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Cycle 5 (2015 Deadline)

History and diversification of floodplain forest bird communities in Amazonia: towards an integrated conservation plan

PI: Camila Ribas (, Instituto Nacional de Pesquisas da Amazonia, Ministry of Science, Technology, and Innovation, and co-PI Alexandre Aleixo, Museu Paraense Emílio Goeldi
U.S. Partner: Joel Cracraft, American Museum of Natural History
Project Dates: December 2016 - November 2018

Project Overview:

The research proposed here is crucial, given that Amazonian countries are focusing on building hydroelectric dams, which will impose a significant impact to the biota specialized in flooded habitats through habitat loss, fragmentation, and changes in sediment dynamics. This biota has a unique, complex, and still poorly known history, as wetlands probably dominated western Amazonia for a large portion of the Neogene, and significant changes on the drainage pattern have occurred since then. Although birds are one of the best-known groups of vertebrates, flooded habitat bird assemblages are still poorly known and have been very little explored using molecular techniques. Based on the dynamic history of flooded habitats (with their frequent cycles of building and erosion due to sedimentary processes), bird species from these habitats were assumed to have high dispersal ability and consequently to lack genetic structure. However, recent studies of phenotypic and genomic variation have shown that this is not the case. Substantial cryptic diversity and endemism have been found within some of these taxa, which indicates that patterns and processes underlying these patterns are not well understood. Within the context of the developmental plans for energy generation, this constitutes a major threat to a significant portion of Amazonian biodiversity that is little known. Dr. Ribas and her colleagues will generate a multidisciplinary dataset, including genomic, ecologic, and spatial biotic and abiotic data that will be integrated to (1) advance our knowledge on the evolution of Amazonian flooded habitats and their biota and (2) provide information that can be used for assessing the impact of proposed hydroelectric dams and for identifying areas of conservation priority. This will be accomplished in collaboration with the NSF-funded project led by Dr. Cracraft, which aims to reconstruct the history and evolution of the Amazonian biota and its environment, focusing mainly on the upland forest biota, and will provide background information on methods and analysis, as well as complementary data.

Hydroelectric energy generation is considered a source of clean and renewable energy, but current environmental impact assessments ignore the long-term irreversible impacts that dams have on Amazonian flooded habitats. There are 121 established, and 303 planned, dams for the Amazon region, most of them in Brazil. In the Amazonian lowlands, 51 dams already exist and 130 more are planned. Among the ten largest planned dams, three are built or nearing completion: Santo Antônio and Jirau (Madeira River) and Belo Monte (Xingu River). The remaining seven are still in planning stages, reinforcing the need for immediate attention to the impacts of these projects. Most planned dams in the Amazonian lowlands will adopt the “run of the river” system, in which large extensions of flooded habitat are kept permanently flooded, submerging river islands and disrupting the hydrologic cycle. The resulting loss of species in flooded habitats may impact the upland biota as well, as taxa from both habitats are interconnected by ecological processes, and thus have important consequences for large portions of Amazonian protected areas and indigenous lands, affecting availability of resources for both the ecosystem and traditional and indigenous communities. To assess the impact of planned dams on the Amazonian biota it is essential to understand the history and distribution of flooded habitats’ biological diversity, as well as the importance of the hydrological cycle in developing and maintaining this diversity. For this, an interdisciplinary framework is necessary that considers the evolution of the current landscape and its possible responses to the dams. Dr. Ribas has assembled a multidisciplinary team that will study population genomics, ecological affinities, biological diversification, and species distribution patterns for flooded habitat birds and relate these patterns to spatial distribution and chronology of flooded habitats, sediment dynamics responsible for building or erosion of flooded substrates, and hydrology of the most threatened Amazonian basins. As a result, they expect to produce and disseminate data and integrative analytical methods that will inform environmental impact assessments related to planning and execution of developmental projects taking place in the future and especially over the coming decade in Brazil.

Summary of Recent Activities

During April through June 2017, Dr. Ribas focused on planning and discussing graduate student projects that will be part of the main PEER project. She and her co-PI have selected three Master’s students and three PhD students who will develop their theses and dissertations in the context of the funded project. All of them have received fellowships from Brazilian funding agencies and they are enrolled in three different graduate programs at INPA and MPEG. The team has also been successful in obtaining one more postdoctoral fellowship from a Brazilian sponsor for a researcher who will work with co-PI Dr. Alexandre Aleixo at MPEG, so this brings the total size of the team to four postdocs, three PhD students, and three Master’s students working with the PI and co-PI, all of them fully funded.

The portable acoustic data recorders ordered in the previous quarter have been tested, and one of the PhD students was trained on the use of the relevant software for data collection and analysis. Data collection for the acoustic monitoring will start in September 2017, and the team has made contacts with the administration at Santo Antônio Energia to receive access to the area. They also plann to collect acoustic data in a joint expedition to the Xingu River, close to the Belo Monte Dam, a trip that will be funded by a separate project headed by Dr. Andre Sawakuchi. As for genomic data, the 279 samples already sent for sequencing are still being processed by Rapid Genomics as of July 2017. The PI has also submitted tissue loan requests to five American collections and is awaiting their replies so that she and her group can proceed with DNA extractions. A sample collection expedition is planned to the lower Solimões River in October/November due to the high flooding this year. Meanwhile, other members of the team are working on gathering georeferenced data, downloading and processing satellite imagery that will be used for habitat and inundation classification, and developing a classification scheme for wetland habitats that is both aligned with the proposed classification systems existing in the literature, and compatible with the scale and nature of satellite land cover mapping.

At the May 2017 USAID/Brazil Environment Program Annual Partners Meeting, Dr. Ribas and Dr. Aleixo initiated conversations with IPE and ICMBio about their biodiversity monitoring initiatives and species distribution analyses. They plan to propose a joint meeting to discuss their common interests. In addition, the meeting provided an opportunity to establish contact with the PEER-funded project headed by Dr. Jean Ometto at INPE, which is gathering remote sensing data for the Amazon.

In addition to the field expeditions noted above, other planned activities for the second half of 2017 include (1) obtaining the samples requested from American collections, extracting DNA, and sending them out for sequencing; (2) selecting samples from four remaining species after receiving some preliminary data; (3) sending the remaining samples from the Brazilian collections for sequencing; and (4) building a genomic database and starting preliminary analyses. Once the classification scheme is defined, a system for collecting ground truthing samples based on expert interpretation of high-resolution Google Earth imagery will be implemented, to build a large and robust dataset that can be used to effectively train machine learning algorithms for habitat classification. Based on these samples, test runs of different classification algorithms will be applied to various locations to assess classification accuracy. High resolution imagery will be solicited from USAID’s GeoCenter Remote Sensing Program, to support validation of classification efforts. During the planned expedition for acoustic monitoring in August/September the team will perform the first ground truthing of the classification scheme. During the coming months they will also continue assembling the datasets of occurrence localities for the 30 focal species (for which genomic data is also being collected) and expand this dataset for all species characterized as associated with Amazonian flooded habitats (around 200 species). The researchers have already started discussing this approach with researchers from their U.S. partner’s project, which is focusing on specific taxonomic groups mostly associated with upland forests. Based on the first classifications of flooded habitats, spatial ecological analysis will be initiated to define sampling strategies for the acoustic monitoring and the methodological approach for evaluating connectivity among populations associated with each kind of habitat. Dr. Ribas and her team plan to submit their first manuscript on the evolution of flooded and upland habitats by the end of August 2017. During their upcoming field work they will collect additional data for chronological analyses of sediments along the main Amazonian rivers. This will help provide a better understanding of the temporal dynamics of flooded habitats and the impacts of the dams on the historical patterns of erosion and sediment deposition.

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