Instituto Amazónico de Investigaciones Científicas Sinchi

Conserving plant diversity is integral to sustainable forest management. This study aims at diversifying tools to map spatial distribution of species richness. We develop a sampling strategy of using rapid assessments by local communities to gather prior information on species richness distribution to drive census cell selection by sampling with covariate designs. An artificial neural network model is built to predict the spatial patterns. Accuracy and consistency of rapid assessment factors, sample selection methods, and sampling intensity of census cells were tested in a simulation study with seven 25–50-ha census plots in the tropics and subtropics. Results showed that identifying more plant individuals in a rapid assessment improved accuracy and consistency, while transect was comparable to or slightly better than nearest-neighbor assessment, but knowing more species had little effects. Results of sampling with covariate designs depended on covariates. The covariate Ifreq, inverse of the frequency of the rapidly assessed species richness strata, was the best choice. List sampling and local pivotal method with Ifreq increased accuracy by 0.7%–1.6% and consistency by 7.6%–12.0% for 5% to 20% sampling intensity. This study recommends a rapid assessment method of selecting 20 individuals at every 20-m interval along a transect. Knowing at least half of the species in a forest that are abundant is sufficient. Local pivotal method is recommended at 5% sampling intensity or less. This study presents a methodology to directly involve local communities in probability-based forest resource assessment to support decision-making in forest management.

Neotropical landscapes are often characterized as mosaics of actively grazed pastures and forest fragments at various stages of succession. Restoring abandoned pastures requires intervening with actions informed by local ecological succession. Here we evaluate how litter production, a key component of nutrient cycling in forests, varies between physiographic landscapes (hill and lowland mountain), among stand age groups (early-secondary: 0–20 year, intermediate-secondary: 20–40 year, and old-growth forests: > 40 year), and in response to climatic (precipitation and irradiation) and forest structure and biodiversity variables (stand density, basal area, species density, diversity), in a tropical humid forest chronosequence. Total and leaf litter production was higher in the lower elevation hill landscape. Leaf litter production increased with stand age in both landscapes but only correlated positively with forest structure and biodiversity in the hill landscape. Lack of correlation in the mountain landscape is attributed to greater variance in structure and species composition in the subset of plots selected from this landscape for this study. Both landscapes exhibited an asynchronous, bimodal regime of leaf fall in response to precipitation. Leaf litter peaks prior to the wet season likely occur in response to water stress, while peaks after the wet season that coincided with increasing solar irradiation are likely the result of a leaf turnover strategy to optimize photosynthesis. Ecological succession in these landscapes does not appear limited in leaf litter production, but further research on the drivers of leaf litter production recovery is necessary to adequately guide intervention efforts.

Typhlomyrmex Mayr is a genus of small and cryptic ants of the subfamily Ectatomminae. Here, we provide taxonomic notes on the ants of the genus Typhlomyrmex Mayr from Colombia, along with the description of Typhlomyrmex encanto sp. nov. based on the worker caste, and the re-description / description of the worker caste of T. clavicornis Emery and T. prolatus Brown. Finally, we offer a key for the known species of Typhlomyrmex, and distribution maps for the three species this study focuses on.

The neotropical Apicotermitinae is a common and widespread clade of mostly soil-feeding soldierless termites. With few exceptions, species of this group were originally assigned to the genus Anoplotermes Müller, 1873. The application of internal worker morphology coupled with genetic sequencing has recently shed light on the true diversity of this subfamily. Herein, Anoplotermes susanae Scheffrahn, Carrijo & Castro, sp. nov. and four new species in four new genera are described: Hirsutitermes kanzakii Scheffrahn, Carrijo & Castro, gen. nov. et sp. nov., Krecekitermes daironi Scheffrahn, Carrijo & Castro, gen. nov. et sp. nov., Mangolditermes curveileum Scheffrahn, Carrijo & Castro, gen. nov. et sp. nov., and Ourissotermes giblinorum Scheffrahn, Carrijo & Castro, gen. nov. et sp. nov. Worker descriptions are based mainly on worker gut morphology, including the enteric valve, while imagoes were described based on external characters. A Bayesian phylogenetic tree of New World Apicotermitinae was constructed using the complete mitogenome to infer genera relationships and corroborate the taxonomic decisions. Distribution maps and a dichotomic key to the known Neotropical Apicotermitinae genera are provided.

In this study, we revised the lichen collection at the Herbario Amazonico Colombiano (coah) in Bogotá, Colombia. The collection has a total of nearly 2,400 specimens, with some duplicates in the Herbario Nacional (col) and in the herbarium of the Botanic Garden in Berlin (b). The revision of 1,861 specimens revealed 574 species in 142 genera and 44 families, among which there are 28 species new to science and seven new combinations. Previously, 324 species had been reported from the Colombian Amazon, and our revision resulted in a new total of 666 species, more than doubling the previous number. All 666 species are enumerated here in the first comprehensive checklist of lichens from the Colombian Amazon. A total of 157 new country records (53 already reported in the new Catalogue of Fungi of Colombia) increase the number of lichens known from Colombia to 2,827. The following species are described as new: Allographa exuens, differing from A. argentata by the lirellae with the corticiform layer soon flaking off and exposing the black labia, the only finely inspersed hymenium, and the narrower ascospores; A. guainiae, differing from Graphis syzygii in the prominent ascomata with lateral thalline margin and whitish thallus remnants between the striae; A. labiata, differing from A. immersa in the prominent lirellae with conspicuous, entire, exposed labia, an inspersed hymenium, longer ascospores, and stictic acid as secondary compound; A. lichexanthonica, differing from A. sitiana in producing lichexanthone; A. sessilis, differing from A. contortuplicata in the muriform ascospores; A. suprainspersata, differing from A. angustata in the very thin thalline cover of the ascomata and the apically inspersed hymenium; Astrothelium bireagens, differing from A. cinnamomeum by the broader, apically flattened perithecia covered by a thin, ferruginous-red, K+ deep purple pruina and internally with an ochraceous-yellow, K+ deep yellow pigment; A. stromatolucidum, differing from A. neovariolosum in the distinctly pseudostromatic ascomata; Carbacanthographis submultiseptata, differing from C. multiseptata in the narrower ascospores and the indistinct periphysoids; Chapsa inconspicua, differing from C. angustispora in the smooth to uneven versus farinose thallus and in the much shorter ascospores; Coenogonium velutinellum, differing from C. pineti in the finely velvety, rather thick thallus composed of irregular to erect, densely packed algal threads covered by a thin pseudocortex; Fellhanera naevioides, differing from F. naevia in the finely dispersed, minutely crenulate thallus and the blackish apothecia; Fissurina sipmanii, differing from F. amazonica in the shorter and broader, slightly gaping, somewhat chroodiscoid ascomata, and the amyloid ascospores; Glyphis lirellizans, differing from Glyphis substriatula in the erumpent vs. prominent lirellae with lateral thalline margin and the exposed disc; Graphis papillifera, differing from G. stellata in the lirellae lacking a thalline margin, very elongate and irregularly to radiately branched and not in stellate clusters, and in the 5-septate ascospores; G. pseudoglyphis, differing from Graphis stellata in the non-verrucose thallus, the branched lirellae which do not, however, form stellate clusters, and the shorter ascospores; Malmidea flavimarginata, differing from M. bacidinoides in the pale yellow, K+ deep yellow medulla and yellow, K+ deep yellow excipular crystals, as well as the smaller ascospores; M. isidiopiperina, differing from M. taytayensis in the smaller ascospores; M. papillitrailiana, differing from M. trailiana in the papillose apothecial margins; Myriotrema araracuarense, differing from Myriotrema muluense in the non-annulate pores of the apothecia and in the longer ascospores; Ocellularia areolata, differing from Ocellularia rhicnoporoides in the pigmented medulla and the larger, more prominent apothecia with completely carbonized excipulum; O. caquetensis, differing from Ocellularia rotundifumosa in the absence of a columella; O. inspersipallens, differing from O. viridipallens in the inspersed hymenium and the 5–7-septate ascospores; O. rufocinctoides, differing from O. rufocincta in the thallus lacking large and irregular crystal clusters, in the more prominent apothecia and in the smaller ascospores; O. sipmanii, differing from Ocellularia abbayesiana in the smaller, 3-septate ascospores; Pseudopyrenula daironii, differing from all other species of the genus in the aggregate perithecia with shared ostiole and the internal orange-red pigment granules lining the perithecial wall; Pyrenula asymmetrica, differing from Pyrenula papilligera in the longer, almost rectangular ascospores; and Redingeria pseudostromatica, differing from other species in the genus in the pseudostromatic ascomata with small, rounded apothecia, in combination with 1-septate ascospores. In addition, the following seven new combinations are proposed: Bacidina cyanophila (≡ Bacidina simplex var. cyanophila), Malmidea sorediifera (≡ Lecanora sorediifera), Ocellularia fuscescens (≡ Thelotrema fuscescens), Phaeographis cymbegrapha (≡ Graphis cymbegrapha; = Phaeographis amazonica Staiger], Polyblastidium flavosquamosum (≡ Heterodermia flavosquamosa), Polyblastidium lamelligerum (≡ Parmelia lamelligera), and Polyblastidium rottboellii (≡ Anaptychia hypoleuca var. rottboellii).

The Colombian Amazon is a megadiverse region with high potential for commercial use in the pharmaceutical, food, and cosmetic industries, constantly expanding and looking for new alternatives from natural resources; unfortunately, few characterization reports of its profitable non-timber species in Colombia have been conducted. This work aimed to perform a comprehensive analysis of traditionally used species: Carapa guianensis (Andiroba), Euterpe precatoria (Asai), Mauritia flexuosa (Miriti), Astrocaryum murumuru (Murumuru), Plukenetia volubilis (Sacha Inchi), and Caryodendron orinocense H.Karst (Cacay). For this purpose, oil and fat quality indices, phytosterol, carotenoid, tocopherol, and tocotrienol content, as well as density and refractive index, were measured to establish their quality level. Multivariate analysis showed four groups of samples; such differences were mainly due to the composition rather than quality indices and physical properties, especially the content of saturated and unsaturated fatty acids. All species reported a precise composition , which makes them noninterchangeable, and Miriti oil arose as the most versatile ingredient for the industry. The Colombian Amazon region is a promising source of quality raw material, especially for oils/fats and unsaturated fatty acids; this resulted in the most interest for pharmaceutical, food, and cosmetic purposes.

Despite the importance of earthworms for soil formation, more is needed to know about how Pre-Columbian modifications to soils and the landscape. Gaining a deeper understanding is essential for comprehending the historical drivers of earthworm communities and the development of effective conservation strategies in the Amazon rainforest. Human disturbance can significantly impact earthworm diversity, especially in rainforest soils, and in the particular case of the Amazonian rainforest, both recent and ancient anthropic practices may be important. Amazonian Dark Earths (ADEs) are fertile soils found throughout the Amazon Basin, created by sedentary habits and intensification patterns of pre-Colombian societies primarily developed in the second part of the Holocene period. We have sampled earthworm communities in three Brazilian Amazonian (ADEs) and adjacent reference soils (REF) under old and young forests and monocultures. To better assess taxonomic richness, we used morphology and the barcode region of the COI gene to identify juveniles and cocoons and delimit Molecular Operational Taxonomic Units (MOTUs). Here we suggest using Integrated Operational Taxonomical units (IOTUs) which combine both morphological and molecular data and provide a more comprehensive assessment of diversity, while MOTUs only rely on molecular data. A total of 970 individuals were collected, resulting in 51 taxonomic units (IOTUs, MOTUs, and morphospecies combined). From this total, 24 taxonomic units were unique to REF soils, 17 to ADEs, and ten were shared between both soils. The highest richness was found in old forest sites for ADEs (12 taxonomic units) and REFs (21 taxonomic units). The beta-diversity calculations reveal a high species turnover between ADEs and REF soils, providing evidence that ADEs and REFs possess distinct soil biota. Furthermore, results suggest that ADE sites, formed by Pre-Columbian human activities, conserve a high number of native species in the landscape and maintain a high abundance, despite their long-term nature.

Cleistes rosea and 10 other taxa comprise a complex widely distributed in various open vegetation types from eastern South America to Panama. The taxonomic identity of most of these taxa is unclear and their relationships with C. rosea have never been satisfactorily discussed or tested. Here, we employ molecular phylogenetics, morphometrics and morphological, ecological and geographic distribution data to investigate the relationships and taxonomy of Cleistes rosea and related species. Our results confirm that Cleistes rosea and Cleistes castaneoides are sister species and although highly similar in general floral morphology, they differ in vegetative characters, distribution, habitat, floral scent, and lip characters. Both species show local variations regarding floral characters, particularly the flower colour, and such differences were used here to delimit infraspecific taxa within the C. rosea/C. castaneoides clade. While C. rosea var. guianensis var. nov. is restricted to French Guiana, and C. rosea var. buenaventurae stat. & comb. nov. is restricted to low altitudes on the western side of the Cordillera Occidental in the Chocó region of Colombia, C. castaneoides var. castaneoides and C. castaneoides var. augusta comb. nov. are sympatric throughout their distribution. Cleistes abdita, formerly known as C. rosea f. pallida, is similar to C. castaneoides but distinguished by the smaller flowers and restricted distribution to Amazonian savannas. Cleistes rosea is distributed throughout the north of the Andes and northern South America. In turn, C. castaneoides occurs mainly in South-eastern and Central-western Brazil. Still, the distribution of these three species overlaps in the Guiana Shield, where the differentiation between them is less evident. Our results provide evidence of the plasticity of the floral morphology of Cleistes, especially the lip, and highlight that hitherto neglected characters, such as vegetative morphology, habitat, and floral scent, are particularly informative for the characterization of species and taxonomy of the genus.

Chaetolepis es un pequeño género de 11 especies de arbustos y hierbas de zonas montañosas, en su mayoría neotropicales. Como producto de la revisión de la familia Melastomataceae para el proyecto Flora de Bogotá, se hizo la descripción, ilustración y mapeo de una nueva especie del género y se establecieron las diferencias con especies morfológicamente cercanas.

Noteworthy new records of 12 species of mosses and liverworts, with notes on their taxonomy, distribution and ecology

Bats are natural reservoirs of protozoal, viral, fungal and bacterial pathogens. However, little has been described about their endoparasites, especially in the Neotropics, despite the fact that this region represents a high taxonomic and functional bat diversity. In this study, we describe gastrointestinal parasites found in faecal samples of Neotropical bats from the Amazon rainforest of Colombia. We characterise the prevalence of parasites by employing flotation and McMaster techniques. We obtained 222 samples, but only 15 bats (6.8%) of the species Carollia brevicauda (n = 9), C. perspicillata (n = 3), Artibeus planirostris (n = 1), A. lituratus (n = 1) and Gardnerycteris crenulatum (n = 1) were positive for gastrointestinal parasites. This is the first survey of bat gastrointestinal parasites conducted in the Colombian Amazon. We report for the first time coccidian parasites in phyllostomid bats from Colombia. We also found nematodes in gestating females, which may suggest a transfer of parasites to the foetus during pregnancy in fruit bats. Besides insectivorous bats, frugivores can also represent a source for gastrointestinal parasites in the Neotropics, but the factors that determine their hosting capacity are still not fully understood. Further research should explore the interactions of wild and domestic hosts with parasites, which could be useful for analysing potential risks to the human population.

Accurate estimates of forest biomass stocks and fluxes are needed to quantify global carbon budgets and assess the response of forests to climate change. However, most forest inventories consider tree mortality as the only aboveground biomass (AGB) loss without accounting for losses via damage to living trees: branchfall, trunk breakage, wood decay. Here we use ~151,000 annual records of tree survival and structural completeness to compare AGB loss via damage to living trees to total AGB loss (mortality + damage) in seven tropical forests widely distributed across environmental conditions. We find that 42% (3.62 Mg ha-1 yr-1 ; 95% CI 2.36-5.25) of total AGB loss (8.72 Mg ha-1 yr-1 ; CI 5.57-12.86) is due to damage to living trees. Total AGB loss was highly variable among forests, but these differences were mainly caused by site variability in damage-related AGB losses rather than by mortality-related AGB losses. We show that conventional forest inventories overestimate stand-level AGB stocks by 4% (1-17% range across forests) because assume structurally complete trees, underestimate total AGB loss by 29% (6-57% range across forests) due to overlooked damage-related AGB losses, and overestimate AGB loss via mortality by 22% (7-80% range across forests) because of the assumption that trees are undamaged before dying. Our results indicate that forest carbon fluxes are higher than previously thought. Damage on living trees is an underappreciated component of the forest carbon cycle that is likely to become even more important as the frequency and severity of forest disturbances increase.

Deforestation in the tropics is one of the greatest biodiversity crises of the Anthropocene. In response, tropical countries such as Colombia have committed to restoring degraded lands and reconnecting forest fragments. To contribute to this mission, we evaluated how easy-to-measure seed functional traits predicted germination requirements and early seedling growth rates (RGRs) for 11 tree species native to the Andean-Amazon piedmont region. Pre-sowing treatments followed a 3 × 3 factorial design: three light conditions (full, partial, and no light) and three pre-germination treatments (hot water, abrasion, and control). A cluster analysis grouped species into three groups driven chiefly by highly correlated variables of seed size and mass. However, species within and among functional groups differed in their response to pre-germination treatments. One exception includes the small-seeded species group responding with little-to-no germination to the absence of light. Since functional traits were highly correlated, we used Principal Component Regression (PCR) to predict germination metrics (germination percentage, velocity, and vigor) and RGRs. The multivariate trait axis of seed size and seed mass measurements (PC1) correlated negatively with germination metrics and positively with RGRs. Our results highlight the challenges associated with using easy-to-measure functional traits to deduce the most effective pre-sowing treatment. Other more relevant functional traits can be measured in lab, but a shotgun approach to testing pre-germination treatments may be more cost-effective. High germination in small-sized seed species highlights the early-successional niche these species occupy, but reduced RGR may represent a tradeoff associated with having relatively few resources stored in seed.

In a time of rapid global change, the question of what determines patterns in species abundance distribution remains a priority for understanding the complex dynamics of ecosystems. The constrained maximization of information entropy provides a framework for the understanding of such complex systems dynamics by a quantitative analysis of important constraints via predictions using least biased probability distributions. We apply it to over two thousand hectares of Amazonian tree inventories across seven forest types and thirteen functional traits, representing major global axes of plant strategies. Results show that constraints formed by regional relative abundances of genera explain eight times more of local relative abundances than constraints based on directional selection for specific functional traits, although the latter does show clear signals of environmental dependency. These results provide a quantitative insight by inference from large-scale data using cross-disciplinary methods, furthering our understanding of ecological dynamics.

Pastures and crops have been expanding at an accelerated rate in the forests of the Colombian Amazon since the peace accords were signed in 2016. The rapid loss of tropical rainforests is threatening the integrity of protected areas and connectivity in the Amazon and other natural regions. In the context of the post-conflict stage, a set of land use and land cover change scenarios were constructed for the Colombian Amazon for the year 2040, using expert coherent narratives. Three scenarios were designed: trend, extractivist, and sustainable development. Historic land use change and driving factors were analyzed throughout 14 transitions between the years 2002 and 2016, based on the interpretation of Landsat images and their relationship with 29 driving factors using artificial neural networks. The Markov chain model was calculated for the transitions, and the change allocation model was parameterized to spatially simulate the scenarios. The results showed that the LULC model calibration and validation were satisfactory (0.91). The sustainable development scenario that considers strong policies for the conservation of forests and implementation of sustainable production projects was the option with greater values for conserved forests and secondary vegetation in recovery, adding ~ 42 million hectares by 2040. The other scenarios showed that the Colombian Amazon will lose ~ 2 million hectares of forests in the trend scenario and ~ 4.3 million hectares in the extractivist scenario, based on the reference year (2016). In the trend scenario, pastures and crops could increase by 48%; and, in the extractivist scenario, these would increase by 117%, changing from ~ 3.9 to ~ 8.6 million hectares. We hope that the scientific contribution of this study will be relevant for informed discussion in decision-making and provide a framework for building a peaceful territory.

The gulupa (Passiflora edulis Sims f. edulis) is one of the main fruit trees that are part of Colombia's export supply. The objective of this research was to determine the effect of chemical fertilizers alone (control) or together with integrated fertilization (humic acids or vermicompost; two separate treatments), on the yield and quality of gulupa fruit during two consecutive production cycles in the Colombian Amazon foothills. The climatic conditions were monitored and the phenological state of the plant was related to the average temperature, relative humidity, precipitation, solar radiation, and vapor pressure deficit. The integrated fertilization with vermicompost offered better values in productive parameters (fresh weight, number of fruits and equatorial diameter) irrespective of the cycle considered, but the fruit quality attributes were similar irrespective of the fertilization treatment tested. The fluctuations of the climatic variables of precipitation, relative humidity and solar radiation in both cycles (the second rainiest and affected by the ENSO phenomenon) reduced the quality of the fruit (whole fruit firmness by 19%, dry matter and pulp total titratable acidity by 24%, total soluble solids by 8%, individual sugars by 49%, organic acids by 63% and antioxidant capacity by 67%) as well as the productive parameters during the second cycle. These results demonstrate the high degree of influence exerted by the climate on productive and fruit quality attributes that are decisive in the production and marketing of the fruit.

The Colombian Amazon region is part of the Neotropical rainforest (humid forest biome) covering an area of 483,163 km2 and includes tributaries of both the Amazon and Orinoco River basins. The aquatic ecosystems found there include: rivers and alluvial plains originating in Andean headwaters, on eroded soils of tropical forests in the lowlands, and Guiana Shield formations, comprising a dense fluvial drainage network in the lowlands, with Paleogene/Neogene geological formations (terra firme streams in higher places that don’t usually flood) and Paleozoic (shield streams); and Andean and Guiana Shield streams above 200–250 m a.s.l. We present here an exhaustive compilation of published information, supported by fish collections, consisting of a list of 1104 species distributed in 375 genera, 53 families, and 16 orders. We include occurrence data of these species in each sub-basin. The presence/absence species matrix was analyzed using a dendrogram and non-metric multidimensional scaling (NMDS) analysis to identify patterns of similarity between basins and sub-basins. We evaluated species composition between basins and among the different geological origins using PERMANOVA. The dendrogram shows co-occurrences of 404 species in the two basins. It also shows two clear groupings of the sub-basins of the Amazon (except Guainía-Negro drainages) and those of the Orinoco. Within the Amazon Basin, there are two nodes according to the geological origin: systems of Andean origin and those of the lowlands. The dendrogram results are consistent with the NMDS analysis, which shows a clear grouping according to the connectivity of the basins; the Guainía-Negro is included in the Amazon basin. Species distribution patterns were supported by the PERMANOVA, and differed significantly between basins (F = 4.3, R = 0.26, P = 0.003) and geological origin (F = 3.6, R = 0.23, P = 0.003). The number of species in this study represents almost a fifth of the ichthyofauna of the Neotropics and about a third of that of the Amazon River basin; clearly supporting Colombia’s status among the countries with the greatest diversity of freshwater fish species of the planet. We include here a significant number of new records (75 spp), provide a first approximation of the distribution patterns, and a framework for future biogeographical studies.

Increasing biodiversity in highly diverse plant communities can jointly increase ecosystem function and ecosystem vulnerability. This paradox requires further attention. This study analyzed the functional response of plant communities to above- and below-ground parameters along the chronosequence (degraded pastures (DP), early forests (EF), intermediate forests (IF), and old-growth forests (OF)) in two highly fragmented landscapes of the Colombian Amazon as an estimate of the level of functional vulnerability. Three sets of functional attributes were evaluated: (i) functional composition based on the community-weighted mean (CWM) of five traits; (ii) functional diversity based on the multi-trait indices and functional dispersion (FDis) of each individual trait; and (iii) the functional vulnerability at the community-level and species-level. The individual traits did not show a clear pattern along the chronosequence. However, the trend indicated an increase in the values of resource conservation traits with the age of abandonment. The functional response of the community did not vary between landscapes. Between DP and OF, there was a significant increase in functional diversity and a decrease in functional redundancy, which increased community-level vulnerability. Consequently, the more vulnerable species were observed in the IF and OF plots. In addition, a decrease in environmental parameters, such as penetration resistance, bulk density and Ca content, and an increase in slope, precipitation, electric conductivity, pH, clay, organic material, and P and N contents increased the vulnerability. We elucidated the need for secondary forest management in terms of conservation and restoration to maintain the capacity to respond to changing environmental conditions in highly fragmented landscapes in the Andean–Amazonian transition.

Determining the relative importance of dispersal and vicariance events across neotropical regions is a major goal in biogeography. These events are thought to be related to important landscape changes, notably the transition of Amazonia toward its modern hydrological configuration ca. 10 million years ago. We investigated the spatio-temporal context of the diversification of one of the major lineages of Pristimantis, a widespread and large genus of direct-developing Neotropical frogs. We gathered a spatially and taxonomically extensive sampling of mitochondrial DNA sequences from 754 Pristimantis gr. conspicillatus specimens, which led to delimiting 75 Operational Taxonomic Units (OTUs). Complete mitogenomes of 35 of these OTUs were assembled and collated with two nuDNA loci to reconstruct a time-calibrated phylogeny. We identified five major clades that diverged around the Oligocene-Miocene transition and that are largely restricted to distinct Neotropical regions i.e. Western Amazonia (P. conspicillatus clade), the Brazilian Shield (P. fenestratus clade), the Atlantic Forest (P. ramagii clade), the Guiana Shield (P. vilarsi clade) and the northern Andes (P. nicefori clade). The majority of the diversification events within these clades occurred in-situ from the early Miocene onward. Yet, a few ancient dispersal/vicariance events are inferred to have occurred among trans-Andean forests, the Atlantic Forest, the Brazilian and the Guiana Shields, but almost none in the last 10 Ma. The radical landscape transformations during the Miocene caused by the Andean orogeny and hydrological barriers such as the Pebas System and the subsequent transcontinental configuration of the Amazon drainage is a likely explanation for the isolation of the different clades within the P. gr. conspicillatus.