CE03 - Interactions Humains-Environnement

The Starch Food Niche: Human Adaptation, Genes and Culture – Starch4Sapiens

Starch4Sapiens

The Starch Food Niche: Human Adaptation, Genes, and Culture

Biological and behavioral changes that made possible efficient starchy food metabolization

Starch4Sapiens aims to analyze and compare the biological and behavioral changes that made possible efficient starchy food metabolization which occurred in Eurasia between the Upper Pleistocene and Neolithic (from ca 126 ka to 12 ka, 6). Our hypothesis is that regular consumption of large amounts of dietary carbohydrates required molecular adaptations to permit positive selection under constraining environmental conditions and this favored Homo sapiens expansion. We aim to read the history of genotypic changes from genomes, which are also noticeable in fossil remains and cultural behavior, in order to determine the extent to which they were introduced by regular starch-rich food consumption well before the Neolithic transition. Thus, the project risk-hypothesis is to show that continuous and massive dietary carbohydrate consumption was only possible due to co-evolution between genetic adaptation, which allowed the effective digestion of starch-rich foods contained in dietary carbohydrates (CNV analysed by P2), and lifestyle transformations, on the level of socially-learned culture and behavior patterns (mechanical processing of starchy plants into staple food by means of ground stones and probably associated to thermal treatment, namely wet-cooking; analyzed by P3). These modifications may have led to better health conditions (visible by change in bones, teeth and pathology from EAHS and HS) (studied by P1) necessary and essential for a constant increase in the HS population and, consequently, to the disappearance of other humans (notably Neandertals and Denisovans).

Starch4Sapiens is rooted in the transdisciplinary concept that genes, environment and culture are dovetailed factors to be considered together when unfolding the complexity of the starch-based diet emerging at the dawn of the colonization of Eurasia by Homo sapiens.
P1: 1. Establishment of a protocol for the implementation of a reproducible method to assess the oral status of archaic fossils and all current and prehistoric populations of Homo sapiens. 2. Analysis with this protocol of 4 unpublished Homo sapiens populations (3 historical and 1 Neolithic), of the Mesolithic population of Taforalt and of several Neanderthal and Gravettian sites.
P2: Estimation of copy number values directly on hg19 to realize an exploratory analysis of the data. Second, in order to obtain the most recent gene copy number estimation, we translated the signal of hg19 on the most recent genome assembly hg38. This was performed using the ENSEMBL gene ID identifiers correspondence between the two genome assemblies and by resolving a large number of technical problems due to the gene mapping between the hg19 and hg38 reference genomes. We produced 16 datasets of data for the 16 ancient genomes that will be provided to the community as well as the procedure that allows to obtain the estimations through upcoming publications.
P3: 1. Preparation and analysis of archaeological samples collected from materials from Vindija (Croatia) and Krems (Austria) as well as Denisova Analysis of said samples using both the optical microscope (OM) and the scanning electron microscope (SEM) was also continued during the last 6 months.2. Expanding the reference collection composed of modern plants. Samples prepared by P3 at the DAIS (Venice) were observed and photographed with the optical microscope, and some were selected to be photographed using the SEM. 3.The plant reference collection was also expanded by considering plants that had been modified, either by the action of amylase (e.g., wheat, oats, acorns, flax, etc.), but also by artificial ageing in a climatic chamber (e.g., acorns, hemp, etc.) and grinding activities (acorns, horseradish, etc.).

P1: a: Establish an indisputable methodological protocol for collecting data on human fossils; b: With this protocol study of Neanderthal, Gravettian, Western and Central European fossils; c:Collect data for oral health status on modern humans and Neolithic unpublished collections
P2: Estimation of Copy Number Variation (CNV) in ancient genomes. Collected from 16 genomes from Neandertal (n=8), Denisovan (n=2) and Early Sapiens (n=6) for which we estimated CNV for approximately 18000 genes. The haploid gene copy number estimation, was performed using a classical method based on the computation of genes and chromosomes coverage based on read depth. The ancient genomes collected were mapped on the genome reference assembly hg19 in previous publications. In order to obtain the most recent gene copy number estimation, we translated the signal of hg19 on the most recent genome assembly hg38. This step is done for ancient genomes and it is in progress for modern ones.
P1 +P3: a: Preparation and analysis of archaeological samples notably samples collected from materials from Vindija (Croatia) and Krems (Austria); b: Expanding the reference collection composed of modern plants; c: Work on plant fibers was also important given that we have been finding numerous fibers in the archaeological samples we have studied.

P1 Prevision: extend the study to fossils from other Neolithic collections, and from Eastern Europe and Russia as planned in the ANR project!
P2: Prevision: Calculations of CNV for modern Homo sapiens genomes have to be finalized. A large selection of modern genomes, spreading over Eurasia, Africa and South Eastern Asia has been realized starting from existing databases.
P1 +P2 + P3: Prevision: publish these new and important data

bioRxiv preprint doi: doi.org/10.1101/2021.10.30.466563

Data base on line , anthropologicaldata.free.fr ; enlargement and update with data of studies in the framework of the ANR

The Starch Food Niche: Human Adaptation, Genes, and Culture
Principal coordinator: S Condemi ( AMU); partners: A. Carbone (SU) and L. Longo (UniVe-IT)

Today Homo sapiens (HS) is the only human species on earth. This has not always been the case: 40,000 years ago, HS shared the planet with at least four other human hominins (Neanderthals, Denisovans, Flores and Luzonensis). HS not only supplanted these other Eurasian archaic humans (EAHs), with a constant demographic growth, but became adapted to nearly all latitudes and climates. This "success" is often linked to the switch from an economy based on foraging and collecting (Paleolithic hunter-gatherers-fishers) to one of production (Neolithic breeders and farmers, starting circa 12.000 years ago). HS's spectacular population growth was made possible due to a regular and starch-rich diet following crop domestication.

Starch4Sapiens is devoted to understanding the origins of the starch-rich diet. Our purpose is to establish the timing for the emergence of the Starch Food Niche (SFN) by comparing changes between EAHs and early HS prior the Neolithic in (i) biology (i. e. anatomical variations), (ii) genetics (genes CNV) expressing enzymes related to starch metabolization and (iii) task-specific behavior in foraging and processing dietary carbohydrates. The originality and novelty of our approach lies in its complementary and interrelated analysis. Our objective is to seek and confront data to demonstrate changes in dietary behavior from EAHs to early HS and until today. We aim to read the history of genotypic changes from genomes, which are also noticeable in fossil remains and cultural behavior, in order to determine the extent to which these changes were introduced by regular starch-rich food consumption well before the Neolithic transition. If this hypothesis is correct, starch food processing and the efficient metabolization of dietary carbohydrates was the key to the appropriation of a different nutriotope allowing HS to enhance its fitness.

Project coordination

Silvana Condemi (Anthropologie bio-culturelle, Droit, Ethique et Santé)

The author of this summary is the project coordinator, who is responsible for the content of this summary. The ANR declines any responsibility as for its contents.

Partner

CaF-UV Ca Foscari - Universita’ di Venezia
ADES Anthropologie bio-culturelle, Droit, Ethique et Santé
CQB Biologie Computationnelle et Quantitative

Help of the ANR 431,460 euros
Beginning and duration of the scientific project: December 2020 - 36 Months

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