Markus Gastauer

Avoiding inaccuracies in tree calibration and phylogenetic community analysis using Phylocom 4.2

There is an increased interest in phylogenetic approaches for conservation biology and community analysis. Many of these analyses are carried out using the Phylocom 4.2 package. With this computational tool, already existing trees are pruned to species from community to be studied. For plant communities, a variety of megatrees including all angiosperm families are available for phylogenetic community analysis. Using the bladj algorithm, internal nodes of community trees derived from these megatrees are calibrated on time scales from fossil or molecular data provided in an ages file. The higher precision of tree calibration, the better is the ecological interpretation if we assume that the closest related species have the most superposed set of traits, the highest probability of co-occurrence in case of environmental filter effects and the highest ratio of competitive exclusion. Together with the Phylocom 4.2 package comes an ages file based on Wikstroms dating of angiosperm families (wikstrom.ages). But there are inconsistencies in syntax and/or nomenclature between internal node names of trees and the ages file from phylocom that influence the tree calibration and the subsequent analysis. To avoid that, we classified all online available megatrees according to their syntax and nomenclatureof internal nodes. For each of the four classes we provide a new, fully compatible ages file in the supplement material. Each online available megatree, pruned to the species from an example community from the Atlantic Rainforest, was calibrated twice running the bladj algorithm using once the original wikstrom.ages file and, additionally, the new ages file prepared for that tree class. Outcomes from trees calibrated by different methods have been compared. To avoid inconsistencies that push results beyond the realistic, we recommend a strict application of the four ages files provided as supplementary files.

Interactions, Environmental Sorting and Chance: Phylostructure of a Tropical Forest Assembly

Density dependence, environmental sorting and chance have been discussed for the purpose of understanding, predicting and explaining the species richness, composition and structural parameters of living communities. Different ecological mechanisms occur individually in an overlapping manner, so the structure of each local community is influenced by an independent mixture of these factors. To identify which of these factors prevails in organizing the species-rich tree community from 100 plots of 10 × 10 m in a primary forest patch (the Forest of Seu Nico – FSN, from the Atlantic Forest domain), we analyzed species-environment correlations via canonical correspondence analysis and identified two different pedo-environments. We analyzed the community’s phylogenetic structure using Phylocom 4.2 software to calculate the net relatedness index (NRI) and the nearest taxon index (NTI). Furthermore, we partitioned the total phylogenetic diversity into independent α and β components (ΠST). To reveal the overlap of ecological mechanisms such as neutrality, environmental filtering and density-dependent factors, we analyzed the phylogenetic structure in both pedo-environments. The species-environment correlations observed in the FSN are weak in comparison with those found in other studies, although the permanent plot presents a short environmental gradient, dividing the plot into an upper, more acidic hillside and a lower, more fertile bottom. The overall phylogenetic structure of the FSN community shows strong and significant phylogenetic overdispersion. This overdispersion indicates that density-dependent factors, such as interspecific competition, play an important role in maintaining the species richness and community structure in megadiverse ecosystems such as the FSN when we assume traits to be conserved within evolutionary lineages. The NRI and NTI are correlated positively with the soil pH and negatively with the soil’s aluminum concentration, so the bottom plots show higher phylogenetic overdispersion and lower ΠST values than the hillside plots. This pattern can be explained by the greater importance of environmental filters in more acidic soils that form less favorable habitats, while the influence of competition and therefore also the rate of competitive exclusion are higher in the more favorable, less acidic plots.

Environmental filtering of agroforestry systems reduces the risk of biological invasion

Abstract Prevention is the most effective way of mitigating the negative impacts of exotic species invasions on biodiversity. Preventative measures include inhibiting the further dispersal and recruitment of established invasive species. We expect coffee production in agroforestry systems to reduce the recruitment of exotic species relative to monoculture stands because intercropped trees function as environmental filters that select for individuals with traits such as shade tolerance. If ecologically similar species are also closely related phylogenetically, such environmental filters should reduce phylogenetic diversity, supporting the coexistence of closely related species. Here, we test whether the taxonomic and phylogenetic diversity of native and exotic species in agroforestry systems is lower than in monocultures. We sampled the understory in 180 plots distributed in both habitats in three study sites within the Araponga municipality, Brazil, and measured understory light availability. Phylogenetic diversity was calculated as the net relatedness index (NRI) and the nearest taxon index (NTI). Understory light availability was lower in agroforestry systems. Of the 48 species found, 25 occurred in agroforestry systems, three of which were exotics. Forty-two species were found in monoculture stands (including 13 exotics). As expected, NRI and NTI indicated lower phylogenetic diversity in agroforestry systems than in monoculture stands. Agroforestry systems provide less favorable habitats for exotic species, filtering them from the understory. The mechanisms that select against exotic species remain unknown; however, shading might exclude predominantly heliophytic exotic species from the agricultural matrix. Therefore, agroforestry systems may function as buffer zones preventing invasion into sensitive ecosystems.

Community dynamics in a species-rich patch of old-growth forest in a global changing scenario

Ecological theory predicts that, in mature ecosystems, species richness, the number of individuals and the biomass of individuals will remain in a relatively stable state of equilibrium. The aim of this study was to test that theory. In 2001 and 2010, we conducted censuses of all trees with a circumference at breast height ≥ 10 cm in a one-hectare plot in a seasonal semideciduous old-growth forest in southeastern Brazil. We compared the two censuses in terms of species richness and diversity, computing growth, recruitment and mortality rates, as well as gains and losses of basal area. Between 2001 and 2010, species richness declined from 224 to 218 species and the basal area increased from 37.86 to 40.16 m2 ha−1. Overall turnover (the mean difference between mortality and recruitment) was lower than would be expected for a seasonal semideciduous forest, indicating stability and slight successional advance. This interpretation is supported by the observation that pioneer species and canopy species both showed higher mortality than recruitment. However, uncommon species (< 10 individuals in the 2001 census) showed higher mortality than recruitment and became rarer, whereas most species that were abundant in 2001 became more abundant by 2010. These observations, as well as the decline in species richness, although statistically not significant, match the predictions of ecological theory for scenarios in which formerly contiguous ecosystems become fragmented and the remnants become isolated within the landscape. Nevertheless, further censuses are needed in order to test the idea that the observed patterns are not explained by natural oscillations but are consequences of environmental changes related to human activity.

PRESERVATION OF PRIMARY FOREST CHARACTERISTICS DESPITE FRAGMENTATION AND ISOLATION IN A FOREST REMNANT FROM VIÇOSA, MG, BRAZIL1

Segundo seus proprietarios, a Floresta de Seu Nico (FSN), situada no Municipio de Vicosa, Minas Gerais, Brasil, nunca sofreu corte raso, porem e considerada floresta primaria. No entanto, o fragmento florestal sofreu impactos por extracao seletiva de madeira e produtos nao madeireiros, alem de fragmentacao e isolamento. O objetivo desse estudo foi testar se a FSN, apesar de impactos, preservou caracteristicas de florestas primarias, que sao porcentagens elevadas de especies nao pioneiras (>80%), especies dispersas por animais (>90%), especies de sub-bosque (> 50%) e especies endemicas (~40%). Para isso, todas as arvores com diâmetro a altura do peito igual ou superior a 3,2 cm, dentro de uma parcela de 100 x 100 m, foram identificadas. Com 218 especies de arvores encontradas dentro da parcela, a riqueza de especies da FSN e elevada na regiao. As porcentagens de especies nao pioneiras (92 %), dispersas por animais (85%), de sub-bosque (55%) e endemicas (39,2%) da FSN cumprem os criterios propostos para florestas primarias. Porem, conclui-se que a FSN manteve suas caracteristicas como floresta primaria, que destaca a sua importância para a conservacao dos recursos bioticos da regiao, onde fragmentos semelhantes estao faltando ou, ainda, nao foram descritos.

Handling sticky resin by stingless bees (Hymenoptera, Apidae)

For their nest defense, stingless bees (Meliponini) collect plant resins which they stick on intruders like ants or cleptobiotic robber bees causing their immobilization. The aim of this article is to identify all parts of stingless bee workers contacting these sticky resins. Of special interest are those body parts with anti-adhesive properties to resin, where it can be removed without residues. For that, extensive behavioral observations during foraging flight, handling and application of the resin have been carried out. When handling the resin, all tarsi touch the resin while walking above it. For transportation from plants to the nest during foraging flight, the resin is packed to the corbicula via tarsi and basitarsi of front and middle legs. Once stuck to the resin or after the corbicula had been unloaded, the bees legs have to be cleaned thoroughly. Only the tips of the mandibles, that form, cut and apply the sticky resin, seem to have at least temporarily resin-rejecting properties.

The hypothesis of sympatric speciation as the dominant generator of endemism in a global hotspot of biodiversity

Abstract Allopatric or sympatric speciation influence the degree to which closely related species coexist in different manners, altering the patterns of phylogenetic structure and turnover among and between communities. The objective of this study was to examine whether phylogenetic community structure and turnover in the Brazilian Atlantic Forest permit conclusions about the dominant process for the formation of extant angiosperm richness of tree species. Therefore, we analyzed phylogenetic community structure (MPD, MNTD) as well as taxonomic (Jaccard similarity) and phylogenetic turnover (betaMPD, betaMNTD) among and between 49 tree communities distributed among three different habitat types. Mean annual precipitation and mean annual temperature in each survey area were estimated. Phylogenetic community structure does not differ between habitat types, although MPD reduces with mean annual temperature. Jaccard similarity decreases and betaMNTD increases with spatial distance and environmental differences between study sites. Spatial distance explains the largest portions of variance in the data, indicating dispersal limitation and the spatial aggregation of recently formed taxa, as betaMNTD is related to more recent evolutionary events. betaMPD, that is related to deep evolutionary splits, shows no spatial or environmental pattern, indicating that older clades are equally distributed across the Brazilian Atlantic Forest. While similarity pattern indicates dispersal limitations, the spatial turnover of betaMNTD is consistent with a high degree of sympatric speciation generating extant diversity and endemism in the Brazilian Atlantic Forest. More comprehensive approaches are necessary to reduce spatial sampling bias, uncertainties regarding angiosperm diversification patterns and confirm sympatric speciation as the dominant generator for the formation of extant species diversity in the Brazilian Atlantic Forest.

Tree Diversity and Dynamics of the Forest of Seu Nico, Viçosa, Minas Gerais, Brazil

Abstract Background To understand future changes in community composition due to global changes, the knowledge about forest community dynamics is of crucial importance. To improve our understanding about processes and patterns involved in maintaining species rich Neotropical ecosystems, we provide here a dataset from the one hectare Forest of Seu Nico (FSN) Dynamics Plot from Southeastern Brazil. New information We report diameter at breast height, basal area and height measurements of 2868 trees and treelets identified from two census spanning over a nine-year period. Furthermore, soil properties and understory light availability of all 100 10 x 10m subplots from the one hectare FSN Dynamics Plot during the second census are given.

Conserving relics from ancient underground worlds: assessing the influence of cave and landscape features on obligate iron cave dwellers from the Eastern Amazon

The degradation of subterranean habitats is believed to represent a serious threat for the conservation of obligate subterranean dwellers (troglobites), many of which are short-range endemics. However, while the factors influencing cave biodiversity remain largely unknown, the influence of the surrounding landscape and patterns of subterranean connectivity of terrestrial troglobitic communities have never been systematically assessed. Using spatial statistics to analyze the most comprehensive speleological database yet available for tropical caves, we first assess the influence of iron cave characteristics and the surrounding landscape on troglobitic communities from the Eastern Amazon. We then determine the spatial pattern of troglobitic community composition, species richness, phylogenetic diversity, and the occurrence of frequent troglobitic species, and finally quantify how different landscape features influence the connectivity between caves. Our results reveal the key importance of habitat amount, guano, water, lithology, geomorphology, and elevation in shaping iron cave troglobitic communities. While mining within 250 m from the caves influenced species composition, increasing agricultural land cover within 50 m from the caves reduced species richness and phylogenetic diversity. Troglobitic species composition, species richness, phylogenetic diversity, and the occurrence of frequent troglobites showed spatial autocorrelation for up to 40 km. Finally, our results suggest that the conservation of cave clusters should be prioritized, as geographic distance was the main factor determining connectivity between troglobitic communities. Overall, our work sheds important light onto one of the most overlooked terrestrial ecosystems, and highlights the need to shift conservation efforts from individual caves to subterranean habitats as a whole.

Early Acacia invasion in a sandy ecosystem enables shading mediated by soil, leaf nitrogen and facilitation

Australian species of the genus Acacia are amongst the most invasive trees. As nitrogen fixers, they are able to invade oligotrophic ecosystems and alter ecosystem functioning to their benefit. We aimed to answer three questions: How does early Acacia invasion influence nitrogen and light in a sandy savanna? How does early Acacia invasion impact biodiversity? Does early invasion alter ecosystem functioning towards the dominance of Acacia? We analyzed (using generalized linear mixed models and richness estimators) paired plots focused on plants of Acacia mangium (Fabaceae) and plants of Marcetia taxifolia (Melastomataceae) by taking hemispherical photos and sampling plants, leaves and soil for measurements of light, richness, leaf nitrogen, leaf δ15N, soil nitrogen and soil coarse sand. The results suggest that early Acacia invasion alters the control of soil and of leaf nitrogen and increases shading, enabling a much wider range of light variation. The δ15N results suggest that the nitrogen taken up by Acacia is transferred to neighboring plants and influences the light environment, suggesting facilitation. The enrichment of plant species observed during early Acacia invasion is consistent with the wider range of light variation, but the forecasted leaf nitrogen conditions during the established phase of Acacia invasion might cause loss of light-demanding species because of increased shading. If early Acacia invasion turns into an established phase with highly increased shading, Acacia seedlings might be favored and ecosystem functioning might change towards its dominance.