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138 results for “community phylogenetic”
Data from: Species interactions mediate phylogenetic community structure in a hyper-diverse lizard assemblage from arid Australia
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Diversity and phylogenetic community structure across elevation during climate change in a family of hyperdiverse neotropical beetles (Staphylinidae)
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Data from: Phylogenetic structure and host abundance drive disease pressure in communities
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Data from: Using trait and phylogenetic diversity to evaluate the generality of the stress-dominance hypothesis in eastern North American tree communities
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Data from: Deconstructing Darwin’s naturalization conundrum in the San Juan Islands using community phylogenetics and functional traits
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Data from: Trophic position determines functional and phylogenetic recovery after disturbance within a community
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Data from: The contribution of rare species to community phylogenetic diversity across a global network of forest plots
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Scale-dependent shifts in functional and phylogenetic structure of Mediterranean island plant communities over two centuries
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Data from: Phylogenetic plant community structure along elevation is lineage specific
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Data from: Using functional and phylogenetic diversity to infer avian community assembly along elevational gradients
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Relatedness and the composition of communities over time: evaluating phylogenetic community structure in the late Cenozoic record of bivalves
Understanding the mechanisms that prevent or promote the coexistence of taxa at local scales is critical to understanding how biodiversity is maintained. Competitive exclusion and environmental filtering are two processes thought to limit which taxa become established in a community. However, determining the relative importance of the two processes is a complex task, especially when the critical initial stages of colonization cannot be directly observed. Here, we explore the use of phylogenetic community structure for identifying filtering mechanisms in a fossil community. We integrated a time-calibrated molecular phylogeny of bivalve genera with a spatial dataset of late Cenozoic bivalves from the Pacific coast of North America to characterize how the community that was present in the semi-restricted San Joaquin Basin (SJB) embayment of present-day California was phylogenetically structured. We employed phylogenetic distance-based metrics across six time bins spanning 27-2.5 Ma and found no evidence of significant clustering or evenness in the SJB community when compared to communities randomly assembled from the regional source pool. Additionally, we found that new colonizers into the SJB were not significantly more or less closely related to native taxa than expected by chance. These findings suggest that neither competitive exclusion nor environmental filtering were overwhelmingly influential factors shaping the composition of the SJB community over time. We further discuss interpretations of these patterns in light of current understandings in community phylogenetics and reiterate the critical role historical perspectives play in how community assembly rules are assessed.
Data from: Phylogenetic structure and formation mechanism of shrub communities in arid and semi-arid areas of the Mongolian Plateau
<p>The mechanisms of species coexistence within a community have always been the focus in ecological research. Community phylogenetic structure reflects the relationship of historical processes, regional environments and interactions between species, and studying it is imperative to understand the formation and maintenance mechanisms of community composition and biodiversity.</p> <p>We studied the phylogenetic structure of the shrub communities in arid and semiarid areas of the Mongolian Plateau. First, the phylogenetic signals of four plant traits (height, canopy, leaf length and leaf width) of shrubs and subshrubs were measured to determine the phylogenetic conservation of these traits. Then the net relatedness index (NRI) of shrub communities was calculated to characterize their phylogenetic structure. Finally, the relationship between the NRI and current climate and paleoclimate (since the Last Glacial Maximum, LGM) factors was analyzed to understand the formation and maintenance mechanisms of these plant communities. We found that desert shrub communities showed a trend towards phylogenetic overdispersion, that is, limiting similarity was predominant in arid and semi-arid areas of the Mongolian Plateau despite the phylogenetic structure and formation mechanisms differing across habitats. The typical desert and sandy shrub communities showed a significant phylogenetic overdispersion, while the steppified desert shrub communities showed a weak phylogenetic clustering. It was found that mean winter temperature (i.e. in the driest quarter) was the major factor limiting steppified desert shrub phylogeny distribution. Both cold and drought (despite having opposite consequences) differentiated the typical desert to steppified desert shrub communities. The increase in temperature since the LGM is conducive to the invasion of shrub plants into steppe grassland, and this process may be intensified by global warming.</p>
Reappraising plastid markers of the red algae for phylogenetic community ecology in the gnomic era
<p>Selection of appropriate genetic markers to quantify phylogenetic diversity is crucial for phylogenetic community ecology studies. Yet, systematic evaluation of marker genes for this purpose is scarcely done. Recently, the combined effort of the phycological community has produced a rich plastid genome resource with taxonomic representation spanning all of the major lineages of the red algae (Rhodophyta). As a proof-of-concept study, we leverage this resource to develop and apply a phylogenomic strategy to seek candidate plastid markers that best capture the identity of component species in an eDNA metabarcoding study. We ranked the core plastid genes of 107 published plastid genomes based on various sequence-derived properties and their tree distance to plastid genome phylogenies and found that the most widely used marker, <i>rbc</i>L,<i> </i>is not necessarily the optimal marker, while more informative markers might have been overlooked. We designed and tested PCR primers for several candidate marker genes, and successfully amplified one of these, <i>rpoC1</i>, for a taxonomically broad set of red algal specimens. We suggest that our general marker identification methodology and the <i>rpoC1</i> primers will be useful to the phycological community for eDNA metabarcoding of the red algae.</p>
Data from: A new promising phylogenetic marker to study the diversity of fungal communities: the Glycoside Hydrolase 63 gene
In molecular ecology, the development of efficient molecular markers for fungi remains an important research domain. Nuclear ribosomal internal transcribed spacer (ITS) region was proposed as universal DNA barcode marker for fungi, but this marker was criticized for Indel-induced alignment problems and its potential lack of phylogenetic resolution. Our main aim was to develop a new phylogenetic gene and a putative functional marker, from single-copy gene, to describe fungal diversity. Thus, we developed a series of primers to amplify a polymorphic region of the Glycoside Hydrolase GH63 gene, encoding exo-acting α-glucosidases, in basidiomycetes. These primers were validated on 125 different fungal genomic DNAs, and GH63 amplification yield was compared with that of already published functional markers targeting genes coding for laccases, N-acetylhexosaminidases, cellobiohydrolases and class II peroxidases. Specific amplicons were recovered for 95% of the fungal species tested, and GH63 amplification success was strikingly higher than rates obtained with other functional genes. We downloaded the GH63 sequences from 483 fungal genomes publicly available at the JGI mycocosm database. GH63 was present in 461 fungal genomes belonging to all phyla, except Microsporidia and Neocallimastigomycota divisions. Moreover, the phylogenetic trees built with both GH63 and Rpb1 protein sequences revealed that GH63 is also a promising phylogenetic marker. Finally, a very high proportion of GH63 proteins was predicted to be secreted. This molecular tool could be a new phylogenetic marker of fungal species as well as potential indicator of functional diversity of basidiomycetes fungal communities in term of secretory capacities.
Data from: Phylogenetic composition of host plant communities drives plant-herbivore food web structure
1. Insects tend to feed on related hosts. The phylogenetic composition of host plant communities thus plays a prominent role in determining insect specialization, food web structure, and diversity. Previous studies showed a high preference of insect herbivores for congeneric and confamilial hosts suggesting that some levels of host plant relationships may play more prominent role that others. 2. We aim to quantify the effects of host phylogeny on the structure of quantitative plant-herbivore food webs. Further, we identify specific patterns in three insect guilds with different life histories and discuss the role of host plant phylogeny in maintaining their diversity. 3. We studied herbivore assemblages in three temperate forests in Japan and the Czech Republic. Sampling from a canopy crane, a cherry picker and felled trees allowed a complete census of plant-herbivore interactions within three 0.1 ha plots for leaf chewing larvae, miners, and gallers. We analyzed the effects of host phylogeny by comparing the observed food webs with randomized models of host selection. 4. Larval leaf chewers exhibited high generality at all three sites, whereas gallers and miners were almost exclusively monophagous. Leaf chewer generality dropped rapidly when older host lineages (5-80 myr) were collated into a single lineage but only decreased slightly when the most closely related congeneric hosts were collated. This shows that leaf chewer generality has been maintained by feeding on confamilial hosts while only a few herbivores were shared between more distant plant lineages and, surprisingly, between some congeneric hosts. In contrast, miner and galler generality was maintained mainly by the terminal nodes of the host phylogeny and dropped immediately after collating congeneric hosts into single lineages. 5. We show that not all levels of host plant phylogeny are equal in their effect on structuring plant-herbivore food webs. In the case of generalist guilds, it is the phylogeny of deeper plant lineages that drives the food web structure whereas the terminal relationships play minor roles. In contrast, the specialization and abundance of monophagous guilds is affected mainly by the terminal parts of the plant phylogeny and does not generally reflect deeper host phylogeny.
Data from: Non-linear effects of phylogenetic distance on early-stage establishment of experimentally introduced plants in grassland communities
1. The phylogenetic distance of an introduced plant species to a resident native community may play a role in determining its establishment success. While Darwin's naturalization hypothesis predicts a positive relationship, the preadaptation hypothesis predicts a negative relationship. Rigorous tests of this now so-called Darwin's naturalization conundrum require not only information on establishment successes but also of failures, which is frequently not available. Such essential information, however, can be provided by experimental introductions. 2. Here, we analysed three datasets from two field experiments in Germany and Switzerland. In the Swiss experiment, alien and native grassland species were introduced as seeds only with and without disturbance (tilling). In the German experiment, alien and native grassland species were introduced both as seeds and as seedlings with and without disturbance (tilling), and with and without fungicide application. For the seedling introduction experiment, there was an additional herbivore-exclusion treatment. 3. Phylogenetic distance affected establishment in the three datasets differently, with success peaking at intermediate distances for the seed datasets, but decreasing with increasing distances in the seedling dataset. Disturbance favored seedling survival, most likely by weakening the resident community. 4. Synthesis: By analyzing experimental introductions, we show that the relationship between phylogenetic distance and establishment, at least for seedling emergence, may actually be non-linear with an optimum at intermediate distances. Therefore, Darwin´s naturalization hypothesis and the preadaptation hypothesis need not be in conflict. Rather, the mechanisms underlying them can operate simultaneously or alternately depending on the life stage and on the environmental conditions of the resident community.
Data from: Resident-invader phylogenetic relatedness, not resident phylogenetic diversity, controls community invasibility
A central goal of invasion biology is to elucidate mechanisms regulating community invasibility. Darwin's naturalization hypothesis, one of the oldest hypotheses in invasion biology, emphasizes the importance of phylogenetic relatedness (PR) between resident and invader species for predicting invasibility. Alternatively, a recent extension of the diversity-invasibility hypothesis predicts that phylogenetic diversity (PD) of resident communities influences invasibility. Neither of these hypotheses has undergone rigorous experimental testing, and the relative contributions of PR and PD, whose effects tend to be confounded with each other, to community invasibility are unknown. Here we consider both perspectives together by independently manipulating PR and PD in laboratory bacterial assemblages. We found that while invader abundance declined significantly as PR increased, it was unaffected by PD. Likewise, we found that resident-invader functional similarity, not functional diversity of resident communities, was a significant predictor of invader abundance. Nevertheless, invader abundance was better predicted by PR than functional similarity. These results highlight the importance of considering species evolutionary relationships, especially the phylogenetic relatedness between resident and invader species, for the prediction, prevention and management of biological invasions.
Data from: Phylogenetic diversity is maintained despite richness losses over time in restored tallgrass prairie plant communities
Ecosystem restoration is an important tool for mitigating biodiversity loss and recovering critical ecosystem services to humanity, but restoration rarely takes into account the evolutionary attributes of the community being restored. Phylogenetic diversity (PD) represents a potentially valuable measure of restoration success because it can correlate with functional trait diversity that drives ecosystem function. However, PD patterns in restored communities are rarely assessed. We surveyed plant communities in restored tallgrass prairies 2–19 years old and calculated two PD measures, SESMNTD and SESMPD, of the communities and seed mixture applied to sites. We also identified high-threat exotic species present in each site to determine whether PD of the seed mixture applied was related to resistance against invasion. We show that PD in North American tallgrass prairie restorations, as measured by both SESMNTD and SESMPD, is maintained over time even as richness declines. Neither the resulting community PD nor invasion by high-threat exotic species was affected by PD of the seed mixture used in site restoration. Thus, simply maximizing PD of seed mixtures without considering the particular component species is unlikely to help achieve restoration goals. Synthesis and applications. These results suggest that species losses over time are not biased towards species with or without close relatives in the community. If phylogenetic diversity (PD) reflects functional trait diversity in communities, then local declines in species richness may not necessarily mean the loss of ecosystem function in restoration projects. However, PD of restored communities may be limited by low establishment rates for most species. Conservation practitioners should consider PD with careful planning to maintain overall community diversity and potentially maximize ecosystem function and services in restorations. This perspective will require a deeper understanding of the relationships between phylogenetic relatedness and traits associated with competition and fitness.
Data from: Species richness, but not phylogenetic diversity, influences community biomass production and temporal stability in a re-examination of 16 grassland biodiversity studies
1.Hundreds of experiments have now manipulated species richness of various groups of organisms and examined how this aspect of biological diversity influences ecosystem functioning. Ecologists have recently expanded this field to look at whether phylogenetic diversity among species, often quantified as the sum of branch lengths on a molecular phylogeny leading to all species in a community, also predicts ecological function. Some have hypothesized that phylogenetic divergence should be a superior predictor of ecological function than species richness because evolutionary relatedness represents the degree of ecological and functional differentiation among species. But studies to date have provided mixed support for this hypothesis. 2.Here, we re-analyze data from 16 experiments that have manipulated plant species richness in grassland ecosystems and examined the impact on aboveground biomass production over multiple time points. Using a new molecular phylogeny of the plant species used in these experiments, we quantified how the phylogenetic diversity of plants impacts average community biomass production as well as the stability of community biomass production through time. 3.Using four complementary analyses we show that, after statistically controlling for variation in species richness, phylogenetic diversity (the sum of branches in a molecular phylogenetic tree connecting all species in a community) is neither related to mean community biomass nor to the temporal stability of biomass. These results run counter to past claims. However, after controlling for species richness, phylogenetic diversity was positively related to variation in community biomass over time due to an increase in the variances of individual species, but this relationship was not strong enough to influence community stability. 4.In contrast to the non-significant relationships between phylogenetic diversity, biomass, and stability, our analyses show that species richness per se tends to increase the mean biomass production of plant communities, after controlling for phylogenetic diversity. The relationship between species richness and temporal variation in community biomass was either positive, non-significant or negative depending on which analysis was used. However, the increases in community biomass with species richness, independently of phylogenetic diversity, always led to increased stability. These results suggest that phylogenetic diversity is no better as a predictor of ecosystem functioning than species richness. 5.Synthesis. Our study on grasslands offers a cautionary tale when trying to relate phylogenetic diversity to ecosystem functioning suggesting that there may be ecologically important trait and functional variation among species that is not explained by phylogenetic relatedness. Our results fail to support the hypothesis that the conservation of evolutionarily distinct species would be more effective than the conservation of species richness as a way to maintain productive and stable communities under changing environmental conditions.
FIGURE 1 in Using community phylogenetics to assess phylogenetic structure in the Fitzcarrald region of Western Amazonia
FIGURE 1 | Maps depicting the location and year of collection expeditions in (purple dots) and near (orange dots) the Fitzcarrald region of Southwestern Amazonia. Collections from 77 localities in four river basins (black circles in lower-left image) collected over four field seasons. False-color map images generated from a DEM by Paulo Petry.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.