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PARTNERSHIPS FOR ENHANCED ENGAGEMENT IN RESEARCH (PEER)
Cycle 5 (2015 Deadline)


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


PI: Camila Ribas (camilaribas@gmail.com), Instituto Nacional de Pesquisas da Amazonia (INPA), Ministry of Science, Technology, and Innovation, and co-PI Alexandre Aleixo, Museu Paraense Emílio Goeldi (MPEG)
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

The second quarter of 2018 was another very busy period for this PEER time. They conducted one field expedition to the flooded environments along the Branco River between May 2-25. This was important to complement sampling in this region, which is currently the subject of new environmental impact studies due to plans to build a dam on the Branco River. The last of the four field expeditions for acquiring acoustic data for the project ran from June 24 through July 15. In the three previous expeditions (September 2017, December 2017, and March 2018) a total of almost 140,000 recordings were made. Preliminary analysis of the acoustic data from September 2017 revealed 154 species and from December 2017, 121 species.

Back in the lab, the team received sequencing results from 192 samples sent for processing in November 2017 and from 131 samples sent in early April 2018. The students involved in the project received training and are processing the data. The project involves implementing population structure analyses for each species and demographic trend analyses to assess population size changes through time. Preliminary results show population structure for some species, with different levels of admixture between populations. Ultimately the results should help to highlight which species are particularly vulnerable to climate and habitat changes. The researchers have also obtained occurrence data from museum collections for 233 species specialized in Amazonian flooded environments, a total of almost 130,000 records. Geographic coordinates are being obtained for all the records, and maps with occurrence points are being built for each species. Activities in recent months also included the organization of luminescence and radiocarbon ages and preparation of a manuscript about the development of the current Amazonian floodplain. Understanding the past fluvial sedimentary dynamics responsible for the expansion and retraction of Amazonian floodplains is critical to forecasting the resilience of flooded forests under future scenarios of climate (precipitation) and/or anthropogenic (deforestation and river impoundment) changes.

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).

Another key focus of work for the group has been habitat mapping. Preliminary applications of the machine learning models have resulted in accuracies of 70%-80%, using five habitat classes (forests, woodlands, shrubs, herbaceous, open water), by combining ALOS PALSAR and Landsat 5 imagery, and they expect to increase this accuracy by optimizing models and applying model ensembles. In addition to working to address the lack of extensive ground sampling in many of the locations through other technical means, the team has also made progress on a Web mapping application to be used to collect ground truth information from the large accumulated field expertise among project participants and collaborators. A preliminary version of the app can be accessed at https://ecodyn.shinyapps.io/PEER_app/, and this link will be periodically updated until the final operational version is ready, likely by the end of July 2018.

As for future plans, Dr. Ribas has set the dates (September 18-21) and agenda for a workshop with key Brazilian stakeholders and fellow researchers working on related topics. An initial version of the group’s habitat map will be presented in order to gather feedback. In the second semester of 2018, she and her colleagues will organize a joint graduate course at INPA focused on Amazonian biogeography and the history and threats to the flooded habitats. The team’s bird survey and inventory at the RESEX do Baixo Juruá will proceed from July 9 through August 5, in collaboration with the Instituto de Desenvolvimento Sustentável Mamirauá, for complementing the sampling for the project and contributing to the management plan of the RESEX. Now that the acoustic monitoring surveys are complete, the team will continue analyzing and mapping their data. Several manuscripts are in preparation, and the researchers will also present some of their findings at the Brazilian Ornithological Congress next September. Considering the amount of data generated so far and all the students and personnel involved, it is likely that a one-year extension will be issued on the project.
 
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