The identification of high-performance indicator taxa that combine practical feasibility and ecological value requires an understanding of the costs and benefits of surveying different taxa. We present a generic and novel framework for identifying such taxa, and illustrate our approach using a large-scale assessment of 14 different higher taxa across three forest types in the Brazilian Amazon, estimating both the standardized survey cost and the ecological and biodiversity indicator value for each taxon. Survey costs varied by three orders of magnitude, and dung beetles and birds were identified as especially suitable for evaluating and monitoring the ecological consequences of habitat change in our study region. However, an exclusive focus on such taxa occurs at the expense of understanding patterns of diversity in other groups. To improve the cost-effectiveness of biodiversity research we encourage a combination of clearer research goals and the use of an objective evidence-based approach to selecting study taxa.

Rivers have been suggested to have played an important role in shaping present-day patterns of ecological and genetic variation among Amazonian species and communities. Recent molecular studies have provided mixed support for the hypothesis that large lowland Amazonian rivers have functioned as significant impediments to gene flow among populations of neotropical species. To date, no study has systematically evaluated the impact that riverine barriers might have on structuring whole Amazonian communities. Our analyses of the phylogeography of frogs and small mammals indicate that a putative riverine barrier (the Juruá River) does not relate to present-day patterns of community similarity and species richness. Rather, our results imply a significant impact of the Andean orogenic axis and associated thrust-and-fold lowland dynamics in shaping patterns of biotic diversity along the Juruá . Combined results of this and other studies significantly weaken the postulated role of rivers as major drivers of Amazonian diversification.

BackgroundTiti monkeys, Callicebus, comprise the most species-rich primate genus—34 species are currently recognised, five of them described since 2005. The lack of molecular data for titi monkeys has meant that little is known of their phylogenetic relationships and divergence times. To clarify their evolutionary history, we assembled a large molecular dataset by sequencing 20 nuclear and two mitochondrial loci for 15 species, including representatives from all recognised species groups. Phylogenetic relationships were inferred using concatenated maximum likelihood and Bayesian analyses, allowing us to evaluate the current taxonomic hypothesis for the genus.ResultsOur results show four distinct Callicebus clades, for the most part concordant with the currently recognised morphological species-groups—the torquatus group, the personatus group, the donacophilus group, and the moloch group. The cupreus and moloch groups are not monophyletic, and all species of the formerly recognized cupreus group are reassigned to the moloch group. Two of the major divergence events are dated to the Miocene. The torquatus group, the oldest radiation, diverged c. 11 Ma; and the Atlantic forest personatus group split from the ancestor of all donacophilus and moloch species at 9–8 Ma. There is little molecular evidence for the separation of Callicebus caligatus and C. dubius, and we suggest that C. dubius should be considered a junior synonym of a polymorphic C. caligatus.ConclusionsConsidering molecular, morphological and biogeographic evidence, we propose a new genus level taxonomy for titi monkeys: Cheracebus n. gen. in the Orinoco, Negro and upper Amazon basins (torquatus group), Callicebus Thomas, 1903, in the Atlantic Forest (personatus group), and Plecturocebus n. gen. in the Amazon basin and Chaco region (donacophilus and moloch groups).Electronic supplementary materialThe online version of this article (doi:10.1186/s12983-016-0142-4) contains supplementary material, which is available to authorized users.

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Until the recent construction of hydroelectric dams, a series of 18 rapids divided the upper and lower Madeira River, and these rapids were thought to separate two species of Amazonian freshwater dolphins (boto): Inia boliviensis (above) and I. geoffrensis (below). Some reports and articles, however, mention the occurrence of botos within the rapids region and that they occasionally cross the rapids, but without mentioning the species concerned. Based on our previous studies, it is likely that I. boliviensis occurs in the region of the rapids. To test this supposition, we sampled 18 individuals from this region, and collected mitochondrial (control region, cytochrome b and cytochrome oxidase I) and nuclear (10 microsatellite loci) DNA data, in order to test if there is connectivity between the dolphins that were found within the rapids region and dolphins collected upstream and downstream of the rapids, and investigate population structuring between these localities. All animals in our study were molecularly identified using three mitochondrial markers as belonging to the species I. boliviensis. Animals upstream of the Teotônio waterfall, the main and highest waterfall of the region, had nuclear genome of I. boliviensis, while most dolphins downstream of the waterfall had nuclear genome of I. geoffrensis. Inia boliviensis collected in the rapids region above the Teotônio waterfall belong to a management unit (MU) distinct from the I. boliviensis MU occupying Bolivian rivers. Downstream of Teotônio waterfall most dolphins are I. boliviensis/ geoffrensis hybrids, with remaining individuals being migrant I. boliviensis.

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Mitochondrial DNA remains a cornerstone for molecular ecology, especially for study species from which high-quality tissue samples cannot be easily obtained. Methods using mitochondrial markers are usually reliant on reference databases, but these are often incomplete. Furthermore, available mitochondrial genomes often lack crucial metadata, such as sampling location, limiting their utility for many analyses. Here, we assembled 205 new mitochondrial genomes for platyrrhine primates, most from the Amazon and with known sampling locations. We present a dated mitogenomic