Okinawa and Kyushu Islandsduring the Yayoi Period. This trade route is of primaryimportance during these periods as pigs may have beentraded in exchange for these shells as they were producedin Okinawa.

The existence of several deposits of cone shells at theShimizu shell midden on Kume Island (fig. 1) mayindicate that this site was a trading port like the Gushibarushell midden on Ie Island. Moreover, the discovery ofmany Chinese coins issued in the 2nd century BC andthe 7th century AD from other sites on Kume Island (i.e.Kitahara shell midden, dating from Yayoi to the Heianperiod; Okinawa Prefectural Board of Education, 1995)suggests that the inhabitants of the island had tradecontacts with the Asian continent. The molecular andarchaeological evidence suggests that some of the Susremains from Kume Island may be of domesticated pigs.These pigs might have been brought to the island as amajor import product through this trade.

In light of these results, it seems clear that prehistoricpeople from the Okinawan Islands and the KoreanPeninsula kept domesticated pigs and traded them bet-ween the islands. The earliest pig keeping appears tohave occurred about 7,000 BP at the Jomon period NoguniB shell midden. These pigs had high 15N ratio in theirskeletons and were even smaller than the modern Ryukyuwild boar.

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Akira MatsuiCenter for Archaeological OperationsNara National Cultural Properties Research Institute2–9–1 Nijyo-choNara 630–8577JapanE-mail: [email protected]

Naotaka IshiguroObihiro University of Agricultureand veterinary MedicineInada-choObihiroHokkaido 080–8555JapanE-mail: [email protected]

Hitomi HongoPrimate Research InstituteKyoto University KanrinInuyamaAichi 484–8506JapanE-mail: [email protected]

Masao MinagawaGraduate School of Environmental Earth ScienceHokkaido UniversitySapporo060–0810JapanE-mail: [email protected]

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