Sunday, March 18, 2018

A partial nuclear genome of the Jomons who lived 3000 years ago in Fukushima, Japan


The Jomon period of the Japanese Archipelago, characterized by cord-marked ‘jomon’ potteries, has yielded abundant human skeletal remains. However, the genetic origins of the Jomon people and their relationships with modern populations have not been clarified. We determined a total of 115 million base pair nuclear genome sequences from two Jomon individuals (male and female each) from the Sanganji Shell Mound (dated 3000 years before present) with the Jomon-characteristic mitochondrial DNA haplogroup N9b, and compared these nuclear genome sequences with those of worldwide populations. We found that the Jomon population lineage is best considered to have diverged before diversification of present-day East Eurasian populations, with no evidence of gene flow events between the Jomon and other continental populations. This suggests that the Sanganji Jomon people descended from an early phase of population dispersals in East Asia. We also estimated that the modern mainland Japanese inherited < 20% of Jomon peoples’ genomes. Our findings, based on the first analysis of Jomon nuclear genome sequence data, firmly demonstrate that the modern mainland Japanese resulted from genetic admixture of the indigenous Jomon people and later migrants.

Monday, March 12, 2018

Ethnic derivation of the Ainu inferred from ancient mitochondrial DNA data

Noboru Adachi, Tsuneo Kakuda, Ryohei Takahashi, Hideaki Kanzawa-Kiriyama, Ken-ichi Shinoda
American Journal of Physical Anthropology
11 October 2017
(Link) open access



The Ainu, the indigenous people living on the northernmost island of Japan, Hokkaido, have long been a focus of anthropological interest because of their cultural, linguistic, and physical identity. A major problem with genetic studies on the Ainu is that the previously published data stemmed almost exclusively from only 51 modern-day individuals living in Biratori Town, central Hokkaido. To clarify the actual genetic characteristics of the Ainu, individuals who are less influenced by mainland Japanese, who started large-scale immigration into Hokkaido about 150 years ago, should be examined. Moreover, the samples should be collected from all over Hokkaido.

Materials and methods

Mitochondrial DNA haplogroups of 94 Ainu individuals from the Edo era were successfully determined by analyzing haplogroup-defining polymorphisms in the hypervariable and coding regions. Thereafter, their frequencies were compared to those of other populations.


Our findings indicate that the Ainu still retain the matrilineage of the Hokkaido Jomon people. However, the Siberian influence on this population is far greater than previously recognized. Moreover, the influence of mainland Japanese is evident, especially in the southwestern part of Hokkaido that is adjacent to Honshu, the main island of Japan.


Our results suggest that the Ainu were formed from the Hokkaido Jomon people, but subsequently underwent considerable admixture with adjacent populations. The present study strongly recommends revision of the widely accepted dual-structure model for the population history of the Japanese, in which the Ainu are assumed to be the direct descendants of the Jomon people.

Sunday, March 11, 2018

A Common Variation in EDAR Is a Genetic Determinant of Shovel-Shaped Incisors

Ryosuke Kimura, Tetsutaro Yamaguchi, Mayako Takeda, Osamu Kondo, Takashi Toma, Kuniaki Haneji, Tsunehiko Hanihara, Hirotaka Matsukusa, Shoji Kawamura, Koutaro Maki, Motoki Osawa, Hajime Ishida, and Hiroki Oota
American Journal of Human Genetics
2009 Oct 9; 85(4): 528–535
(Link) open access


Shovel shape of upper incisors is a common characteristic in Asian and Native American populations but is rare or absent in African and European populations. Like other common dental traits, genetic polymorphisms involved in the tooth shoveling have not yet been clarified. In ectodysplasin A receptor (EDAR), where dysfunctional mutations cause hypohidrotic ectodermal dysplasia, there is a nonsynonymous-derived variant, 1540C (rs3827760), that has a geographic distribution similar to that of the tooth shoveling. This allele has been recently reported to be associated with Asian-specific hair thickness. We aimed to clarify whether EDAR 1540C is also associated with dental morphology. For this purpose, we measured crown diameters and tooth-shoveling grades and analyzed the correlations between the dental traits and EDAR genotypes in two Japanese populations, inhabitants around Tokyo and in Sakishima Islands. The number of EDAR 1540C alleles in an individual was strongly correlated with the tooth-shoveling grade (p = 7.7 × 10−10). The effect of the allele was additive and explained 18.9% of the total variance in the shoveling grade, which corresponds to about one-fourth of the heritability of the trait reported previously. For data reduction of individual-level metric data, we applied a principal-component analysis, which yielded PC1-4, corresponding to four patterns of tooth size; this result implies that multiple factors are involved in dental morphology. The 1540C allele also significantly affected PC1 (p = 4.9 × 10−3), which denotes overall tooth size, and PC2 (p = 2.6 × 10−3), which denotes the ratio of mesiodistal diameter to buccolingual diameter.

Friday, March 9, 2018

A Re-Examination of Sundadonty Origin Models

Shannon A. Klainer and G. Richard Scott
AAPA 2018, Meeting Program Abstracts
April 11-14, 2018


The Sinodont and Sundadont dental complexes distinguish East Asians from Southeast Asians. There are two models regarding the origin of Sundadonty: (1) it was a longstanding complex throughout Asia that was ultimately ancestral to the specialized Sinodont complex in northeast Asia; and (2) it arose through gene flow between East Asian Neolithic farmers (Sinodonts) and Austral-Melanesians, the original inhabitants of Southeast Asia. To address these models, frequencies were analyzed for 23 crown and root traits in 15 groups from East Asia, Southeast Asia, Polynesia, Micronesia, and Australia using the Mean Measure of Divergence distance statistic and cluster analysis. Two distinct clusters were found. The first cluster includes four Australian populations, differentiated at a high level from all Asian populations. The second cluster shows two major subclusters: the first contains five East Asian groups, with Japan linked tightly with Mongolia (Urga) and north China (An-yang) while the second includes ten Southeast Asian and Pacific populations. In Japan, modern Japanese exhibit the Sinodont pattern while the ancient Jomon and recent Ainu exhibit Sundadonty. It seems unlikely that the Sundadont pattern was a product of Sinodont X Austral-Melanesian admixture given that the earlier populations of Japan and the widely dispersed populations of the Pacific were all Sundadonts. The pattern of dental variation is more consistent with the idea that Sundadonty is an ancient dental complex in Asia that was ancestral to the Sinodont complex that arose in north Asia during the late Pleistocene.

Thursday, March 8, 2018

Evaluating the self-domestication hypothesis of human evolution

Marcelo R. Sánchez-Villagra and Carel P. Van Schaik
AAPA 2018, Meeting Program Abstracts
April 11-14, 2018
Early XXth century studies posited how the very traits that are so variable in humans are precisely those recorded as highly variable among domesticated species subject of intense selective breeding, as in dog breeds. The current version of the self-domestication hypothesis posits that the effects of selection against aggression in morphology, physiology, behavior and psychology reported for domestic animals operated in human evolution too. This hypothesis attempts to explain the behavioral and morphological changes in human evolution from the Middle Pleistocene to recent times, in particular, our reduced aggressiveness and the shortening of the upper facial skeleton and a reduction in brow ridge projection: these changes are tied to physiological changes connected to the rise of high levels of social tolerance and its cognitive consequences.

Unfortunately, the self-domestication hypothesis cannot easily be reconciled with the complex and multivariate empirical record of morphological features of humans. Its full evaluation requires (1) data on rate and variation in human evolution (currently lacking); (2) specification of the time window (if the Holocene is included, the confounding effects of agriculture and sedentary life must be removed); (3) a complete test of the neural crest mechanisms that would be associated with the coupling of traits in domestication (hardly testable for mammals, and although testable in chickens using developmental genetics tools, this model may not be applicable to a primate, because clades of tetrapods vary in the relation between neural crest development and adult morphology).

Monday, March 5, 2018

Plio-Pleistocene climate proxies and hominin evolution in East Africa

Kaye E. Reed, David A. Feary, John Rowan, Christopher J. Campisano
AAPA 2018, Meeting Program Abstracts
April 11-14, 2018


Experimental studies suggest that the evolutionary success of C4 grasses in tropical environments is in part due to a greater physiological tolerance for low CO2 levels compared to C3 plants (i.e., trees and shrubs).  Such studies predict that C4 biomass inversely tracks atmospheric pCO2 levels through geological time, which should be reflected in the structure of terrestrial ecosystems, including mammal communities.

We apply these conclusions to the Plio-Pleistocene fossil record of East Africa to better characterize environmental parameters as hominins evolved. We used mammalian species occurrence and dietary data from 96 eastern African fossil sites as a proxy for grassy versus woody habitats, and pCO2 data were derived from ice cores (back to 800 ka), and boron-based proxies for the older record.

We show a statistically significant inverse relationship between deviations in pCO2 and grazer abundances (r=-0.36, p=0.002) over the last ~4.5 Ma; before 3.4 Ma grazers comprise <20% of the total fauna when pCO2 is >250 ppm, and before 1 Ma they are <32% when pCO2 is <200 ppm. In contrast, browsers often exceed 30% of the total fauna before 3.4 Ma, but decline when pCO2 drops below 250 ppm.

Australopithecus appeared in eastern Africa when pCO2 was greater than 350 ppm, and Homo appeared at <300 ppm coincident with grassland expansion. Our findings have important implications for the role of paleoclimate in human evolution, as well as for the future stability of eastern Africa’s grassland habitats in the face of CO2 increases over the next century.

Sunday, March 4, 2018

Big Questions and Bigger Data: Solutions to the problem of data integration for addressing major questions in human evolution

Denne Reed
AAPA 2018, Meeting Program Abstracts
April 11-14, 2018


The future of paleoanthropology lies with our ability to address big-picture questions by integrating heterogeneous data from disparate sources. For example, simply cataloging early hominin fossils from Africa and their distribution in space and time is difficult because the necessary information is spread across numerous institutions.

This paper demonstrates data integration using PaleoCore (, an open-source, geospatial data management infrastructure. Hominin fossil specimen data, taxonomic designations, locations, geological contexts, dates, anatomical descriptions, measurements, images, and bibliographic references were aggregated from publicly available online resources. These data were cleaned, and aligned to the PaleoCore data standard and conceptual data model to produce a comprehensive digital catalog of over 2700 hominin fossils recovered from over 20 African sites in the time span between the Late Miocene to the start of the Pleistocene (Messinian to Gelasian stages, ca 7.25 - 1.8 Ma). This database was used to calculate and visualize the temporo-spatial distribution of hominin fossils during this time span.

The database marks the first phase of a broader initiative to document the entire hominin fossil record, and to link hominin fossils to a wider host of archaeological, geological, climatic and ecological data using linked open data protocols and facilitated by machine learning algorithms. This digital infrastructure provides the foundation for the collaborative efforts of research consortia now coming together to address broad questions in human evolution and to fulfill the vision of developing comprehensive evolutionary explanations for the patterns we observe in the paleoanthropological record.

Saturday, March 3, 2018

Teeth on trial: What can dental morphology really tell us about hominin phylogeny?

Shara E. Bailey, Lucas K. Delezene, Jacopo Moggi-Cecchi and Matthew M. Skinner
AAPA 2018, Meeting Program Abstracts
April 11-14, 2018


Results of studies on cusp homology, experimental studies of dental growth and development and the dental morphology of new fossil hominins like Homo floresiensis and H. naledi force us to re-examine to what extent we can rely on dental morphological data to reconstruct evolutionary relationships. H. floresiensis has primitive deciduous lower canines and primitive permanent lower third and fourth premolars. However, its small, four-cusped lower molars are morphologically derived towards H. sapiens. Rather than indicating a unique phylogenetic link with H. sapiens, it is possible that the simplified molars of H. floresiensis are a result of diminutive tooth size, similar to that seen in the Middle Pleistocene hominins from Sima de los Huesos.

But what about the opposite end of the spectrum? The talonid expansion observed in Paranthropus lower deciduous molars and lower permanent premolars and molars has been traditionally understood as derived characters that link P. robustus and P. boisei into a monophyletic clade. However, certain dental morphological characteristics of H. naledi force us to question this interpretation. The permanent lower third premolar and six out of nine deciduous teeth represented by that sample show greatest morphological similarity to P. robustus and/or A. africanus (ui1, li2, lc, udm1, ldm1 and ldm2). Yet, a number of other morphological traits are derived towards later Homo (e.g., lack of upper and lower molar accessory cusps) or unique within the hominin clade (upper molar cusp height and spacing). Here we present alternative ways to interpret these conflicting signals.

Friday, February 23, 2018

The easternmost Middle Paleolithic (Mousterian) from Jinsitai Cave, North China

Feng Li, Steven L. Kuhn, Fuyou Chen, Yinghua Wang, John Southon , Fei Peng, Mingchao Shan, Chunxue Wang, Junyi Ge, Xiaomin Wang, Tala Yun, Xing Gao
Journal of Human Evolution
Volume 114, January 2018, Pages 76-84
(Link) open access


The dispersal of Neanderthals and their genetic and cultural interactions with anatomically modern humans and other hominin populations in Eurasia are critical issues in human evolution research. Neither Neanderthal fossils nor typical Mousterian assemblages have been reported in East Asia to date. Here we report on artifact assemblages comparable to western Eurasian Middle Paleolithic (Mousterian) at Jinsitai, a cave site in North China. The lithic industry at Jinsitai appeared at least 47–42 ka and persisted until around 40–37 ka. These findings expand the geographic range of the Mousterian-like industries at least 2000 km further to the east than what has been previously recognized. This discovery supplies a missing part of the picture of Middle Paleolithic distribution in Eurasia and also demonstrates the makers' capacity to adapt to diverse geographic regions and habitats of Eurasia.

Thursday, February 22, 2018

Neanderthals and Modern Humans in the Indus Valley? The Middle and Late (Upper) Palaeolithic Settlement of Sindh, a Forgotten Region of the Indian Subcontinent

Paolo Biagi and Elisabetta Starnini
Springer Publishing
December 8th, 2017
(Link) not open access but available for purchase for $30


This paper discusses the Middle and Late (Upper) Palaeolithic sites of Sindh (Pakistan), a region of the Indian Subcontinent of fundamental importance for the study of the spread of both Neanderthals and Anatomically Modern Humans (AMH) in south Asia.

Most of the Middle Palaeolithic assemblages known to date were collected during the geological surveys carried out during the 1970s in Lower Sindh by Professor A.R. Khan, and the short visits paid to Upper Sindh by B. Allchin. More finds were discovered by the Italian Archaeological Mission during the last 30 years mainly at Ongar, near Hyderabad (Lower Sindh), and the Rohri Hills, near Rohri (Upper Sindh).

The presence of characteristic Levallois Mousterian assemblages at Ongar, and other sites west of the Indus River, opens new perspectives to the study of the dispersal of Neanderthal groups, whose south-easternmost spread has systematically been avoided by most authors.

Although the presence of typical Levallois Mousterian assemblages attributed to Neanderthals has been recorded from Iran, Afghanistan, Uzbekistan, and former Soviet Central Asia, the presence of similar complexes in the Indian Subcontinent is very scarce. The occurrence of typical Levallois cores, flakes, blades, points, Mousterian scrapers and one Mousterian point at Ongar is suggested to mark the south-easternmost limit of this cultural aspect. In contrast, the Middle Palaeolithic of the Indian Subcontinent is mainly characterized by unretouched flake assemblages and scrapers. Levallois points and flakes have already been described as a minor component of the so-called “Late Soan” complexes of the Punjab along the same western bank of the Indus in north Pakistan.

Even more complex is the definition of the earliest Late (Upper) Palaeolithic assemblages in the study region. In contrast with what previously suggested, Late (Upper) Palaeolithic sites are quite common in some areas of Lower Sindh, among which are the Mulri Hills (Karachi) and Jhimpir (Thatta). The assemblages from Karachi region sites are characterized by subconical cores with bladelet detachments, curved, backed points, bladelets, lunates of different shape and size, and, in a few cases, a high percentage of burins. The situation in Upper Sindh is absolutely different. The Rohri Hills yielded evidence of an impressive number of Late (Upper) Palaeolithic flint workshops, characterized by subconical bladelet and bladelet-like flakelet cores, and impressive amounts of debitage products. A similar situation has been recorded also from Ongar (Milestone 101), where modern limestone quarrying still underway has destroyed all the archaeological sites.

To conclude: Sindh is a very important region for the study of the Palaeolithic of the Indian Subcontinent and its related territories. It is unfortunate that our knowledge of this important territory is very scarce, and its archaeological heritage is under systematic destruction. 

Wednesday, February 21, 2018

Ancient human DNA: How sequencing the genome of a boy from Ballito Bay changed human history

Marlize Lombard, Mattias Jakobsson, Carina Schlebusch
South African Journal of Science
January/February 2018
(Link) pdf

From the article: 

"The context of the three Stone Age hunter–gatherers (who displayed no recent admixture with migrating farmers and pastoralists), coupled with the high-quality DNA coverage obtained for the boy from Ballito Bay, provided us with the unique opportunity to recalculate the genetic time depth for our species (Homo sapiens) to between 350 000 and 260 000 years ago. Previously, the deepest genetic split was considered to have been between about 160 000 and 100 000 years ago.  And, based on fossil material from Ethiopia, the oldest modern humans were thought to have lived about 190 000 years ago in East Africa. Our work demonstrates that it is the context of human remains that matters when looking at potential deep splits in our lineage, and not their age. However, full-genome data from older remains may yet reveal more surprising outcomes. For example, any additional gene flow into southern African Stone Age populations, predating 2000 years ago, will increase the time depth of the first H. sapiens population split."

"The new genetic split-time estimate1 coincides with the interpretation of fossil material from Morocco in North Africa, dated to about 300 000 years ago16, which is seen as anatomically transitional between archaic and modern H. sapiens. It is also consistent with the age of the Florisbad skull that was found in the Free State, South Africa, dated to 260 000 years ago.  The Florisbad remains were discovered with Middle Stone Age artifacts, and have been referred to as archaic H. sapiens, representing a combination of archaic and modern characteristics with a cranial volume similar to that of modern humans of about 1300 mL. Other human remains from South Africa dating to between 300 000 and 200 000 years ago are those from Hoedjiespunt, currently ascribed to H. heidelbergensis, because although they are morphologically modern, they seemed larger than modern Africans."

The Kocabaş hominin (Denizli Basin, Turkey) at the crossroads of Eurasia: New insights from morphometric and cladistic analyses

Amélie Vialet, Sandrine Prat, Patricia Will, Mehmet Cihat Alçiçek
Comptes Rendus Palevol
3 February 2018
(Link) open access


The Kocabaş skullcap (Denizli Basin), dated between 1.2 and 1.6 Ma, is the only ancient hominin fossil from Turkey and is part of discussions focusing on the first settlement outside the African continent. Our morphometric study tends to link this specimen with the African fossils, Homo ergaster and early Homo erectus, and to distinguish it from the specimens from Dmanisi and Asian Homo erectus. These results are confirmed by a cladistic analysis, which shows a separation of Kocabaş from the Eurasian clade comprising the Dmanisi hominins and grouping it with the African fossils dated to around 1 Ma (KNM-OL 45500, Daka-Bouri BouVP2/66, Buia UA31). As in the Kocabaş fossil, the divergence of the frontal bone is not very marked on these latter fossils and the temporal lines are separated on the parietal bone. The Kocabaş skull seems to point to a different evolutionary history than that of the Dmanisi fossils, and could reflect a later “out-of-Africa” expansion.

Wednesday, February 7, 2018

The biomechanical significance of the frontal sinus in Kabwe 1 (Homo heidelbergensis)

Ricardo Miguel Godinho, Paul O'Higgins
Journal of Human Evolution
Volume 114, January 2018, Pages 141-153
(Link) open access


Paranasal sinuses are highly variable among living and fossil hominins and their function(s) are poorly understood. It has been argued they serve no particular function and are biological ‘spandrels’ arising as a structural consequence of changes in associated bones and/or soft tissue structures. In contrast, others have suggested that sinuses have one or more functions, in olfaction, respiration, thermoregulation, nitric oxide production, voice resonance, reduction of skull weight, and craniofacial biomechanics. Here we assess the extent to which the very large frontal sinus of Kabwe 1 impacts on the mechanical performance of the craniofacial skeleton during biting. It may be that the browridge is large and the sinus has large trabecular struts traversing it to compensate for the effect of a large sinus on the ability of the face to resist forces arising from biting. Alternatively, the large sinus may have no impact and be sited where strains that arise from biting would be very low. If the former is true, then infilling of the sinus would be expected to increase the ability of the skeleton to resist biting loads, while removing the struts might have the opposite effect. To these ends, finite element models with hollowed and infilled variants of the original sinus were created and loaded to simulate different bites. The deformations arising due to loading were then compared among different models and bites by contrasting the strain vectors arising during identical biting tasks. It was found that the frontal bone experiences very low strains and that infilling or hollowing of the sinus has little effect on strains over the cranial surface, with small effects over the frontal bone. The material used to infill the sinus experienced very low strains. This is consistent with the idea that frontal sinus morphogenesis is influenced by the strain field experienced by this region such that it comes to lie entirely within a region of the cranium that would otherwise experience low strains. This has implications for understanding why sinuses vary among hominin fossils.