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The Casiquiare River is a unique biogeographic corridor between the Orinoco and Amazonas basins. We investigated the importance of this connection for Neotropical fishes using peacock cichlids (Cichla spp.) as a model system. We tested whether the Casiquiare provides a conduit for gene flow between contemporary populations, and investigated the origin of biogeographic distributions that span the Casiquiare. Using sequences from the mitochondrial control region of three focal species (C. temensis, C. monoculus, and C. orinocensis) whose distributions include the Amazonas, Orinoco, and Casiquiare, we constructed maximum likelihood phylograms of haplotypes and analyzed the populations under an isolation-with-migration coalescent model. Our analyses suggest that populations of all three species have experienced some degree of gene flow via the Casiquiare. We also generated a mitochondrial genealogy of all Cichla species using >2000 bp and performed a dispersal-vicariance analysis (DIVA) to reconstruct the historical biogeography of the genus. This analysis, when combined with the intraspecific results, supports two instances of dispersal from the Amazonas to the Orinoco. Thus, our results support the idea that the Casiquiare connection is important across temporal scales, facilitating both gene flow and the dispersal and range expansion of species.

Riama is the most speciose genus of the Neotropical lizard family Gymnophthalmidae. Its more than 30 montane species occur throughout the northern Andes, the Cordillera de la Costa (CC) in Venezuela, and Trinidad. We present the most comprehensive phylogenetic analysis of Riama to date based on a total evidence (TE) approach and direct optimization of molecular and morphological evidence. Analyses use DNA sequences from four loci and 35 phenotypic characters. The dataset consists of 55 ingroup terminals representing 25 of the 30 currently recognized species of Riama plus five undescribed taxa, including an endemic species from the Sierra Nevada de Santa Marta (SNSM) in Colombia, and 66 outgroup terminals of 47 species. Analysis results in a well‐supported hypothesis in which Riama is polyphyletic, with its species falling into three clades. The Tepuian Anadia mcdiarmidi nests within one clade of Riama, and the recently resurrected Pantodactylus nests within Cercosaura. Accordingly, we propose a monophyletic taxonomy that reflects historical relationships. Analysis of character evolution indicates that the presence/absence of prefrontals—a cornerstone of the early genus‐level taxonomy of cercosaurines—is optimally explained as having been plesiomorphically present in the most recent common ancestor of Cercosaurinae and lost in that of the immediately less inclusive clade. Multiple independent reversals to present and subsequent returns to absent occur within this clade. To evaluate the impact of phenotypic evidence on our results, we compare our TE results with results obtained from analyses using only molecular data. Although phenotypic evidence comprises only 1.2% of the TE matrix, its inclusion alters both the topology and support values of the clades that do not differ. Finally, current phylogenetic evidence reveals a SNSM–CC–Trinidad–tepuis biogeographical link. We hypothesize that an ancient connection facilitated the exchange of species between the SNSM and the CC.

The pygmy marmoset, Cebuella pygmaea, the smallest of the New World monkeys, has one of the largest geographical distributions of the Amazonian primates. Two forms have been recognized: Cebuella pygmaea pygmaea (Spix, 1823), and C. p. niveiventris Lönnberg, 1940. In this study, we investigated if the separation of pygmy marmosets into these two clades can be corroborated by molecular data. We also examine and compare coloration of the pelage in light of the new molecular results. We analyzed the mtDNA cytochrome b gene and, for the first time for any Neotropical primate, we used a reduced representation genome sequencing approach (ddRADseq) to obtain data for recently collected, geographically representative samples from the Rio Japurá, a northern tributary of the Rio Solimões and from the Javarí, Jutaí, Juruá, Madeira and Purus river basins, all tributaries south of the Solimões. We estimated phylogenies and diversification times under both maximum likelihood and Bayesian inference criteria. Our analysis showed two highly supported clades, with intraclade divergences much smaller than interclade divergences, indicating two species of Cebuella: one from the Rio Japurá and one to the south of Solimões. The interpretation of our results in light of the current taxonomy is not trivial however. Lönnberg stated that the type of Spix's pygmy marmoset (type locality 'near Tabatinga') was obtained from the south of the Solimões, and his description of the distinct niveiventris from Lago Ipixuna, south of the Solimões and several hundred kilometres east of Tabatinga, was based on a comparison with specimens that he determined as typical pygmaea that were from the upper Rio Juruá (south of the Solimões). As such it remains uncertain whether the name pygmaea should be applicable to the pygmy marmosets north of the Rio Solimões (Tabatinga type locality) or south (near Tabatinga but across the Solimões). Finally, our analysis of pelage coloration revealed three phenotypic forms: (1) south of the Rio Solimoes, (2) Eirunepé-Acre, upper Juruá basin; and (3) Japurá. More samples from both sides of Solimões in the region of Tabatinga will be necessary to ascertain the exact type locality for Spix's pygmaea and to resolve the current uncertainties surrounding pygmy marmoset taxonomy.

Morphological variants of Cichla temensis, readily differentiated by their striking color pattern differences, are found in several Amazon basin flood pulse river systems. The adult variants have at times been thought to represent different species or sexual dimorphism. A three part study was performed in two regions in Brazil (rio Igapó Açú and rio Caures) to elucidate the nature of the variants. In part one; selected diagnostic morphometric characters were compared intraspecifically among the variants and interspecifically with C. monoculus and C. orinocensis. All of the C. temensis variants were found to differ significantly from their sympatric congeners while not differing among each other. In part two, mitochondrial DNA samples were compared intraspecifically among the variants and interspecifically with their sympatric congeners. There were no diagnostic molecular synapomorphies that would unambiguously distinguish the variants and all C. temensis variants were clearly diagnosable and divergent from their sympatric congeners. In part three, color pattern variation in both sexes was compared to a gonadosomatic index (GSI). A significant correlation between color pattern variation and gonadosomatic index was found. The results of this study demonstrate that Cichla temensis variants are confirmed to be members of a single species and that the variation does not represent a sexual dimorphism. The color pattern variation is a cyclically occurring secondary sexual characteristic and is indicative of the specific degree of an individual's seasonal sexual maturation.Variantes morfológicas de Cichla temensis, facilmente diferenciados por seus padrões de coloração marcantes, são encontrados em vários rios do sistema de inundação da várzea da bacia Amazônica. Variantes dos indivíduos adultos têm sido cogitados como pertencerem a uma diferente espécie ou apresentarem dimorfismo sexual. Um estudo em três etapas foi realizado em duas regiões no Brasil (rio Igapó Açú e rio Caures) para elucidar a natureza desta variação. Na primeira parte, caracteres morfométricos diagnósticos foram comparados intraespecificamente entre os variantes e interespecificamente com C. monoculus e C. orinocensis. Todos os variantes de C. temensis apresentaram diferenças significativas quando comparados com seus congêneres simpátricos enquanto não diferiram entre si. Na segunda parte, sequências de DNA mitocondrial foram comparadas intraespecificamente entre os variantes e interespeficamente com seus congêneres simpátricos. Não houve sinapomorfias moleculares diagnósticas para diferenciar inequivocamente os variantes e todos os variantes de C. temensis foram claramente divergentes de seus congêneres simpátricos. Na terceira parte, a variação no padrão de cor em ambos os sexos foi comparado ao índice gonadossomático (GSI). Foi encontrada uma correlação significativa entre a variação na coloração e o índice gonadossomático. Os resultados deste estudo demonstram que os variantes em Cichla temensis são membros de uma única espécie e que a variação ...

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Abstract 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.