A Molecular Perspective on Systematics, Taxonomy and Classification Amazonian Discus Fishes of the Genus Symphysodon

With the goal of contributing to the taxonomy and systematics of the Neotropical cichlid fishes of the genus Symphysodon, we analyzed 336 individuals from 24 localities throughout the entire distributional range of the genus. We analyzed variation at 13 nuclear microsatellite markers, and subjected the data to Bayesian analysis of genetic structure. The results indicate that Symphysodon is composed of four genetic groups: group PURPLE—phenotype Heckel and abacaxi; group GREEN—phenotype green; group RED—phenotype blue and brown; and group PINK—populations of Xingú and Cametá. Although the phenotypes blue and brown are predominantly biological group RED, they also have substantial contributions from other biological groups, and the patterns of admixture of the two phenotypes are different. The two phenotypes are further characterized by distinct and divergent mtDNA haplotype groups, and show differences in mean habitat use measured as pH and conductivity. Differences in mean habitat use is also observed between most other biological groups. We therefore conclude that Symphysodon comprises five evolutionary significant units: Symphysodon discus (Heckel and abacaxi phenotypes), S. aequifasciatus (brown phenotype), S. tarzoo (green phenotype), Symphysodon sp. 1 (blue phenotype) and Symphysodon sp. 2 (Xingú group)

Mapping the Hidden Diversity of the \u3cem\u3eGeophagus sensu stricto\u3c/em\u3e Species Group (Cichlidae: Geophagini) From the Amazon Basin

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

Reduction of genetic diversity of the Harpy Eagle in Brazilian tropical forests

Habitat loss and fragmentation intensify the effects of genetic drift and endogamy, reducing genetic variability of populations with serious consequences for wildlife conservation. The Harpy Eagle (Harpia harpyja) is a forest dwelling species that is considered near threatened and suffers from habitat loss in the forests of the Neotropical region. In this study, 72 historical and current samples were assessed using eight autosomal microsatellite markers to investigate the distribution of genetic diversity of the Harpy Eagle of the Amazonian and Atlantic forests in Brazil. The results showed that the genetic diversity of Harpy Eagle decreased in the regions where deforestation is intense in the southern Amazon and Atlantic Forest. © 2016 Banhos et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

A Multilocus Approach to Understanding Historical and Contemporary Demography of the Keystone Floodplain Species Colossoma macropomum (Teleostei: Characiformes)

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

Lizards from central Jatapú River, Amazonas, Brazil

The present study reports an inventory of lizard species from a region at the central Jatapú River located in the state of Amazonas, Brazil. The lizard fauna was surveyed using three sampling methods: diurnal and nocturnal visual search, pitfall traps with drift fences, and incidental collections. We recorded 24 lizard species belonging to 18 genera and eight families. Non-parametric estimators of richness (Bootstrap, Chao 2, Jackknife 1, Ace) were used to estimate the percentage of total richness sampled. Expected species richness varied from 27 species estimated via Bootstrap to 30 species with Jackknife 1. The composition of the lizard fauna encountered in the rio Jatapú plot was compared with seven other published surveys carried out in the region of the Brazilian Guiana Shield. The composition of the Jatapú lizard fauna was most similar to FLOTA Faro (84%) and least similar to ESEC Grão-Pará Center (66%). There was no association between faunal similarity and geographic distance. The present species list contributes to our knowledge of lizards of the southern portion of the Guiana Shield in Brazil

Genomic resources for the conservation and management of the harpy eagle (Harpia harpyja, Falconiformes, Accipitridae)

We report the characterization and optimization of 45 heterologous microsatellite loci, and the development of a new set of molecular sex markers for the conservation and management of the Neotropical harpy eagle (Harpia harpyja L. 1758). Of the 45 microsatellites tested, 24 were polymorphic, six monomorphic, 10 uncharacterizable due to multiple bands and five did not amplify. The observed gene diversity of the analyzed sample of H. harpyja was low and similar to that of other threatened Falconiformes. While a high proportion of the microsatellite markers were highly variable, individuals of H. harpyja could be differentiated by a joint analysis of just three (p = 2.79 × 10-4) or four markers (p = 2.89 × 10-4). Paternity could be rejected with 95.23% and 97.83% probabilities using the same three and four markers, respectively. The sex determination markers easily and consistently differentiated males from females even with highly degraded DNA extracted from naturally shed feathers. The markers reported in this study potentially provide an excellent set of molecular tools for the conservation and management of wild and captive H. harpyja and they may also prove useful for the enigmatic Neotropical crested eagle (Morphnus guianensis Daudin 1800). Copyright by the Brazilian Society of Genetics

Boto (Inia geoffrensis—Cetacea: Iniidae) aggregations in two provisioning sites in the lower Negro River—Amazonas, Brazil: are they related?

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

Anfíbios de Santa Isabel do Rio Negro, Amazônia Brasileira.

No presente estudo fornecemos uma lista de espécies de anfíbios de Santa Isabel do Rio Negro na Amazônia Brasileira. As amostragens foram realizadas de março a abril de 2012 em dois conjuntos de trilhas de 3 km de extensão, usando os seguintes métodos: (1) armadilhas de interceptação e queda com cerca direcionadora; (2) amostragens visuais e auditivas simultâneas; (3) encontros ocasionais. As trilhas foram instaladas ao norte (rio Daraá) e ao sul (rio Ayuanã) do rio Negro. Registramos 40 espécies de anuros e uma espécie de salamandra, pertencentes a 20 gêneros e nove famílias. A composição de espécies foi comparada com as de 16 outros estudos desenvolvidos nas áreas de endemismo Guiana, Imeri e Jaú, onde a riqueza de espécies variou de 21 a 63, e a similaridade, de 23 a 100%. A anurofauna das duas áreas estudadas foi mais similar à de Flota Faro, localizada na Amazônia Oriental, do que à de um sítio mais próximo, Departamento del Guainía, Colômbia. O índice de similaridade foi extremamente variável entre os sítios da mesma ou de distintas áreas de endemismo. Esse padrão também foi observado nas análises de agrupamento. Como esperado, áreas geograficamente mais próximas foram mais similares na composição da anurofauna. No entanto, a anurofauna do Parque Nacional do Jaú (área de endemismo Jaú) foi mais similar à de Manaus (área de endemismo Guiana) do que à do rio Ayuanã, que pretence à mesma área de endemismo que o Parque Nacional do Jaú. Os limites das áreas de endemismo podem ser melhor definidos para outros vertebrados terrestres, como aves e mamíferos, do que para anfíbios e répteis Squamata.A species list of amphibians from Santa Isabel do Rio Negro in Brazilian Amazonia is provided. Collections were made from March–April 2012 along each of two 3-km trails with the following sampling methods: (1) pitfall traps with drift fences; (2) visual and auditory surveys; and (3) chance encounters. The trail at Daraá is north of the Rio Negro, whereas the other in Ayuanã is south of the river. Forty species of anurans and one salamander species representing 20 genera and nine families were recorded. The species composition was compared with those of 16 other studies conducted in the Guiana, Imeri, and Jaú areas of endemism, where species richness varies from 21–63, and similarity indices range from 23–100%. The anuran fauna at our sites resembles that of Flota Faro in eastern Amazonia more than it does that of the nearest site in the Departamento del Guainía of Colombia. The index of similarity is extremely variable between sites of the same and distinct areas of endemism. This pattern also was observed in the cluster analysis. As expected, geographically close areas have similar faunal compositions. However, the anuran fauna of Parque Nacional do Jaú (Jaú area of endemism) resembles that of Manaus (Guiana area of endemism) more closely than it does that of the Ayuanã River, which belongs to the same area of endemism as Parque Nacional do Jaú. The limits of the areas of endemism are better defined by the presence / absence of other terrestrial vertebrates, such as birds and mammals, than by the assemblage of amphibians and squamate reptiles

Remarkable Geographic Structuring of Rheophilic Fishes of the Lower Araguaia River

Rapids and waterfalls, and their associated fauna and flora are in peril. With the construction of each new hydroelectric dam, more rapids and waterfalls are destroyed, leading to the disappearance of associated fauna and flora. Areas of rapids harbor distinct, highly endemic rheophilic fauna and flora adapted to an extreme environment. Rheophilic habitats also have disjunct distribution both within and across rivers. Rheophilic habitats thus represent islands of suitable habitat separated by stretches of unsuitable habitat. In this study, we investigated to what extent, if any, species of cichlid and anostomid fishes associated with rheophilic habitats were structured among the rapids of Araguaia River in the Brazilian Amazon. We tested both for population structuring as well as non-random distribution of lineages among rapids. Eight of the nine species had multiple lineages, five of these nine species were structured, and three of the eight species with multiple lineages showed non-random distribution of lineages among rapids. These results demonstrate that in addition to high levels of endemicism of rheophilic fishes, different rapids even within the same river are occupied by different lineages. Rheophilic species and communities occupying different rapids are, therefore, not interchangeable, and this realization must be taken into account when proposing mitigatory/compensatory measures in hydroelectric projects, and in conservation planning

Evidence of multiple paternal contribution in Podocnemis sextuberculata (Testudines: Podocnemididae) detected by microsatellite markers

Evidência de contribuição paterna múltipla em Podocnemis sextuberculata (Chelonia: Podocnemididae) por meio de marcadores microssatélites. Encontramos evidências de paternidade múltipla em uma amostra de 80 recém-eclodidos de sete ninhos de Podocnemis sextuberculata situados ao longo do rio Amazonas, no município de Barreirinha, AM, Brasil, e 54 indivíduos recém-eclodidos de cinco ninhos na Reserva Biológica Abufari, Tapauá, AM, Brasil. Como observado em outras espécies do gênero, P. sextuberculata apresentou comportamento poliândrico. Por meio da frequência alélica e variação em seis locos microssatélite para cada localidade, a ocorrência de paternidade múltipla em ninhos amostrados dessa espécie foi inferida, mesmo o genótipo da mãe sendo desconhecido. Para um dos ninhos, um mínimo de quatro machos contribuíram para a prole, enquanto que para quase todos os outros ninhos, pelo menos dois machos contribuíram. Apenas um dos 12 ninhos não mostrou evidência clara de contribuição de mais de um macho. Esta é a primeira evidência genética de paternidade múltipla em P. sextuberculata.Evidence of multiple paternity in Podocnemis sextuberculata (Testudines: Podocnemididae) detected by microsatellite markers. We found evidence of multiple paternity in a sample of 12 Podocnemis sextuberculata nests including seven nests (80 hatchlings) collected along the Amazonas River, in the municipality of Barreirinha, AM, Brazil and five nests in the Abufari Biological Reserve, Tapauá, AM, Brazil (54 hatchlings). As observed in other species of the genus, P. sextuberculata also presented polyandric behavior. By means of allelic frequency and variation in six microsatellite loci for each location, the occurrence of multiple paternity in sampled nests of this species was inferred, even though the maternal genotype was unknown. For one of the nests, a minimum of four males contributed to the clutch, whereas for nearly all remaining nests at least two males contributed. Only one of the twelve nests did not show clear evidence for contributions from more than one male. This is the first genetic evidence of multiple paternity in P. sextuberculat