A method to incorporate the effect of taxonomic uncertainty on multivariate analyses of ecological data

Researchers in ecology commonly use multivariate analyses (e.g. redundancy analysis, canonical correspondence analysis, Mantel correlation, multivariate analysis of variance) to interpret patterns in biological data and relate these patterns to environmental predictors. There has been, however, little recognition of the errors associated with biological data and the influence that these may have on predictions derived from ecological hypotheses. We present a permutational method that assesses the effects of taxonomic uncertainty on the multivariate analyses typically used in the analysis of ecological data. The procedure is based on iterative randomizations that randomly re-assign non identified species in each site to any of the other species found in the remaining sites. After each re-assignment of species identities, the multivariate method at stake is run and a parameter of interest is calculated. Consequently, one can estimate a range of plausible values for the parameter of interest under different scenarios of re-assigned species identities. We demonstrate the use of our approach in the calculation of two parameters with an example involving tropical tree species from western Amazonia: 1) the Mantel correlation between compositional similarity and environmental distances between pairs of sites, and; 2) the variance explained by environmental predictors in redundancy analysis (RDA). We also investigated the effects of increasing taxonomic uncertainty (i.e. number of unidentified species), and the taxonomic resolution at which morphospecies are determined (genus-resolution, family-resolution, or fully undetermined species) on the uncertainty range of these parameters. To achieve this, we performed simulations on a tree dataset from southern Mexico by randomly selecting a portion of the species contained in the dataset and classifying them as unidentified at each level of decreasing taxonomic resolution. An analysis of covariance showed that both taxonomic uncertainty and resolution significantly influence the uncertainty range of the resulting parameters. Increasing taxonomic uncertainty expands our uncertainty of the parameters estimated both in the Mantel test and RDA. The effects of increasing taxonomic resolution, however, are not as evident. The method presented in this study improves the traditional approaches to study compositional change in ecological communities by accounting for some of the uncertainty inherent to biological data. We hope that this approach can be routinely used to estimate any parameter of interest obtained from compositional data tables when faced with taxonomic uncertainty

The Role of Guadua Bamboo in Land Management and Indigenous Perspectives on Bamboo Ecosystems in Southwestern Amazonia

We examine the Indigenous uses, oral histories, and knowledge of native Guadua bamboo species in southwestern Amazonia. Two Guadua species form dense stands in which individual plants die en masse at regular intervals of about 28 years. Scholars suggested that pre-colonial earth builders took advantage of these die-off events as a natural aid in removing the forest to construct geometric earthworks. Our results show that Guadua species have a significant position in Indigenous socio-cosmologies, land use, and as a protector of diverse resources. Indigenous ontological understandings cannot be separated from discussions of the abundance and geographical distribution of Guadua as a critical controlling factor in the vegetation structure and function of southwestern Amazonian rain forests. Furthermore, oral histories point to the connection between land management and bamboo, as well as bamboo and the use of fire, conforming to the suggestion of opening ceremonial spaces in bamboo patches in pre-colonial earthwork societies.Peer reviewe

Geologically recent rearrangements in central Amazonian river network and their importance for the riverine barrier hypothesis

The riverine barrier hypothesis is a central concept in Amazonian biogeography. It states that large rivers limit species distributions and trigger vicariant speciation. Although the hypothesis has explanatory power, many recent biogeographical observations addressing it have produced conflicting results. We propose that the controversies arise because tributary arrangements in the Amazon river system have changed in geologically recent times, such that large tracts of forest that were on the same side of a river at one time got separated to different sides at another. Based on topographical data and sediment dating, we map about 20 major avulsion and river capture events that have rearranged the river network in central Amazonia during the late Pleistocene and Holocene. We identify areas where past riverine barrier effects might still linger in the absence of a major river, as well as areas where such effects may not yet have accumulated across an existing river. These results call for a reinterpretation of previous biogeographical studies and a reorientation of future works to take into account the idiosyncratic histories of individual rivers

Urban Power Line Corridors as Novel Habitats for Grassland and Alien Plant Species in South-Western Finland

Regularly managed electric power line corridors may provide habitats for both early-successional grassland plant species and disturbance-dependent alien plant species. These habitats are especially important in urban areas, where they can help conserve native grassland species and communities in urban greenspace. However, they can also provide further footholds for potentially invasive alien species that already characterize urban areas. In order to implement power line corridors into urban conservation, it is important to understand which environmental conditions in the corridors favor grassland species and which alien species. Likewise it is important to know whether similar environmental factors in the corridors control the species composition of the two groups. We conducted a vegetation study in a 43 kilometer long urban power line corridor network in south-western Finland, and used generalized linear models and distance-based redundancy analysis to determine which environmental factors best predict the occurrence and composition of grassland and alien plant species in the corridors. The results imply that old corridors on dry soils and steep slopes characterized by a history as open areas and pastures are especially suitable for grassland species. Corridors suitable for alien species, in turn, are characterized by productive soils and abundant light and are surrounded by a dense urban fabric. Factors controlling species composition in the two groups are somewhat correlated, with the most important factors including light abundance, soil moisture, soil calcium concentration and soil productivity. The results have implications for grassland conservation and invasive alien species control in urban areas.</p

The Role of Guadua Bamboo in Land Management and Indigenous Perspectives on Bamboo Ecosystems in Southwestern Amazonia

We examine the Indigenous uses, oral histories, and knowledge of native Guadua bamboo species in southwestern Amazonia. Two Guadua species form dense stands in which individual plants die en masse at regular intervals of about 28 years. Scholars suggested that pre-colonial earth builders took advantage of these die-off events as a natural aid in removing the forest to construct geometric earthworks. Our results show that Guadua species have a significant position in Indigenous socio-cosmologies, land use, and as a protector of diverse resources. Indigenous ontological understandings cannot be separated from discussions of the abundance and geographical distribution of Guadua as a critical controlling factor in the vegetation structure and function of southwestern Amazonian rain forests. Furthermore, oral histories point to the connection between land management and bamboo, as well as bamboo and the use of fire, conforming to the suggestion of opening ceremonial spaces in bamboo patches in pre-colonial earthwork societies.</p

Foliar element distributions in Guadua bamboo, a major forest dominant in southwestern Amazonia

Silica is the best-known component filling the spaces that form phytoliths in many plants, but phytoliths may also contain other elements. We used scanning electron microscopy with energy-dispersive X-ray spectroscopy (SEM-EDX) to map element distributions in the leaves of Guadua bamboo, which is a successful competitor in southwestern Amazonian forests. We emphasize immobile elements that can be mineralized (silicon and calcium) as well as potassium, an abundant mobile nutrient with many vital functions. We discovered high silicon (Si) content with little or no calcium (Ca) or potassium (K) in bulliform cells, bilobate shaped short cells and stomata, all of which can form phytoliths, and moderately high Si content in the bundle sheet, prickle tips and papillae. K often surrounded Si-loaded cells, Si and K had overlapping distributions in the intercostal areas near vein margins, and Ca showed abundant spotted distribution in the intercostal areas. The dark inside content of the costal zones of some samples in light microscopy showed no mineralization but prominently contained sulfur. Adjacent fusoid cells showed different Si, K and Ca combinations, which may suggest potentially variable functions of these cells. Widespread Si deposition strengthens Guadua bamboo leaves and may help it to outcompete tree species during periods of drought

Impact of spatial configuration of training data on the performance of Amazonian tree species distribution models

Remote sensing can provide useful explanatory variables for tree species distribution modeling, but only a few studies have explored this potential in Amazonia at local scales. Particularly for tropical forest management it would be useful to be able to predict the potential distribution of important tree taxa in areas where field data is as yet missing. Forest concessions produce valuable census data that cover large areas with high sampling effort and can be used as occurrence data in species distribution models (SDM). Nevertheless, these tree records are often spatially clumped and possibly only provide accurate predictions over areas close to where the training occurrence records are located. Here, we aim at investigating to what degree SDM performance and spatial predictions differ between models that have different spatial configurations of the occurrence data. For this, we divided the available occurrence data from a forest concession census in Peruvian Amazonia into different spatial configurations (narrow, elongated and compact), each of which contained approximately 20% of the full dataset. We then modelled the distributions of five tree taxa using Landsat data and elevation. More elongated configurations of the training data were more representative of the available environmental space, and also produced more robust SDMs. Average model performance (expressed as AUC) was 5% higher and variation in model performance 50% lower when elongated rather than compact configurations of training area were used. This confirms that covering only a small fraction of the environmental variability in the area of interest may lead to misleading SDM predictions, which needs to be taken into account when forest management decisions are based on SDMs.</p

Dating flowering cycles of Amazonian bamboo-dominated forests by supervised Landsat time series segmentation

Bamboo-dominated forests are unusual and interesting because their structure and biomass fluctuate in decades-long cycles corresponding to the flowering and mortality rhythm of the bamboo. In southwestern Amazonia, these forests have been estimated to occupy an area of approximately 160 000 km(2), and a single reproductively synchronized patch can cover up to thousands of square kilometers. Accurate mapping of these forests is challenging, however: the forests are spatially heterogeneous, with bamboo densities varying widely among adjacent sites; much of the area is inaccessible, so field verification of bamboo presence is difficult to obtain and georeferenced records of past flowering events virtually non-existent; and detectability of the bamboo by remote sensing varies considerably during its life cycle. In this study, we develop a supervised time series segmentation approach that allows us to identify both the presence of bamboo forests and the years in which the bamboo flowering and subsequent mortality have occurred. We then apply the method to the entire Landsat TM/ETM+ archive from 1984 to the end of 2018 and validate the classification by visual interpretation of very high resolution imagery. Collecting accurate ground reference data of bamboo presence and bamboo mortality timing is notably difficult in these forests, and we therefore developed a methodology that takes advantage of imperfect reference data obtained from the Landsat time series itself. Our results show that bamboo forests can be differentiated from non-bamboo forests using any of the infrared bands, but band 5 produces the highest classification accuracy. Interestingly, there appears to be a temporal difference in the spectral responses of the three infrared bands to bamboo flowering and mortality: near infrared (band 4) reflectance reacts to the event earlier than shortwave infrared (bands 5 and 7) reflectance. The long Landsat TM/ETM+ archive allows our methodology to detect some areas with two mortality events, with a theoretical maximum interval of 29 years. Analysis of these pixels with repeated mortality confirms that the life cycles of the local bamboo species (Guadua sarcocarpa and G. weberbauerii) last typically 28 years

Geologically recent rearrangements in central Amazonian river network and their importance for the riverine barrier hypothesis

The riverine barrier hypothesis is a central concept in Amazonian biogeography. It states that large rivers limit species distributions and trigger vicariant speciation. Although the hypothesis has explanatory power, many recent biogeographical observations addressing it have produced conflicting results. We propose that the controversies arise because tributary arrangements in the Amazon river system have changed in geologically recent times, such that large tracts of forest that were on the same side of a river at one time got separated to different sides at another. Based on topographical data and sediment dating, we map about 20 major avulsion and river capture events that have rearranged the river network in central Amazonia during the late Pleistocene and Holocene. We identify areas where past riverine barrier effects might still linger in the absence of a major river, as well as areas where such effects may not yet have accumulated across an existing river. These results call for a reinterpretation of previous biogeographical studies and a reorientation of future works to take into account the idiosyncratic histories of individual rivers.</p