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138 results for “community phylogenetic”
Inventory of High-resolution phylogenetic profiles of the planktonic microbial communities (via 16S and 18S rRNA gene amplicons) from Shark River Slough and Taylor Slough, Everglades National Park (FCE LTER), Florida, USA, 2017 - ongoing
Planktonic microbial communities mediate many vital biogeochemical processes in wetland ecosystems, yet compared to other aquatic ecosystems, like oceans, lakes, rivers, or estuaries, they remain relatively underexplored. Our study site, the Florida Everglades (USA)—a vast iconic wetland consisting of a slow-moving system of shallow rivers connecting freshwater marshes with coastal mangrove forests and seagrass meadows—is a highly threatened model ecosystem for studying salinity and nutrient gradients, as well as the effects of sea level rise and saltwater intrusion. This dataset provides the first high-resolution phylogenetic profiles of planktonic bacterial and eukaryotic microbial communities (using 16S and 18S rRNA gene amplicons) from these environments. The dataset contains 16S and 18S rRNA data from 2017, and contains 16S rRNA data for monthly (2019) and quarterly water samples (2020-ongoing). The 2017 data are published in Laas et al. 2022. A detailed list of sequence data and their accession numbers in GenBank is provided and will be updated as more data are published. This data package is an inventory of sequence read archive (SRA) entries available through GenBank BioProject PRJNA525456 (at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA525456) and BioProject PRJNA1018945 (at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1018945). This data package is associated with the following publication: Laas, P., Ugarelli, K., Travieso, R., Stumpf, S., Gaiser, E. E., Kominoski, J. S., & Stingl, U. (2022). Water column microbial communities vary along salinity gradients in the Florida Coastal Everglades wetlands. Microorganisms, 10(2), 215. https://doi.org/10.3390/microorganisms10020215 Instead of citing this package, which is an inventory, please cite the original GenBank data or journal article, as appropriate. Citation guidance for the journal article is available on the respective publisher's website.
Data from: Resource addition drives taxonomic divergence and phylogenetic convergence of plant communities
1. Anthropogenic environmental changes are known to affect the Earth's ecosystems. However, how these changes influence assembly trajectories of the impacted communities remains a largely open question. 2. In this study, we investigated the effect of elevated nitrogen (N) deposition and increased precipitation on plant taxonomic and phylogenetic β-diversity in a 9-year field experiment in the temperate semi-arid steppe of Inner Mongolia, China. 3. We found that both N and water addition significantly increased taxonomic β-diversity, whereas N, not water, addition significantly increased phylogenetic β-diversity. After the differences in local species diversity were controlled using null models, the standard effect size of taxonomic β-diversity still increased with both N and water addition, while water, not N, addition, significantly reduced the standard effect size of phylogenetic β-diversity. The increased phylogenetic convergence observed in the water addition treatment was associated with the colonization of different, but phylogenetically closely related, species into different replicate plots of the treatment. Species colonization in this treatment was found to be trait-based, with leaf nitrogen concentration being the key functional trait. 4. Synthesis. Our analyses demonstrate that anthropogenic environmental changes may affect the assembly trajectories of plant communities at both taxonomic and phylogenetic scales. Our results also suggest that while stochastic processes may cause communities to diverge in species composition, deterministic process could still drive communities to converge in phylogenetic community structure.
Data from: Trechus (Coleoptera: Carabidae) of Appalachia: A phylogenetic insight into the history of high elevation leaf litter communities
<p>Elevation gradients provide a wealth of habitats for a wide variety of organisms. The southern Appalachian Mountains in eastern United States are known for their high biodiversity and rates of endemism in arthropods, including in high-elevation leaf-litter taxa that are often found nowhere else on earth. Trechus Clairville (Coleoptera: Carabidae) is a genus of litter inhabitants with a near-global distribution and over 50 Appalachian species. These span two subgenera, Trechus s. str. and Microtrechus Jeannel, largely restricted to north and south of the Asheville basin, respectively. Understanding the diversification of these 3–5 mm flightless beetles through geological time can provide insights into how the litter-arthropod community has responded to historical environments, and how they may react to current and future climate change. We identified beetles morphologically and sequenced six genes to reconstruct a phylogeny of the Appalachian Trechus. We confirmed the Asheville Basin as a biogeographical barrier with a split between the north and south occurring towards the end of the Pliocene. Finer scale biogeography, including mountain-range occupancy, was not a reliable indication of relatedness, with group ranges overlapping and many instances of species-, species group-, and subgeneric sympatry. This may be because of the recent divergence between modern species and species groups. Extensive taxonomic revision of the group is required for Trechus to be useful as a bioindicator, but their high population density and speciose nature make them worth additional time and resources.</p>
Dataset of Rainy years counteract negative effects of drought on taxonomic, functional, and phylogenetic diversity: resilience in annual plant communities
<p>Data used in the article: </p> <p><strong>Rainy years counteract negative effects of drought on taxonomic, functional, and phylogenetic diversity: resilience in annual plant communities</strong></p> <p><strong>Abstract</strong></p> <p>1- Climate models forecast changes in the amounts and distribution of rain, which may affect ecosystems worldwide, especially in drylands where water is already the limiting factor for plant life. Annual plant communities are common in drylands where they can complete their entire life cycle during the rainy period while avoiding the dry season. Moreover, seed dormancy allows them to disperse over time by remaining in the seed bank for long periods. However, the extent to which these communities will be able to tolerate increasing drought is uncertain.</p> <p>2- We performed a five-year rainfall reduction treatment under field conditions and determined its effects on annual plant communities in a Mediterranean gypsum ecosystem. We assessed the taxonomic, functional, and phylogenetic diversity of these communities each year for five years.</p> <p>3-The taxonomic and functional diversity decreased under the rainfall reduction treatment whereas the phylogenetic diversity increased. Moreover, the relative importance of species with drought-resistant functional designs increased in the community assemblages. However, after a rainy season with above average rainfall, all of the diversity values recovered completely even under the rainfall reduction treatment.</p> <p>4- Our results provide important insights into the responses of these plant communities under a climate change scenario, where they indicate high losses of diversity during drought events but rapid recovery in milder years.</p> <p><em>Synthesis</em> Our findings highlight the great resilience of annual plant communities in drylands, which may allow them to tolerate increased drought under the present climate change scenario.</p>
Community level phylogenetic diversity does not differ between rare and common lineages across tallgrass prairies in northern Great Plains
<p class="MsoNormal">In some cases, rare lineages provide resistance to invasions, serve as keystone species, and contribute unique functional or phylogenetic diversity to their communities. In other cases, rare species may be functionally redundant with common species and do not significantly contribute to phylogenetic diversity. How rare and common species coexist and contribute to local species pools may depend upon attributes of their communities and remains an open question in ecology. Niche differentiation has served as an explanation for species coexistence, and phylogenetic relatedness provides a means to approximate how ecologically similar species are to each other. To explore the contribution of rare species to community phylogenetic diversity, we sampled twenty-one plant communities across the Prairie Coteau ecoregion, home of the largest tracts of untilled northern tallgrass prairie and of high conservation concern. We used breakpoint analysis through iterative addition of less abundant species to the phylogenetic tree for each community. We also assessed the phylogenetic signal of abundance classes using Blomberg's K statistic and calculated the phylogenetic similarity between rare and common species using a phylogenetic beta diversity metric (D<sub>nn</sub>). To estimate the phylogenetic structuring of these prairie communities, we calculated two common metrics that capture evolutionary relatedness between species (MPD, and MNTD) and examine the correlation between these metrics and species richness. Overall, we found rare species do not contribute higher levels of phylogenetic diversity than more common species in the Prairie Coteau ecoregion. Eight of 21 communities had significant breakpoints, where the addition of a less common species resulted in a shift in phylogenetic diversity, with only four communities having an increasing trend for the rarest species. Phylogenetic signal for abundance was low and unsignificant across 18 communities, while four sites did show significant low phylogenetic signal. We additionally found our communities had lower phylogenetic diversity than expected from the regional species pool. Finally, we found weak to no correlation when using MPD and MNTD. Our results indicate niche differentiation does not explain rare species persistence in tallgrass prairies. We found species were more closely related than expected from random community assembly, suggesting high functional redundancy within this system. This is promising for the long term viability of this ecosystem, but only insofar as enough species remain in the system to create redundancy. With ongoing biodiversity loss, it is essential we understand the role rare species play in their communities. Phylogenetic diversity could be an important tool for researchers and managers to utilize for conservation of critically threatened systems such as tallgrass prairies.</p>
Data from: Mycorrhizal symbiosis increases plant phylogenetic diversity and regulate community assembly
<p>The intricate mechanisms shaping plant diversity and community composition are the cornerstone of ecological understanding. Yet, the role of mycorrhizal symbiosis, the fundamental partnership between fungi and plant roots, in influencing community composition has often been underestimated. Here, we use extensive species survey data from 1,315 terrestrial ecosystem sites to elucidate the influence of mycorrhizal symbiosis on plant phylogenetic diversity and its implications for community assembly processes. Our findings demonstrate that increasing mycorrhizal symbiotic potential leads to greater phylogenetic dispersion within plant communities. Furthermore, we unveil a distinct dichotomy in the assembly processes governed by mycorrhizal status. Mycorrhizal species predominantly influence deterministic processes, suggesting a role in niche-based community assembly. Conversely, non-mycorrhizal species exert a stronger influence on stochastic processes, highlighting the importance of random events in shaping community structure. These results underscore the crucial but often hidden role of mycorrhizal symbiosis in driving plant community diversity and assembly. This study provides valuable insights into the complex mechanisms shaping ecological communities and the way for more informed conservation and management practices that acknowledge the complex interplay between symbiosis and ecological community dynamics.</p>
FIGURE 2 in Using community phylogenetics to assess phylogenetic structure in the Fitzcarrald region of Western Amazonia
FIGURE 2 | Ultrametric cladogram of the Fitzcarrald region fish fauna (modified from S2) showing distributions of species in habitats and river basins. Red boxes indicate species presences in: Rivers, Stream, Lakes, Purus, Yuruá, Urubamba and Las Piedras. Note phylogenetic clustering in the Urubamba basin and the stream habitat.
FIGURE 3 in Taxonomic and phylogenetic beta diversity in headwater stream fish communities of the Paraná and Paraguai River basins
FIGURE 3 | Turnover and nestedness components of taxonomic and phylogenetic beta diversity in streams of the Paraná and Paraguai River basins. Clockwise from top left: total, turnover and nestedness components of taxonomic beta diversity; at the bottom, total, turnover and nestedness components of phylogenetic beta diversity. Filled circles correspond to Paraná streams and triangles to Paraguai streams.
FIGURE 2 in Taxonomic and phylogenetic beta diversity in headwater stream fish communities of the Paraná and Paraguai River basins
FIGURE 2 | Phylogenetic hypothesis for fish collected in headwater streams of the Paraná and Paraguai River basins.
FIGURE 1 in Taxonomic and phylogenetic beta diversity in headwater stream fish communities of the Paraná and Paraguai River basins
FIGURE 1 | Headwater streams sampled in the Paraná and Paraguai River basins. Blue circles represent streams of the Paraguai basin, and black triangles represent streams of the Paraná basin. The stars represent waterfalls. The color indicates the variation in altitude.
Species introductions cause phylogenetically structured successional pathways in natural wood-inhabiting fungal communities
<p>These files include the data and the scripts for reproducing the results presented in the manuscript "Species introductions cause phylogenetically structured successional pathways in natural wood-inhabiting fungal communities".</p> <p>Description of the files can be found from the README.docx file.</p>
Data for: Historical and contemporary processes drive global phylogenetic structure across geographical scales: Insights from bat communities
<p><strong>Aim</strong>: Patterns of evolutionary relatedness among co-occurring species are driven by scale-dependent contemporary and historical processes. Yet, we still lack a detailed understanding of how these drivers impact the phylogenetic structure of biological communities. Here, we focused on bats – one of the most speciose and vagile groups of mammals – and test the predictions of three general biogeographical hypotheses that are particularly relevant to understanding how paleoclimatic stability, local diversification rates, and geographical scales shaped their present-day phylogenetic community structure.</p> <p><strong>Location</strong>: Worldwide, across restrictive geographical extents: global, east-west hemispheres, biogeographical realms, tectonic plates, biomes, and ecoregions.</p> <p><strong>Time period</strong>: Last Glacial Maximum (~22,000 years ago) to the present.</p> <p><strong>Major taxa studied</strong>: Bats (Chiroptera)</p> <p><strong>Methods</strong>: We estimated bat phylogenetic community structure across restrictive geographical extents and modelled it as a function of paleoclimatic stability, and in situ net diversification rates.</p> <p><strong>Results</strong>: Limiting geographical extents from larger to smaller scales strongly changed the phylogenetic structure of bat communities. The magnitude of these effects is less noticeable in the western hemisphere, where frequent among-realm biota interchange could have been maintained through bats' adaptive traits. Highly phylogenetically related bat communities are generally more common in regions that changed less in climate since the last glacial maximum, supporting the expectation that stable climates allow for increased phylogenetic clustering. Finally, increased in situ net diversification rates are associated with greater phylogenetic clustering in bat communities.</p> <p><strong>Main conclusions</strong>: We show that the worldwide phylogenetic structure of bat assemblages varies as a function of geographical extents, dispersal barriers, paleoclimatic stability and in situ diversification. The integrative framework used in our study, which can be applied to other taxonomic groups, has proven useful to not only explain the evolutionary dynamics of community assembly but could also help tackle questions related to scale dependence in community ecology and biogeography.</p>
Data for: Environmental responses of fruiting fungal communities are phylogenetically structured
<p class="MsoNormal"><span>Through their ephemeral reproductive structures (fruiting bodies), ectomycorrhizal forest soil fungi provide a resource for a plethora of organisms. Thus, resolving what biotic and abiotic factors determine the occurrence and abundance of fruiting bodies is fundamental for understanding the dynamics of forest trophic networks. While the influence of abiotic factors such as moisture and temperature on fungal fruiting are relatively well established, little is known about how these processes interact with the evolutionary history of fungal species to determine when, where, and in which abundance fungal fruiting bodies will emerge. A specific knowledge gap relates to whether species' responses to their environment are phylogenetically structured. Here, we ask whether related fungal taxa respond similarly to climatic factors and forest habitat characteristics, and whether such correlated responses will affect the assembly of fungal fruiting communities. To resolve these questions, we fitted joint species distribution models combining data on the species composition and abundance of fungal fruiting bodies, environmental variation, and phylogenetic relationships among fungal taxa. Our results show that both site-level forest characteristics (dominant tree species and forest age) and climatic factors related to phenology (effective heat sum) greatly influence the occurrence and abundance of fruiting bodies. More importantly, while different fungal species responded unequally to their shared environment, there was a strong <span>phylogenetic signal in their responses, so that related fungal species tended to fruit under similar environmental conditions. </span>Thus, not only are fruiting bodies short-lived and patchily distributed, but the availability of similar resources will be further aggregated in time and space. These strong constraints on resource availability for fungus-associated taxa highlight the potential of fungus-based networks as a model system for studies on the ecology and evolution of resource–consumer relations in ephemeral systems of high spatiotemporal patchiness.</span></p>
Data for: Environmental responses of fruiting fungal communities are phylogenetically structured
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Data from: Trechus (Coleoptera: Carabidae) of Appalachia: A phylogenetic insight into the history of high elevation leaf litter communities
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Data and code from: Mechanisms of community assembly through the lens of phylogenetic diversity: A critical reappraisal
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Data from: Resource addition drives taxonomic divergence and phylogenetic convergence of plant communities
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Data from: Mycorrhizal symbiosis increases plant phylogenetic diversity and regulate community assembly
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Data for: Historical and contemporary processes drive global phylogenetic structure across geographical scales: Insights from bat communities
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Community level phylogenetic diversity does not differ between rare and common lineages across tallgrass prairies in northern Great Plains
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International Brain Laboratory public data
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OpenNeuro
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