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Peru ranks among the three countries with the highest bird species diversity globally and a majority of those species are found in the Peruvian Amazon. However, birds in this area are currently facing serious anthropogenic threats. Genetic and genomic methods are becoming important tools for avian biodiversity monitoring and conservation planning. Comprehensive molecular libraries that are publicly available are key to the effective deployment of these tools. We analyze the information gaps for four molecular markers in the most important genetic sequence databases, Barcode of Life Data Systems (BOLD) and NCBI GenBank, for bird species of the Peruvian Amazonia. We found that 64% of Peruvian Amazonian bird species have gene sequences for COI, 59.5% have CYTB sequences, 16.4% have 12S sequences, and only 0.6% have 18S sequences. However, these numbers decrease drastically to 4.3% for COI sequences when we only consider specimens sampled in Peru. Our data also showed that 43.8% of Peruvian Amazonian endemic species (n = 32) are missing sequences of any screened marker uploaded to GenBank or BOLD. Our results will encourage and guide efforts of the scientific community to complete reference libraries for Peruvian avian species that will be useful for future DNA-based monitoring projects that include birds. [ABSTRACT FROM AUTHOR]

Innovative techniques, such as environmental DNA (eDNA) metabarcoding, are now promoting broader biodiversity monitoring at unprecedented scales, because of the reduction in time, presumably lower cost, and methodological efficiency. Our goal was to assess the efficiency of established inventory techniques (live‐trapping grids, pitfall traps, camera trapping, mist netting) as well as eDNA for detecting Amazonian mammals. For terrestrial small mammals, we used 32 live‐trapping grids based on Sherman and Tomahawk traps (total effort of 10,368 trap‐nights); in addition to 16 pitfall traps (1,408 trap‐nights). For bats, we used mist nets at 8 sites (4,800 net hours). For medium and large mammals, we used 72 camera trap stations (5,208 camera‐days). We identified vertebrate and mammal taxa based on eDNA analysis (12S region, with V05 and Mamm01 markers) from water samples, including a total of 11 3‐km transects for stagnant water sampling and seven small streams for running water sampling. A total of 106 mammal species were recorded. Building on sample‐based rarefaction and extrapolation curves, both trapping grids and pitfall were successful, recording 91.16% and 82.1% of the expected species for these techniques (~22 and ~9 species), and 16.98% and 6.60% of the total recorded mammal species, respectively. Mist nets recorded 83.2% of the expected bat species (~48), and 34.91% of the total recorded species. Camera trapping recorded 99.2% of the predicted large‐ and medium‐sized species (~31), and 33.02% of the total recorded species. eDNA recorded 75.4% of the expected mammal species for this technique (~68), and 47.0% of the total recorded species. eDNA resulted in a useful tool that saves on effort and reduces sampling costs. This study is among the first to show the large potential of eDNA metabarcoding for assessing Amazonian mammal communities, providing, in combination with conventional techniques, a rapid overview of mammal diversity with broad applications to monitoring, management and conservation. By including appropriate genetic markers and updated reference databases, eDNA metabarcoding method can be extended to the whole vertebrate community. [ABSTRACT FROM AUTHOR]

Aim: Community‐level assessments of how biodiversity responds to disturbance within forest habitats are often biased towards terrestrial‐based surveys. However, recent research suggests that arboreal communities of several indicator groups (ants, amphibians, beetles and butterflies) are more susceptible to human disturbance than their terrestrial counterparts, but what about wildlife at higher trophic levels? We assess responses to disturbance, from forest floor to canopy, of a key conservation flagship group: medium to large rainforest mammals. Location: The Manu Biosphere Reserve, southeast Peru. Methods: We deploy both arboreal and terrestrial camera traps to directly compare the response of arboreal and terrestrial mammal communities to rainforest degradation and disturbance. Results: We show that the arboreal mammal community is more susceptible to habitat disturbance than the terrestrial community. Furthermore, the largest‐bodied arboreal species, which are major seed dispersers, showed the greatest negative response to forest disturbance. The strongest predictors of occupancy probability for arboreal communities were focal tree connectivity and canopy cover, whereas surrounding forest loss and canopy height were there strongest predictors of terrestrial community occupancy, although these also had effects similar in size and magnitude on the arboreal community. Main conclusions: Conservation conclusions drawn from camera‐based studies focused on the terrestrial realm likely underestimate the impact of rainforest degradation to arboreal communities and on arboreal rainforest biodiversity in general. We highlight the importance of implementing arboreal research methods, capable of investigating conservation implications of anthropogenic disturbance across all vertical strata, for accurate conservation assessments and improving rainforest management and restoration strategies. [ABSTRACT FROM AUTHOR]

The adult sphingid communities of three sites in southeastern Peru representative of the moist tropical forest of the lowland Amazon, the pluvial tropical forest of the upper Amazon and Andean foothills, and the montane cloud forest of the eastern slopes of the Andes were sampled during 2004-2006 by using mercury vapor light traps. In total, 119 species of Sphingidae were documented. Species diversity was highest in the upper Amazon and Andean foothills, with 94 species (21 genera), followed by 80 species (21 genera) in the Amazonian lowlands, and 43 species (17 genera) in the montane cloud forest. The greatest number of endemics (22) was registered at the upper Amazon-Andean foothills site. The montane cloud forest site was characterized by the highest relative percentage of endemic species. The species assemblages of the lowland Amazon and the Andean foothills were more similar in composition to each other than to the montane assemblage. All three assemblages proved to be more distinctive than expected based on the proximity of the sampled sites and seemingly good flight capabilities of sphingid moths. This was reflected by the endemics accounting for nearly 40% of the total species pool. By contrast, cosmopolitans numbered only 26 species, or 22% of the total assemblage. We hypothesize that the composition and distribution of sphingid species along this elevational gradient may reflect floristic similarities and differences between the study sites and the extent to which different species are adapted to cope with certain environmental conditions, such as temperature and air humidity. [ABSTRACT FROM AUTHOR]

The lowland tapir Tapirus terrestris is the largest herbivore in the Neotropics and feeds on a large quantity of fruits, often ingesting the seeds and defecating them intact. Seed dispersal by the lowland tapir in the southwestern Amazon was studied by examining seeds from 135 dung samples collected between 2005 and 2007. Seeds of a total of 122 plant species were identified, representing 68 genera and 33 families. The species accumulation curve showed that more species can be expected with further sampling. Many species (45%) were only encountered once, and only 10 percent of all species were found in >10 samples, indicating that the lowland tapir is an opportunistic forager. Seed diversity showed a clear seasonal pattern and was highly correlated with fruit availability. Seed diameter ranged from <1 to 25 mm with 81 percent <10 mm diam. The size distribution of seeds found in lowland tapir dung generally followed that of seeds found in the forest, but had a lower proportion of seeds in the smallest size class (<2.5 mm) and a larger proportion found in the largest size class (20–25 mm). The diversity of seeds encountered in dung of the lowland tapir in this study was much higher than in previous studies. We conclude that the lowland tapir is a potential disperser for a large number of plant species, including many that previously have been thought to be dispersed only by large primates. Abstract in Spanish is available at . [ABSTRACT FROM AUTHOR]

Mammal inventories in tropical forests are often difficult to carry out, and many elusive species are missed or only reported from interviews with local people. Camera traps offer a new tool for conducting inventories of large- and medium-sized terrestrial mammals. We evaluated the efficiency of camera traps based on data from two surveys carried out at a single site during 2 consecutive years. The survey efforts were 1440 and 2340 camera days, and 75 and 86% of the 28 large- and medium-sized terrestrial mammal species known to occur at the site were recorded. Capture frequencies for different species were highly correlated between the surveys, and the capture probability for animals that passed in front of the cameras decreased with decreasing size of the species. Camera spacing and total survey area had little influence on the number of species recorded, with survey effort being the main factor determining the number of recorded species. Using a model we demonstrated the exponential increase in survey effort required to record the most elusive species. We evaluated the performance of different species richness estimators on this dataset and found the Jackknife estimators generally to perform best. We give recommendations on how to increase efficiency of camera trap surveys exclusively targeted at species inventories. [ABSTRACT FROM AUTHOR]

We evaluated the usefulness of herbarium collection databases for assessing patterns of species diversity and distribution based on a dataset from the flowering plant families Moraceae and Myristicaceae from the Peruvian Amazon. For Moraceae, a total of 3523 collections were used representing 134 species. The Myristicaceae were represented by 2113 collections of 46 species. We evaluated the distribution of collections based on 252 grid cells (0.5° size) covering all lowland rainforest in the Peruvian Amazon. We found that collections were concentrated in a few cells and that species diversity clearly increases in relation to collection density. Moraceae were collected in only 45% and Myristicaceae in only 31% of the 252 grid cells. Fifty percent of the collections came from just six and three cells, respectively. Most species were represented by only a small number of collections and collected only in a few grid cells, meaning a few widespread common species tend to dominate the collection records. Not surprisingly, most collections were made close to towns and transport routes. We evaluated the usefulness of rarefaction curves and diversity estimators for comparing diversity between regions. These techniques seem to be of little use for botanical collections due to violations of underlying assumptions. Problems such as accuracy of geographic and taxonomic data and strong bias in the spatial representation of the whole dataset are important to consider when basing conservation analysis, planning, and decision-making on seemingly large databases of biodiversity collections and are discussed in detail. [ABSTRACT FROM AUTHOR]

Abstract: The complex floodplains of large rivers offer a striking example of how geomorphology, by dictating patterns in the frequency and duration of soil saturation and surface flooding, influences ecosystem structure and function. This study draws on multiple sources of data from remote sensing, together with ground observations and water sampling, to distinguish floodplain ecosystems in the Madre de Dios River, a tributary of the Amazon River in Perú. This remote tropical river meanders across sub-Andean alluvial deposits in a tectonically active region and creates floodplain surfaces of varying ages, including terraces that are above the reach of present-day river floods. Data from Landsat ETM+ (optical multispectral), JERS-1 (L-band radar), and the Shuttle Radar Topography Mission (C-band interferometric Digital Elevation Models) were integrated in an object-oriented image analysis approach to distinguish five classes of floodplain vegetation. Vegetation classes generally correspond with successional age and reflect the activity of the riverine meander belt. Stage data for the river show erratic fluctuations and an annual range exceeding 8 m, but the maximum depth of floodplain inundation varied from >1 m close to the river to approximately 0.1 m on more elevated terraces. The major ion composition of standing waters on the floodplain during the dry season indicated the importance of emergence of local groundwater in maintaining saturated soils, particularly further from the river, where backswamp vegetation is distinct and includes palm swamps. Thus, a hydrological continuum exists from deep but sporadic river inundation near the river to constant soil saturation by groundwater emergence in distal backswamps, reflecting the geomorphological origin and age of the floodplain deposits. This hydrogeomorphic continuum results in fundamental ecological differences. The exceptionally rich biodiversity of the sub-Andean region may be ascribed in part to the enhanced biodiversity associated with fluvial geomorphological features, and, thus, conservation planning must account for the diverse landforms created by fluvial dynamics. [Copyright &y& Elsevier]

We compare the historical demographies of two Müllerian comimetic butterfly species: Heliconius erato and Heliconius melpomene. These species show an extensive parallel geographic divergence in their aposematic wing phenotypes. Recent studies suggest that this coincident mosaic results from simultaneous demographic processes shaped by extrinsic forces over Pleistocene climate fluctuations. However, DNA sequence variation at two rapidly evolving unlinked nuclear loci, Mannose phosphate isomerase (Mpi) and Triose phosphate isomerase (Tpi), show that the comimetic species have quite different quaternary demographies. In H. erato, despite ongoing lineage sorting across the Andes, nuclear genealogical estimates showed little geographical structure, suggesting high historical gene flow. Coalescent-based demographic analysis revealed population growth since the Pliocene period. Although these patterns suggest vicariant population subdivision associated with the Andean orogeny, they are not consistent with hypotheses of Pleistocene population fragmentation facilitating allopatric wing phenotype radiation in H. erato. In contrast, nuclear genetic diversity, theta, in H. melpomene was reduced relative to its comimic and revealed three phylogeographical clades. The pattern of coalescent events within regional clades was most consistent with population growth in relatively isolated populations after a recent period of restricted population size. These different demographic histories suggest that the wing-pattern radiations were not coincident in the two species. Instead, larger effective population size (N(e)) in H. erato, together with profound population change in H. melpomene, supports an earlier hypothesis that H. erato diversified first as the model species of this remarkable mimetic association.