In 2021, more than 28.4 million people were estimated to reside within the Legal Amazon area in Brazil. Since 1970, the resident population in the region has quadrupled. The Legal Amazon in Brazil extends across nine Brazilian states, with the the largest area located in the state of Amazonas.

The Amazon rainforest is known for being one of the most diverse ecosystems on Earth. According to the source, this biome located in South America was home to one in every ten known species on the planet. The Amazon basin spans across nine South American countries or territories: Brazil, Bolivia, Peru, Ecuador, Colombia, Venezuela, Guyana, Suriname, and French Guiana. The region occupies an area of 2.6 million square miles, which represents around 40 percent of the total South American territory.

Abstract The Southwestern Region of the Brazilian Amazon is formed by forests dominated by bamboos. The genus Guadua is endemic to the Americas, and little is known about the genetic diversity and structure of species of this genus. This study aimed to evaluate the genetic diversity and structure of two native Guadua species in natural populations in the Southwestern region of the Brazilian Amazon. Therefore, the genetic diversity and structure of Guadua aff. chaparensis and Guadua aff. lynnclarkiae were evaluated with the use of microsatellite molecular markers (SSR). It was verified that the average genetic diversity for the populations studied was considered high ( H ^ e =0.5) compared to other species of bamboo. All populations had rare and private alleles, and none of them presented significant values of inbreeding. The populations were divergent ( G ^ ST = 0.46), resulting in a low apparent gene flow. The Bayesian analysis showed that among the 350 individuals analyzed, five groups (K=5) were formed, with little similarity among the groups (Populations), although two of them presented clonal individuals. According to the results obtained, it can be conclude that populations should be treated as having unique characteristics, mainly when accessed for management and for in situ and ex situ conservation studies.

Obligate river dolphins occur only in the rivers of Asia and South America, where they are increasingly subject to damaging pressures such as habitat degradation, food competition and entanglement in fishing gear as human populations expand. The Amazon basin hosts two, very different, dolphins—the boto or Amazon river dolphin (Inia geoffrensis) and the smaller tucuxi (Sotalia fluviatilis). Both species have wide geographical ranges and were once considered to be relatively abundant. Their IUCN Red List conservation status of Data Deficient (DD), due to limited information on threats, ecology, population numbers and trends, did not initially cause alarm. However, the development of dolphin hunting to provide fish bait at around the beginning of this millennium broadly coincided with the onset of a widespread perception that numbers of both species were in decline. Consequently, the need for population trend data to inform conservation advice and measures became urgent. This paper presents a 22-year time series of standardised surveys for both dolphins within the Mamirauá Reserve, Amazonas State, Brazil. Analysis of these data show that both species are in steep decline, with their populations halving every 10 years (botos) and 9 years (tucuxis) at current rates. These results are consistent with published, independent information on survival rates of botos in this area, which demonstrated a substantial drop in annual survival, commencing at around the year 2000. Mamirauá is a protected area, and is subject to fewer environmental pressures than elsewhere in the region, so there is no reason to suspect that the decline in dolphins within the Reserve is more pronounced than outside it. If South America's freshwater cetaceans are to avoid following their Asian counterparts on the path to a perilous conservation status, effective conservation measures are required immediately. Enforcement of existing fishery laws would greatly assist in achieving this.

Artibeus obscurus (Mammalia: Chiroptera) is endemic to South America, being found in at least 18 Brazilian states. Recent studies revealed that different populations of this genus present distinct phylogeographic patterns; however, very little is known on the population genetics structure of A. obscurus in the Amazon rainforest. Here, using a fragment (1010bp) of the mitochondrial gene cytochrome b from 87 samples, we investigated patterns of genetic divergence among populations of A. obscurus from different locations in the Brazilian Amazon rainforest and compared them with other Brazilian and South American regions. Analysis of molecular variance (AMOVA), fixation index (Fst) analysis, and phylogeographic patterns showed divergence between two major monophyletic groups, each one corresponding to a geographic region associated with the Atlantic and Amazon forest biomes. The Atlantic forest clusters formed a monophyletic group with a high bootstrap support and a fragmented distribution that follows the pattern predicted by the Refuge Theory. On the other hand, a different scenario was observed for the Amazon forest, where no fragmentation was identified. The AMOVA results revealed a significant geographic heterogeneity in the distribution of genetic variation, with 70% found within populations across the studied populations (Fst values ranging from 0.05864 to 0.09673; φST = 0.55). The intrapopulational analysis revealed that one population (Bragança) showed significant evidence of population expansion, with the formation of 2 distinct phylogroups, suggesting the occurrence of a subspecies or at least a different population in this region. These results also suggest considerable heterogeneity for A. obscurus in the Amazon region.

The 2003 Santarem dataset consists of 8 interconnected datasets and 1 linking file. The primary unit of analysis is the rural property or lot. Each lot in the sample contains a minimum of 1 household with a mean of 1.33 households per lot in the final sample. Within households, data were collected on subsets of individuals as well as additional properties used by the households in the study. These 2003 Santarem data come from interviews with farm families in an agricultural zone south of the city of Santarem in the Brazilian state of Para. Santarem is a relatively old settlement within the Brazilian Amazon that has experienced waves of regional settlement in the 1930s, mid-century, and the 1970s. The study region is adjacent to the confluence of the Amazon and Tapajos Rivers and the northern terminus of the BR-163 (the Cuiaba-Santarem Highway). BR-163 links intensive agropastoral production (particularly mechanized soybean farming) in the state of Mato Grosso to Santarem, where the multinational corporation Cargill runs a deepwater port (opened in 2003) for loading soybeans onto oceangoing ships. The opening of this port has accelerated the process of urbanization and led to a transformation from a landscape of small family farming to a landscape of mechanized agriculture (description adapted from VanWey, Leah K., and Kara B. Cebulko, 2007, Journal of Marriage and the Family 69: 1257-1270). The discourse on deforestation has focused on the alarming rates of deforestation in the Amazon Basin to the neglect of the dynamic and reciprocal influences between the human population and the environment. Deforestation is a process mediated by human intervention, from the act of clearing to how such a clearing is used and managed over time. It would be helpful to know whether observable rates of forest removal represent a stage in the developmental cycle of households or represents the simple and direct impact of increasing population in these environments. From the point of view of theory and method, it is necessary to develop new approaches that effectively link demographic process to the interactive relationship of population to specific aspects of an environmental matrix. This project addressed multiple scales, from household dynamics to landscape dynamics and has developed methods by which to scale between them. We hypothesize that as households occupy frontier areas past the first generation, they move from a strategy of managing their land under the constraints of available household labor to a strategy that gives greater recognition of the constraints posed by land quality and of the risks to their farm operation coming from external socioeconomic forces and biophysical constraints. In the first generation, the labor available to a household is determined by the size of the household making the initial trip to the frontier (primarily young couples is common in frontier regions) and later by the fertility of these initial migrants. As these initial migrants age and their children enter adulthood (thereby becoming the second generation), labor supply is determined by the reproductive and land use choices of these children. Given the precipitous decline in female fertility, other factors gain salience in the second generation: the suitability of the land for various uses, the availability of off-farm employment and educational opportunities (both locally and those requiring migration), and macroeconomic factors affecting the economic viability of farming. These decisions then directly determine the entries into and exits from the household. This study investigated five basic questions: (1) Does the changing availability of household labor over the household life cycle affect the trajectory of deforestation and land use change in the same way for later generations of Amazonian farmers as for first generation in-migrants? (2) What are the determinants of changing household labor supply? Specifically, what are the biophysical and socioeconomic determinants of entries into and exits from the household through fertility, migration, and marriage? (3) How are the decisions of households regarding land use and labor allocation constrained by soil quality, access to water supplies, interannual drought events (e.g. El Nino type events), and other resource scarcities? (4) Are there notable differences in land use choices made by la

We compiled and presented a dataset for all timber species reported in the Amazon region from all nine South American Amazonian countries. This was based on official information from every country, as well as from two substantial scientific references. We verified the standard taxonomic names from each individual source, using the Taxonomic Name Resolution Service (TNRS) and considered all Amazonian tree species with DBH ≥ 10 cm. We also obtained estimates of the current population size for most species from a published approach based on data from 1,900 tree inventory plots (1-hectare each) distributed across the Amazon region and part from the Amazon Tree Diversity Network (ATDN). We then identified the hyperdominant timber species. In addition, we overlapped our timber species list with data for species that are used for commercial purposes, according to the International Tropical Timber Organization (ITTO), the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) and the International Union for Conservation of Nature (IUCN) taxa assessment and Red List categories. Finally, we also included IUCN Red List categories based on combined deforestation, and climate change scenarios for these species. Our final Amazonian timber species dataset contains 1,112 unique species records, which belong to 337 genera and 72 families from the lowland Amazonian rainforest, with associated information related to population, conservation, and trade status of each species. The authors of this research expect that the information provided will be useful to strengthen the public forestry policies of the Amazon countries, inform ecological studies, as well for forest management purposes.

Biogeographic barriers such as rivers have been shown to shape spatial patterns of biodiversity in the Amazon basin, yet relatively little is known about the distribution of genetic variation across continuous rainforest. Here, we characterize the genetic structure of the brilliant-thighed poison frog (Allobates femoralis) across an 880-km-long transect along the Purus-Madeira interfluve south of the Amazon river, based on 64 individuals genotyped at 7609 single-nucleotide polymorphism loci. A population tree and clustering analyses revealed 4 distinct genetic groups, one of which was strongly divergent. These genetic groups were concomitant with femoral spot coloration differences, which was intermediate within a zone of admixture between two of the groups. The location of these genetic groups did not consistently correspond to current ecological transitions between major forest types. A multimodel approach to quantify the relative influence of isolation-by-geographic distance (IBD) and isolation-by-environmental resistance (IBR) nevertheless revealed that, in addition to a strong signal of IBD, spatial genetic differentiation was explained by IBR primarily linked to dry season intensity (r2 = 8.4%) and canopy cover (r2 = 6.4%). We show significant phylogenetic divergence in the absence of obvious biogeographical barriers and that finer-scaled measures of genetic structure show patterns that are associated with environmental variables also known to predict the density of A. femoralis.

Methods

Extraction of DNA and single-nucleotide polymorphism (SNP) discovery was carried out at Diversity Arrays Technology sequencing Pty. Ltd. (DArTseq) facility (Canberra, Australia; more detail, please see the Supplementary Information in the article). A modified double-digest restriction-site associated DNA sequencing protocol was performed on libraries prepared using a combination of Pstl-Hpall restriction enzymes. The Pstl enzyme adaptor also contained an Illumina adaptor sequence, a primer sequence and a variable-length barcode. The Hpall adaptor contained an Illumina flow cell attachment and overhang sequence. Following enzymatic digestion, fragments were amplified and sequenced on an Illumina HiSeq2500. DNA sequences were aligned via BLAST using the Nanorana parkeri reference genome. To check for contamination, sequences were also blasted to bacterial and fungal genomes (NCBI).

Usage Notes

This data set was filtered for missing data using the filter_dart function of the R package RADIATOR v. 0.010. Only individuals and loci with ≥95% SNPs geno- typed were retained. SNPs were also screened for allele coverage, with any SNPs displaying a local and global minor allele frequency threshold of less than 1% removed from the dataset. In cases where multiple SNPs were found within the same read, only one locus was retained (chosen randomly per RAD tag) to avoid statistical bias from physical linkage. Two samples from M14 had <95% of loci genotyped and were removed, which resulted in 64 individuals from 13 populations genotyped at 10 275 SNPs (please see the article Table S2 for summary of filtering steps).

The identification of ecological and evolutionary mechanisms that might account for the elevated biotic diversity in tropical forests is a central theme in evolutionary biology. This issue is especially relevant in the Neotropical region, where biological diversity is the highest in the world, but where few studies have been conducted to test factors causing population differentiation and speciation. We used mtDNA sequence data to examine the genetic structure within white-backed fire-eye (Pyriglena leuconota) populations along the Tocantins River valley in the south-eastern Amazon Basin, and we confront the predictions of the river and the Pleistocene refuge hypotheses with patterns of genetic variation observed in these populations. We also investigated whether these patterns reflect the recently detected shift in the course of the Tocantins River. We sampled a total of 32 individuals east of, and 52 individuals west of, the Tocantins River. Coalescent simulations and phylogeographica...

The Amazon River is known as a region of intense biochemical reactivity. As a result of increased anthropogenic impacts in its catchment (e.g. population growth, agriculture, and deforestation), The Amazon River is undergoing fundamental changes. The RV METEOR cruise M174 (https://doi.org/10.1594/PANGAEA.935041) aimed to provide an integrated overview of nitrogen cycling processes in areas influenced by the Amazon River, which is crucial to estimate the ecosystem's health and productivity. During this cruise, a MUC was deployed at eight stations to collect short sediment cores, in order to explore the influence of the river on sediments. This dataset presents the results of porewater nutrients collected with rhizons and measured on board with an autoanalyzer (Quaatro seal analytics).

Aim: We tested if historical demographic changes of populations occurring on the floodplains of a major Amazon Basin tributary could be associated with range expansions from upper and middle sections of the river, following the establishment of widespread river-created environments during the Late Pleistocene and Holocene. Location: Solimões River, Western Amazon, South America. Taxon: Myrmoborus lugubris, Thamnophilus cryptoleucus and Myrmotherula assimilis. Methods: We explored spatial patterns of genetic diversity and connectivity among sampled localities using thousands of Ultra-Conserved Elements. Range expansions were tested with alternative methods. We quantified habitat preference for the analyzed species to test whether the occupation of dynamic habitats could predict spatial patterns of genetic diversity. Results: Our study did not support shared population range expansions related to historical regionalized changes in habitat availability. We found considerable variation in the spatial distribution of the genetic diversity between studied taxa, and that species with higher levels of specialization to dynamic environments have a more heterogeneous distribution of genetic diversity and reduced levels of gene flow across space. Main conclusions: Our results suggest that demographic expansions along the Solimões River might be linked to spatially homogeneous oscillation in the distribution of floodplain environments, promoting effective population size changes but not range expansion. We found that habitat specificity might be a good predictor of population connectivity along the Amazonian floodplains.

All fishes data with coordinates

Habitat fragmentation remains a major focus of research by ecologists decades after being put forward as a threat to the integrity of ecosystems. While studies have documented myriad biotic changes in fragmented landscapes, including the local extinction of species from fragments, the demographic mechanisms underlying these extinctions are rarely known. However, many of them – especially in lowland tropical forests – are thought to be driven by one of two mechanisms: (1) reduced recruitment in fragments resulting from changes in the diversity or abundance of pollinators and seed dispersers or (2) increased rates of individual mortality in fragments due to dramatically altered abiotic conditions, especially near fragment edges. Unfortunately, there have been few tests of these potential mechanisms due to the paucity of long-term and comprehensive demographic data collected in both forest fragments and continuous forest sites. Here we report 11 years (1998-2009) of demographic data from populations of the Amazonian understory herb Heliconia acuminata (LC Rich.) found at Brazil's Biological Dynamics of Forest Fragments Project (BDFFP). The resulting data set comprises >66000 plant×year records of 8586 plants, including 3464 seedlings that became established after the initial census. Seven populations were in experimentally isolated fragments (one in each of four 1-ha fragments and one in each of three 10-ha fragments), with the remaining six populations in continuous forest. Each population was in a 50×100m permanent plot, with the distance between plots ranging from 500 m-60 km. The plants in each plot were censused annually, at which time we recorded, identified, marked, and measured new seedlings, identified any previously marked plants that died, and recorded the size of surviving individuals. Each plot was also surveyed 4-5 times during the flowering season to identify reproductive plants and record the number of inflorescences each produced. These data have been used to investigate topics ranging from the way fragmentation-related reductions in germination influence population dynamics to statistical methods for analyzing reproductive rates. This breadth of prior use reflects the value of these data to future researchers. In addition to analyses of plant responses to habitat fragmentation, these data can be used to address fundamental questions in plant demography, the evolutionary ecology of tropical plants, and for developing and testing demographic models and tools. Though we welcome opportunities to collaborate with interested users, there are no restrictions on the use this data set. However, we do request that those using the data for teaching or research inform us of how they are doing so and cite this paper and the data archive when appropriate. Any publication using the data must also include a BDFFP Technical Series Number in the Acknowledgments. Authors can request this series number upon the acceptance of their article by contacting the BDFFP's Scientific Coordinator or E. M. Bruna.

Abstract Arapaima is a widely-distributed fish of enormous economic importance in the Amazon region. In the present study, a total of 232 specimens were sampled, 121 from five sites in the Amazon basin and 111 from five sites in the Tocantins-Araguaia basin. The analyses investigated fragments of the Cytochrome b, Control Region, Cytochrome Oxidase I, NADH dehydrogenase subunit 2 and seven loci microsatellites. The analyses revealed the existence of two mitochondrial lineages within the general area, with no haplotypes shared between basins, and genetic variability significantly higher in the Amazon than in the Tocantins-Araguaia basin. Two divergent, but sympatric mitochondrial lineages were found in the Amazon basin, but only a single lineage in the Tocantins-Araguaia basin. The existence of these two mitochondrial lineages indicates that past events, probably occurring during the Pleistocene, resulted in the separation of the populations of this species and molded its evolutionary history, which is reflected directly in its mitochondrial DNA. The analysis of the arapaima population structure identified distinct levels of diversity within the distribution of the species, indicating specific geographic regions that will require special attention for the development of conservation and management strategies.

ABSTRACT This paper examines changes over time for a full generation of migrant settlers in the Northern Ecuadorian Amazon (NEA). Data were collected from a 2014 household survey covering a subsample of households surveyed previously in 1990 and 1999. We observed changes in demographic behavior, land use, forest cover, and living conditions. As the frontier develops, human fertility is continuing to decline with contraceptive prevalence rising. Meanwhile, out-migration from colonist households, largely to destinations within the region, persists. More households have secure land tenure than in 1999, and are better off as measured by possession of assets. There is continued growth in pasture, largely at the expense of forest. Farms still serve as an important livelihood source for families, though growing cities in the NEA are creating more non-agricultural economic opportunities. Our findings provide a snapshot of demographic, economic, land use, and livelihood changes occurring in the NEA during the past quarter century, providing useful information for policymakers seeking to balance economic and environmental goals in order to promote sustainable development as well as protect biodiversity.

Despite the recent malaria burden reduction in the Americas, focal transmission persists across the Amazon Basin. Timely analysis of surveillance data is crucial to characterize high-risk individuals and households for better targeting of regional elimination efforts. Here we analyzed 5,480 records of laboratory-confirmed clinical malaria episodes combined with demographic and socioeconomic information to identify risk factors for elevated malaria incidence in Mâncio Lima, the main urban transmission hotspot of Brazil. Overdispersed malaria count data clustered into households were fitted with random-effects zero-inflated negative binomial regression models. Random-effect predictors were used to characterize the spatial heterogeneity in malaria risk at the household level. Adult males were identified as the population stratum at greatest risk, likely due to increased occupational exposure away of the town. However, poor housing and residence in the less urbanized periphery of the town were also found to be key predictors of malaria risk, consistent with a substantial local transmission. Two thirds of the 8,878 urban residents remained uninfected after 23,975 person-years of follow-up. Importantly, we estimated that nearly 14% of them, mostly children and older adults living in the central urban hub, were free of malaria risk, being either unexposed, naturally unsusceptible, or immune to infection. We conclude that statistical modeling of routinely collected, but often neglected, malaria surveillance data can be explored to characterize drivers of transmission heterogeneity at the community level and provide evidence for the rational deployment of control interventions.

Freshwater turtles are a valuable food resource for riverine human communities and have been historically overharvested throughout all major tropical large river basins, with consequent gradual population decreases. Even species considered to be abundant are declining, and in many cases were brought to a condition of near extinction. The collection of adult females during breeding season on nesting beaches is considered a major factor in population decline and subsequent loss of food sources for humans. There is growing consensus that adult females constitute the category which turtle populations can least afford to lose. In the Negro River Basin, the podocnemidid big-headed Amazon River turtle, Peltocephalus dumerilianus, is heavily exploited for consumption and poached for illegal trade among riverine communities and cities. Between 1997 and 2002 and in 2019, we measured live turtles and carapaces of big-headed turtles in the city of Barcelos and its surroundings, and among the riverine families living in the Jaú National Park. We compared body sizes and sex ratios between areas, periods, and between consumed and traded individuals. We found no differences between areas, even those close to Barcelos and the ones belonging to remote areas where pressure levels are lower. The individuals consumed in Jaú National Park are larger than those poached for illegal trade in both areas. There was an increase in average size between 1997 and 2002. Sex ratio was slightly skewed toward males, which were larger, and did not differ between areas and periods. Results indicate stability on size of harvested populations, which may be supporting current extraction levels. Data suggest this could be related to the absence of adult female capture during nesting for this species. We recommend protection strategies for other Amazon Podocnemidid species that focus on the protection of nesting beaches and surrounding areas where adults occupy, specifically in areas under communal protection.

README for all data filesREAD ME.txtManaus Fisheries datasee READMEProchCatchEffortLen.txtLittoralVarssee READMEDrawdown factor Dsee READMED.txt

We studied the natural populations of a flagship fish species of the Amazon, Colossoma macropomum which in recent years has been suffering from severe exploitation. Our aim was to investigate the existence or not of genetic differentiation across the wide area of its distribution and to investigate changes in its effective population size throughout its evolutionary history. We sampled individuals from 21 locations distributed throughout the Amazon basin. We analyzed 539 individuals for mitochondrial genes (control region and ATPase gene 6/8), generating 1,561 base pairs, and genotyped 604 individuals for 13 microsatellite loci obtaining, on average, 21.4 alleles per locus. Mean HE was 0.78 suggesting moderate levels of genetic variability. AMOVA and other tests used to detect the population structure based on both markers indicate that C. macropomum comprises a single and large panmitic population in the main channel of the Solimões-Amazonas River basin, on the other hand localities in the headwaters of the tributaries Juruá, Purus, Madeira, Tapajós, and localities of black water, showed genetic structure. The greatest genetic differentiation was observed between the Brazilian Amazon basin and the Bolivian sub-basin with restricted genetic flow between the two basins. Demographic analyzes of mitochondrial genes indicated population expansion in the Brazilian and Bolivian Amazon basins during the Pleistocene, and microsatellite data indicated a population reduction during the Holocene. This shows that the historical demography of C. macropomum is highly dynamic. Conservation and management strategies should be designed to respect the existing population structure and minimize the effects of overfishing by limiting fisheries C. macropomum populations.

Pairwise FST values across all sampled populations of Rhinella marina.