Periodic Reporting for period 1 - DOPAMICS (Domestication and adaptation in Neotropical palms: a microevolutionary history)
Reporting period: 2022-09-01 to 2025-02-28
Amazonia is the most diverse forest on earth but it is facing a significant biodiversity loss due to increasing human pressures and climate change. However, the state of diversity in lowland Amazonia and underlying evolutionary processes are largely under-documented, making it difficult to anticipate future changes and to elaborate knowledge-driven mitigation strategies. Moreover, very little attention has been paid to the recent evolution of plant populations through the Holocene that witnessed the rise of pre-Columbian societies. Although South America is commonly credited as a major centre of plant domestication, most studies focused on a few major crops with an obvious domestication syndrome, leaving aside most Amazonian species with tenuous evidence of domestication.
DOPAMICS will challenge the domestication syndrome paradigm in the light of "incipiently domesticated" palm species of ancient agroecosystems of Amazonia. I will build upon emblematic archaeological sites - the so-called "ring-ditches" - and implement an interdisciplinary methodology at the crossroads between ecology, evolution and human sciences to illustrate the diversity of domestication histories in Neotropical palms in a multi-species setting. DOPAMICS aims to retrace the pre-Columbian history of contemporary wild landscapes, disentangle natural and anthropogenic evolutionary processes that shaped patterns of genomic and phenomic diversity (with a focus on fruit metabolism and fibre biomechanics) and forecast the future of palm populations under scenarios of fast genetic diversity loss (e.g. selective logging, maladaptation to future conditions).
DOPAMICS will provide extensive field observational data, a fine knowledge of the microevolutionary history of domestication in Neotropical palms, and new avenues towards the sustainable use of Amazonian landscapes to reconcile environmental concerns raised by the loss of wild diversity with local socio-economic needs.
DOPAMICS will challenge the domestication syndrome paradigm in the light of "incipiently domesticated" palm species of ancient agroecosystems of Amazonia. I will build upon emblematic archaeological sites - the so-called "ring-ditches" - and implement an interdisciplinary methodology at the crossroads between ecology, evolution and human sciences to illustrate the diversity of domestication histories in Neotropical palms in a multi-species setting. DOPAMICS aims to retrace the pre-Columbian history of contemporary wild landscapes, disentangle natural and anthropogenic evolutionary processes that shaped patterns of genomic and phenomic diversity (with a focus on fruit metabolism and fibre biomechanics) and forecast the future of palm populations under scenarios of fast genetic diversity loss (e.g. selective logging, maladaptation to future conditions).
DOPAMICS will provide extensive field observational data, a fine knowledge of the microevolutionary history of domestication in Neotropical palms, and new avenues towards the sustainable use of Amazonian landscapes to reconcile environmental concerns raised by the loss of wild diversity with local socio-economic needs.
The first period focused on extensive field sample collection, sample management, and preliminary data acquisition. Through an interdisciplinary approach, we established standardised sampling transects spanning varying conditions within three study sites in French Guiana, and developed innovative protocols for field collection and data acquisition. Field expeditions, conducted across three major campaigns, led to an extensive inventory, mapping and sampling of palm species. These transects offer a long-term research framework that is particularly valuable for monitoring the impacts of climate change on palm populations.
A postdoc in geoarchaeology, produced the most accurate archaeo-environmental dataset on pre-Columbian impacts in French Guiana to date. Soil samples analyses and radiocarbon dating provided a detailed account of the human history and the landscape-scale extent of anthropogenic disturbances in the study sites. Beyond primary objectives, we conducted an exploratory study on the morphology and morphometry of Neotropical palm phytoliths using Scanning Electron Microscopy to reconstruct paleoenvironments through future work.
In parallel, we are exploring the genomic and phenomic diversity in palm populations. A first PhD student research focuses on the biomechanical properties of palm leaves through vibratory mechanics and tensile testing to evaluate how fibre mechanical properties vary with water content, relevant to traditional palm use, and how biomechanical properties vary within and across species. He developed an informatic pipeline to monitor fibre deformation by Digital Image Correlation, allowing standardised, semi-automated acquisition of biomechanics data. He experimentally evaluated DIC method following a cross-validation with a laser extensometer. Regarding metabolomics, we processed palm fruits in the lab, including weighing, lyophilization, systematic photography for morphometric analysis and manual dissection for metabolomic profiling. Preliminary metabolite extraction and metabolomic profiling tests were carried out, providing encouraging results. A second PhD student was recently hired to study the genomic and metabolomic diversity in palm populations. He is developing the bioinformatics pipeline for NGS data processing using the first set of genomic data acquired.
DOPAMICS team is also engaged in disseminating the work and results of the project to the general public and local communities. For example, we co-organized the Science Nature Festival in Saül in 2023 in collaboration with the Amazonian Park in French Guiana. This event was therefore an exceptional opportunity to present the DOPAMICS project and to share scientific and cultural knowledge with local people.
All protocols, codes and data generated will be made open access on dedicated repositories complying with FAIR principles.
A postdoc in geoarchaeology, produced the most accurate archaeo-environmental dataset on pre-Columbian impacts in French Guiana to date. Soil samples analyses and radiocarbon dating provided a detailed account of the human history and the landscape-scale extent of anthropogenic disturbances in the study sites. Beyond primary objectives, we conducted an exploratory study on the morphology and morphometry of Neotropical palm phytoliths using Scanning Electron Microscopy to reconstruct paleoenvironments through future work.
In parallel, we are exploring the genomic and phenomic diversity in palm populations. A first PhD student research focuses on the biomechanical properties of palm leaves through vibratory mechanics and tensile testing to evaluate how fibre mechanical properties vary with water content, relevant to traditional palm use, and how biomechanical properties vary within and across species. He developed an informatic pipeline to monitor fibre deformation by Digital Image Correlation, allowing standardised, semi-automated acquisition of biomechanics data. He experimentally evaluated DIC method following a cross-validation with a laser extensometer. Regarding metabolomics, we processed palm fruits in the lab, including weighing, lyophilization, systematic photography for morphometric analysis and manual dissection for metabolomic profiling. Preliminary metabolite extraction and metabolomic profiling tests were carried out, providing encouraging results. A second PhD student was recently hired to study the genomic and metabolomic diversity in palm populations. He is developing the bioinformatics pipeline for NGS data processing using the first set of genomic data acquired.
DOPAMICS team is also engaged in disseminating the work and results of the project to the general public and local communities. For example, we co-organized the Science Nature Festival in Saül in 2023 in collaboration with the Amazonian Park in French Guiana. This event was therefore an exceptional opportunity to present the DOPAMICS project and to share scientific and cultural knowledge with local people.
All protocols, codes and data generated will be made open access on dedicated repositories complying with FAIR principles.
DOPAMICS advances research on tropical biodiversity by applying an interdisciplinary, data-intensive approach to study Neotropical palms. DOPAMICS holds significant scientific and societal value. The data generated are anticipated to inform conservation strategies in the context of increasing anthropogenic pressures and ongoing climate change, by empirically analysing how populations adapt to natural and human-mediated pressures. Our research further illustrates the long-standing relationship between humans and these ecosystems, providing a new perspective on sustainable land use and cultural heritage.
DOPAMICS already made significant contributions to the understanding of the history of Amazonian landscapes in French Guiana through pre-Columbian times, focusing on emblematic but still misunderstood earthworks – the so-called “ring ditches”. Extensive soil surveys revealed that the sites were occupied from the 5th to the 15th centuries, with two main occupation periods. Local enrichments in chemical indicators, along with soil colour variations extending beyond ring ditch enclosures, revealed that pre-Columbian societies made extensive use of their landscapes, leaving long-term imprints on present-day, seemingly wild, Amazonian landscapes. Interestingly, however, soil properties did not meet all the characteristics of the so-called Amazonian Dark Earths (ADEs). ADEs are often considered the most meaningful evidence of long-term pre-Columbian impacts on Amazonian landscapes. However, ADEs are rare in interfluvial regions, and soil modification by human activities is a multidirectional and gradual process that leads to various degrees of soil transformation. Our study thus advocates a paradigm shift towards a better integration of “Amazonian Brown Earths” into the definition of anthropogenic soils in Amazonia. Soil disturbances were also associated with local enrichments in macro- and micro-charcoals that support in situ fire management that could be attributed to forest clearance and/or slash-and-burn cultivation.
Additionally, by engaging with local communities, we promote knowledge sharing and local skill development, while our methodologies and findings will be openly accessible to the global research community through a dedicated database, encouraging further research and applied conservation efforts in tropical biodiversity.
DOPAMICS already made significant contributions to the understanding of the history of Amazonian landscapes in French Guiana through pre-Columbian times, focusing on emblematic but still misunderstood earthworks – the so-called “ring ditches”. Extensive soil surveys revealed that the sites were occupied from the 5th to the 15th centuries, with two main occupation periods. Local enrichments in chemical indicators, along with soil colour variations extending beyond ring ditch enclosures, revealed that pre-Columbian societies made extensive use of their landscapes, leaving long-term imprints on present-day, seemingly wild, Amazonian landscapes. Interestingly, however, soil properties did not meet all the characteristics of the so-called Amazonian Dark Earths (ADEs). ADEs are often considered the most meaningful evidence of long-term pre-Columbian impacts on Amazonian landscapes. However, ADEs are rare in interfluvial regions, and soil modification by human activities is a multidirectional and gradual process that leads to various degrees of soil transformation. Our study thus advocates a paradigm shift towards a better integration of “Amazonian Brown Earths” into the definition of anthropogenic soils in Amazonia. Soil disturbances were also associated with local enrichments in macro- and micro-charcoals that support in situ fire management that could be attributed to forest clearance and/or slash-and-burn cultivation.
Additionally, by engaging with local communities, we promote knowledge sharing and local skill development, while our methodologies and findings will be openly accessible to the global research community through a dedicated database, encouraging further research and applied conservation efforts in tropical biodiversity.