Co-occurrence pattern of congeneric tree species provides conflicting evidence for competition relatedness hypothesis
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ABSTRACT:
SUBMITTER: Watanabe S
PROVIDER: S-EPMC8570171 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:The competition-relatedness hypothesis (CRH) predicts that the strength of competition is the strongest among closely related species and decreases as species become less related. This hypothesis is based on the assumption that common ancestry causes close relatives to share biological traits that lead to greater ecological similarity. Although intuitively appealing, the extent to which phylogeny can predict competition and co-occurrence among species has only recently been rigorously tested, with mixed results. When studies have failed to support the CRH, critics have pointed out at least three limitations: (i) the use of data poor phylogenies that provide inaccurate estimates of species relatedness, (ii) the use of inappropriate statistical models that fail to detect relationships between relatedness and species interactions amidst nonlinearities and heteroskedastic variances, and (iii) overly simplified laboratory conditions that fail to allow eco-evolutionary relationships to emerge. Here, we address these limitations and find they do not explain why evolutionary relatedness fails to predict the strength of species interactions or probabilities of coexistence among freshwater green algae. First, we construct a new data-rich, transcriptome-based phylogeny of common freshwater green algae that are commonly cultured and used for laboratory experiments. Using this new phylogeny, we re-analyse ecological data from three previously published laboratory experiments. After accounting for the possibility of nonlinearities and heterogeneity of variances across levels of relatedness, we find no relationship between phylogenetic distance and ecological traits. In addition, we show that communities of North American green algae are randomly composed with respect to their evolutionary relationships in 99% of 1077 lakes spanning the continental United States. Together, these analyses result in one of the most comprehensive case studies of how evolutionary history influences species interactions and community assembly in both natural and experimental systems. Our results challenge the generality of the CRH and suggest it may be time to re-evaluate the validity and assumptions of this hypothesis.
| S-EPMC4286037 | biostudies-literature
Project description:The distribution and co-occurrence of species are partly the outcome of their interactions with environmental drivers. Drought is a key driver related to the distribution of plant species. Drought events continue to increase in frequency and severity and identifying those aspects of plant function that are related to drought is critical. Here, we perform a community-level analysis of gene expression in relation to experimental drought and relate the similarity in gene set enrichment across species to their natural co-occurrence. Species with similar gene set enrichment in response to experimental drought tend to non-randomly co-occur in a natural stand. We demonstrate that similarity in the transcriptomic response of species to drought is a significantly better indicator of natural co-occurrence than measures of functional trait similarity and phylogenetic relatedness and that transcriptomics has the capacity to greatly enhance ecological investigations of species distributions and community structure.
| S-EPMC5722877 | biostudies-literature
Project description:Co-occurrence patterns are used in ecology to explore interactions between organisms and environmental effects on coexistence within biological communities. Analysis of co-occurrence patterns among microbial communities has ranged from simple pairwise comparisons between all community members to direct hypothesis testing between focal species. However, co-occurrence patterns are rarely studied across multiple ecosystems or multiple scales of biological organization within the same study. Here we outline an approach to produce co-occurrence analyses that are focused at three different scales: co-occurrence patterns between ecosystems at the community scale, modules of co-occurring microorganisms within communities, and co-occurring pairs within modules that are nested within microbial communities. To demonstrate our co-occurrence analysis approach, we gathered publicly available 16S rRNA amplicon datasets to compare and contrast microbial co-occurrence at different taxonomic levels across different ecosystems. We found differences in community composition and co-occurrence that reflect environmental filtering at the community scale and consistent pairwise occurrences that may be used to infer ecological traits about poorly understood microbial taxa. However, we also found that conclusions derived from applying network statistics to microbial relationships can vary depending on the taxonomic level chosen and criteria used to build co-occurrence networks. We present our statistical analysis and code for public use in analysis of co-occurrence patterns across microbial communities.
| S-EPMC4102878 | biostudies-literature
Project description:BackgroundMicrobial interactions shape the structure and function of microbial communities; microbial co-occurrence networks in specific environments have been widely developed to explore these complex systems, but their interconnection pattern across microbiomes in various environments at the global scale remains unexplored. Here, we have inferred an Earth microbial co-occurrence network from a communal catalog with 23,595 samples and 12,646 exact sequence variants from 14 environments in the Earth Microbiome Project dataset.ResultsThis non-random scale-free Earth microbial co-occurrence network consisted of 8 taxonomy distinct modules linked with different environments, which featured environment specific microbial co-occurrence relationships. Different topological features of subnetworks inferred from datasets trimmed into uniform size indicate distinct co-occurrence patterns in the microbiomes of various environments. The high number of specialist edges highlights that environmental specific co-occurrence relationships are essential features across microbiomes. The microbiomes of various environments were clustered into two groups, which were mainly bridged by the microbiomes of plant and animal surface. Acidobacteria Gp2 and Nisaea were identified as hubs in most of subnetworks. Negative edges proportions ranged from 1.9% in the soil subnetwork to 48.9% the non-saline surface subnetwork, suggesting various environments experience distinct intensities of competition or niche differentiation. Video abstract CONCLUSION: This investigation highlights the interconnection patterns across microbiomes in various environments and emphasizes the importance of understanding co-occurrence feature of microbiomes from a network perspective.
| S-EPMC7273686 | biostudies-literature
Project description:Plant-plant interactions are driven by environmental conditions, evolutionary relationships (ER) and the functional traits of the plants involved. However, studies addressing the relative importance of these drivers are rare, but crucial to improve our predictions of the effects of plant-plant interactions on plant communities and of how they respond to differing environmental conditions. To analyze the relative importance of -and interrelationships among- these factors as drivers of plant-plant interactions, we analyzed perennial plant co-occurrence at 106 dryland plant communities established across rainfall gradients in nine countries. We used structural equation modeling to disentangle the relationships between environmental conditions (aridity and soil fertility), functional traits extracted from the literature, and ER, and to assess their relative importance as drivers of the 929 pairwise plant-plant co-occurrence levels measured. Functional traits, specifically facilitated plants' height and nurse growth form, were of primary importance, and modulated the effect of the environment and ER on plant-plant interactions. Environmental conditions and ER were important mainly for those interactions involving woody and graminoid nurses, respectively. The relative importance of different plant-plant interaction drivers (ER, functional traits, and the environment) varied depending on the region considered, illustrating the difficulty of predicting the outcome of plant-plant interactions at broader spatial scales. In our global-scale study on drylands, plant-plant interactions were more strongly related to functional traits of the species involved than to the environmental variables considered. Thus, moving to a trait-based facilitation/competition approach help to predict that: 1) positive plant-plant interactions are more likely to occur for taller facilitated species in drylands, and 2) plant-plant interactions within woody-dominated ecosystems might be more sensitive to changing environmental conditions than those within grasslands. By providing insights on which species are likely to better perform beneath a given neighbour, our results will also help to succeed in restoration practices involving the use of nurse plants.
| S-EPMC4407970 | biostudies-literature
Project description:Climatic change will affect elevational vegetation distribution because vegetation distribution is related to thermal conditions. However, how elevational species distributions are determined by biotic and abiotic factors is not clear. The long-term plot census along an elevational gradient is indispensable to clarify mechanisms of elevational distribution of tree species. Two congeneric conifers, the less shade-tolerant Abies veitchii and shade-tolerant A. mariesii, dominate at low and high elevations, respectively, in the subalpine zone in Japan. This study investigated the population dynamics of the two species at three elevations (low, middle, high) for 13 years to examine why the two species dominated the different elevations from the viewpoints of competition and disturbance. This study showed that growth and survival rates were not highest at the most dominant elevations for each species. At the high elevation where A. mariesii dominated and small disturbances frequently occurred, the recruitment rate of A. mariesii was highest among the three elevations and that of A. veitchii was largely decreased by tree competition. However, A. veitchii was dominant earlier than A. mariesii at the low elevation after large disturbances by the high growth rate of individual trees. Therefore, A. mariesii was superior to A. veitchii at the high elevation because of its high recruitment rate and large reduction of recruitment of A. veitchii due to competition, while A. veitchii was superior to A. mariesii at the low elevation after large disturbances because of higher growth rate than A. mariesii. It is suggested that the elevational distributions of the two species were determined by elevational changes in population dynamics in relation to competition and disturbance. Long-term observational studies of forest dynamics among various elevations are indispensable to predict the effects of climatic change on vegetation distribution.
| S-EPMC8858215 | biostudies-literature
Project description:BackgroundKarst caves are considered as extreme environments with nutrition deficiency, darkness, and oxygen deprivation, and they are also the sources of biodiversity and metabolic pathways. Microorganisms are usually involved in the formation and maintenance of the cave system through various metabolic activities, and are indicators of changes environment influenced by human. Zhijin cave is a typical Karst cave and attracts tourists in China. However, the bacterial diversity and composition of the Karst cave are still unclear. The present study aims to reveal the bacterial diversity and composition in the cave and the potential impact of tourism activities, and better understand the roles and co-occurrence pattern of the bacterial community in the extreme cave habitats.ResultsThe bacterial community consisted of the major Proteobacteria, Actinobacteria, and Firmicutes, with Proteobacteria being the predominant phylum in the rock, soil, and stalactite samples. Compositions and specialized bacterial phyla of the bacterial communities were different among different sample types. The highest diversity index was found in the rock samples with a Shannon index of 4.71. Overall, Zhijin cave has relatively lower diversity than that in natural caves. The prediction of function showed that various enzymes, including ribulose-bisphosphate carboxylase, 4-hydroxybutyryl-CoA dehydratase, nitrogenase NifH, and Nitrite reductase, involved in carbon and nitrogen cycles were detected in Zhijin cave. Additionally, the modularity indices of all co-occurrence network were greater than 0.40 and the species interactions were complex across different sample types. Co-occurring positive interactions in the bacteria groups in different phyla were also observed.ConclusionThese results uncovered that the oligotrophic Zhijin cave maintains the bacterial communities with the diverse metabolic pathways, interdependent and cooperative co-existence patterns. Moreover, as a hotspot for tourism, the composition and diversity of bacterial community are influenced by tourism activities. These afford new insights for further exploring the adaptation of bacteria to extreme environments and the conservation of cave ecosystem.
| S-EPMC7257168 | biostudies-literature
Project description:Interspecific competition is an important driver of community assembly in plants and animals, but phylogenetic evidence for interspecific competition in bacterial communities has been elusive. This could indicate that other processes such as habitat filtering or neutral processes are more important in bacterial community assembly. Alternatively, this could be a consequence of the lack of a consistent and meaningful species definition in bacteria. We hypothesize that competition in bacterial community assembly has gone undetected at least partly because overly broad measures of bacterial diversity units were used in previous studies. First, we tested our hypothesis in a simulation where we showed that how species are defined can dramatically affect whether phylogenetic overdispersion (a signal consistent with competitive exclusion) will be detected. Second, we demonstrated that using finer-scale Operational Taxonomic Units (OTUs) (with more stringent 16S rRNA sequence identity cutoffs or based on fast-evolving protein coding genes) in natural populations revealed previously undetected overdispersion. Finally, we argue that bacterial ecotypes, diversity units incorporating ecological and evolutionary theory, are superior to OTUs for the purpose of studying community assembly.
| S-EPMC3930319 | biostudies-literature
Project description:Climate-driven sympatry may lead to competition for food resources between species. Rapid warming in the West Antarctic Peninsula (WAP) is coincident with increasing gentoo penguin and decreasing Adélie penguin populations, suggesting that competition for food may exacerbate the Adélie penguin decline. On fine scales, we tested for foraging competition between these species during the chick-rearing period by comparing their foraging behaviors with the distribution of their prey, Antarctic krill. We detected krill aggregations within the horizontal and vertical foraging ranges of Adélie and gentoo penguins, and found that krill selected for habitats that balance the need to consume food and avoid predation. In overlapping Adélie and gentoo penguin foraging areas, four gentoo penguins switched foraging behavior by foraging at deeper depths, a strategy which limits competition with Adélie penguins. This suggests that climate-driven sympatry does not necessarily result in competitive exclusion of Adélie penguins by gentoo penguins. Contrary to a recent theory, which suggests that increased competition for krill is one of the major drivers of Adélie penguin population declines, we suggest that declines in Adélie penguins along the WAP are more likely due to direct and indirect climate impacts on their life histories.
| S-EPMC4702144 | biostudies-literature
Project description:Tree diversity in forests is an important driver of ecological processes including herbivory. Empirical evidence suggests both negative and positive effects of tree diversity on herbivory, which can be, respectively, attributed to associational resistance or associational susceptibility. Tree diversity experiments allow testing for associational effects, but evidence regarding which pattern predominates is mixed. Furthermore, it is unknown if herbivory on tree species of native vs. exotic origin is influenced by changing tree diversity in a similar way, or if exotic tree species escape natural enemies, resulting in lower damage that is unrelated to tree diversity. To address these questions, we established a young tree diversity experiment in temperate southwestern Germany that uses high planting density (49 trees per plot; plot size 13 m2). The species pool consists of six congeneric species pairs of European and North American origin (12 species in total) planted in monocultures and mixtures (1, 2, 4, 6 species). We assessed leaf damage by leaf-chewing insects on more than 5,000 saplings of six broadleaved tree species. Plot-level tree species richness increased leaf damage, which more than doubled from monocultures to six-species mixtures, strongly supporting associational susceptibility. However, leaf damage among congeneric native and exotic species pairs was similar. There were marked differences in patterns of leaf damage across tree genera, and only the genera likely having a predominately generalist herbivore community showed associational susceptibility, irrespective of the geographical origin of a tree species. In conclusion, an increase in tree species richness in young temperate forests may result in associational susceptibility to feeding by generalist herbivores.
| S-EPMC5161486 | biostudies-literature