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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 the last quarter of 2017, the main project activities included field work; molecular data generation, management, and preliminary analysis; acoustic data acquisition, management, and preliminary analysis; and construction of a database of occurrence localities for species from Amazonian flooded habitats. The main project expedition for bird and spatial data collection along the Solimões River ended on November 13. Dr. Ribas and her colleagues collected blood or tissue samples from 488 birds specialized on Amazonian flooded habitats, filing many sampling gaps that will allow a better assessment of phylogeographic patterns and population connectivity for the species selected for the project. From the collected samples, 118 sampled individuals belong to 19 of the 30 focal species selected for the project. All specimens and samples have been prepared, identified, and deposited in the Bird and Genetic Resources Collections of INPA (the National Institute of Amazonian Research) and the Genetic Resources Collection of MPEG (Museu Paraense Emílio Goeldi). A smaller expedition was carried out between November 7 and December 4 to sample birds in the Madeira River watershed in Mapinguari and Campos Amazônicos National Parks. During this expedition, the team collected 224 samples, which have been deposited in the INPA Genetic Resources Collection. The second expedition for acoustic data collection along the Madeira River took place from November 28 through December 23. During this period, two regions were sampled upstream and downstream of the Santo Antonio Dam, after which the data were all uploaded to the Arbimon server. The researchers have started extracting species lists for each locality based on a sample of the recorded data. They began by identifying birds from 100 recordings from each locality in order to understand the general species composition. Subsequently they will proceed with the analysis of temporal patterns of occupancy by constructing identification models for selected species.

5-009 Toucan5-009 Sample Analysis
The team conducted field expeditions to gather samples from a number of species.Following data collection, the team organized and collated collected samples (photo courtesy of Dr. Ribas).

Regarding the molecular aspects of their project, during the last quarter of 2017 the researchers sent two more plates for sequencing (plates 4 and 5) and received the results from plate 3 (each plate includes 96 samples). They have organized data from the first three plates in a common database and have started processing the raw data. In the meantime, they have also focused on defining the list of Amazonian bird species specialized in flooded environments for which they will collect occurrence data. These will include all 30 species selected for the genetic analyses, plus all other species that occur primarily in Amazonian flooded environments—their preliminary list includes 271 species. They are now revising the list to exclude taxa that have most of their distributions outside Amazonia, generalists that also occupy upland forests and other habitats, and widespread aquatic taxa. In parallel, they have also started to gather occurrence data from online databases, including the Global Biodiversity Information Facility and other repositories.

In September 2017, Dr. Ribas was awarded a PEER supplement of U.S. $5,000 to organize a workshop on “Integrating knowledge about species and areas vulnerability in a spatial framework for planning hydroelectric energy generation in Amazonia.” The event will take place May 16-18, 2018, at the Auditorio da Ciência, INPA, Manaus. All invited stakeholder institutions have agreed to participate, including the Instituto de Pesquisas Ecológicas (IPE), the Empresa de Pesquisa Energética (EPE), the Brazilian Institute of Environment and Renewable Natural Resources (IBAMA) and the Chico Mendes Institute for Biodiversity Conservation (ICMBio). Efforts are now under way to define the detailed aims and agenda and arrange the logistics. One of the three days of the workshop will be open to students and the broader scientific community.

In February 2018, the team will conduct a small field expedition to the upper Amazon River, between the cities of Obidos and Santarem, to obtain specific samples to cover sampling gaps. They also will execute their third expedition for acoustic data collection on the Madeira River in April, and another expedition for acoustic data collection on the Xingu River (to cover the high water period) will happen in March. At least two additional plates will be sent for sequencing during the first half of the year, including the samples collected in the recent field campaigns. The team will also receive data from the two plates sent for sequencing in December.

Dr. Ribas has been invited by the Center for Latin American and Caribbean Studies at Duke University to participate as a presenter at the fourth annual Global Brazil Conference, to be held April 5-6, 2018, at Duke University in Durham, NC, with the theme “Amazon Frontiers.” After the conference at Duke, Dr. Ribas will spend a week at the American Museum of Natural History in New York to discuss project activities with U.S. partner Dr. Joel Cracraft. Funding for the visit will be provided by Duke University and no PEER funds will be used.

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