Characterizing primate home‐ranges in Amazonia : Using ferns and lycophytes as indicators of site quality

The habitats present in research sites across Amazonia have usually been characterized only very broadly, for example, as inundated or non-inundated (terra firma) forests. However, within each of these categories there is considerable variation in soil properties and floristic composition. This variation is likely to determine habitat quality for animal populations through its effects on primary productivity and food availability, thereby affecting carrying capacity. Therefore, comparison of edaphic properties across sites could provide new insight into which factors affect animal foraging patterns, population densities, and home-range sizes. We provide an example from Estacion Biologica Quebrada Blanco in Peruvian Amazonia, where behavioral studies on primates (especially tamarins) have been conducted for more than three decades but little is known about the edaphic or floristic characteristics of the forest they occupy. We used indicator plant species to estimate and map soil base cation concentration and its variability at Estacion Biologica Quebrada Blanco. We found that soils in the study area are relatively cation-poor in a western Amazonian context, which probably translates into low primary productivity. Some differences in soils among the home-ranges of three tamarin groups were also observed, illustrating the usefulness of the method for detailed habitat mapping. in Spanish is available with online material.Peer reviewe

A case study on joint species distribution modelling with bird atlas data: revealing limits to species' niches

Growing interest in biodiversity mapping has spurred the development of species distribution atlases, often mainly based on citizen-science projects. Atlas data have been frequently exploited to model species' ecological niches and distributions on a species-by-species basis. However, spatial autocorrelation and phylogenetic relatedness among species complicate the statistical description of species' niches. Also, the effects of species' traits and co-occurrences on species-habitat relationship are commonly disregarded. In this work, we build a hierarchical multi-species model based on a major citizen-science project (the third Spanish breeding bird atlas) that simultaneously accounts for spatial, phylogenetic and trait-based dependencies. We predict the distributions of species niches, species richness and community traits along regional ecological gradients. Climate, habitat associations and species' traits all contribute (in this order) to structuring species' distributions. Species richness increases towards intermediate climatic conditions and with aquatic habitat cover and decreases with increasing forest and woody agricultural land cover. Species were distributed along regional climate gradients in accordance with their global thermal niches. Forest habitats favoured assemblages dominated by generalist, small-sized and cold-dwelling species with limited migratory behaviour. Increasing sampling effort augmented the model performance. Model performance was weaker for rare species and those with decreasing population sizes, likely due to their low niche saturation. Overall, we show that ecological relationships generalize from local to large scales and may be eludicated from atlases based on citizen-science mapping effortsWe wholeheartedly thank JS worked within the REMEDINAL4 network (TE-CM S2018/EMT-4338) during the preparation of the manuscript with no specific funding for this study; he is part of the project Grant (NextDive; PID2021-124187NB-I00) funded by MCIN/AEI/ 10.13039/ 501100011033 and by “ERDF A way of making Europe”. AE was funded by Organismo Autonomo ´ Parques Nacionales of Spain through the project 2745/2021. MJ was supported by the Academy of Finland's ‘Thriving Nature’ profiling action. OO was funded by the Academy of Finland (grant no. 309581), the Jane and Aatos Erkko Foundation, the Research Council of Norway's Centres of Excellence Funding Scheme (223257), and the European Research Council under the Horizon 2020 research and innovation programme (grant agreement No 856506; ERC Synergy project LIFEPLAN). The CSC – IT Center for Science, Finland is acknowledged for computational resource

The first arriving virus shapes within-host viral diversity during natural epidemics

Viral diversity has been discovered across scales from host individuals to populations. However, the drivers of viral community assembly are still largely unknown. Within-host viral communities are formed through co-infections, where the interval between the arrival times of viruses may vary. Priority effects describe the timing and order in which species arrive in an environment, and how early colonizers impact subsequent community assembly. To study the effect of the first-arriving virus on subsequent infection patterns of five focal viruses, we set up a field experiment using naïve Plantago lanceolata plants as sentinels during a seasonal virus epidemic. Using joint species distribution modelling, we find both positive and negative effects of early season viral infection on late season viral colonization patterns. The direction of the effect depends on both the host genotype and which virus colonized the host early in the season. It is well established that co-occurring viruses may change the virulence and transmission of viral infections. However, our results show that priority effects may also play an important, previously unquantified role in viral community assembly. The assessment of these temporal dynamics within a community ecological framework will improve our ability to understand and predict viral diversity in natural systems

Predicting environmental gradients with fern species composition in Brazilian Amazonia

Conclusions: Fern species composition can be used as an indicator of soil cation concentration, which can be expected to be relevant also for other components of rain forests. Presence-absence data are adequate for this purpose, which makes the collecting of additional data potentially very rapid. Comparison with earlier studies suggests that edaphic preferences of fern species have good transferability across geographical regions within lowland Amazonia. Therefore, species and environmental data sets already available in the Amazon region represent a good starting point for generating better environmental and floristic maps for conservation planning.</p

Characterizing primate home-ranges in Amazonia: Using ferns and lycophytes as indicators of site quality

The habitats present in research sites across Amazonia have usually been characterized only very broadly, for example, as inundated or non-inundated (terra firma) forests. However, within each of these categories there is considerable variation in soil properties and floristic composition. This variation is likely to determine habitat quality for animal populations through its effects on primary productivity and food availability, thereby affecting carrying capacity. Therefore, comparison of edaphic properties across sites could provide new insight into which factors affect animal foraging patterns, population densities, and home-range sizes. We provide an example from Estacion Biologica Quebrada Blanco in Peruvian Amazonia, where behavioral studies on primates (especially tamarins) have been conducted for more than three decades but little is known about the edaphic or floristic characteristics of the forest they occupy. We used indicator plant species to estimate and map soil base cation concentration and its variability at Estacion Biologica Quebrada Blanco. We found that soils in the study area are relatively cation-poor in a western Amazonian context, which probably translates into low primary productivity. Some differences in soils among the home-ranges of three tamarin groups were also observed, illustrating the usefulness of the method for detailed habitat mapping.in Spanish is available with online material

Mixed-species groups in bats : non-random roost associations and roost selection in neotropical understory bats

Publisher Copyright: © 2021, The Author(s).Background: Mixed-species groups in animals have been shown to confer antipredator, foraging and other benefits to their members that may provide selective advantages. In most cases, however, it is unclear whether functional benefits are a principal driver of heterospecific groups, or whether groups simply result from simultaneous exploitation of common resources. Mixed-species groups that form independently of environmental conditions may, however, evidence direct benefits of species associations. Bats are among the most gregarious mammals, with sometimes thousands of individuals of various species roosting communally. Despite numerous potential functional benefits of such mixed-species roosting groups, interspecific attraction has never been shown. To explore alternative explanations for mixed-species roosting, we studied roost selection in a speciose neotropical understory bat community in lowland rainforest in Costa Rica. Long term roost data were recorded over 10 years in a total of 133 roosts comprising both natural roosts and structurally uniform artificial roosts. We modelled bat roost occupancy and abundance in each roost type and in forest and pasture habitats to quantify the effects of roost- and environmental variability. Results: We found that bat species presence in natural roosts is predictable from habitat and structural roost parameters, but that the presence and abundance of other bat species further modifies roost choice. One third of the 12 study species were found to actively associate with selected other bat species in roosts (e.g. Glossophaga commissarisi with Carollia sowelli). Other species did not engage in communal roosting, which in some cases indicates a role for negative interspecific interactions, such as roost competition. Conclusions: Mixed-species roosting may provide thermoregulatory benefits, reduce intraspecific competition and promote interspecific information transfer, and hence some heterospecific associations may be selected for in bats. Overall, our study contributes to an improved understanding of the array of factors that shape diverse tropical bat communities and drive the dynamics of heterospecific grouping in mammals more generally.Peer reviewe

Mixed‑species groups in bats: non‑random roost associations and roost selection in neotropical understory bats

Background: Mixed-species groups in animals have been shown to confer antipredator, foraging and other benefits to their members that may provide selective advantages. In most cases, however, it is unclear whether functional benefits are a principal driver of heterospecific groups, or whether groups simply result from simultaneous exploitation of common resources. Mixed-species groups that form independently of environmental conditions may, however, evidence direct benefits of species associations. Bats are among the most gregarious mammals, with sometimes thousands of individuals of various species roosting communally. Despite numerous potential functional benefits of such mixed-species roosting groups, interspecific attraction has never been shown. To explore alternative explanations for mixed-species roosting, we studied roost selection in a speciose neotropical understory bat community in lowland rainforest in Costa Rica. Long term roost data were recorded over 10 years in a total of 133 roosts comprising both natural roosts and structurally uniform artificial roosts. We modelled bat roost occupancy and abundance in each roost type and in forest and pasture habitats to quantify the effects of roost- and environmental variability. Results: We found that bat species presence in natural roosts is predictable from habitat and structural roost parameters, but that the presence and abundance of other bat species further modifies roost choice. One third of the 12 study species were found to actively associate with selected other bat species in roosts (e.g. Glossophaga commissarisi with Carollia sowelli). Other species did not engage in communal roosting, which in some cases indicates a role for negative interspecific interactions, such as roost competition. Conclusions: Mixed-species roosting may provide thermoregulatory benefits, reduce intraspecific competition and promote interspecific information transfer, and hence some heterospecific associations may be selected for in bats. Overall, our study contributes to an improved understanding of the array of factors that shape diverse tropical bat communities and drive the dynamics of heterospecific grouping in mammals more generally.Peer reviewe

The legacy of human use in Amazonian palm communities along environmental and accessibility gradients

Aim: Palms are iconic and dominant elements of neotropical forests. In the Amazon region, palms have been used and managed by humans for food, material, medicine and other purposes for millennia. It is, however, debated to what extent the structure of modern palm communities reflects long term human modification. Here, we investigate the complex interplay of ecological and societal factors that influence the distributions of both human used and non used palms in western Amazonia.Location: Amazonia.Time period: Present.Major taxa studied: Palms (Arecaceae).Methods: We used Bayesian hierarchical joint species distribution models to predict the distributions and environmental niche dimensions of 78 western Amazonian species, and to explore their relationships with their diversity of human uses and with specific uses (food, construction and medicine). The models were parameterized with a comprehensive set of field-and satellite-derived environmental predictors.Results: Our results suggest that a combination of ecological and anthropogenic factors drive the present day distributions of Amazonian palms. The modelled ecological niches of the species revealed use-related species-sorting along soil, climatic, accessibility and drainage gradients. We found peaks in the proportions of useful palms and their diversity of uses in fertile soils, close to rivers, and on floodplains. These are habitats favourable for human settlement, although they harbour naturally restricted palm species pools. We also found a negative correlation between predicted palm species richness and number of human uses across western Amazonia.Main conclusions: Soil characteristics, accessibility, and species pool size all contribute to defining palm- human relationships. At the basin scale, the signature of human use on palm communities was predicted to be stronger in the species poor southwest than in central-western Amazonia. Overall, we conclude that environmental conditions have influenced modern Amazonian palm distributions both directly and indirectly, by regulating human settlement patterns and natural resource use over extended time periods.Peer reviewe

Multispectral canopy reflectance improves spatial distribution models of Amazonian understory species

Species distribution models are required for the research and management of biodiversity in the hyperdiverse tropical forests, but reliable and ecologically relevant digital environmental data layers are not always available. We here assess the usefulness of multispectral canopy reflectance (Landsat) relative to climate data in modelling understory plant species distributions in tropical rainforests. We used a large dataset of quantitative fern and lycophyte species inventories across lowland Amazonia as the basis for species distribution modelling (SDM). As predictors, we used CHELSA climatic variables and canopy reflectance values from a recent basin-wide composite of Landsat TM/ETM+ images both separately and in combination. We also investigated how species accumulate over sites when environmental distances were expressed in terms of climatic or surface reflectance variables. When species accumulation curves were constructed such that differences in Landsat reflectance among the selected plots were maximised, species accumulated faster than when climatic differences were maximised or plots were selected in a random order. Sixty-nine species were sufficiently frequent for species distribution modelling. For most of them, adequate SDMs were obtained whether the models were based on CHELSA data only, Landsat data only or both combined. Model performance was not influenced by species’ prevalence or abundance. Adding Landsat-based environmental data layers overall improved the discriminatory capacity of SDMs compared to climate-only models, especially for soil specialist species. Our results show that canopy surface reflectance obtained by multispectral sensors can provide studies of tropical ecology, as exemplified by SDMs, much higher thematic (taxonomic) detail than is generally assumed. Furthermore, multispectral datasets complement the traditionally used climatic layers in analyses requiring information on environmental site conditions. We demonstrate the utility of freely available, global remote sensing data for biogeographical studies that can aid conservation planning and biodiversity management.Peer reviewe