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Beyond species richness and community composition: Using plant functional diversity to measure restoration success in jarrah forest

Aim: The importance of restoring ecosystem functions to native systems that have been degraded, damaged or destroyed is increasingly recognised. Yet few studies have measured the effect of restoration efforts on ecosystem functioning or the functional diversity (FD) that underpins it. Here we assessed change in FD of restored assemblages one to 25 years after the onset of post-mine restoration. Location: Northern Jarrah (Eucalyptus marginata Donn ex Sm.) Forest bioregion of south-western Australia. Methods: Functional richness, evenness, divergence and dispersion were derived from five plant functional traits relevant to community reassembly. Effects of three explanatory variables (i.e., age, year restoration was initiated, and time since fire) on six response variables (i.e., four FD indices, species richness, and compositional similarity to nearby reference forest) were analysed using linear mixed models for a dataset with repeated measures of plots through time (n= 810 plots), and linear models for a sub-set of one-time measures of different aged assemblages (i.e., space-for-time approach; n= 490 plots). Results: Functional evenness and functional dispersion increased with age, while functional divergence and functional richness decreased with age. Functional dispersion increased with time since fire, while functional richness decreased with time since fire. Species richness decreased with age, but at 25-years, species richness was comparable to that observed in reference forest. In contrast, similarity showed no relationship with age of restored forest, and at 25-years, similarity of restored forest to reference was low compared with similarity of reference forest to itself. Three of four FD indices had not reached those of reference jarrah forest 25-years after restoration had been initiated. Conclusions: Reassembly of FD suggests importance of environmental filtering and high functional redundancy. A longer time frame may be needed to assess FD of restored assemblages, and in the meantime, species richness is not an adequate surrogate of FD.

Energy-water and seasonal variations in climate underlie the spatial distribution patterns of gymnosperms species richness in China

Studying the pattern of species richness is crucial in understanding the diversity and distribution of organisms in the earth. Climate and human influences are the major driving factors that directly influence the large-scale distributions of plant species, including gymnosperms. Understanding how gymnosperms respond to climate, topography, and human-induced changes is useful in predicting the impacts of global change. Here, we attempt to evaluate how climatic and human-induced processes could affect the spatial richness patterns of gymnosperms in China. Initially, we divided a map of the country into grid cells of 50 × 50 km2 spatial resolution and plotted the geographical coordinate distribution occurrence of 236 native gymnosperm taxa. The gymnosperm taxa were separated into three response variables: (i) all species, (ii) endemic species, and (iii) non-endemic species, based on their distribution. The species richness patterns of these response variables to four predictor sets were also evaluated: (i) energy-water, (ii) climatic seasonality, (iii) habitat heterogeneity, and (iv) human influences. We performed generalized linear models (GLMs) and variation partitioning analyses to determine the effect of predictors on spatial richness patterns. The results showed that the distribution pattern of species richness was highest in the southwestern mountainous area and Taiwan in China. We found a significant relationship between the predictor variable set and species richness pattern. Further, our findings provide evidence that climatic seasonality is the most important factor in explaining distinct fractions of variations in the species richness patterns of all studied response variables. Moreover, it was found that energy-water was the best predictor set to determine the richness pattern of all species and endemic species, while habitat-heterogeneity has a better influence on non-endemic species. Therefore, we conclude that with the current climate fluctuations as a result of climate change and increasing human activities, gymnosperms might face a high risk of extinction.

Environmental range per unit space determines a unimodal pattern of species richness along a heterogeneity gradient

Although many studies have focused on the effects of the environment and area on local patterns of species richness, few studies have demonstrated how to reconcile the availability of more niches with smaller habitat areas in heterogeneous localities. Here, the environmental range that a species prefers was defined as a niche; a space was defined as an available space if the environmental range of the space matches a niche; and the metric "environmental range per unit space (ERUS)" was presented to describe the heterogeneity of localities. Because the spaces with stressful environmental ranges, outside the niche, increased with increasing heterogeneity, available spaces did not continue to indefinitely increase, but the proportion of available spaces in spaces was low at high heterogeneous localities. Consequently, the probability of species occurring in their respective available spaces was unimodal. Due to the presence of large spaces in homogenous localities and more spaces in heterogeneous localities, the interval distances between nonadjacent spaces were large in these localities. Together, the changes in the number and proportion of available spaces and distance between spaces determined the unimodal probability of species dispersing into their respective available spaces. Thus, the probability of species coexisting was unimodal because it is important for coexisting species to grow in their respective available spaces. The probability of population extinction increased with increasing heterogeneity because the available spaces became narrower. In this way, the ERUS strongly influence species richness: a unimodal richness along the heterogeneity gradient occurred in suitable, suboptimal and stressful environments, and a unimodal algae richness occurred in a lake and river. These results challenge the viewpoint that richness increases with heterogeneity, providing information about the conservation of richness in very homogeneous and heterogeneous regions, and highlighting the importance of balancing the roles of environment and space in understanding and predicting richness.

Role of species richness and human-impacts in resisting invasive species in tropical forests

The biotic resistance hypothesis suggests that biodiversity rich areas should be resistant to biological invasions. Globally, conservationists use this hypothesis to protect diverse ecosystems. However, supporting data are often contradictory, possibly due to several confounding factors. Complexity in inferences increase in the tropics, which are sparsely studied. We hypothesize that human impacts, forest type and climate would modulate the relationship between native and invasive plant richness. To understand these interacting and varying effects of native richness and human disturbance on plant invasions, we sampled 354 grids of 25 km2 with equal representation of protected areas and multi-use areas to record abundance of native and non-native plants from 34 protected areas across five forest types in tropical India. We used linear mixed effect models to investigate occurrence and abundance of invasive plants with respect to varying native richness, human impacts, forest types and climate. Human use of forests increased richness and abundance of invasive plants across all forest types. After accounting for human-use, native species richness of tropical wet forests had a negative relationship with invasive plants richness and abundance, while the relationship reversed with increasing aridity and temperature. Human infrastructure facilitated invasions within protected areas. Synthesis. The biotic resistance hypothesis explained a lower number of invasions within protected tropical wet forests but not within dry forests. Human-free protected areas had lower richness and abundance of invasive plants across all systems, especially in wet tropical forests. Our results support the contextual importance of the biotic resistance hypothesis, while stressing the importance of protected areas, insulated from human impacts, to preserve the integrity of vulnerable natural systems.

The role of island physiography and oceanographic factors in shaping species richness and turnover of nesting seabird assemblages on islands across the southeastern Pacific

For seabirds, food supplies and nest sites are largely driven by oceanographic gradients and island habitats, respectively. Research into seabirds' ecological roles in insular ecosystems is crucial to understanding processes that structure seabird nesting assemblages. We examined the influence of island physiography and oceanographic factors on the spatial variation in α and β-diversity of nesting seabird assemblages. Location Southeastern Pacific Ocean. Taxon Birds Methods We compiled data from 53 seabirds breeding on 41 coastal and oceanic islands using different sources: our field records, online databases, environmental reports, and literature. We used generalized linear models (GLM) to describe the effect of island physiography (area, elevation, and isolation) and oceanographic factors (surface temperature, salinity, and primary productivity) on seabird species richness (α-diversity). We applied multivariate GLM to test the effects of physiographic and oceanographic predictors on species composition (β-diversity). We used Jaccard dissimilarities on species occurrences per island to calculate β-diversity partitioned into turnover and nestedness. Polynomial models allowed us to model these metrics against geographical and environmental gradients and so analyze patterns in seabird β-diversity across spatial scales. Results Species richness was highest in Galápagos, Pitcairn, and Rapa Nui. Changes in seabird α-diversity across islands were determined by island area and distance to South America but not by oceanographic variables. Physiographic and oceanographic factors were significant in determining β-diversity. Changes in β-diversity were mostly due to species replacement (β-turnover) across three major island Systems (Galápagos Archipelago, Chilean coastal islands, and oceanic islands of the southeastern Pacific). The contribution of β-nestedness was restricted to small scales (within archipelagos). Main conclusions Physiographic and oceanographic factors explain species diversity of seabird assemblages on islands of the southeastern Pacific. Oceanographic variables did not affect species richness but significantly influenced species composition. Change in species composition reflects gradients across three marine biogeographical realms: Temperate South, Eastern Indo-Pacific, and Tropical Eastern Pacific. The low degree of species nestedness may reflect multiple evolutionary origins.

Figure 4 in The Herpetofauna from Ilha Grande (Angra dos Reis, Rio de Janeiro, Brazil): updating species composition, richness, distribution and endemisms

Figure 4. Specimen of Corallus hortulanus (not collected) found in Vila do Aventureiro village, Ilha Grande (Photo by F.B.S. Telles).

Figure 3 in The Herpetofauna from Ilha Grande (Angra dos Reis, Rio de Janeiro, Brazil): updating species composition, richness, distribution and endemisms

Figure 3. New records of snakes for Ilha Grande. (A) Dipsas indica (Photo by D. Cunha-Passos); (B) Echinantera cephalostriata (Photo by P. Fatorelli).

Figure 1 in The Herpetofauna from Ilha Grande (Angra dos Reis, Rio de Janeiro, Brazil): updating species composition, richness, distribution and endemisms

Figure 1. Image of Ilha Grande with the localities where the species were recorded, and their respective density points of species. CAX = Caxadaço trail; CDM = Costão do Demo, RBEPS; EAD = Abraão-Dois Rios road; FPS = Forest of Praia do Sul; JAR = Jararaca trail, Dois Rios; LPM = Lopes Mendes; PAP = Pico do Papagaio; PRN = Parnaioca trail; RPS = Restinga of Praia do Sul; VAB = Vila do Abraão; VAV = Vila do Aventureiro; VDR = Vila Dois Rios.

Figure 2 in The Herpetofauna from Ilha Grande (Angra dos Reis, Rio de Janeiro, Brazil): updating species composition, richness, distribution and endemisms

Figure 2. New records of amphibians for Ilha Grande. (A) Ischnocnema bolbodactyla; (B) Leptodactylus latrans; (C) Leptodactylus flavopictus (Photos by F.B.S. Telles).

opencc-by-4.0Aug 2021View details →

Tree species richness differentially affects the chemical composition of leaves, roots and root exudates in four subtropical tree species - Sampling Raw Data

Sampling Raw Data for the manuscript "Tree species richness differentially affects the chemical composition of leaves, roots and root exudates in four subtropical tree species "  R Code for producing the sunburst plots from the data obtained by classyFire

opencc-by-4.0Aug 2021View details →

Reptiles of the Iron Quadrangle: a species richness survey in one of the most human exploited biodiversity hotspots of the world - species vouchers

The material present here is the supplementary Material of the paper: Reptiles of the Iron Quadrangle: a species richness survey in one of the most human exploited biodiversity hotspots of the world, published in Cuadernos de Herpetologia (2021).  *Abstract: Currently, more than 10,700 species of reptiles are known to occur worldwide, of these 842 occur in Brazil. The Iron Quadrangle (IQ) is an important region in southeastern Brazil, in the state of Minas Gerais, due to the intense iron mining activity, its rich and unique biodiversity. However, data available for the reptile fauna are scattered in the literature which make the diversity of this group in the IQ remains poorly known. Here we aimed to characterize the reptile fauna of the IQ, representing the first inventory for the area. We found 128 reptile species occurring in the IQ, which corresponds to 49.23% of the reptile fauna for the state of Minas Gerais, and 15.20% of the Brazilian reptile biodiversity. Among these, three species are included in at least one national or international red-list category, four have their type-locality inside the limits of the IQ, seven had not been previously documented for the area, and four have their range extensions to be included in the IQ.

Effects of released farmed mallards on species richness of breeding waterbirds and amphibians in natural, restored, and constructed wetlands

Common practices in current game management are wetland restoration and creation, as well as releases of quarry species. We studied the impact of releases of mallard ducklings on species richness of wild waterbirds and amphibians on three types of wetlands: natural, constructed and restored. Data on species richness, macrophyte cover and water characteristics (total phosphorous and pH) were collected at 32 sites in an agricultural landscape in southern Sweden. In total, 14 species of waterbirds were recorded, ranging from zero to seven per wetland and survey. Amphibians were present in 24 of the 32 wetlands; in total five species were found, ranging from zero to three per wetland. By using generalized linear modelling we found that wetland type best predicted waterbird species richness. Constructed wetlands had significantly more waterbird species, regardless of whether they were used for mallard releases or not. There were breeding amphibians in 62% of natural, 100% of restored and 77% of constructed wetlands. Breeding amphibians were present in 84% of wetlands without, and in 62% of wetlands with releases. However, included variables did not explain amphibian species richness in the wetlands. Releasing large numbers of mallards on a wetland and providing food ad libitum is likely to affect water quality, nutrient availability and predation pressure. Indeed, phosphorous levels were significantly higher in release wetlands, but no differences were found between wetland types.This means that mallard releases may increase nutrient loads in environments that are already eutrophied. However, in our study system releases did not influence species richness of waterbirds and amphibians locally. Constructing wetlands for mallard releases can thus have positive local effects on species richness.

opencc-zeroSep 2021View details →

Temporal stability in species richness but reordering in species abundances within avian assemblages of a Tropical Andes conservation hot spot

As the pace of environmental change increases, there is an urgent need for quantitative data revealing the temporal dynamics of local communities in tropical areas. Here we quantify the stability of avian assemblages in the highly threatened, but poorly studied, Andean biodiversity hot spot. We evaluated the temporal variation in species richness and community composition of local bird assemblages in three habitat types (native forest, introduced forest, native shrub) using a unique, relatively long-term data series from Cajas National Park and Mazán Reserve in the Southern Andes of Ecuador. We sampled birds with mist nets using a standardized protocol over 11 years, from 2006 to 2016. Species richness remained stable over time across habitats, but community composition changed in the native forest. In particular, we observed taxonomic reordering in the native forest, in which the evenness in the distribution of abundances of taxa decreased over time. This finding is consistent with other studies where species richness remained constant over time while community composition changed. Our study highlights the value of long-term studies in the tropical Andes as we show that species composition of birds in a montane forest is changing, consistent with global trends in biodiversity change.

opencc-zeroSep 2021View details →

Data from: Rapid post-fire re-assembly of species-rich bryophyte communities in Afroalpine heathlands

Questions: In some fire-prone ecosystems, bryophytes play a crucial role by providing the surface fuel that controls the fire-return interval. Afroalpine heathlands are such an ecosystem, yet almost nothing is known about the bryophytes in this system. We do not know the level of species richness, or if there is a successive accumulation of species over time, or if some species are adapted to specific phases along the successional gradient, for example early-successional species sensitive to competition. Location: Afroalpine heathlands in Ethiopia Methods: We made an inventory of all bryophytes in 48 plots of 5 x 5 m, distributed along a chronosequence from 1 to 25 years post-fire. The heathlands are located around 3500-3800 m asl, and are managed by traditional pasture burning with fire intervals of around 8-20 years. Results: We found in total 111 taxa of bryophytes. Post-fire mortality was almost 100%. The youngest plots had only a few cosmopolitan species often found after fire. Species richness increased monotonically and seemed to start levelling off at around 15 years after fire, when many plots had around 30 species and a high cover of Breutelia diffracta, which is a key ground-living species, important as surface fuel. Most species were found with sporophytes, a pattern even stronger for the most frequent species. Conclusions: Interestingly, bryophyte diversity is already remarkably high by only 15 years after total eradication. The relatively slow accumulation of species in the first years suggest that dispersal in space, and not time, is the major mechanism by which sites regain their diversity (i.e. spore banks play a small role). This indicates that the high species richness is built up through colonization from surrounding heathlands, and perhaps also from higher altitude alpine grasslands and lower altitude forests, and that the bryophyte diversity in this system is maintained by the traditional fire and grazing management.

opencc-by-4.0Nov 2022View details →

Urbanization decreases species richness, and increases abundance in dry climates whereas decreases in wet climates: A global meta-analysis

Soil invertebrates have an essential role in decomposition, nutrient turnover and soil structure formation, all of which are strongly threatened by urbanization. Sealing, compaction by trampling and pollution destroy and degrade city soils and potentially damage soil-living invertebrates. The existing literature on how urbanization affects soil invertebrates is inconsistent, presenting both negative and positive effects. Therefore, here we aimed to synthesize the effects of urbanization on soil invertebrates considering their taxonomic (Acari, Annelida, Carabidae, Collembola, Gastropoda, Isopoda, Myriapoda, Nematoda) and functional (soil living vs. soil-related; mobility) identities, as well as to examine how the overall effect is modulated by climatic conditions (total annual precipitation, annual mean ambient temperature), urban heat island effect (based on ambient temperature differences between urban and rural areas) and city population. In a systematic review using hierarchical and categorical meta-analyses, we extracted 158 effect sizes from 75 studies on abundance and 125 effect sizes from 84 studies on species richness. Invertebrate abundance showed an increase, whereas species richness significantly decreased with increasing urbanization. The reason behind this could be that a few generalist species can adapt well to the urban environment and achieve strongly elevated densities. The species richness of annelids, springtails, and snails decreased with advancing urbanization, most probably because these animals are sensitive to soil compaction and pollution, both of which are common consequences of urbanization. The temperature did not modify the effects of urbanization, but precipitation modified the effects on abundance. Abundance increased with advancing urbanization in drier climates, probably because irrigation increased soil moisture, whereas it decreased in wet climates, as urban areas were drier than their surroundings. Making future cities more climate-neutral could better sustain soil biodiversity.

opencc-zeroNov 2022View details →

Nutrient addition drives declines in grassland species richness primarily via enhanced species loss

Declines in grassland diversity in response to nutrient addition are a general consequence of global change. This decline in species richness may be driven by multiple underlying processes operating at different timescales. Nutrient addition can reduce diversity by enhancing the rate of local extinction via competitive exclusion, or by reducing the rate of colonization by constraining the pool of species able to colonize under new conditions. Partitioning net change into extinction and colonization rates will better delineate the long-term effect of global change in grasslands. We synthesized changes in richness in response to experimental fertilization with nitrogen, phosphorus, and potassium with micronutrients across 30 grasslands. We quantified changes in local richness, colonization, and extinction over 8-10 years of nutrient addition, and compared these rates against control conditions to isolate the effect of nutrient addition from background dynamics. Total richness at steady state in the control plots was the sum of equal, relatively high rates of local colonization and extinction. On aggregate, 30-35% of initial species were lost and the same proportion of new species was gained at least once over a decade. Absolute turnover increased with site-level richness but was proportionately greater at lower-richness sites relative to starting richness. Loss of total richness with nutrient addition, especially N in combination with P or K, was driven by enhanced rates of extinction with a smaller contribution from reduced colonization. Enhanced extinction and reduced colonization were disproportionately among native species, perennials, and forbs. Reduced colonization plateaued after the first few (< 5) years after nutrient addition, while enhanced extinction continued throughout the first decade. Synthesis: Our results indicate a high rate of colonizations and extinctions underlying the richness of ambient communities, and that nutrient enhancement drives overall declines in diversity primarily by the exclusion of previously established species. Moreover, enhanced extinction continues over long time scales, suggesting continuous, long-term community responses and a need for long-term study to fully realize the extinction impact of increased nutrients on grassland composition.

opencc-zeroNov 2022View details →

Productivity, niche availability, species richness and extinction risk: Untangling relationships using individual-based simulations

It has been widely hypothesised that the productivity of an ecosystem affects the number of species that it can support. Despite decades of study, the nature, extent, and underlying mechanisms of this relationship are unclear. One suggested mechanism is the "more individuals" hypothesis (MIH). This proposes that productivity controls the number of individuals in the ecosystem, and that more individuals can be divided into a greater number of species before their population size is sufficiently small for each to be at substantial risk of extinction. Here, we test this hypothesis using REvoSim: an individual-based eco-evolutionary system that simulates the evolution and speciation of populations over geological time, allowing phenomena occurring over timescales that cannot be easily observed in the real world to be evaluated. The individual-based nature of this system allows us to remove assumptions about the nature of speciation and extinction that previous models have had to make. Many of the predictions of the MIH are supported in our simulations: rare species are more likely to undergo extinction than common species, and species richness scales with productivity. However, we also find support for relationships that contradict the predictions of the strict MIH: species population size scales with productivity, and species extinction risk is better predicted by relative than absolute species size. Furthermore, we show that the scaling of species richness with productivity depends upon the ability of species to partition niche space. Consequently, we suggest that the MIH is applicable only to ecosystems where niches are not already saturated with species, and where partitioning is therefore still possible. Some hypotheses regarding patterns of biodiversity implicitly or explicitly overlook niche theory in favour of neutral explanations, as has historically been the case with the MIH. Our simulations demonstrate that niche theory exerts a control on the applicability of the MIH. --

opencc-zeroNov 2022View details →

Estimating total species richness: fitting rarefaction by asymptotic approximation

Estimating the number of species in a community is important for assessments of biodiversity. Previous species richness estimators are mainly based on non-parametric approaches. Although parametric asymptotic models have been applied, they received limited attention due to specific limitations. Here, we introduce parametric models fitting the probability-based rarefied species richness curve that allow us to estimate the 'Total Expected Species' (TES) in a community based on species' abundance data. We develop two approaches to calculate TES (termed 'TESa' and 'TESb'), based on two slightly different mathematical assumptions regarding Expected Species (ES) models. We provide R functions to calculate both these estimation approaches and their standard deviation. The function also enables users to visualize the estimation. We test the performance of TESa, TESb and their average (TESab) across simulated and empirical data, and compare their bias, precision and accuracy with other, commonly used, non-parametric species richness estimators; the bias-corrected (bc-)Chao1 and the Abundance-based Coverage Estimator (ACE). Simulation reveals that in small samples, TESa shows a tendency to over-estimate and TESb to under-estimate overall species richness. TESab performs well in bias, precision and accuracy when compared to (bc-)Chao1 and ACE estimators. Results from empirical data shows that the variance generated from TES estimates is comparable to that for (bc-)Chao1 and ACE. Our study demonstrates that rarefaction theory in combination with parametric approximation models provides a valuable new approach to estimate the species richness of incompletely sampled communities. <a name="_Hlk114347649"></a>Robust estimates are likely to be obtained where the observed number of species is greater than half of the TES estimation. When the ratio of TESa to the observed richness is >> 2, we suggest the use of TESb or TESab. Although more comprehensive comparisons with other estimators are suggested, we encourage researchers to consider the TES approach in their biodiversity studies as a complement to current existing estimators.

opencc-zeroDec 2022View details →

Data for: Contemporizing island biogeography theory with anthropogenic drivers of species richness

Aim: Island biogeography theory states that species richness increases with habitat diversity and decreases with isolation from source pools. However, ecological theory must incorporate effects of human activity to explain contemporary patterns of biodiversity. We contemporized island biogeography theory by conceptualizing island trajectories of how species richness changes over time with accelerating land development and economic trade, which increase extinction and immigration rates, respectively. With this contemporized theory, we then articulate and empirically assess expected relationships of native, introduced, and total species richness with natural and anthropogenic metrics of habitat diversity and isolation from source pools. Location: Greater Caribbean region. Time period: Database finalized in 2020. Methods: We built a database of 1075 native and introduced reptiles and amphibians (herps) for 840 Caribbean islands. For each island, we calculated natural and anthropogenic metrics of island habitat diversity and isolation from source pools and used linear model averaging to assess the expected relationships under the contemporized theory for 15 major herp clades. Results: Natural habitat diversity metrics exhibited positive relationships with native and introduced species richness, strengthening total species richness–area relationships across herp clades. Geographic isolation exhibited negative relationships with native and positive relationships with introduced species richness, weakening total species richness–isolation relationships. Economic area, based on developed land, and economic isolation, based on maritime trade, exhibited negative relationships with native species richness, but positive and negative relationships, respectively, with introduced species richness. Total species richness relationships with these two anthropogenic metrics were strongest in clades with many introduced species. Main conclusion: A contemporized island biogeographic theory that includes the effects of land development and economic trade on species extinction and immigration explained current Caribbean herp species richness patterns. As human activity continues to accelerate, the contemporized theory we articulate here will increasingly predict island biogeography of the Anthropocene.