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Areas of endemism are the smallest units in biogeography and can be defined as biologically unique areas comprising taxa with common geographic limits to their distributions. High beta diversity within Amazonia is often related to turnover among these areas. For decades, evolutionary biologists have tried to comprehend the mechanisms generating and maintaining the spatial structure and high diversity of free-living Amazonian organisms, particularly birds. However, few studies have tried to analyze these patterns among their parasites. Host and parasite associations involve shared history that may allow us to better understand the fine-scale evolutionary history of the host. Here we compare the coevolutionary patterns among 2 avian host species with distinct patterns of genetic structure in northern Amazonia, Dendrocincla fuliginosa (Aves: Dendrocolaptidae) and Dixiphia pipra (Aves: Pipridae), and their ectoparasitic lice (Insecta: Phthiraptera), Furnaricola sp. ex Dendrocincla fuliginosa, Myrsidea sp. ex Dixiphia pipra, and Tyranniphilopterus sp. ex Dixiphia pipra. We obtained sequences of the mitochondrial gene cytochrome oxidase subunit I from hosts and parasites collected on opposite banks of the Negro and Japurá rivers, which delimit 3 areas of endemism in northern Amazonia: Napo, Jau, and Guiana. Our results demonstrate that the Negro River is a geographical barrier for both Furnaricola sp. and its avian host, Dendrocincla fuliginosa. Phylogenies of both hosts, Dendrocincla fuliginosa, and the parasites, Furnaricola sp., show monophyletic clades on opposite margins of the river that are not sister taxa. These clades have a mean uncorrected p-distance of 17.8% for Furnaricola sp. and 6.0% for Dendrocincla fuliginosa. Thus, these parasite clades constitute distinct evolutionary lineages and may even be distinct species. In contrast, Dixiphia pipra has no population structure associated with either river. Accordingly, data from their lice Myrsidea sp. indicate weak support for different clades on opposite margins of the Negro River, whereas data from their lice Tyranniphilopterus sp. indicate weak structure across the Japurá. This study is a first step toward understanding the effects of biogeographic history on permanent ectoparasites and suggests that host biogeographic history is to some extent a determinant of the parasite's history. Furthermore, the parasite's evolutionary history is an additional source of information about their hosts' evolution in this highly diverse region of northern Amazonia.

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Hydroelectric dams represent an important threat to seasonally flooded environments in the Amazon basin. We aimed to evaluate how a dam in the Madeira River, one of the largest tributaries of the Amazonas River, affected floodplain avifauna. Bird occurrence was recorded through simultaneous passive acoustic monitoring in early successional vegetation and floodplain forest downstream from the dam and upstream in sites impacted by permanent flooding after dam reservoir filling. Species were identified through manual inspection and semi-automated classification of the recordings. To assess the similarity in vegetation between downstream and upstream sites, we used Landsat TM/ETM+ composite images from before (2009-2011) and after (2016-2018) reservoir filling. Downstream and upstream floodplain forest sites were similar before, but not after dam construction. Early successional vegetation sites were already different before dam construction. We recorded 195 bird species. While species richness did not differ between upstream and downstream sites, species composition differed significantly. Ten species were indicators of early successional vegetation upstream, and four downstream. Ten species were indicators of floodplain forest upstream, and 31 downstream. Seven of 24 floodplain specialist species were detected by the semi-automated classification only upstream. While we found some bird species characteristic of early successional vegetation in the upstream sites, we did not find most species characteristic of tall floodplain forest. Predominantly carnivorous, insectivorous, and nectarivorous species appear to have been replaced by generalist and widely distributed species.

Barragens hidroelétricas representam uma importante ameaça a ambientes sazonalmente alagados na Amazônia. Avaliamos como uma barragem no Rio Madeira, um dos maiores tributários do Rio Amazonas, afetou a comunidade de aves de várzea. A ocorrência de aves foi registrada através de monitoramento acústico passivo simultâneo em vegetação em estágio sucessional inicial e floresta de várzea a jusante e em áreas a montante alagadas permanentemente após a formação do reservatório. Espécies foram identificadas por inspeção manual e classificação semi-automática das gravações. Para acessar a similaridade entre a vegetação a jusante e montante, utilizamos composições de imagens Landsat TM/ETM+ de antes (2009-2011) e após (2016-2018) a formação do reservatório. Sítios de floresta de várzea foram similares antes, mas não após o reservatório. Sítios de vegetação sucessional inicial já diferiam antes do reservatório. Registramos 195 espécies de aves. A riqueza de espécies não diferiu entre os sítios a jusante e montante, mas a composição de espécies diferiu significativamente. Dez espécies foram indicadoras de vegetação sucessional inicial a montante e quatro a jusante. Dez espécies foram indicadoras de floresta de várzea a montante e 31 a jusante. Sete de 24 espécies especialistas de várzea foram detectadas apenas a montante pelas classificações semi-automáticas. Encontramos algumas espécies típicas de vegetação sucessional inicial a montante, porém não encontramos a maioria de espécies típicas the floresta alta de várzea. Predominantemente, aves carnívoras, insetívoras e nectarívoras aparentam ter sido substituídas por espécies generalistas e amplamente distribuídas.

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ABSTRACT Hydroelectric dams represent an important threat to seasonally flooded environments in the Amazon basin. We aimed to evaluate how a dam in the Madeira River, one of the largest tributaries of the Amazonas River, affected floodplain avifauna. Bird occurrence was recorded through simultaneous passive acoustic monitoring in early successional vegetation and floodplain forest downstream from the dam and upstream in sites impacted by permanent flooding after dam reservoir filling. Species were identified through manual inspection and semi-automated classification of the recordings. To assess the similarity in vegetation between downstream and upstream sites, we used Landsat TM/ETM+ composite images from before (2009-2011) and after (2016-2018) reservoir filling. Downstream and upstream floodplain forest sites were similar before, but not after dam construction. Early successional vegetation sites were already different before dam construction. We recorded 195 bird species. While species richness did not differ between upstream and downstream sites, species composition differed significantly. Ten species were indicators of early successional vegetation upstream, and four downstream. Ten species were indicators of floodplain forest upstream, and 31 downstream. Seven of 24 floodplain specialist species were detected by the semi-automated classification only upstream. While we found some bird species characteristic of early successional vegetation in the upstream sites, we did not find most species characteristic of tall floodplain forest. Predominantly carnivorous, insectivorous, and nectarivorous species appear to have been replaced by generalist and widely distributed species.

RESUMO Barragens hidroelétricas representam uma importante ameaça a ambientes sazonalmente alagados na Amazônia. Avaliamos como uma barragem no Rio Madeira, um dos maiores tributários do Rio Amazonas, afetou a comunidade de aves de várzea. A ocorrência de aves foi registrada através de monitoramento acústico passivo simultâneo em vegetação em estágio sucessional inicial e floresta de várzea a jusante e em áreas a montante alagadas permanentemente após a formação do reservatório. Espécies foram identificadas por inspeção manual e classificação semi-automática das gravações. Para acessar a similaridade entre a vegetação a jusante e montante, utilizamos composições de imagens Landsat TM/ETM+ de antes (2009-2011) e após (2016-2018) a formação do reservatório. Sítios de floresta de várzea foram similares antes, mas não após o reservatório. Sítios de vegetação sucessional inicial já diferiam antes do reservatório. Registramos 195 espécies de aves. A riqueza de espécies não diferiu entre os sítios a jusante e montante, mas a composição de espécies diferiu significativamente. Dez espécies foram indicadoras de vegetação sucessional inicial a montante e quatro a jusante. Dez espécies foram indicadoras de floresta de várzea a montante e 31 a jusante. Sete de 24 espécies especialistas de várzea foram detectadas apenas a montante pelas classificações semi-automáticas. Encontramos algumas espécies típicas de vegetação sucessional inicial a montante, porém não encontramos a maioria de espécies típicas the floresta alta de várzea. Predominantemente, aves carnívoras, insetívoras e nectarívoras aparentam ter sido substituídas por espécies generalistas e amplamente distribuídas.

RESUMEN

Hydroelectric dams represent an important threat to seasonally flooded environments in the Amazon basin. We aimed to evaluate how a dam in the Madeira River, one of the largest tributaries of the Amazonas River, affected floodplain avifauna. Bird occurrence was recorded through simultaneous passive acoustic monitoring in early successional vegetation and floodplain forest downstream from the dam and upstream in sites impacted by permanent flooding after dam reservoir filling. Species were identified through manual inspection and semi-automated classification of the recordings. To assess the similarity in vegetation between downstream and upstream sites, we used Landsat TM/ETM+ composite images from before (2009-2011) and after (2016-2018) reservoir filling. Downstream and upstream floodplain forest sites were similar before, but not after dam construction. Early successional vegetation sites were already different before dam construction. We recorded 195 bird species. While species richness did not differ between upstream and downstream sites, species composition differed significantly. Ten species were indicators of early successional vegetation upstream, and four downstream. Ten species were indicators of floodplain forest upstream, and 31 downstream. Seven of 24 floodplain specialist species were detected by the semi-automated classification only upstream. While we found some bird species characteristic of early successional vegetation in the upstream sites, we did not find most species characteristic of tall floodplain forest. Predominantly carnivorous, insectivorous, and nectarivorous species appear to have been replaced by generalist and widely distributed species.(AU)

Barragens hidroelétricas representam uma importante ameaça a ambientes sazonalmente alagados na Amazônia. Avaliamos como uma barragem no Rio Madeira, um dos maiores tributários do Rio Amazonas, afetou a comunidade de aves de várzea. A ocorrência de aves foi registrada através de monitoramento acústico passivo simultâneo em vegetação em estágio sucessional inicial e floresta de várzea a jusante e em áreas a montante alagadas permanentemente após a formação do reservatório. Espécies foram identificadas por inspeção manual e classificação semi-automática das gravações. Para acessar a similaridade entre a vegetação a jusante e montante, utilizamos composições de imagens Landsat TM/ETM+ de antes (2009-2011) e após (2016-2018) a formação do reservatório. Sítios de floresta de várzea foram similares antes, mas não após o reservatório. Sítios de vegetação sucessional inicial já diferiam antes do reservatório. Registramos 195 espécies de aves. A riqueza de espécies não diferiu entre os sítios a jusante e montante, mas a composição de espécies diferiu significativamente. Dez espécies foram indicadoras de vegetação sucessional inicial a montante e quatro a jusante. Dez espécies foram indicadoras de floresta de várzea a montante e 31 a jusante. Sete de 24 espécies especialistas de várzea foram detectadas apenas a montante pelas classificações semi-automáticas. Encontramos algumas espécies típicas de vegetação sucessional inicial a montante, porém não encontramos a maioria de espécies típicas the floresta alta de várzea. Predominantemente, aves carnívoras, insetívoras e nectarívoras aparentam ter sido substituídas por espécies generalistas e amplamente distribuídas.(AU)

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To elucidate the relationships and spatial range evolution across the world of the bird genus Turdus (Aves), we produced a large genomic dataset comprising ca 2 million nucleotides for ca 100 samples representing 53 species, including over 2000 loci. We estimated time-calibrated maximum-likelihood and multispecies coalescent phylogenies and carried out biogeographic analyses. Our results indicate that there have been considerably fewer trans-oceanic dispersals within the genus Turdus than previously suggested, such that the Palaearctic clade did not originate in America and the African clade was not involved in the colonization of the Americas. Instead, our findings suggest that dispersal from the Western Palaearctic via the Antilles to the Neotropics might have occurred in a single event, giving rise to the rich Neotropical diversity of Turdus observed today, with no reverse dispersals to the Palaearctic or Africa. Our large multilocus dataset, combined with dense species-level sampling and analysed under probabilistic methods, brings important insights into historical biogeography and systematics, even in a scenario of fast and spatially complex diversification.

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The Amazonian landscape evolution is the result of the combined effect of Andean tectonism, climate and the Earth's interior dynamics. To reconstruct the landscape evolution and its influence on paleoenvironmental variations within Amazonia since the Oligocene, we conducted numerical experiments that incorporate different surface and geodynamic processes, reproducing many paleogeographic features as inferred from the sedimentary record. We show that the evolution of the drainage pattern gradually reduced the area of sedimentation derived from the Guiana and Brazilian shields while expanded the Andean derived deposits during the Miocene, affecting the nutrient availability. First order biotic habitats were inferred from these paleogeographical reconstructions, showing an eastward expansion of várzea and terra firme forests and consequent retraction of igapó forests, with a millennial-scale reconfiguration of a mosaic of habitats in the lowlands. We conclude that this dynamism probably guided the observed patterns of speciation in the most biodiverse biome on Earth.

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The spiny rats, genus Proechimys, have the highest species richness within the Echimyidae family, as well as species with high genetic variability. The genus distribution includes tropical South America and Central America south to Honduras. In this study, we evaluate the phylogeographic histories of Proechimys guyannensis and P. cuvieri using cytochrome b, in a densely sampled area in northeastern Amazon where both species are found in sympatry in different environments. For each species, Bayesian and Maximum Likelihood phylogenetic analysis were congruent and recovered similar clades in the studied area. Bayesian phylogenetic analysis using a relaxed molecular clock showed that these clusters of haplotypes diversified during Pleistocene for both species. Apparently, the large rivers of the region did not act as barriers, as some clades include specimens collected from opposite banks of Oiapoque, Araguari and Jari rivers. Bayesian skyline plot analysis showed recent demographic expansion in both species. The Pleistocene climatic changes in concert with the geologic changes in the Amazon fan probably acted as drivers in the diversification that we detected in these two spiny rats. Proechimys cuvieri and P. guyannensis show genetic structure in the eastern part of the Guiana region. Greater genetic distances observed in P. guyannensis, associated with highly structured groups, suggest that more detailed studies of systematics and ecology should be directed to this species.

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