Trait-based filtering from the regional species pool into local grassland communities

Aims For plants to establish in a local community from a pool of possible colonizers from the region, it must pass through a series of filters. Which of the filters is most important in this process has been much debated. In this study, we explored how species are filtered from the regional species pool into local communities. The aim was to determine if differences in species abundance and functional traits could explain which species from the regional species pool establish at the local scale and if the filtering differed between grassland communities.Methods This study took place in a cultivated landscape in southeastern Sweden. We estimated plant species abundance in 12 ex-arable field sites and 8 adjacent seminatural grassland sites and in a 100-m radius around the center of each site. We used Monte Carlo simulations to examine if species abundance and functional traits (height, seed mass, clonal abilities, specific leaf area and dispersal method) controlled the filtering of species from the regional pool into local communities.Important findings On average, only 28% of species found in the regional pool established in the ex-arable field sites and 45% in the seminatural grassland sites, indicating that the size of the regional species pool was not limiting local richness. For both grassland types, species abundance in the regional pool was positively correlated with species occurrence at the local scale. We found evidence for both species interaction filtering and dispersal limitation influencing the local assembly. Both local and regional processes were thus influencing the filtering of species from the regional species pool into local communities. In addition, the age of the communities influenced species filtering, indicating that community assembly and the importance of different filters in that process change over succession.     

局域和区域过程共同控制着群落的物种多样性:种库假说

解释群落的物种多样性大小是生态学研究的一个重要的理论和实践问题。人们提出了群落物种多样性的多种假说, Zobel等人提出的种库假说(species pool hypothesis)是生物多样性理论研究的重要发展。该假说认为, 一个群落的物种多样性不仅与环境条件和生态过程(ecological process)(如竞争、捕食)有关, 也受区域种库(regional species pool)的限制。区域种库是指一个地区可进入某一群落的潜在物种数量, 它由地史过程(如冰期、地质年代)和区域过程(物种形成、迁移扩散以及消亡)所决定。按照种库假说, 某一生境类型的面积越大, 地质年代越古老, 物种形成的机会也就越多, 因而能适应和分布于该生境的物种也就越多, 实际群落中的物种丰富度也就越高。种库在空间上主要有两个层次: 区域种库和实际种库, 前者指某一生境所拥有的潜在物种数量, 主要由生物地理过程(biogeographic processes)所决定; 后者则为调查的群落中实际出现的物种数量, 主要由竞争等生态过程和区域种库共同决定。本文对种库假说的基本概念、主要内容、种库确定方法等作了介绍, 并阐述了作者对这些问题的理解和认识。     

Phytophagous insect assemblages and the regional species pool: patterns and asymmetries

We describe three models predicting relationships between: (a) the taxonomic composition of the regional species pool of phytophagous insects and the composition of the phytophagous insect fauna on a host taxon; and (b) the faunal composition of two host taxa. The predictions of these models were compared with empirical data representing the regional pool of phytophages in Central Europe and the faunas of two plant taxa: the cabbage plants (Brassicaceae) and the thistles (Asteraceae: Cardueae). Three important findings emerge at a general level. (1) Different taxonomic levels of insects (orders, families, genera) of the regional pool and on the investigated host taxa are well correlated in terms of species richness, but there is no consistent trend in the variance explained by this correlation across taxonomic levels. (2) The model considering evolutionary interactions and speciation processes is consistent with patterns found in the empirical data. (3) Asymmetries in sampled species numbers of insect families on both host taxa may be accounted for by reference to the biology of these insects. We conclude that the faunas of single host taxa can provide the basis for extrapolating to the regional pool, at least at high taxonomic levels.     

Effects of fishing and regional species pool on the functional diversity of fish communities

The potential population and community level impacts of fishing have received considerable attention, but little is known about how fishing influences communities' functional diversity at regional scales. We examined how estimates of functional diversity differed among 25 regions of variable richness and investigated the functional consequences of removing species targeted by commercial fisheries. Our study shows that fishing leads to substantial losses in functional diversity. The magnitude of such loss was, however, reduced in the more speciose regions. Moreover, the removal of commercially targeted species caused a much larger reduction in functional diversity than expected by random species deletions, which was a consequence of the selective nature of fishing for particular species traits. Results suggest that functional redundancy is spatially variable, that richer biotas provide some degree of insurance against the impact of fishing on communities' functional diversity and that fishing predominantly selects for particular species traits. Understanding how fishing impacts community functional diversity is key to predict its effects for biodiversity as well as ecosystem functioning.     

Predicting distributions of species richness and species size in regional floras: Applying the species pool hypothesis to the habitat templet model

The species pool hypothesis is applied here to the interpretation of ‘hump-shaped’ (unimodal) species richness patterns along gradients of both habitat fertility and disturbance level (the habitat templet). A ‘left-wall’ effect analogous to that proposed for the evolution of organismal complexity predicts a right-skewed unimodal distribution of historical habitat commonness on both gradients. According to the species pool hypothesis, therefore, the distribution of opportunity for net species accumulation (speciation minus extinction) should also have a corresponding unimodal central tendency on both habitat gradients. Two assumptions of this hypothesis are illustrated with particular reference to highly fertile, relatively undisturbed habitats: (i) such habitats have been relatively uncommon in space and time, thus providing relatively little historical opportunity for the origination of species with the traits necessary for effective competitive ability under these habitat conditions; and (ii) species that have evolved adaptation to these habitats are relatively large, thus imposing fundamental ‘packing’ limitations on the number of species that can ‘fit’ within such habitats. Based on these assumptions, the species pool hypothesis defines two associated predictions that are both supported by available data: (a) resident species richness will be relatively low in highly fertile, relatively undisturbed contemporary habitats; and (b) species sizes within regional floras should display as a right-skewed unimodal (log-normal) distribution. The latter is supported here by an analysis of data for 2,715 species in the vascular flora of northeastern North America.     

Ecosystem consequences of fish parasites*

In most aquatic ecosystems, fishes are hosts to parasites and, sometimes, these parasites can affect fish biology. Some of the most dramatic cases occur when fishes are intermediate hosts for larval parasites. For example, fishes in southern California estuaries are host to many parasites. The most common of these parasites, Euhaplorchis californiensis, infects the brain of the killifish Fundulus parvipinnis and alters its behaviour, making the fish 10–30 times more susceptible to predation by the birds that serve as its definitive host. Parasites like E. californiensis are embedded in food webs because they require trophic transmission. In the Carpinteria Salt Marsh estuarine food web, parasites dominate the links and comprise substantial amount of biomass. Adding parasites to food webs alters important network statistics such as connectance and nestedness. Furthermore, some free‐living stages of parasites are food items for free‐living species. For instance, fishes feed on trematode cercariae. Being embedded in food webs makes parasites sensitive to changes in the environment. In particular, fishing and environmental disturbance, by reducing fish populations, may reduce parasite populations. Indirect evidence suggests a decrease in parasites in commercially fished species over the past three decades. In addition, environmental degradation can affect fish parasites. For these reasons, parasites in fishes may serve as indicators of environmental impacts.     

Introducing the biogeographic species pool

The species pool concept has played a central role in the development of ecological theory for at least 60 yr. Surprisingly, there is little consensus as to how one should define the species pool, and consequently, no systematic approach exists. Because the definition of the species pool is essential to infer the processes that shape ecological communities, there is a strong incentive to develop an ecologically realistic definition of the species pool based on repeatable and transparent analytical approaches. Recently, several methodological tools have become available to summarize repeated patterns in the geographic distribution of species, phylogenetic clades and taxonomically broad lineages. Here, we present three analytical approaches that can be used to define what we term ‘the biogeographic species pool’: distance‐based clustering analysis, network modularity analysis, and assemblage dispersion fields. The biogeographic species pool defines the pool of potential community members in a broad sense and represents a first step towards a standardized definition of the species pool for the purpose of comparative ecological, evolutionary and biogeographic studies.     

How to determine a regional species pool: a study in two Swedish regions

The species pool hypothesis has been proposed as one of the possible explanations for the local species richness of plant communities. For testing and validating this theory, it is of crucial importance to determine the dimension of the regional pool, which is the reservoir of species that are potentially able to exist in a community. The main purpose of this study was to develop and test different methods for the determination of the regional species pool. Two regions in Sweden served as study areas, Öland and Uppland. In both regions, three different vegetation types were treated: dry calcareous grasslands, coastal meadows and deciduous forests. For the determination of the regional pool two main groups of methods are proposed: 1) six ecological approaches, based on Ellenberg species indicator values, and 2) two phytosociological approaches, based on the occurrence of species in different syntaxa in the framework of the Braun-Blanquet system. The different screening methods were tested using Sørensen's index expressing the similarity between the community species pool and the regional species pool. Two types of error were recognized which may result in low index values. For the six ecological methods Sørensen's index values were below 50%. The methods differed considerably from each other in accuracy, due to large differences in errors of both types. The phytosociological methods resulted in higher similarity values of up to almost 70%. The two approaches differed in error type but gave similar results.     

Importance of functional traits and regional species pool in predicting long-distance dispersal in savanna ecosystems

Long-distance dispersal (LDD) of plants is difficult to measure but disproportionately important for various ecological and evolutionary processes. Dispersal of seeds of gallery-forest trees in savanna provides an opportunity for the study of colonisation processes and species coexistence driven by LDD. Investigations were carried out on 91 isolated trees along four gallery forests sampled in the Biosphere Reserve of Pendjari, Benin. The abundance of adult trees within nearest gallery forest was combined with functional traits (species maximum height, seed weight, morphological adaptation for dispersal by wind, water, birds and mammals) to explain the floristic composition of forest seedlings and saplings under isolated trees and in savanna. Stepwise negative binomial regression was used to identify the most significant variables explaining abundance of seedlings and saplings beneath isolated trees and in savanna and then derive colonisation from seedlings and persistence from saplings. The maximum height of species and seed weight explained the highest proportion of variance in species colonisation. Morphological dispersal syndromes by wind and birds had poor explanatory importance. Species rare in gallery forest had higher potential to colonise new environments through LDD whilst abundant species had higher persistence abilities. Contrary to the predictions of the seedling-size effect, small-seeded species dominated the sapling stage. The findings revealed the strong dependence of LDD and subsequent colonisation and persistence processes on species traits specialised for a variety of dispersal vectors. They also suggest that LDD towards isolated trees established far away from gallery forest can be difficult.     

Ecosystem consequences of herbicides: the role of microbiome

Non-target organisms are globally exposed to herbicides. While many herbicides – for example, glyphosate – were initially considered safe, increasing evidence demonstrates that they have profound effects on ecosystem functions via altered microbial communities. We provide a comprehensive framework on how herbicide residues may modulate ecosystem-level outcomes via alteration of microbiomes. The changes in soil microbiome are likely to influence key nutrient cycling and plant–soil processes. Herbicide-altered microbiome affects plant and animal performance and can influence trophic interactions such as herbivory and pollination. These changes are expected to lead to ecosystem and even evolutionary consequences for both microbes and hosts. Tackling the threats caused by agrochemicals to ecosystem functions and services requires tools and solutions based on a comprehensive understanding of microbe-mediated risks.     

Global and regional importance of the tropical peatland carbon pool

Accurate inventory of tropical peatland is important in order to (a) determine the magnitude of the carbon pool; (b) estimate the scale of transfers of peat‐derived greenhouse gases to the atmosphere resulting from land use change; and (c) support carbon emissions reduction policies. We review available information on tropical peatland area and thickness and calculate peat volume and carbon content in order to determine their best estimates and ranges of variation. Our best estimate of tropical peatland area is 441 025 km² (～11% of global peatland area) of which 247 778 km² (56%) is in Southeast Asia. We estimate the volume of tropical peat to be 1758 Gm³ (～18–25% of global peat volume) with 1359 Gm³ in Southeast Asia (77% of all tropical peat). This new assessment reveals a larger tropical peatland carbon pool than previous estimates, with a best estimate of 88.6 Gt (range 81.7–91.9 Gt) equal to 15–19% of the global peat carbon pool. Of this, 68.5 Gt (77%) is in Southeast Asia, equal to 11–14% of global peat carbon. A single country, Indonesia, has the largest share of tropical peat carbon (57.4 Gt, 65%), followed by Malaysia (9.1 Gt, 10%). These data are used to provide revised estimates for Indonesian and Malaysian forest soil carbon pools of 77 and 15 Gt, respectively, and total forest carbon pools (biomass plus soil) of 97 and 19 Gt. Peat carbon contributes 60% to the total forest soil carbon pool in Malaysia and 74% in Indonesia. These results emphasize the prominent global and regional roles played by the tropical peat carbon pool and the importance of including this pool in national and regional assessments of terrestrial carbon stocks and the prediction of peat‐derived greenhouse gas emissions.     

Correlation between richness per unit area and the species pool cannot be used to demonstrate the species pool effect

Abstract. Significant correlation between the size of the species pool and richness per unit area is usually taken as a demonstration of the effect of the species pool on the species richness per unit area. This is not logically necessary. It has to be emphasized that such a correlation cannot be interpreted as a demonstration of the effect of species pool on the species richness per unit area. More generally, correlation cannot be used to demonstrate a one‐directional effect of one variable upon another, since several types of (functional) relationships could produce correlations between such variables; the same caution has to be taken when analysing the species pool vs. richness per unit area correlation. In this paper, a simple Monte Carlo simulation model is used to demonstrate that (1) statistical processes acting only at the local scale (such as competitive exclusion) can generate exactly the same correlation that has been used to infer the effect of the species pool on richness per unit area; (2) this correlation would be deemed significant even if the mathematical dependency between species pool and richness per unit area is taken into account; and (3) the strength of this relation depends on beta diversity within the contiguous area used to determine the species pool.     

Mathematical consequences of the genealogical species concept

A genealogical species is defined as a basal group of organisms whose members are all more closely related to each other than they are to any organisms outside the group ("exclusivity"), and which contains no exclusive group within it. In practice, a pair of species is so defined when phylogenies of alleles from a sample of loci shows them to be reciprocally monophyletic at all or some specified fraction of the loci. We investigate the length of time it takes to attain this status when an ancestral population divides into two descendant populations of equal size with no gene exchange, and when genetic drift and mutation are the only evolutionary forces operating. The number of loci used has a substantial effect on the probability of observing reciprocal monophyly at different times after population separation, with very long times needed to observe complete reciprocal monophyly for a large number of loci. In contrast, the number of alleles sampled per locus has a relatively small effect on the probability of reciprocal monophyly. Because a single mitochondrial or chloroplast locus becomes reciprocally monophyletic much faster than does a single nuclear locus, it is not advisable to use mitochondrial and chloroplast DNA to recognize genealogical species for long periods after population divergence. Using a weaker criterion of assigning genealogical species status when more than 50% of sampled nuclear loci show reciprocal monophyly, genealogical species status depends much less on the number of sampled loci, and is attained at roughly 4-7 N generations after populations are isolated, where N is the historically effective population size of each descendant. If genealogical species status is defined as more than 95% of sampled nuclear loci showing reciprocal monophyly, this status is attained after roughly 9-12 N generations.     

Mutational consequences of dNTP pool imbalances in E. coli

The accuracy of DNA synthesis depends on the accuracy of the polymerase as well as the quality and concentration(s) of the available 5′-deoxynucleoside-triphosphate DNA precursors (dNTPs). The relationships between dNTPs and error rates have been studied in vitro, but only limited insights exist into these correlations during in vivo replication. We have investigated this issue in the bacterium Escherichia coli by analyzing the mutational properties of dcd and ndk strains. These strains, defective in dCTP deaminase and nucleoside diphosphate kinase, respectively, are characterized by both disturbances of dNTP pools and a mutator phenotype. ndk strains have been studied before, but were included in this study, as controversies exist regarding the source of its mutator phenotype. We show that dcd strains suffer from increased intracellular levels of dCTP (4-fold) and reduced levels of dGTP (2-fold), while displaying, as measured using a set of lacZ reversion markers in a mismatch-repair defective (mutL) background, a strong mutator effect for G·C→T·A and A·T→T·A transversions (27- and 42-fold enhancement, respectively). In contrast, ndk strains possess a lowered dATP level (4-fold) and modestly enhanced dCTP level (2-fold), while its mutator effect is specific for just the A·T→T·A transversions. The two strains also display differential mutability for rifampicin-resistant mutants. Overall, our analysis reveals for both strains a satisfactory correlation between dNTP pool alterations and the replication error rates, and also suggests that a minimal explanation for the ndk mutator does not require assumptions beyond the predicted effect of the dNTP pools.     

Parasites and the regional distribution of bumblebee species

Parasites and regional processes may be important to structure local species assemblages In particular, it has been hypothesized that widely distributed and abundant species should harbour more parasite species which could give them a competitive advantage in local species assemblages Empirical evidence bearing on these points are scarce and mainly restricted to vertebrate hosts or plants The aim of this study was to provide data in insect hosts and to test whether the patterns in field populations conform with those correlates expected from the parasite-host distribution hypothesis We investigated species assemblages of bumblebees at 12 different sites in a mesoscale region with their parasites over two consecutive years Parasites included dipteran and hymenopteran parasitoids. nematodes, mites, and protozoa The mean number of parasite species per host species ranged from 1 to 8 To account for sampling effort, all data were corrected for sample size effects The number of parasite species per average host individual (parasite load) ranged from 0 09 to 0 75 In cross-species comparisons, the number of parasite species per host species was positively correlated with regional distribution, i e the number of sites a host species occupied m the region, and with the average local host abundance The same relationships were found for parasite load In addition, parasite load correlated positively with average colony size of the host species, but not with body size of the individuals Bumblebee species were bimodally distributed When separated into widely-distributed and locally-occurring species, common hosts harboured more parasite species than rare ones Moreover, workers of common species individually had higher parasite loads From these results, we conclude that some of the necessary preconditions for parasites being able to affect the distribution and occurrence of their hosts are met in bumblebees The findings support a general pattern that parasite loads correlate positively with local abundance and geographical distribution of their hosts, also on mesoscales usually considered in ecological studies     

The species pool hypothesis: the necessity to shift emphasis

The species pool of a biological community is determined as a group of species that inhabit some area and potentially can be included in a given community. The species pool hypothesis, i.e. the assumption that the size of species pool strongly influences species richness of local community can be confirmed if there is positive linear relationship between these two variables. The results of hypothesis testing however are not obvious. For example, correlation between local richness and species pool size can be caused by their dependence on the third variable--capacity of environment. It seems that in case of decreasing area occupied by local community the environmental conditions become more important than species pool size. If that is true, the influence of species pool on local species richness is not significant. However one can estimate the degree of unsaturation of species pool on the basis of relationships between the number of species in small locations occupied by similar local communities and their species pool. We think, that study of local and regional species richness should shift the emphasis--from the analysis of species pool influence on local community richness to the estimation of historical, ecological and anthropogenic factors in variation of species pool size. The local species richness should be considered rather as a tool (allowing to compare the species capacity of biological communities), than as an object of such study.     

The importance of species pool size for community composition

We investigated if an increase in species pool size leads to more pronounced turnover in local communities and assessed if this increase relates to stronger competition for environmental niches or to more random placement of species. We compared compositional turnover of pteridophytes (ferns and lycophytes) at 15 sites in mountain ecosystems on 13 islands in southeast Asia and Melanesia that mainly differed in the size of their species pool. Each site was sampled with 16 plots of 20 × 20 m². Using multiple regression on distance matrices, we investigated the relationship between environmental distance and compositional turnover at different spatial extents within sites with different species pool sizes. Additionally, we tested the hypothesis that the intensity of competition increases with increasing species pool size. This was done by assessing how realized niche overlap and unevenness of communities relate to environmental distance and species pool size. With increasing species pool size, there was an increase in: a) proportional turnover in community composition, b) the importance of environmental distance for explaining turnover in community composition and c) a decrease in environmental niche overlap between species indicating an increasing importance of competition for community composition. Our results support the idea that increasing species pool size increases the competition for available environmental niches, and thereby leads to a tighter connection between environmental factors and community composition.