Periodic Reporting for period 1 - CODEV (Co-diversification and co-evolution of human populations and cereals in Africa)
Période du rapport: 2019-08-01 au 2021-07-31
The transition to agriculture, from hunter-gathering lifestyle, is one of the most important events in the last few thousand years of human history. Starting in different places and at different times across the continents, this process led to profound cultural and material changes, setting the foundation of modern societies. Plant domestication played a crucial role in the establishment of agricultural food production systems. Under this evolutionary process, species evolve dramatic functional and phenotypic changes under human selection for characters that fit the agricultural environment and human necessities (such as taste, yield, cultivation, harvesting and storage practices). Around 2500 plants have undergone domestication, grasses (e.g. wheat and rice) being the most important group by far.
Agriculture boosted demographic growth and long-distance migrations that greatly shaped the make up of human populations. New environments and lifestyles have resulted in important local adaptations in our specie, e.g. to pathogens, climate or dietary regimes. Likewise, following human movements, many domesticated plants dispersed and experienced local diversification (e.g. shapes, color, taste and usages) to adapt to new physical environments and human preferences.
Despite the connection between human Neolithic transitions and crop domestication, the genetic consequences of these processes are usually addressed separately in humans and plants. The main aim of this project is to jointly analyze the genetic structure of human populations and their domesticated crops to better understand how the common history of migration and expansion of humans and plants shaped the genetic make-up of each species. This project leverages the information on the species past history stored in the genomes, using population genetics approaches and complementary geographical, environmental and ethno-linguistic information. We focus on Africa, where agriculture transitions are still poorly characterized and show distinctive features from other continents, since plant cultivation started late, in multiple areas and spread more slowly and patchily than elsewhere.
Agriculture boosted demographic growth and long-distance migrations that greatly shaped the make up of human populations. New environments and lifestyles have resulted in important local adaptations in our specie, e.g. to pathogens, climate or dietary regimes. Likewise, following human movements, many domesticated plants dispersed and experienced local diversification (e.g. shapes, color, taste and usages) to adapt to new physical environments and human preferences.
Despite the connection between human Neolithic transitions and crop domestication, the genetic consequences of these processes are usually addressed separately in humans and plants. The main aim of this project is to jointly analyze the genetic structure of human populations and their domesticated crops to better understand how the common history of migration and expansion of humans and plants shaped the genetic make-up of each species. This project leverages the information on the species past history stored in the genomes, using population genetics approaches and complementary geographical, environmental and ethno-linguistic information. We focus on Africa, where agriculture transitions are still poorly characterized and show distinctive features from other continents, since plant cultivation started late, in multiple areas and spread more slowly and patchily than elsewhere.
We have gathered high quality genome-wide datasets of two African cereals (sorghum and pearl millet) and human populations, as well as generated new genomic resources. Populations genetics analyses of polymorphism data allowed to explore the spatial genetic structure and patterns of linkage disequilibrium of human populations in Sub-Saharan Africa. The spatial gradients observed are consistent with an history of rapid expansion of farmer groups, impacted locally by other processes, such as admixture with local populations of hunter-gatherers or groups of non-African ancestry. Similar approaches are being deployed on the cereal species datasets to identify parallel or idiosyncratic patterns of demographic history.
Analyses of adaptive diversity at candidate genes showed little evidence of local adaptation in human populations so far, suggesting that the differences observed among populations were mostly driven by the genetic drift associated with specific demographic histories. Candidate functional genes in cereals have been identified, thanks also to the study performed on sorghum in the context of a different research project (Burgarella et. al. 2021 Front. Plant Sci. doi:10.3389/fpls.2021.666075). The analysis of their variability in association with environmental information and the comparison with patterns of human diversity will help identify the main evolutionary processes at play.
Analyses of adaptive diversity at candidate genes showed little evidence of local adaptation in human populations so far, suggesting that the differences observed among populations were mostly driven by the genetic drift associated with specific demographic histories. Candidate functional genes in cereals have been identified, thanks also to the study performed on sorghum in the context of a different research project (Burgarella et. al. 2021 Front. Plant Sci. doi:10.3389/fpls.2021.666075). The analysis of their variability in association with environmental information and the comparison with patterns of human diversity will help identify the main evolutionary processes at play.
The results of this project will contribute to a more comprehensive understanding of the interplay of plant domestication and Holocene migrations, which have received the attention of evolutionary biologists for a long time. The genetic characterization of human populations and native plant resources will also have relevance for basic and applied research in Africa, a continent often underrepresented in surveys of genetic diversity.
Within the framework of this project, scientific and academic collaborations have been initiated and strengthened within the European and African research space. Postgraduate teaching material was developed for courses imparted in Sweden and France. Outreach activities for the general public included contributions to three science festivals and focused on the evolutionary and societal impact of domestication and the contribution of archaeogenetics to reconstruct our history. These activities were diffused in different languages (English, Swedish, Spanish and Italian), and an original video has been created and is available online (https://youtu.be/iSY5_1gzFKc).
Within the framework of this project, scientific and academic collaborations have been initiated and strengthened within the European and African research space. Postgraduate teaching material was developed for courses imparted in Sweden and France. Outreach activities for the general public included contributions to three science festivals and focused on the evolutionary and societal impact of domestication and the contribution of archaeogenetics to reconstruct our history. These activities were diffused in different languages (English, Swedish, Spanish and Italian), and an original video has been created and is available online (https://youtu.be/iSY5_1gzFKc).