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Copyright of Biotropica is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

​​​​​​​The so-called arc of deforestation is a major agricultural and industrial frontier in southern Amazonia and northern Cerrado of Brazil. As arboreal mammals, the primates in this region are therefore threatened by forest loss and fragmentation. At the same time, knowledge about the taxonomic diversity and distribution ranges of these taxa is incomplete, which might hamper efficient conservation measurements. New species have been recently discovered in this region, and their ranges remain imprecise because only a few occurrence records are available for each species. Here we present 192 new records of 22 species and subspecies of Alouatta, Aotus, Ateles, Cebus, Chiropotes, Lagothrix, Leontocebus, Pithecia, Plecturocebus, Saimiri, and Sapajus, collected in 56 different localities during 10 field expeditions across the arc of deforestation between 2015 and 2018. Based on these new records, we extend the ranges of Alouatta puruensis, Ateles chamek, and Saimiri collinsi; identify potential hybridization zones between A. puruensis and A. discolor, and between At. chamek and At. marginatus; redefine the range of Plecturocebus moloch; and clarify the ranges of P. baptista and P. hoffmannsi. Moreover, these results and the dataset are valuable for further research on, for example, species distribution and habitat use modeling, for assessing species extinction risks, and for supporting efforts for the conservation of species increasingly threatened on a global deforestation frontier. [ABSTRACT FROM AUTHOR]

The genus Saguinus comprises three principal clades that diverged in the Middle to Late Miocene. Their taxa are ecologically differentiated and allopatrically distributed. These clades were recently recognized as different genera, Saguinus, Tamarinus and Oedipomidas. In Tamarinus, the phylogenetic relationships among species/subspecies are poorly understood. Thus, in this study we present a comprehensive dated genomic phylogeny based on double digest restriction associated DNA for all known species and subspecies of Tamarinus. We also tested whether that Tamarinus imperator and Tamarinus subgrisescens are different species, as morphology‐based taxonomy, phenotypical divergences and mitochondrial genes recognized them as two different species. Additionally, we reconstructed time‐calibrated phylogenetics tree hypotheses of all extant species and subspecies of the genera Saguinus, Tamarinus and Oedipomidas. Our analysis robustly supported the phylogenetic hypothesis of all species/subspecies of the genus Tamarinus; strongly supported a divergence between the three clades, Saguinus, Oedipomidas and Tamarinus; and provided support for T. imperator and T. subgrisescens as distinct species. Therefore, we reiterate and ratify the division of Saguinus into three genera, supporting the taxonomic proposal for these genera. [ABSTRACT FROM AUTHOR]

The discovery and characterization of cryptic diversity is important for conservation and management, especially for ichthyofauna, whose diversity is underestimated and understudied. Cryptic diversity is especially common in widely distributed species, and Pellona flavipinnis is one such species. Thus, the aim of the present study was to investigate and test whether P. flavipinnis harbours cryptic diversity. In this study we used the COI and control region sequences and microsatellite loci of 86–114 specimens from 11–12 locations throughout the Amazon basin, depending on the molecular marker used. We also included two COI GenBank sequences from the type locality of the species, the Paraná River. The results from COI sequences showed that P. flavipinnis from the Amazon basin presented two spatially structured lineages differentiated from P. flavipinnis from the Paraná River by 10.6%–9.8% (depending on the lineages) and 45 mutational steps. The genetic distance between the Amazon lineages was 2.4% using COI, with high population differentiation values (ФST = 0.8686 and ФST = 0.8483 for COI and control region, respectively). Among the five species delimitation methods employed, three indicated two lineages in P. flavipinnis in the Amazon basin, and all five methods indicated that the Amazonian lineages are different from that of Paraná. Results from microsatellite loci also showed that P. flavipinnis from the Amazon basin is composed of two evolutionary units. The results of 13 morphometric measurements indicated that there are no differences in shape between the P. flavipinnis lineages in the Amazon basin. The present findings suggest that there are two sympatric lineages of P. flavipinnis in the Amazon basin. [ABSTRACT FROM AUTHOR]

Currently, 15 species of Amazon marmosets (genus Mico) are known to science. The Amazon marmosets occur primarily in southern Brazilian Amazonia, the arc of deforestation, and are among the least studied primates of the neotropics. This is particularly the case for M. acariensis and M. chrysoleucos, both endemic to the Aripuanã–Sucundurí interfluve, south-central Amazonia. Mico acariensis was not studied beyond the species description, and the only information currently available is the pelage colouration of the holotype, inferred coordinates of the type locality, and a field report with two additional localities of occurrence. Regarding M. chrysoleucos, in addition to the species description, there are taxonomic reviews, the report of a second occurrence record, and a study on the species range. We provide here new occurrence records that extend the distribution of M. chrysoleucos; provide new records for and update the distribution of M. acariensis; and propose the existence of a hybrid zone in the Aripuanã–Sucundurí interfluve, i.e. around the known distribution boundaries of M. acariensis, M. chrysoleucos, and M. melanurus, and we also discuss habitat use patterns of Amazon marmosets. [ABSTRACT FROM AUTHOR]

Background. Semaprochilodus insignis is a migratory fish of commercial and subsistence importance to communities in the Amazon. Despite the high intensity of exploitation, recent studies have not been carried out to assess the genetic status of its stocks. Methods. This study is the first to estimate genetic diversity and to test the existence of spatial and temporal structuring of S. insignis through sequencing of the mtDNA control region (n = 241) and eight microsatellite loci (n = 180) of individuals sampled at 11 sites distributed in the Brazilian Amazon basin. Results. Results for both markers were congruent, revealing a homogeneous genetic diversity in all the sampled locations, in addition to the absence of spatial and temporal genetic structure, indicating that the species forms a large panmictic population in the Brazilian Amazon. Discussion. Although overfishing does not yet appear to have affected the levels of genetic variability of S. insignis, signals of reduction of the effective population size and a bottleneck provide an early alert to the effects of overfishing. Thus, the ever-decreasing populations may threaten S. insignis in the future. Therefore, it is hoped that the results of this study may contribute to the elaboration of management plans or any other measures that aim at the management and conservation of this species of great importance for the Amazon basin. [ABSTRACT FROM AUTHOR]

The Neotropics contain one of the most diverse assemblages of freshwater fishes worldwide. Part of this diversity is shared between the Orinoco and Amazon basins. These basins have been separated for a long time due to the Vaupes Arch, rising between 10-11 Ma. Today, there is only one permanent connection between the Orinoco and Negro (Amazon) basins, known as the Casiquiare Canal. However, alternative corridors allowing fish dispersion between both basins have been proposed. The cardinal tetra (Paracheirodon axelrodi), the most important fish in the ornamental world market, is distributed in both basins. Here we investigated P. axelrodi phylogeography, population structure, and potential routes of migration and connectivity between the two basins. A total of 468 bp of the mitochondrial gene (COI), 555 bp of the nuclear gene fragment (MYH6), and eight microsatellite loci were analyzed. As a result, we found two major genetic clusters as the most likely scenario (K = 2), but they were not discreetly distributed between basins. A gradient of genetic admixture was observed in Cucui and São Gabriel da Cachoeira, between the upper Negro River and the upper Orinoco. Samples from the middle-lower Negro River were highly structured. Cucui (Negro basin) was more similar to the Orinoco than to the rest of the Negro basin populations. However, substructure was also observed by the discriminant analysis, fixation indices and other hierarchichal structure analyses (K = 3-6), showing three major geographic clusters: Orinoco, Cucui, and the remaining Negro basin. Unidirectional migration patterns were detected between basins: via Cucui toward Orinoco and via the remaining of the Negro basin toward Orinoco. Results from the Relaxed Random Walk analysis support a very recent origin of this species in the headwater Orinoco basin (Western Guiana Shield, at late Pleistocene) with a later rapid colonization of the remaining Orinoco basin and almost simultaneously the Negro River via Cucui, between 0.115 until about 0.001 Ma. Historical biogeography and population genetic patterns observed here for Cardinal tetra, seem to be better explained by river capture, physical, or ecological barriers than due to the geographic distance. [ABSTRACT FROM AUTHOR]

The brown or pouchless four-eyed opossums or jupatis represent the genus Metachirus with a wide geographical range in the Neotropics. Recent studies show distinct monophyletic clades with high genetic divergence and recognized two species, Metachirus nudicaudatus and Metachirus myosuros. Nevertheless, there is a need for systematic revision with multiple sources of evidence on the taxonomy of Metachirus, which has never been fully revised. Here we describe a new species of Metachirus for the Brazilian Amazon from the Xingu/Tocantins interfluve using the unification of concepts and evolutionary significant units, morphological, genetic, and geographic data. Our analysis reveals a new species within Metachirus as a differentiated Amazonian clade from the Serra dos Carajás region and the Caxiuanã National Forest, both in the Xingu endemism centre. This new species can be distinguished from the type species, M. nudicaudatus and from M. myosuros through discrete external morphological characters, including cranium and dentition, and molecular data with an average degree of divergence, but ancient divergence time for the mitochondrial cytochrome b gene. The Amazon River delimits the distribution of the new species, which also occurs in areas under strong anthropogenic pressure, reinforcing the importance to guide conservation strategies for the region. [ABSTRACT FROM AUTHOR]

Amazonian mammal diversity is exceptionally high, yet new taxonomic discoveries continue to be made and many questions remain for understanding its diversification through time and space. Here we investigate the diversification of spiny rats in the genus Makalata, whose species are strongly associated with seasonally flooded forests, watercourses and flooded islands. We use a biogeographical approach based on a mitochondrial cytochrome b gene through divergence time estimation and reconstruction of ancestral areas and events. Our findings indicate an ancient origin of Makalata for the Guiana Shield and Eastern Amazonia as ancestral area. A first cladogenetic event led to a phylogeographic break into two broader clades of Makalata through dispersal, implying a pattern of western/Eastern Amazonian clades coinciding with the Purus Arch (middle Miocene). Most of subclades we infer originated between the late Pliocene to the early Pleistocene, with few recent exceptions in the early Pliocene through dispersal and vicariant events. The hypothesis of rivers as dispersal barriers is not corroborated for Makalata, as expected for mammalian species associated with seasonally flooded environments. We identify two key events for the expansion and diversification of Makalata species: the presence of geologically stable areas in the Guiana and Brazilian shields and the transition from lacustrine conditions in western Amazonia (Acre system) to a river system, with the establishment of the Amazon River transcontinental system and its tributaries. Our results are congruent with older geological scenarios for the Amazon basin formation (Miocene), but we do not discard the influence of recent dynamics on some speciation events and, mainly, on phylogeographic structuring processes. [ABSTRACT FROM AUTHOR]

Based on morphological and molecular analysis of Astronotus species, a new species is described from the Orinoco River and Gulf of Paria basins in Venezuela and Colombia. Morphologically, it differs from Astronotus crassipinnis and Astronotus ocellatus in pre-orbital depth, caudal peduncle depth, head width, and caudal peduncle length, with significant differences in average percentage values. Osteologically, it differs from the two described species by lacking a hypurapophysis on the parahypural bone (hypural complex) and having two or three supraneural bones. Another characteristic that helps diagnose the new species is the morphology of the sagitta otolith, which is oval with crenulated dorsal and ventral margins and a rounded posterior edge. Genetically, the new species is distinct from all the other lineages previously proposed for the genus, delimited by five single locus species delimitation methods, and also has unique diagnostic nucleotides. Phylogenetic analyses support the monophyly of the new species as well as all other species/lineages. Astronotus species have considerable genetic, anatomical, and sagitta otolith shape differences, but have few significant traditional morphometric and meristic differences, because there is high variability in counts of spines, soft dorsal-fin rays, and lateral-line scales. It is clear that this new species is genetically and anatomically differentiated from all other species within the genus, and deserves recognition as a new valid species. [ABSTRACT FROM AUTHOR]

Turtles are one of the most threatened groups of vertebrates, with about 60% of species classified at some level of extinction risk. Compounding this extinction crisis are cryptic species and species complexes that are evaluated under a single species epithet but harbor multiple species, each of which needs to be evaluated independently. The Phrynops geoffroanus species group is a classic example. Described first in 1812, it is currently thought to harbor multiple species. To test this hypothesis, we collected mitochondrial and nuclear genomic data, morphometric data, and distribution and associated biome information. We applied statistically rigorous species delimitation analyses, taxonomic hypotheses tests, and fully coalescent phylogenetic reconstruction methods, concluding that the Phrynops geoffroanus species complex comprises four geographically structured species/lineages that diverged during the Pleistocene and are currently geographically structured along the main South American river basins and biomes. These species/lineages show subtle and largely non-significant differences in shape but are characterized by differences in coloration and patterns of marks on the head and plastron. Our results contribute to the understanding of species diversity and diversification of biodiversity in South America and provide an important basis for the conservation of freshwater turtles. [ABSTRACT FROM AUTHOR]

South American freshwater ichthyofauna is taxonomically the most diverse on the planet, yet its diversity is still vastly underestimated. The Amazon basin alone holds more than half of this diversity. The evidence of this underestimation comes from the backlog of morphologically distinct, yet undescribed forms deposited in museum collections, and from DNA-based inventories which consistently identify large numbers of divergent lineages within even well-studied species groups. In the present study, we investigated lineage diversity within the Geophagus sensu stricto species group. To achieve these objectives, we analyzed 337 individuals sampled from 77 locations within and outside the Amazon basin representing 10 nominal and six morphologically distinct but undescribed species. We sequenced the mitochondrial cytochrome c oxidase subunit I (COI) and delimited lineages using four different single-locus species discovery methods (mPTP-15 lineages; LocMin-14 lineages; bGMYC-18 lineages; and GMYC-30 lineages). The six morphologically distinct but undescribed species were also delimited by the majority of the species discovery methods. Five of these lineages are restricted to a single collection site or a watershed and their habitats are threatened by human activities such as deforestation, agricultural activities and construction of hydroelectric plants. Our results also highlight the importance of combining DNA and morphological data in biodiversity assessment studies especially in taxonomically diverse tropical biotas. [ABSTRACT FROM AUTHOR]

Copyright of Journal of Zoological Systematics & Evolutionary Research is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

We report dengue virus type 4 (DENV-4) in Amazonas, Brazil. This virus was isolated from serum samples of 3 patients treated at a tropical medicine reference center in Manaus. All [...]

Species of Neacomys are small cricetid rodents that occur in forested habitats of Central and South America, from eastern Panama to central Bolivia and central/western Brazil. In order to assess species diversity of this poorly known genus, we obtained cytochrome b gene sequences from the most comprehensive taxonomic and geographic sampling analyzed to date. We also conducted morphological analyses on a large series of specimens housed in 15 museums, including types of 10 out of 14 nominal taxa. Our analyses of the genetic data recovered 17 lineages clustered in four distinct clades. Among these lineages, 11 correspond to species currently recognized as valid, and the remaining six are putative new species. In southeastern Amazonia—the geographical scope of this report—four undescribed species were discovered, three of which are named herein: Neacomys marajoara, sp. nov., from the Island of Marajó, Pará state; Neacomys vossi, sp. nov., restricted to the Tapajós center of endemism (between the Tapajós and Xingu rivers); and Neacomys xingu, sp. nov., restricted to the Xingu center of endemism (between the Xingu and Araguaia/Tocantins rivers). The new species can be discriminated from other Neacomys species by the morphology of the nasal bones, zygomatic plate, interorbital region, subsquamosal fenestra, paraoccipital process, incisive foramina, auditory bullae, anterocone and anteroloph of the first upper molar, carotid circulation pattern, and karyotype. Our results substantially improve our understanding of the genus Neacomys by providing morphological, morphometric, and novel molecular insights about these poorly known rodents and demonstrate that the diversity of small Amazonian mammals is still poorly known, even in the relatively accessible southeastern part of the biome. [ABSTRACT FROM AUTHOR]

Phyllomedusa bicolor is a large-sized nocturnal tree frog found in tropical rainforests throughout much of the Amazonian region of Brazil, Colombia, Bolivia, Peru, Venezuela, and the Guianas. Very little is known about P. bicolor genetic diversity and genealogical history of its natural populations. Here, using a sampling design that included populations covering most of its distributional range, we investigated the spatial distribution of genetic variability of this species, and we tested the hypothesis that P. bicolor is composed of deeply structured genetic groups, constituting more than one lineage across the Brazilian Amazonia. The results suggested two main lineages in two geographic mega-regions: Western and Eastern Amazonia, the latter consisting of three population groups distributed in the Guiana and Brazilian Shields. The present findings have implications to taxonomy, to understanding the processes that lead to diversification, and to defining strategies of conservation and medicinal use of the species. [ABSTRACT FROM AUTHOR]

Copyright of Neotropical Ichthyology is the property of Neotropical Ichthyology and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Arapaima, pirarucu or paiche (Arapaima gigas) is one of the largest freshwater fish in the world, and has a long history of commercial exploitation in the Amazon region. To estimate levels of genetic variability and historical and recent connectivity in Arapaima, we examined variation in eleven microsatellite DNA markers in individuals from 22 localities in Brazil, Colombia, and Peru. The results of analysis of molecular variance, Bayesian clustering and discriminant analysis of principal components showed that Arapaima in our samples represents two major populations, one in the Amazonas and one in the Araguaia-Tocantins River basins. The Amazonas population is further structured by isolation-by-distance with the hydrologically largely unconnected Amapá locality representing the eastern-most extreme of this continuum; gene flow predominates at distances of less than 1500 km with localities separated by over 2000 km dominated by genetic drift and effectively forming different populations. We saw no evidence of multiple species of Arapaima in the Amazonas basin, and analysis of pairwise genetic divergence (FST) with Mantel tests and correlograms indicated that this largest population exhibits a large-scale pattern of isolation-by-distance, with which results from MIGRATE-N agreed. The degree and significance of genetic divergence indicates that most sampled localities represent demographically independent sub-populations, although we did identify several recent migration events between both proximal and more distant localities. The levels of genetic diversity were heterogeneous across sites, including low genetic diversity, effective population sizes, and evidence of genetic bottlenecks in several places. On average the levels of gene diversity and rarefied allelic richness were higher for localities along the Amazonas mainstem than in the tributaries, despite these being the areas of highest fishing pressure, while the lowest values were found in tributary headwaters, where landscape modification is a significant threat. We recommend that managers consider the regional and local threats to these populations and tailor strategies accordingly, strategies which should ensure the ability of young A. gigas to disperse through floodplain corridors to maintain genetic diversity among otherwise sedentary adult sub-populations. [ABSTRACT FROM AUTHOR]

The Negro River currently has seven floating houses where tourists can feed and interact with botos, each with its own history of how these aggregations were formed. Some keepers say these groups are familial, even reporting individuals being born into the group. However, behavioral studies have shown that botos are solitary, only forming groups at feeding areas and during the mating season. In the present study we used 12 microsatellite and molecular sex markers to characterize relationships within and between two boto aggregations (ten and seven botos each) in the lower Negro River. Molecular sexing revealed that all botos sampled from both aggregations were males. This may be explained by habitat preference, as male botos are primarily found in the main channels of large rivers, whereas females prefer more protected areas, such as flooded forests and its channels and lakes. Most of the animals were unrelated within each aggregation, demonstrating that these aggregations are not normally formed due to kinship bonds, but are exclusively for feeding, as botos learn that these places provide easy access to food. This study provides important information that helps us understand how human interaction is affecting the social structure and behavior of these animals. [ABSTRACT FROM AUTHOR]

Schneider's dwarf caiman Paleosuchus trigonatus is one of the smallest living crocodilians. Due to its broad distribution, cryptic behavior, and small home range, the species is well suited for the study of phylogeographic patterns on a continental scale. Additionally, this species is under threat due to habitat loss, trade and harvest, but is considered at low conservation risk by the IUCN. In the present study we test the hypothesis that P. trigonatus is comprised of geographically structured lineages. Phylogenetic reconstructions of the mitochondrial cytochrome b gene and single locus species discovery methods revealed the existence of two well-supported lineages within P. trigonatus--an Amazonian and Guianan lineage. Fossil calibrated divergence of these lineages was estimated to have occurred in the Late Miocene (7.5 Ma). The hypothesis that the Atlantic coast drainages might have been colonized from the southeast or central Amazon is supported by demographic metrics and relatively low genetic diversity of the Coastal and upper Branco populations when compared to the Amazon basin populations. The Amazon basin lineage is structured along an eastwest gradient, with a sharp transition in haplotype frequencies to the east and west of the Negro and Madeira rivers. These lineages are already under anthropogenic threat and, therefore, are conservation dependent. Recognition of these lineages will foster discussion of conservation future of P. trigonatus and these lineages. [ABSTRACT FROM AUTHOR]

Several hypotheses have been used to explain diversification in the Neotropics. Integrating evolution with ecology extends the scope of testing the frameworks of these hypotheses. We test diversification hypotheses by integrating phylogeography and ecological niche models (ENMs) using the rodent Hylaeamys megacephalus (Azara's broad-headed oryzomys or large headed rice rat) of the Amazon and dry forests, as a model. We estimated divergence times, ancestral areas, diversification events, historical demography, haplotype sharing, and genetic distances based on the mitochondrial cytochrome b gene. We generated ENMs and tested for niche divergence between lineages; integrated genetic data to predict gene flow corridors; and projected paleodistributions for comparison with historical demography. We found high structuring in northern Amazonia on the left bank of the Amazon River, and less structure but secondary contact in southern Amazonia and dry forests. The Northern Amazonian lineage diverged from the other lineages through dispersal followed by vicariance due to the Amazon River about 1.35 Mya, while the Southern Amazonian and Cerrado lineages diverged through dispersal about 0.78 Mya. Paleodistribution models revealed expansions of dry forest lineages consistent with the Refugia Hypothesis, but not retraction for the humid forest lineage, which were not congruent with historical demography data. Niche divergence was not supported for the Northern Amazonian lineage, whereas habitat corridors linking current lineages suggest environmental continuity to their distributions that is concordant with a riverine barrier. In contrast, niche divergence was supported between the Southern Amazonian and Cerrado lineages, indicating that isolation followed by ecological divergence likely acted on this diversification. The recent Amazon River barrier and ecological differentiation observed here will surely provide insight for future studies and hypotheses of biodiversity diversification in the Neotropics. Studies that integrate evolution and ecology promise to disentangle alternative hypotheses and shed light on the biogeography of this megadiverse region. [ABSTRACT FROM AUTHOR]