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Tropical rain forest diversification: a GLOBAL approach

Periodic Reporting for period 2 - GLOBAL (Tropical rain forest diversification: a GLOBAL approach)

Reporting period: 2022-04-01 to 2023-09-30

Tropical rain forests (TRF) are the most species rich yet highly threatened ecosystems on Earth. They play pivotal roles as global climate regulators and for human wellbeing. Their long term conservation is central for global climate mitigation and biodiversity conservation. Elucidating the evolutionary processes that underpin this immense diversity is critical for improved conservation actions. What evolutionary processes determine TRF diversity? How will human-induced species losses impact the evolutionary history of TRF? Time calibrated phylogenies retain the fingerprint of these patterns and are fundamental prerequisites to maximize the conservation of evolutionary history. However, global densely sampled robust phylogenies are lacking for TRF plants, significantly limiting our ability to properly address these questions. I will generate the largest most comprehensive datasets ever assembled for a major, ecologically important and species-rich pantropical model plant family: Annonaceae (~2500 species). First, I will test major hypotheses about TRF evolution at a global scale and what biotic and abiotic factors drove their diversification. Then, I will predict the impact of plant species extinction on the evolutionary history of TRF. Using the extensive network of European herbaria, I will reconstruct a robust time-calibrated complete species level phylogenomic tree of Annonaceae. I will compile massive morphological, chemical and geographical datasets for all species. Novel paleoclimatic data will be modelled through space at ten discrete periods over the last 100 million years. These data will then be integrated using innovative statistical macroevolutionary comparative approaches to answer the above questions at never achieved levels of precision. GLOBAL will provide improved predictions of TRF evolution informing conservation policies, and set the new standard for next generation evolutionary studies of TRF evolution applicable to other key tropical groups.
The first phase of the project focused on generating and acquiring data. The first task focused on generating a species level phylogeny of all Annonaceae, which has about 2500 species. For that we had to sample these species, and had access to two main sources. First, via a global network of collaborators, we received over 2000 samples of leaves dried in “silica gel”. This type of leaf is ideal for DNA extraction. We also performed several field trips, mainly in the mega diverse country of Ecuador, which led to the discovery of several new species. Second, the botanical engineer of the project, Carlos Rodrigues, sampled as many missing species as possible using a large but undervalued resource: herbarium specimens. These are the basis of plant biodiversity research, and represent plants collected in the field, dried and mounted on paper. Carlos sampled over 3800 specimens representing around 2110 species, some of these only from a single herbarium sheet. DNA is extracted and sequenced in Montpellier by the molecular engineer Vincent Soulé. The oldest specimen we extracted DNA from was collected in 1826! Based on this huge effort, we have now sequenced nearly 85% of all Annonaceae species, which has never been achieved for a tropical plant family. Post doc Francis Nge has been generating phylogenies at high levels of precision linked to the hundreds of genes sequenced for each species. We generated the first complete genus level phylogeny of Annonaceae that will be the basis of an updated classification.
We are also gathering climate data deep into the past for the tropics. Post doc Delphine Tardif has been modeling paleoclimates at local (100km²) and regional scales throughout the last 100 million years at discrete times. She is now exploring how these past climatic variations have impacted the distribution and evolution of Annonaceae.
In parallel, PhD student Paola Santacruz has undertaken an in-depth study of Annonaceae-herbivore interactions in the most biodiverse place in the world, the Yasuní National Park in Amazonian Ecuador. She spent over a year there collecting data on nine different species such as what insects eat their leaves and the chemical composition of their leaves. She discovered a discrete but diverse community of Lepidoptera (butterflies and moths) species feeding on its leaves, as well as several ant species specialized in living on Annonaceae via an association with aphids. We believe that this interaction played a role in the evolution of Annonaceae. To get an idea of chemical composition of all Annonaceae species, we turned once again to herbarium specimens, and using Near Infra red scanning (NIRs), we generated chemical spectra for over 1900 species of Annonaceae (we are still scanning more species). Paola, and other students, will use this data to understand how chemical composition varied throughout the entire family, and if there is a link with evolution.
We are also generating a large dataset of morphological traits for all species. To date we have about 55’000 traits coded for over 1900 species. This is the largest such dataset produced to date. Finally, to get better insights into the distribution and conservation of Annonaceae species, PhD student Serafin Streiff is generating a large distribution dataset, using herbarium specimens. We undertook a citizen science project, where anybody could enter herbarium label information. This was applied within the “herbonautes” project of the largest herbarium in the world located in the museum of Paris, France.
All data generated will be made open access, especially via a website. For that bioinformatician Archimède Patipe is compiling all data and preparing the website.
By sequencing almost all Annonaceae species (e.g. 85% of known diversity), and reconstructing the evolutionary history of this important rain forest plant clade via molecular dating, we will be able to understand at rarely achieved levels of detail how tropical rain biodiversity evolved over millions of years. In addition to the phylogeny, we are generating data on multiple levels, such as geography, chemical and morphological diversity. We aim to have this data for all Annonaceae species, leading to large scale datasets that will be integrated with the phylogeny. For that, we shall apply state of the art methods to test multiple hypotheses about rain forest diversity.
In parallel, we are using near infra-red scanning on herbarium dried leaves. This will be used as a proxy to understand the evolution of chemical diversity across the family. Applying this technology to herbarium specimens is rarely done, at least not on this scale with thousands of species scanned.
By the end of the project we expect to unravel the evolutionary history of Annonaceae in rain forests at global and local levels covering millions of years. We shall infer the impact of human induced extinction of this family and how that impacts multiple dimensions of its biodiversity. In doing so, we shall provide important information about rain forest evolution which contribute towards the conservation of this most biodiverse ecosystems at global levels. All data will be made available online via a dedicated website.
Exploring tropical rain forest in a remote Amazonian region of Ecuador