From hunter-gatherers to food producers: New dental insights into the Nile Valley population history (Late Paleolithic-Neolithic)

OBJECTIVES

This study presents biological affinities between the last hunter-fisher-gatherers and first food-producing societies from the Nile Valley. We investigate odontometric and dental tissue proportion changes between these populations from the Middle Nile Valley and acknowledge the biological processes behind them.

MATERIALS AND METHODS

Dental remains of 329 individuals from Nubia and Central Sudan that date from the Late Pleistocene to the mid-Holocene are studied. Using 3D imaging techniques, we investigated outer and inner metric aspects of upper central incisors, and first and second upper molars.

RESULTS

Late Paleolithic and Mesolithic foragers display homogeneous crown dimensions, dental tissue proportions, and enamel thickness distribution. This contrasts with Neolithic trends for significant differences from earlier samples on inner and outer aspects. Finally, within the Neolithic sample differences are found between Nubian and Central Sudanese sites.

DISCUSSION

Substantial dental variation appears to have occurred around 6000 bce in the Nile Valley, coinciding with the emergence of food-producing societies in the region. Archeological and biological records suggest little differences in dietary habits and dental health during this transition. Furthermore, the substantial variations identified here would have happened in an extremely short time, a few centuries at most. This does not support in situ diet-related adaptation. Rather, we suggest these data are consistent with some level of population discontinuity between the Mesolithic and Neolithic samples considered here. Complex settlement processes could also explain the differences between Nubia and Central Sudan, and with previous results based on nonmetric traits.

Integrative analysis of DNA, macroscopic remains and stable isotopes of dog coprolites to reconstruct community diet

Paleofeces or coprolites are often used to reconstruct diet at archaeological sites, usually using macroscopic analyses or targeted DNA amplification and sequencing. Here we present an integrative analysis of dog coprolites, combining macroscopic analyses, stable isotope measurements, and DNA shotgun sequencing to examine diet and health status. Dog coprolites used in this study were recovered from the Janey B. Goode and East Saint Louis archaeological sites, both of which are located in the American Bottom, an extensive Mississippi River floodplain in Southwestern Illinois. Based on the context of recovery, coprolites are assigned to the Late Woodland and Terminal Late Woodland periods (ca. 600-1050 AD). Given the scarcity of human remains from this time period, these dog coprolites can be useful as a proxy for understanding human diet during the Late Woodland period. We find that the Late Woodland dogs consumed a variety of fish as well as bird and plant taxa, possibly including maize, and also harbored intestinal parasites and pathogenic bacteria. By sequencing the fecal microbiome of the coprolites, we find some similarities to modern dog microbiomes, as well as specific taxa that can be used to discriminate between modern and ancient microbiomes, excluding soil contaminants. As dogs are often used as a surrogate to assess human diet, humans living with these dogs likely had a similar diet and were affected by similar parasites. These analyses, when integrated, show a more comprehensive view of ancient dog and human diet and health in the region during the initial expansion of maize agriculture than any individual method could alone.

Ancient DNA reveals a multistep spread of the first herders into sub-Saharan Africa

How food production first entered eastern Africa ~5000 years ago and the extent to which people moved with livestock is unclear. We present genome-wide data from 41 individuals associated with Later Stone Age, Pastoral Neolithic (PN), and Iron Age contexts in what are now Kenya and Tanzania to examine the genetic impacts of the spreads of herding and farming. Our results support a multiphase model in which admixture between northeastern African-related peoples and eastern African foragers formed multiple pastoralist groups, including a genetically homogeneous PN cluster. Additional admixture with northeastern and western African-related groups occurred by the Iron Age. These findings support several movements of food producers while rejecting models of minimal admixture with foragers and of genetic differentiation between makers of distinct PN artifacts.

Ancient herders enriched and restructured African grasslands

Grasslands are one of the world's most extensive terrestrial biomes and are central to the survival of herders, their livestock and diverse communities of large wild mammals^1-3. In Africa, tropical soils are predominantly nutrient-limited^4-6 but productive grassy patches in wooded grassland savannah ecosystems^2,4 grow on fertile soils created by geologic and edaphic factors, megafauna, fire and termites^4-6. Mobile pastoralists also create soil-fertility hotspots by penning their herds at night, which concentrates excrement-and thus nutrients-from grazing of the surrounding savannahs^7-11. Historical anthropogenic hotspots produce high-quality forage, attract wildlife and increase spatial heterogeneity in African savannahs^4,12-15. Archaeological research suggests this effect extends back at least 1,000 years^16-19 but little is known about nutrient persistence at millennial scales. Here we use chemical, isotopic and sedimentary analyses to show high nutrient and ¹⁵N enrichment in on-site degraded dung deposits relative to off-site soils at five Pastoral Neolithic²⁰ sites (radiocarbon dated to between 3,700 and 1,550 calibrated years before present (cal. BP)). This study demonstrates the longevity of nutrient hotspots and the long-term legacy of ancient herders, whose settlements enriched and diversified African savannah landscapes over three millennia.

Long-distance stone transport and pigment use in the earliest Middle Stone Age

Previous research suggests that the complex symbolic, technological, and socioeconomic behaviors that typify Homo sapiens had roots in the middle Pleistocene <200,000 years ago, but data bearing on human behavioral origins are limited. We present a series of excavated Middle Stone Age sites from the Olorgesailie basin, southern Kenya, dating from ≥295,000 to ~320,000 years ago by argon-40/argon-39 and uranium-series methods. Hominins at these sites made prepared cores and points, exploited iron-rich rocks to obtain red pigment, and procured stone tool materials from ≥25- to 50-kilometer distances. Associated fauna suggests a broad resource strategy that included large and small prey. These practices imply notable changes in how individuals and groups related to the landscape and to one another and provide documentation relevant to human social and cognitive evolution.

Response to Comment on the Paleoenvironment of Ardipithecus ramidus

Cerling et al . contest our interpretation of the woodland habitat preference of Ardipithecus ramidus . However, their reconstruction of a predominantly open grassy environment with riparian woodlands is inconsistent with the totality of the fossil, geological, and geochemical evidence. In the Middle Awash, Ar. ramidus fossils are confined to the western portion of the sampled Pliocene landscape where the species is associated with woodland to grassy woodland habitat indicators.

Macrovertebrate paleontology and the Pliocene habitat of Ardipithecus ramidus

A diverse assemblage of large mammals is spatially and stratigraphically associated with Ardipithecus ramidus at Aramis. The most common species are tragelaphine antelope and colobine monkeys. Analyses of their postcranial remains situate them in a closed habitat. Assessment of dental mesowear, microwear, and stable isotopes from these and a wider range of abundant associated larger mammals indicates that the local habitat at Aramis was predominantly woodland. The Ar. ramidus enamel isotope values indicate a minimal C4 vegetation component in its diet (plants using the C4 photosynthetic pathway), which is consistent with predominantly forest/woodland feeding. Although the Early Pliocene Afar included a range of environments, and the local environment at Aramis and its vicinity ranged from forests to wooded grasslands, the integration of available physical and biological evidence establishes Ar. ramidus as a denizen of the closed habitats along this continuum.

Quantifying dietary macronutrient sources of carbon for bone collagen biosynthesis using natural abundance stable carbon isotope analysis

The diets of laboratory rats were isotopically and nutritionally manipulated using purifiedC3 and/or C4 macronutrients to investigate the routing of dietary carbonto bone collagen biosynthesis. Diets were formulated with purified proteins, carbohydrates andlipids of defined composition and natural abundance stable isotope ratios. Bulk protein and constituent amino acid δ13C values determined for whole diet and bone collagen provided the basis for assessing isotopic fractionation and estimating the degree of routing versus synthesis de novo of essential, non-essential and conditionally indispensable amino acids. Essential and conditionally indispensable amino acids were shown to be routed from diet to collagen with little isotopic fractionation whereas non-essential amino acids differed by up to 20‰. Mathematical modelling of the relationships between macronutrient and tissue δ13C values provided qualitative and quantitative insights into the metabolic and energetic controls on bone collagen biosynthesis. Essential amino acids comprise 21·7% of the carbon in collagen, defining the minimum amount of dietary carbon routing. Estimates of 42 and 28% routing were shown for the non-essential amino acids, glycine and aspartate, respectively. In total, the routing of non-essential and conditionally indispensable amino acids was estimated to equal 29·6% of the carbon in collagen. When the contribution of carbon from the essential amino acids is also considered, we arrive at an overall minimum estimate of 51·3% routing of dietary amino acid carbon into bone collagen.

Prey use by red foxes (Vulpes vulpes) in urban and rural areas of Illinois

Decline of red fox (Vulpes vulpes) populations in Illinois has been attributed to altered geographic landscapes and the eastward expansion of the coyote. To investigate effects of habitat use and competition with coyotes on diets of foxes in intensively farmed landscapes of Illinois, we analyzed carbon and nitrogen isotope ratios (δ13C and δ15N) of foxes, coyotes (Canis latrans), and other local species. Foxes were categorized as rural (agricultural habitat, coyotes present), urban (urban habitat, coyotes absent), or from an agricultural research facility at the University of Illinois (South Farms, agricultural habitat, coyotes absent). Rural foxes had higher fur isotopic values (δ13C and δ15N) than rural coyotes, indicating that coyotes caused foxes to consume prey items from higher trophic levels and eat more C4 plants. Urban foxes had lower isotopic values (δ13C and δ15N) than South Farms foxes, suggesting that habitat use partly determined fox diets; foxes in urbanized habitats consumed prey at lower trophic levels within a largely C3 plant based food web. Models of competitive exclusion by coyotes were better predictors of fox long-term diets, including pup rearing, while habitat use models predicted fox diets on a narrower timescale. Competitive exclusion by coyotes might be an important factor explaining the decline of foxes in the intense farming areas of Illinois.

Natural abundance stable carbon isotope evidence for the routing and de novo synthesis of bone FA and cholesterol

This research reported in this paper investigated the relationship between diet and bone FA and cholesterol in rats raised on a variety of isotopically controlled diets comprising 20% C3 or C4 protein (casein) and C3 and/or C4 nonprotein or energy (sucrose, starch, and oil) macronutrients. Compound-specific stable carbon isotope analysis (delta13C) was performed on the FA (16:0, 18:0, 18:1, and 18:2) and cholesterol isolated from the diet (n = 4) and bone (n = 8) of these animals. The dietary signals reflected by the bone lipids were investigated using linear regression analysis. delta13C values of bone cholesterol and stearic (18:0) acid were shown to reflect whole-diet delta13C values, whereas the delta13C values of bone palmitic (16:0), oleic (18:1), and linoleic (18:2) acids reflected dietary FA delta13C values. Dietary signal differences are a result of the balance between direct incorporation (or routing) and de novo synthesis of each of these bone lipids. Estimates of the degree of routing of these bone lipids gleaned from correlations between delta13C(dlipid-wdiet) (= delta13C(diet lipid) - delta13C(whole diet)) spacings and delta13C(blipid-wdiet) (= delta13C(bone lipid) - delta13C(whole diet)) fractionations demonstrated that the extent of routing, where 18:2 > 16:0 > 18:1 > 18:0 > cholesterol, reflected the relative abundances of these lipids in the diet. These findings provide the basis for more accurate insights into diet when the delta13C analysis of bone fatty FA or cholesterol is employed.

Effects of hydrolysis on the delta13C values of individual amino acids derived from polypeptides and proteins

This study investigates the effects of hydrolysis on the delta13C values of individual amino acids (IAAs) derived from polypeptide standards, and modern and ancient bone collagen. All IAAs were derivatised to their trifluoroacetyl/isopropyl (TFA/IP) esters for delta13C determination using gas chromatography/combustion/isotope ratio mass spectrometry (GC/C/IRMS). Firstly, authentic single poly amino acid standards (SPAAs; n = 5) were hydrolysed for 4, 10, 24 and 48 h. As expected, IAA yields increased as a function of hydrolysis time. Significantly, it was only after 24 h of hydrolysis that IAA delta13C values were statistically identical to bulk SPAA values for all five standards. The accuracy of IAA delta13C values was thus shown to be a function of yield; however, poly phenylalanine demonstrated accurate IAA delta13C values with yields of only 1.4 and 4.3%, after 24 and 48 h of hydrolysis time, respectively. Authentic mixed poly amino acid standards (MPAAs; n = 5) comprising two different amino acids were then hydrolysed for 24 h. Percentage recoveries ranged from 36-95%. Estimates of bulk MPAA delta13C values calculated from measured IAA delta13C values agreed within experimental error with measured bulk MPAA values for three out of the five standards. Finally, the experimental procedure was applied to modern rat (MBCs; n = 20) and ancient ovi-caprine and bovine (ABCs; n = 27) bone collagen samples where the delta13C values of 12 out of its 18 constituent amino acids were determined. Estimated bulk MBC and ABC delta13C values were calculated from constituent amino acid delta13C values using mass balance. With the exclusion of three ABC samples, calculated bulk bone collagen delta13C values (delta13C(BCcal)) were shown to correlate extremely well with measured bone collagen values (delta13C(BCmes)) for both modern and ancient samples, where R2 = 0.91 and 0.84, respectively. Significantly, the variation between calculated and measured bone collagen values (Delta13C(BCcal-BCmes)) exhibited similar ranges for both MBC (from -2.6 to +1.2 per thousand ) and ABC (from -2.7 to +2.2 per thousand ) samples, providing evidence for the preservation of intact collagen in the ancient samples. These results demonstrate that the experimental procedures employed in the acid hydrolytic cleavage of peptides or proteins to their constituent amino acids does not involve significant isotopic fractionation.

Geology and palaeontology of the Late Miocene Middle Awash valley, Afar rift, Ethiopia

The Middle Awash study area of Ethiopia's Afar rift has yielded abundant vertebrate fossils (approximately 10,000), including several hominid taxa. The study area contains a long sedimentary record spanning Late Miocene (5.3-11.2 Myr ago) to Holocene times. Exposed in a unique tectonic and volcanic transition zone between the main Ethiopian rift (MER) and the Afar rift, sediments along the western Afar rift margin in the Middle Awash provide a unique window on the Late Miocene of Ethiopia. These deposits have now yielded the earliest hominids, described in an accompanying paper and dated here to between 5.54 and 5.77 Myr. These geological and palaeobiological data from the Middle Awash provide fresh perspectives on hominid origins and early evolution. Here we show that these earliest hominids derive from relatively wet and wooded environments that were modulated by tectonic, volcanic, climatic and geomorphic processes. A similar wooded habitat also has been suggested for the 6.0 Myr hominoid fossils recently recovered from Lukeino, Kenya. These findings require fundamental reassessment of models that invoke a significant role for global climatic change and/or savannah habitat in the origin of hominids.

Paleolithic technology and human evolution

Human biological and cultural evolution are closely linked to technological innovations. Direct evidence for tool manufacture and use is absent before 2.5 million years ago (Ma), so reconstructions of australopithecine technology are based mainly on the behavior and anatomy of chimpanzees. Stone tool technology, robust australopithecines, and the genus Homo appeared almost simultaneously 2.5 Ma. Once this adaptive threshold was crossed, technological evolution was accompanied by increased brain size, population size, and geographical range. Aspects of behavior, economy, mental capacities, neurological functions, the origin of grammatical language, and social and symbolic systems have been inferred from the archaeological record of Paleolithic technology.

Late Pleistocene human population bottlenecks, volcanic winter, and differentiation of modern humans

The "Weak Garden of Eden" model for the origin and dispersal of modern humans (Harpending et al., 1993) posits that modern humans spread into separate regions from a restricted source, around 100 ka (thousand years ago), then passed through population bottlenecks. Around 50 ka, dramatic growth occurred within dispersed populations that were genetically isolated from each other. Population growth began earliest in Africa and later in Eurasia and is hypothesized to have been caused by the invention and spread of a more efficient Later Stone Age/Upper Paleolithic technology, which developed in equatorial Africa. Climatic and geological evidence suggest an alternative hypothesis for Late Pleistocene population bottlenecks and releases. The last glacial period was preceded by one thousand years of the coldest temperatures of the Later Pleistocene (approximately 71-70 ka), apparently caused by the eruption of Toba, Sumatra. Toba was the largest known explosive eruption of the Quaternary. Toba's volcanic winter could have decimated most modern human populations, especially outside of isolated tropical refugia. Release from the bottleneck could have occurred either at the end of this hypercold phase, or 10,000 years later, at the transition from cold oxygen isotope stage 4 to warmer stage 3. The largest populations surviving through the bottleneck should have been found in the largest tropical refugia, and thus in equatorial Africa. High genetic diversity in modern Africans may thus reflect a less severe bottleneck rather than earlier population growth. Volcanic winter may have reduced populations to levels low enough for founder effects, genetic drift and local adaptations to produce rapid population differentiation. If Toba caused the bottlenecks, then modern human races may have differentiated abruptly, only 70 thousand years ago.

Dietary and environmental reconstruction with stable isotope analyses of herbivore tooth enamel from the Miocene locality of Fort Ternan, Kenya

Tooth enamel of nine Middle Miocene mammalian herbivores from Fort Ternan, Kenya, was analyzed for delta 13C and delta 18O. The delta 18O values of the tooth enamel compared with pedogenic and diagenetic carbonate confirm the use of stable isotope analysis of fossil tooth enamel as a paleoenvironmental indicator. Furthermore, the delta 18O of tooth enamel indicates differences in water sources between some of the mammals. The delta 13C values of tooth enamel ranged from -8.6(-)-13.0/1000 which is compatible with a pure C3 diet, though the possibility of a small C4 fraction in the diet of a few of the specimens sampled is not precluded. The carbon isotopic data do not support environmental reconstructions of a Serengeti-typed wooded grassland with a significant proportion of C4 grasses. This study does not preclude the presence of C3 grasses at Fort Ternan; it is possible that C3 grasses could have had a wider geographic range if atmospheric CO2 levels were higher than the present values.

Stable isotopic analysis of human diet in the Marianas Archipelago, western Pacific

Proportions of marine vs. terrestrial resources in prehistoric human diets in the southern Mariana Islands (Guam, Rota, Saipan), Micronesia, have been estimated by analysis of stable isotope ratios of carbon and nitrogen in bone collagen and of carbon in apatite. The isotopic composition of marine and terrestrial food resources from the Marianas have also been determined. Experimental evidence shows that collagen carbon isotopes mainly reflect those of dietary protein sources and thus overestimate the contribution of marine animal foods. Marine protein consumption apparently ranges from approximately 20% to approximately 50% on these islands. Experiments also demonstrate the carbon isotope ratio of bone apatite carbonate accurately reflects that of the whole diet. Carbonate carbon isotope data suggest some individuals consumed significant amounts of 13C-enriched (C4) plants or seaweeds. Sugar cane is an indigenous C4 crop and seaweeds are eaten throughout the Pacific, but they have not been considered by archaeologists to have been prehistoric dietary staples. Apatite carbon isotope analysis has apparently identified previously unrecognized prehistoric dietary adaptations in the Mariana Islands, but this must be confirmed by archaeobotanical evidence.

Soil Carbon Isotope Evidence for Holocene Habitat Change in the Kenya Rift Valley

In eastern Africa the altitude of the boundary between montane forest and lowland savanna grassland changed substantially in response to climate change during the later Holocene, but this is not clearly reflected in regional pollen records. The carbon-13 to carbon-12 ratios of tropical grasses are higher than those of most other plants, and this difference is preserved in soil organic carbon stable isotope ratios. Soil organic matter (13)C/(12)C ratios in profiles along an altitude transect in the central Rift Valley of Kenya suggest that the forest-savanna boundary advanced more than 300 meters in altitude. This could have implications for understanding the effects of climate change on the configuration of floral zones, prehistoric hunter-gatherer land-use patterns, and the timing of the advent of Neolithic food production.