Am J Hum Biol. 2017 Sep 10;29(5).

An assessment of postcranial indices, ratios, and body mass versus eco-geographical variables of prehistoric Jomon, Yayoi agriculturalists, and Kumejima Islanders of Japan

Noriko Seguchi1,2, Conrad B. Quintyn3, Shiori Yonemoto4, Hirofumi Takamuku5


1Department of Environmental Changes, Faculty of Social and Cultural Studies, Kyushu University, 744 Motooka, Nishi-Ku, Fukuoka City, Fukuoka, Japan 819-0395

2Department of Anthropology, The University of Montana, Missoula, 32 Campus Drive, Missoula, MT 59812 USA

3Department of Anthropology, Bloomsburg University, Centennial Hall 154, 400 East Second Street, Bloomsburg, PA 17815 USA

4The Kyushu University Museum, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka City, Fukuoka, Japan 812-8581

5Department of Anthropology, Doigahama Site Anthropological Museum, 891-8 Kandakami, Houhoku-cho, Shimonoseki City ,Yamaguchi, Japan  759-6121

Correspondence should be addressed to Conrad Quintyn, Bloomsburg University, Department of Anthropology, Bloomsburg, PA. 17815



We explore variations in body and limb proportions of the Jomon hunter-gatherers (14,000–2,500 BP), the Yayoi agriculturalists (2,500–1,700 BP) of Japan, and the Kumejima Islanders of the Ryukyus (1,600–1,800 AD) with 11 geographically diverse skeletal postcranial samples from Africa, Europe, Asia, Australia, and North America using brachial-crural indices, femur head-breadth-to-femur length ratio, femur head-breadth-to-lower-limb-length ratio, and body mass as indicators of phenotypic climatic adaptation. Specifically, we test the hypothesis that variation in limb proportions seen in Jomon, Yayoi, and Kumejima is a complex interaction of genetic adaptation; development and allometric constraints; selection, gene flow and genetic drift with changing cultural factors (i.e., nutrition) and climate. The skeletal data (1127 individuals) were subjected to principle components analysis, Manly’s permutation multiple regression tests, and Relethford-Blangero analysis. The results of Manly’s tests indicate that body proportions and body mass are significantly correlated with latitude, and minimum and maximum temperatures while limb proportions were not significantly correlated with these climatic variables. Principal components plots separated “climatic zones:” tropical, temperate, and arctic populations. The indigenous Jomon showed cold-adapted body proportions and warm-adapted limb proportions. Kumejima showed cold-adapted body proportions and limbs. The Yayoi adhered to the Allen-Bergmann expectation of cold-adapted body and limb proportions. Relethford-Blangero analysis showed that Kumejima experienced gene flow indicated by high observed variances while Jomon experienced genetic drift indicated by low observed variances. The complex interaction of evolutionary forces and development/nutritional constraints are implicated in the mismatch of limb and body proportions.

Key Words: Phenotypic climatic adaptation; body proportion; limb proportion; developmental constraints; nutrition; genetics



Conrad B. Quintyn and Noriko Seguchi

Evolutionary biologists have known since the 19th century that biological organisms are modified by the environments they inhabit, and new migrants to this same environment will also adapt to it and sometimes (i.e., invasive species) will out-compete the local population. For animals, their adaptations are primarily to the natural environment with no complex cultural interactions. For humans, however, adaptation to the natural environment is confounded by complex cultural factors, such as subsistence, diet, and nutrition. And, the complexity increases tenfold when trying to understand from the perspective of human skeletal patterns the regional historic and prehistoric human adaptive complex, specifically the postcranial skeleton (bones below the head). As such, we have attempted to elucidate the extremely complex population history of the Japanese archipelago because craniodental, genome-wide single-nucleotide polymorphism (SNP),  mtDNA, and Y-chromosome DNA studies suggest that the prehistoric Jōmon hunter-gatherers (14,000–2500 BP) and Yayoi agriculturalists (2500–1700 BP) were descendants from Northeast, Central, or Southeast Asia, which has implications for populating the New World. Additionally, delineating Japanese population history is important to modern Japanese people because their origin is the key to national pride. The Kumejima Islanders of the Ryukyus (1600–1800 AD), a third population in the Japanese archipelago, are included in our study because their diet and division of labor, which was based on gender, might be related to their limb proportions and their enigmatic origins.

Before we began this study, we knew from previous research that the Jomon people had longer distal limbs than proximal limbs, which was similar to humans from warmer climates. This is contrary to the Bergmann/Allen rules of adaptation, where populations who were indigenous to cold climates had, on average, a large body mass and small surface area-to-volume in addition to a short limb length and broad body shape. Interestingly, a Jomon person had a large body mass. In contrast, the Yayoi peoples’ limb length and body proportions were short and large, as would be expected in populations indigenous to cold climates (higher latitudes). It is suggested that the Jomon hunter-gatherers had approximately 11,000 years to adapt to the environment of the Japanese Islands after colonization, while the Yayoi agriculturalists had only 800 years—in essence, not enough time to change the ancestral condition.1-2

We applied principal component analysis, Manly’s permutation multiple regression tests, and Relethford-Blangero analysis to accomplish our goal of learning why Jomon cold-adapted their body proportions and warm-adapted their limb proportions. Previous studies have not adequately addressed the mechanisms causing the Jomons’ deviation from the ancestral condition. We collected brachial-crural indices, femur head-breadth-to-femur-length ratios, femur head-breadth-to-lower-limb-length ratios, and body mass from the Jōmon hunter-gatherers, the Yayoi agriculturalists, the Kumejima Islanders of the Ryukyus, and 11 geographically diverse sample groups for comparative purposes. Using these materials and methods, we tested the hypothesis that the Jomons’ mosaic morphology was a complex interaction of natural selection, genetic drift, gene flow, climate, and cultural factors (i.e., migration, population structure, body size, migration, nutrition, and developmental and allometric constraints). Acknowledging the fact that our assessment involved several measures (postcranial indices, ratios, and body mass) and eco-geographical variables, we detailed several goals: (1) to assess the eco-geographical significance of body proportion and size-and-limb proportions and use these measures to compare Jomon, Yayoi, and Kumejima peoples; (2) to assess whether overall body proportion and size-and-limb proportions correlate with latitude, minimum, and maximum temperatures; and (3) to test the hypothesis mentioned above of the interaction of migration and population structure with the evolutionary forces, developmental constraints, and nutrition.

Box plots of z scores for humerus length (HumL), radius length (RadL), maximum femur length (maxFemL), femur length (FemL), femoral head breadth (FHB), and tibia length (TibL) of all groups in general and Jomon, Yayoi, and Kumejima people in particular show a relationship to New World and South Asian sample groups. (See original publication Figure 2.) Specifically, Yayoi groups show similar MaxFemL and FemL with New World sample groups, while the Jōmon show similar FHB with New World groups (i.e., Indian Knoll and Santa Cruz) and the Kumejima. Additionally, the Jomons show HumL, MaxFemL, FemL, and TibL similar to the Alaskan sample group. In contrast, the Kumejimas have shorter HumL, RadL, MaxFemL, FemL, and the shortest, TibL, is similar or smaller than the Phillipine Negrito and Andaman Islander pygmy groups, but the Kumejimas FHB are larger than both pygmy groups. When Jomon, Yayoi, and Kumejima groups are compared, the Yayois’ HumL, RadL, MaxFemL, FemL, TibL, and FHB are different than those of the Jōmons and Kumejimas. Particularly, the Yayois’ FHB are larger than the Jomons and Kumejimas.

Box plots of z scores for brachial (radius length/humerus length) and crural (tibia length/femur length) indices, FHB-femur length and FHB-lower limb length ratios, and body mass measurements for all groups in general, and the Jōmon, Yayoi, and Kumejima in particular, show that the Yayoi and Kumejimas’ brachial indices are similar to sample groups from colder environments in higher latitudes. (See original publication Figure 3.) Interestingly, Kumejima Island is a subtropical environment. And, Jomons also deviated from the north–south clinal distribution because of their high brachial index and, therefore, were similar to groups from tropical environments in lower latitudes, as was observed in earlier studies. For the crural index, the Jomon, Yayoi, and Kumejima groups show indices similar to cold-adapted Native American and Eastern European sample groups. Brachial and crural indices are influenced by climate and dietary-induced stress. For FHB-femur length and FHB-lower limb length ratios, the Jomon, Yayoi, and Kumejima groups are similar to populations from cold-adapted environments. Finally, the Yayoi and Jomon people show a larger body mass, which indicates their adaptation to a cold climate. However, the Jōmons’ body masses were not as large as the Yayoi, Alaskan, Roman British, or East European peoples but more similar to Indian Knoll and Santa Cruz Islanders. In contrast, the Kumejimas showed a small body mass, as is found in tropical populations. Head-adapted body mass can mimic a nutritional response. For instance, Kumejima females obtained their protein from cereals, while the males obtained their protein from animals and fish.3-4 It is possible that the Kumejima people, particularly the females, experienced nutritional stress, which may have impacted their body mass and limb proportions (as mentioned earlier, the Kumejima’s short HumL, RadL, MaxFemL, FemL, and shortest TibL are similar or smaller than the Phillipine Negrito and Andaman Islander pygmy groups). Nonetheless, body mass correlates significantly with latitude and minimum-maximum temperatures, according to Manly’s permutation multiple regression tests.

The Relethford-Blangero analysis (see original publication Tables 5 and 6) indicates that most sample groups did not have much gene flow or admixture, assuming an average heritability of 0.55. Smaller observed variances than expected accompanied negative residuals, indicating little gene flow and more genetic drift or isolation. Moreover, the Jomon and Yayoi groups, which had smaller observed variances than expected with negative residuals, had more restricted gene flow in their regions. The support for these results comes from mitochondrial DNA (mtDNA) sequences and haplogroup N9b, which have a high frequency in the mtDNA of Jōmon and a low frequency in modern Eurasia. This suggests genetic drift or long-term isolation of the Jōmon from continental populations.5-11 In contrast, the Kumejima (larger observed variances than expected) may have received gene flow from other groups.

Based on our analyses, we propose that the late Pleistocene ancestors of the Jomon, who had a broad body shape and large body mass, migrated from a high latitude and colder environment (i.e., Northeast Asia to the Japanese archipelago) where limb proportions may have adapted to the warmer Holocene climate within 11,000 years. While stature (distal limb segment—RadL and TibL) is affected by subsistence and nutrition, body shape and intralimb indices (particularly, the proximal segments—HumL and MaxFemL/FemL) follow eco-geographical patterns that have resulted in a complex morphological pattern. The recent Yayoi migrants have maintained their ancestral limb and body mass proportions with little gene flow from other populations. However, genome-wide, single nucleotide, polymorphism data indicate admixture between the indigenous Jōmons and the later Yayoi migrants in the formation of the modern Japanese population.12

In essence, the Jōmon hunter-gatherers had a relatively small body mass (high brachial and crural index-relatively longer distal limb length) as opposed to the Yayoi agriculturalists, who had a large body mass (low brachial and crural index-relatively shorter distal limb length). There is a suggestion that Jomon came from Southeast Asia.13 But, both groups share ancestry (and genetics, by default) in Northeast Asia, which is indicated by their similar body proportions.14-22 When ancestral differences are minimal but body mass and distal limb length deviate from the ancestral condition, then respective evolutionary forces, diet/nutrition, and subsistence are implicated. In terms of subsistence, hunter-gatherers had an adequate variety of food supplies and suffered less malnutrition than the agriculturalists.23 The agricultural revolution led to infectious and noninfectious disease epidemics (i.e., high salts, sugars, fats, etc.). Disease and malnutrition during growth and development may have impacted the stature (distal limb length) of adults.24-26

In conclusion, natural selection (with the interaction of genetic drift and gene flow) may have been the primary force in the late Pleistocene epoch; however, genetic drift was probably the primary force in the Holocene epoch, which was combined with gene flow and numerous cultural factors.



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