Evidence for community assembly constraints during succession in dune slack plant communities

Community assembly during succession can be constrained by both local and regional factors. Despite an increasing regional species pool size during succession, we found a limit on the number of species in 1 × 1 m plots in dune slacks. Three alternative hypotheses (habitat heterogeneity, dispersal limitation and niche limitation) explaining this community saturation were tested. A null model analysis showed that species richness in the plots had an unusually low variance suggesting that beta habitat diversity was not likely to explain the limitation on species richness. Because we did not find a correlation between the distribution of species over the slack and their dispersal capacity, we also excluded the dispersal limitation hypothesis. Finally, a guild proportionality analysis revealed that the abundances of forb, graminoid and ruderal species showed low an unusually low variance over all age classes involved. This provides evidence for nonrandom community assembly during succession, likely to be determined by competitive exclusion among species of the same guild.     

Riverscape-level patterns of riparian plant diversity along a successional gradient, Willamette river, Oregon

Riparian forest communities dominated by Populus balsamifera ssp. trichocarpa L. (Torr. and Gray ex Hook.) Brayshaw are important contributors to biodiversity in terrestrial and aquatic ecosystems of the Western United States. Species composition along a successional gradient from stand initiation to late-succession of P. balsamifera-dominated riparian forests was investigated along 145 km of the Willamette River, Oregon. There were 151 total species encountered across 28 stands and a mean species richness of 33.3 species per stand. Young stands were dominated by P. balsamifera and Salix tree spp. and opportunistic herbaceous species. Understory trees, shrubs, and herbaceous species as well as late-successional tree species established 12–15 years after stand initiation. Fraxinus latifolia Benth. was the dominant late-successional tree species. Vertical structural diversity, P. balsamifera mean diameter at breast height, large tree biomass, and stand age were strongly correlated with understory species presence and abundance based on non-metric multidimensional scaling (NMS) ordination. There were no young stands on mid and high terraces and this was reflected in geomorphic position being strongly correlated with the stand age gradient. Abundance of Phalaris arundinacea L. an invasive grass species, was also significantly correlated with plant species composition and abundance. This study indicates that Willamette River riparian forests are diverse and therefore important to the biodiversity of the Willamette River valley and that their presence as a mosaic of communities of different successional stages may be threatened by human interventions, including influences exerted by introduced plant species.     

Predation leads to assembly rules in fragmented fish communities

Diamond [Assembly of species communities. In: Ecology and Evolution of Communities (eds Cody, M.L. & Diamond, J.M.). Harvard University Press, Cambridge, pp. 342–444] proposed that resource competition leads to checkerboard-like distributions of competing species. This proposal prompted research that revealed checkerboard patterns within a wide range of communities, but the mechanisms that generate such patterns are still poorly understood. Here we present whole-lake natural experiments and analyses of species–environment relationships in small coastal lake fish communities that were fragmented when land uplift isolated these lakes from the Baltic Sea, showing that a combination of predation and habitat suitability generated checkerboard distributions. Checkerboard patterns developed because two piscivores, northern pike and Eurasian perch, caused the extinction of several prey species in deep lakes. Conversely, low oxygen levels in shallow lakes caused extinction of the piscivores, and these areas served as a refuge for tolerant prey species. Based on these findings, we suggest that habitat suitability and biotic interactions should be viewed simultaneously in null models of assembly rules.     

Resource heterogeneity and community structure: A case study inHeliconia imbricata Phytotelmata

Summary Complex or non-additive differences in the distribution and abundance of arthropod species inhabiting the water-filled bracts ofHeliconia imbricata can be created by simple manipulations of resource levels. The primary resources for these assemblages are the corollas of the flowers that accumulate in the bracts. Removing or adding corollas to individual bracts changes the pattern in the abundance of arthropod species within each bract such that bracts with different treatments ultimately differ in composition and numerical associations among species. These results suggest that direct and indirect resource-mediated factors can structure or significantly affect the distribution and abundance of species in these and perhaps other assemblages. Thus, in natural communities, if resources are heterogeneous among patches (such as among the bracts in this study) structure in a given patch may be a function of the resource level of that patch and can differ significantly from neighboring patches that provide different resource levels.     

Community structure and assembly rules in a dune slack: Variance in richness,guild proportionality,biomass constancy and dominance/diversity relations

There is still disagreement as to whether plant communities can be described as conforming to certain assembly rules. We searched for such rules in the vegetation of four dune slacks in west Wales by examining variance in richness, guild proportionality, biomass constancy and dominance/diversity relations. To test for the occurrence of niche limitation, variance in quadrat species-richness was compared to null models of species occurrence. Using an Overall-model, one site showed a deficit of variance, but this disappeared when a Patch-model analysis was used. It therefore seems likely that the effect observed was due to equality in the species pools adapted to different microenvironments. The proportional representation of functional guilds was examined, in guilds based on morphology and life history. Significant constancy of guild proportions was seen for the annual guild in the only site in which it occurred, perhaps reflecting a regeneration niche. Total biomass per quadrat was examined, and compared to a model in which the biomass of each species was determined at random from the biomasses of that species at the site. Surprisingly, the observed biomasses showed no departure from the null model. However, there was considerable discrepancy from an alternative null model in which biomasses were allocated at random irrespective of species. This would imply that competition limits species coexistence, rather than performance. Examination of the proportions of species from different potential-size classes in each quadrat gave limited confirmation. The local abundance of species (mean biomass) was significantly correlated with the frequency of the species within a site, parallelling the geographical-range/local-abundance correlation previously reported. Five dominance/diversity models were fitted to the biomass data. The best fits were given by the Geometric or the General Lognormal models, though which fitted best varied between and within sites. Between sites, there was some indication of a consistent difference in Preston's gamma. Most of the results are compatible with Gleason's Individualistic concept of the plant community, though there are several pointers that assembly rules have some impact on community structure.     

Phylogenetic diversity and community assembly in a naturally fragmented system

We sought to assess effects of fragmentation and quantify the contribution of ecological processes to community assembly by measuring species richness, phylogenetic, and phenotypic diversity of species found in local and regional plant communities. Specifically, our fragmented system is Craters of the Moon National Monument and Preserve, Idaho, USA. CRMO is characterized by vegetated islands, kipukas, that are isolated in a matrix of lava. We used floristic surveys of vascular plants in 19 kipukas to create a local species list to compare traditional dispersion metrics, mean pairwise distance, and mean nearest taxon distance (MPD and MNTD), to a regional species list with phenotypic and phylogenetic data. We combined phylogenetic and functional trait data in a novel machine‐learning model selection approach, Community Assembly Model Inference (CAMI), to infer probability associated with different models of community assembly given the data. Finally, we used linear regression to explore whether the geography of kipukas explained estimated support for community assembly models. Using traditional metrics of MPD and MNTD neutral processes received the most support when comparing kipuka species to regional species. Individually no kipukas showed significant support for overdispersion. Rather, five kipukas showed significant support for phylogenetic clustering using MPD and two kipukas using MNTD. Using CAMI, we inferred neutral and filtering models structured the kipuka plant community for our trait of interest. Finally, we found as species richness in kipukas increases, model support for competition decreases and lower elevation kipukas show more support for habitat filtering models. While traditional phylogenetic community approaches suggest neutral assembly dynamics, recently developed approaches utilizing machine learning and model choice revealed joint influences of assembly processes to form the kipuka plant communities. Understanding ecological processes at play in naturally fragmented systems will aid in guiding our understanding of how fragmentation impacts future changes in landscapes.     

Heterologous expression and in vitro assembly of the transmembrane cytochrome b6

Folding and assembly studies with alpha-helical membrane proteins are often hampered by the absence of high-level expression systems as well as by missing suitable in vitro refolding procedures. Experimental constraints and requirements for heterologous expression and in vitro assembly of cytochrome b6 have been examined and conditions for in vitro reconstitutions of the protein have been optimized. Cytochrome b6 can serve as an excellent model system for in vitro studies on the dynamic interplay of an apo-protein and heme cofactors during assembly of a transmembrane b-type cytochrome. In vitro assembled cytochrome b6 binds two hemes with different midpoint potentials and both ferri as well as ferro heme bind to the apo-cytochrome. However, the ferro cytochrome appears to be less stable than the ferri form.     

The influence of crop rotation and soil fumigation on a mycorrhizal fungal community associated with soybean

Population densities of mycorrhizal fungal propagules in a western Kentucky field highly productive for soybean were measured by bioassay throughout a soybean production season. The primary experimental variables were crop rotation (soybeans in 1985, then 2 years in corn, milo, fescue, or soybean, then soybean in 1988 on all plots when populations of propagules were determined) and soil fumigation with 67% methyl bromide/33% chloropicrin. Of the 20 species in three genera found, Glomus predominated both in terms of number of species and population densities. Most species of Glomus occurred at higher population densities in rotated plots than in continuous soybean plots. In continuous soybean plots, species of Gigaspora made up a much higher proportion of the mycorrhizal fungal community than in rotated crops. Species richness and diversity were lower, and dominance and equitability higher, in nonfumigated continuous soybean plots than in rotated plots early in the season, but the differences were not present at the end of the season. Soil fumigation killed most propagules in the upper 15 cm of soil, but after production of a crop of soybeans, populations of total propagules and most Glomus spp. recovered to prefumigation densities. However, Gigaspora margarita and Gigaspora gigantea did not recover similarly. Fumigation reduced species richness and diversity and increased dominance, but the effects were ameliorated by the end of the season. Colonization of roots was low during vegetative growth but increased rapidly after the onset of soybean reproduction. There was no evidence for mutualism during the early half of the season, perhaps due to high soil P and low dependency of soybean. Fumigation increased soybean yields. A stable mycorrhizal fungal community appeared to become established with continuous soybean production, and both crop rotation and soil fumigation disrupted the community.     

Patterns in the assembly of an island plant community

Aim  To test for patterns in the assembly of an island plant community.
Location  Islands off the west coast of Vancouver Island, British Columbia, Canada.
Methods  Twenty-seven islands were visited by boat, and the abundance of six woody angiosperm species was quantified. Null models were then used to test whether: (1) some species co-occur less than expected by chance (i.e. co-occurrence assembly rule), (2) the incidence and abundance of some species are inversely related to the abundance of other species (i.e. incidence assembly rule), and (3) support for assembly rules precludes evidence for nestedness, which refers to a pattern in species composition in which the species present on depauperate islands form regular subsets of those occurring on progressively more diverse islands.
Results  Most species co-occurred with other species at frequencies expected by chance. However, one species ( Sambucus racemosa ) co-occurred with other species less frequently than randomized expectations. The observed incidence and abundance patterns of most species were also consistent with randomized patterns. However, the incidence and abundance of S. racemosa declined with the abundance of other plant species. Weak, variable support was found for nestedness of the total plant community. However, stronger, consistent support was found after removing S. racemosa from the matrix prior to analyses.
Main conclusions  Most species were assembled on islands in a manner consistent with randomized expectations. However, non-random distributional patterns were observed in one species whose distribution was consistent with the hypothesis that competition limits the assembly of island communities.     

Robust hypothesis tests for independence in community assembly

The extent to which competition affects the distributions of species at large spatial scales is unclear. To evaluate this question, hypothesis tests that do not depend on parametric assumptions are needed. Here, we develop a broadly applicable test that requires only one parametric assumption. Letting i and j denote the ith and jth colonists to arrive at a site, respectively, and [i j] the event that i and j belong to the same "unit" (e.g., functional group, genus), we show how colonists will be partitioned into units if for all i and j, [i j] is independent of whether i and j share unit membership with the other colonists, conditional on other information about shared units. Our distribution of partitions is useful for inferring competitive effects, because these effects predict that for at least one i and j, P ([i j]) will be less when i and j share unit membership than when they do not.     

华北地区胡桃楸林分布规律及群落构建机制分析

探究植物分布规律和群落构建机制是揭示植物群落空间分布、群落物种多样性的形成、发展及其影响因素的重要途径。该文以华北地区胡桃楸(Juglans mandshurica)林为研究对象, 基于野外84个样方的调查数据, 通过径级分析、典范对应分析等方法研究了胡桃楸林的空间分布规律, 并通过亲缘关系指数计算、植物功能性状等方法研究了胡桃楸林的物种共存机制。结果表明, 华北地区胡桃楸的胸径相对较小(平均5.36 cm), 种群年龄较低; 海拔、坡度、坡位和人为干扰程度是影响华北地区胡桃楸分布的主要因子。研究区域内的胡桃楸大部分生长于山体中下部海拔较低的缓坡, 且人为干扰相对较少的区域, 各分布区域中胡桃楸林的分布规律各异。胡桃楸林物种的构建由生态位机制主导, 其中河北、陕西、天津的胡桃楸林物种共存过程主要受负密度制约的影响, 北京、山西的胡桃楸林的物种共存过程主要受环境选择驱动。     

Traits reveal ecological strategies driving carrion insect community assembly

1. The succession of carrion-associated (necrophilous) insects on decomposing carrion is well documented. To exploit the changing nutritious and dynamic resources available throughout the carrion decomposition process, different species colonise and consume carrion in a predictable temporal sequence. The traits of these necrophilous insects should reflect their ecological strategies. Morphological traits of these insects, such as body size and wing size, however, have not previously been examined during active and advanced decomposition. 2. We used fourth-corner multivariate generalised linear models to identify insect community morphological trait patterns and to quantify their change through time on decomposing rabbit carcasses in grassland and woodland environments. 3. We found that larger-bodied species of flies and carrion-specialist beetles were associated with the early stages of decomposition. The morphological traits of ants, in contrast, showed no changes at carcasses through time and instead showed body size differences between grassland and woodland environments. 4. Our findings indicate that specialist flies and beetles that arrive early in the decomposition process possess traits that enable rapid discovery of carrion at a large scale. Generalist beetles and ants do not share this same trait and are instead adapted to locate and consume a wider variety of resources in their preferred habitat type at their local scale. 5. Our results provide insights into the morphological adaptations linked to the ecological strategies of distinct components of carrion insect communities. Further, our results offer insights into the community assembly dynamics that structure the communities of necrophilous insect species.     

A modified T-vector for simplified assembly of hairpin RNAi constructs

We describe a modified T-vector, pGFPm-T, for direct cloning of RT-PCR products to generate bidirectional restriction fragments for assembly of hairpin-containing RNAi vectors in the popular pFGC and pGSA binary vector backbone. Green fluorescence protein (GFP) is used as a visual reporter for direct selection of recombinants under UV illumination. The simplified cloning process enables a seamless workflow from candidate gene selection and RT-PCR verification to inverted repeat cloning, using a single pair of gene-specific primers.     

Fungal community assembly in soils and roots under plant invasion and nitrogen deposition

Fungal community composition in the Anthropocene is driven by rapid changes in environmental conditions caused by human activities. This study examines the relative importance of two global change drivers – atmospheric nitrogen (N) deposition and annual grass invasion – on structuring fungal communities in a California chaparral ecosystem, with emphasis on arbuscular mycorrhizal fungi. We used molecular markers, functional groupings, generalized linear statistics and joint distribution modeling, to examine how environmental variables structure taxonomic and functional composition of fungal communities. Invasive grasses had a lower richness and relative abundance of symbiotic fungi (both AMF and other fungi) compared to native shrubs. We found a higher richness and abundance of rhizophilic (e.g. Glomeraceae) and edaphophilic (e.g. Gigasporaceae) AMF with increasing soil NO₃. Our findings suggest that invasive persistence may decrease the presence of multiple soil symbionts that native species depend on for pathogen protection and increased access to soil resources.     

Guilds and assembly rules in lawn communities

Abstract. The community structure of 11 lawn sites in New Zealand and Fiji was examined in terms of guilds, seeking assembly rules based on guild proportionality. First, associations were analysed, using a new patch model which examined the mean of associations within patches of about 4 cm x 4 cm. As expected from the previously-demonstrated existence of niche limitation at this scale in lawns, the majority of associations between individual species were negative. Even in a lawn only four months old there were significant associations (mostly negative, and one positive). At some sites those species with the most negative associations were those whose morphology might be expected to restrict co-existence with other species. Much ecological theory is based on the assumption that there are limitations to coexistence, related to the resource usage of the species, such that species that are too similar in resource use are less likely to coexist. This theory was tested by looking for evidence of guild proportionality. We defined two guilds, graminoids and forbs. Using these guilds, three of the sites showed significant evenness in proportional representation from the two guilds in quadrats containing four species, i.e. there was less variation in the graminoid:forb ratio than expected on a random basis. Inclusion of species-poor quadrats in a joint analysis over all richness categories overwhelmed this effect, though there was still a strong trend for two of the New Zealand sites: the two species-rich grass lawns. Preliminary analyses of alternative guild delimitations gave no indication that other guild delimitations would have revealed stronger community structure. There was a strong and significant tendency in most sites for the graminoid guild to be more strongly represented in species-poor quadrats, an effect caused by species frequencies.