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82 results for “community assemblage”
Data from: Assemblage Accumulation Curves: A framework for resolving species accumulation in biological communities using chloroplast genome sequences
The timing and tempo of the processes involved in community assembly are of substantial concern to community ecologists and conservation managers. The fossil record is a valuable source of data for studying past changes in community composition, but it is not always detailed enough to allow the process of community assembly to be resolved at regional or site scales while tracing the trajectories of known species with associated known traits. We present a three‐step framework for studying present‐day species accumulation through time: DNA sampling from multiple individuals from multiple species within a community; estimates of coalescence times for each species using molecular dating methods; and plotting the accumulation of present‐day species through time using the inferred population ages. Our approach is illustrated using whole chloroplast genomes from plants from three rainforest communities in eastern Australia. Expected times to coalescence for multiple species in each community were inferred from pooled high‐throughput sequence libraries. Local assemblage accumulation curves for each community were constructed. We also explored the variation in assemblage accumulation curves of species with different functional traits. Models of equilibrium species richness informed our null hypothesis and largely explained the shape of the assemblage accumulation curves and indicated that the complexities of the accumulation process should be explored with additional parameters, for example allowing species classes with different extinction rates. The assemblage accumulation curves for the study sites showed evidence of recent population expansions within each of the communities. This signal of recent accumulation is consistent with the increase in suitable rainforest habitat that followed the Last Glacial Maximum. Our method of constructing assemblage accumulation curves provides a simple approach for visualizing species‐accumulation data. It can be used to test hypotheses such as the relative survival potential of species‐specific ecological attributes. Although our example used single‐nucleotide polymorphisms derived from whole‐chloroplast sequencing, this framework can be applied to mitochondrial genomes and to communities of other organisms.
Population asynchrony alone does not explain stability in species rich soil animal assemblages: the stabilising role of forest age on oribatid mite communities
<p>1. The importance of microbial and plant communities in the control of the diversity and structure of soil animal communities has been clarified over the last decade. Previous research focused on abiotic factors, niche separation and spatial patterns. Significant gaps still exist in our knowledge of the factors that control the stability of these communities over time.</p> <p>2. We analysed a nine-year data set form the national Long-term Ecological Research Network of Latvia. We focused on 117 oribatid species from three Scots pine forests of different age (<40 yrs, 65 yrs, and >150 yrs) and structure. For each forest type, 100 samples were collected each year, providing very high replication and long of time series for a soil community. We assessed different aspects of stability: we used a dynamic null model, parametrised on observed growth rates, to test the hypothesis that asynchrony in species populations stabilises total community size; we also analysed alpha and beta diversity over time to test the hypothesis that temporal variation in species composition and relative abundances is controlled by forest attributes.</p> <p>3. Real communities can be more stable than their stochastic counterparts if species are asynchronous, confirming for the first time the role of asynchrony in stabilising soil communities. Yet, while some real communities were more stable and had higher abundance and growth rates than others, they were not necessarily more asynchronous than the less stable communities. Species composition and relative abundances were also less variable in the more stable communities.</p> <p>4. Species asynchrony generally stabilises species rich communities but is not sufficient to explain different levels of stability between forests. Forest age is a key factor explaining different levels of overyielding and so stability. Data suggests that both asynchrony and high diversity of microhabitat structure of Scots pine forests promote stability of soil animal communities.</p>
Data from: Validating the power of mitochondrial metagenomics for community ecology and phylogenetics of complex assemblages
1. The biodiversity of mixed-species samples of arthropods can be characterized by shotgun sequencing of bulk genomic DNA and subsequent bioinformatics assembly of mitochondrial genomes. Here, we tested the power of mitochondrial metagenomics by conducting Illumina sequencing on mixtures of >2600 individuals of leaf beetles (Chrysomelidae) from 10 communities. 2. Patterns of species richness, community dissimilarity and biomass were assessed from matches of reads against three reference databases, including (i) a custom set of mitogenomes generated for 156 species (89% of species in the study); (ii) mitogenomes obtained by the de novo assembly of sequence reads from the real-world communities; and (iii) a custom set of DNA barcode (cox1-5′) sequences. 3. Species detection against the custom-built reference genomes was very high (>90%). False presences were rare against mitogenomes but slightly higher against the barcode references. False absences were mainly due to the incompleteness of the reference databases and, thus, more prevalent in the de novo data set. Biomass (abundance × body length) and read numbers were strongly correlated, demonstrating the potential of mitochondrial metagenomics for studies of species abundance. 4. A phylogenetic tree from the mitogenomes showed high congruence with known relationships in Chrysomelidae. Patterns of taxonomic and phylogenetic dissimilarity between sites were highly consistent with data from morphological identifications. 5. The power of mitochondrial metagenomics results from the possibility of rapid assembly of mitogenomes from mixtures of specimens and the use of read counts for accurate estimates of key parameters of biodiversity directly from community samples.
Andean non-volant small mammals: a dataset of community assemblages of non-volant small mammals from the high Andes
<p><span>Information from diversity inventories is used to study patterns of biodiversity and species distribution; likewise, it may be useful to identify priority areas for conservation, and to guide future sampling efforts. In this context, we compiled information on non-volant small mammal communities from the high Andes (> 2,000 m.). Here we present an open resource data set containing information diversity (species composition, number of individuals captured ), inventory design (type of traps, sampling efforts), and environment (habitat) for both unpublished and published information. This study covers 630 mammalian communities, geographically distributed throughout the Andes in Venezuela, Colombia, Ecuador, Peru, Bolivia, Argentina, and Chile</span><span>. </span><span>We compiled a total of </span><span>26,412 individual records belonging to 240 species; the order with greatest number of records was Rodentia (n=25,319, 96.06%), followed by Didelphimorphia (n=373, 1.42%), Eulipotyphla (n=358, 1.36%) and Paucituberculata, (n=307, 1.16%). </span><span>Andean non-volant small mammal communities harbor </span><span>a range of 1-17 species</span><span>, </span><span>with 93.06 % of sites being composed of one to five species</span><span>, 27.78% of sites ranging in richness from six to ten species, and 4.17% are composed by more than ten species. </span><span>Multiple sampling methods were used to survey non-volant small mammals; the most representative methods being the use of snap-traps and Sherman traps, or a combination of both, in more than 81% of the studies.</span> <span>The <em>Andean Non-Volant Small Mammals</em> Data Paper represents the first </span><span>large dataset of faunal species inventories for Andes. </span><span>There are no copyright restrictions </span><span>associated with the use of this data se</span><span>t</span><span>. Please cite this Data Paper when its data are used total or partially in research</span><span> or teaching</span><span>.</span></p>
Spatial assemblage of grassland communities and interrelationships with productivity
<p><span>Knowledge on the fine-scale spatial structure is very important for understanding plant community dynamics, as interactions among sessile plants mainly occur in the neighborhood. However, the spatial assemblage mechanism and interrelationships with productivity remain poorly understood. Here, species segregation index (Ms<sub>com</sub>) was used to quantify the interspecific segregation (or intraspecific aggregation) of the neighborhood in plant communities from three contrasting plateaus. We employed the coordinates for 125,726 individual plants (within 1 m<sup>2</sup> plots) sampled in natural grassland communities across Loess Plateau (LP), Mongolian Plateau (MP), and Tibetan Plateau (TP) to elucidate the assembly mechanisms of Ms<sub>com</sub> and interrelationships with above-ground net primary productivity (ANPP). We found that these grassland communities tended to assemble in intraspecific aggregations; the phenomena were more apparent in desert grassland communities. </span><span>Apart from the controls of self-organization, climatic heterogeneity also plays an important role in determining Ms<sub>com</sub>. In grassland communities on LP and MP, Ms<sub>com</sub> was predominantly affected by </span><span>reproductive allocation</span><span> (RA); whereas on TP, Ms<sub>com</sub> was more responsive and sensitive to climatic heterogeneity (especially precipitation and low temperatures).</span><span> We also found that Ms<sub>com</sub> better explained the overall variations in ANPP than species diversity, and mediated the response of ANPP to environmental variations; Ms<sub>com</sub> and environmental effects jointly explained 22.7, 19.1, and 49.8% of the variations in ANPP on LP, MP, and TP, respectively. Our findings provide new insights into the underlying mechanisms of spatial assemblage of grassland communities, and emphasize the critical role of spatial structure in predicting the impacts of environmental change.</span></p>
Data related to article: Shrubs exhibit competitive interactions with herbaceous plants and shape community assemblage and functional composition in alpine western Himalaya
<p>To understand the interaction between dominant shrubs and herbacous communities in the alpine region of western Himalaya, a field study was conducted along the elevation gradient (3500-5000 masl). During the field survey, we have collected population data, plant functional trait data and soil physico-chemical data from shrub undercanopy and adjacent open habitats. Relative Interaction Index and L0g ratio were calculated using the population data. Further, plant functional traits data and soil physicochemical data were utilised to understand the functional comoposition and resource availability occuring in the contrasting habitats.</p>
Testing the robustness of a coastal biodiversity data protocol in the Mediterranean: Insights from the molluscan assemblages of the sublittoral macroalgae communities
<p>Dataset from NaGISA project, class mollusca.</p>
Data from: Forest plant community as a driver of soil biodiversity: experimental evidence from collembolan assemblages through large-scale and long-term removal of oak canopy trees Quercus petraea
Plant–soil interactions are increasingly recognized to play a major role in terrestrial ecosystems functioning. However, few studies to date have focused on slow dynamic ecosystems such as forests. As they are vertically stratified by multiple vegetation strata, canopy tree removal by thinning operations could alter forest plant community through tree canopy opening. Very little is known about cascading effects on soil biodiversity. We conducted a large-scale, multi-site assessment of collembolan assemblage response to long-term canopy tree removal in sessile oak Quercus petraea temperate forests. A total of 33 experimental plots were studied covering a large gradient of canopy tree basal area, stand age and local abiotic contexts. Collembolan abundance strongly declined with canopy tree removal in early forest successional stage and this was mediated by negative effect of understory plant community composition changes, i.e. shift from moss and forb to tree seedling, fern, shrub and grass species. Negative effect of this composition shift on collembolan species richness was largely offset by positive effect of the increase in understory plant species richness. This gives support to both the plant mass-ratio and functional diversity hypotheses. Collembolan functional groups had contrasting response patterns, which were mediated by different ecological factors. Epedaphic (r-strategist) abundance and species richness increased with canopy tree removal in relation with the increase in understory plant species richness. In contrast, euedaphic (K-strategist) abundance and species richness declined with canopy tree removal in early forest successional stage in relation with changes in understory plant community composition and species richness, as well as microclimatic conditions. Overall, our study provides experimental evidence that forest plant community can be a strong driver of collembolan assemblages. It also emphasizes the role of trees as foundation species of forest ecosystems that can shape soil biodiversity through their regulation of understory plant community and ecosystem abiotic conditions.
Figure 3 in Coral reef tanaidacean assemblages along the SW and SE Gulf of Mexico: biodiversity, geographic distribution and community structure
Figure 3. Dendrograms of each sampling site and grouping of sampling sites with spatial analysis of non-metric multidimensional scaling (MDS) obtained with a dissimilarity matrix using Bray–Curtis indices. Area Natural Protegida Tuxpan–Lobos (ANPT–L), Parque Nacional Sistema Arrecifal Veracruzano (PNSAV) and Sistema Arrecifal Bajos Sisal (SABS).
Figure 1 in Coral reef tanaidacean assemblages along the SW and SE Gulf of Mexico: biodiversity, geographic distribution and community structure
Figure 1. Location of reef systems in the Gulf of Mexico. Area Natural Protegida Tuxpan–Lobos (ANPT–L), Parque Nacional Sistema Arrecifal Veracruzano (PNSAV) and Sistema Arrecifal Bajos Sisal (SABS).
Figure 3 in Autumn community structure in the shallow mixed layer of the subtropical South China Sea reveals a peculiar copepod and zooplankton assemblage
Figure 3. Vertical variation of temperature (A), salinity (B) and chlorophyll a (C) of the six sampling stations.
Figure 6 in Autumn community structure in the shallow mixed layer of the subtropical South China Sea reveals a peculiar copepod and zooplankton assemblage
Figure 6. Clustering dendrogram of different samples using Bray–Curtis similarity and clustering strategy of flexible links in the northern South China Sea.
Figure 2 in Autumn community structure in the shallow mixed layer of the subtropical South China Sea reveals a peculiar copepod and zooplankton assemblage
Figure 2. Monthly averaged information derived from NOAA for sea surface temperature of September 1999.
Figure 1 in Autumn community structure in the shallow mixed layer of the subtropical South China Sea reveals a peculiar copepod and zooplankton assemblage
Figure 1. Map of sampling stations during Ocean Research Vessel III cruise 563, from 27 September to 2 October 1999. Station A6 is the South-East Asia Time Series (SEATS) station in the South China Sea.
A community and functional comparison of coral and reef fish assemblages between four decades of coastal urbanisation and thermal stress.
<p>Urbanised coral reefs experience anthropogenic disturbances caused by coastal development, pollution and nutrient runoff, resulting in turbid, marginal conditions in which only certain species can persist. Mortality effects are exacerbated by increasingly regular thermal stress events, leading to shifts towards novel communities dominated by habitat generalists and species with low structural complexity.</p> <p>There is limited data on the turnover processes that occur due to this convergence of anthropogenic stressors, and how novel urban ecosystems are structured both at the community and functional level. As such, it is unclear how they will respond to future disturbance events.</p> <p>Here, we examine the patterns of coral reef community change, and determine whether ecosystem functions provided by specialist species are lost post-disturbance. We present a comparison of community and functional trait-based changes for scleractinian coral genera and reef fish species assemblages subject to coastal development, coastal modification, and mass bleaching between two time periods, 1975-6 and 2018, in Nakagusuku Bay, Okinawa, Japan.</p> <p>We observed an increase in fish habitat generalists, a dominance shift from branching to massive/ sub-massive corals and increasing site-based coral genera richness between years. Fish and coral communities significantly reassembled, but functional trait-based multivariate space remained constant, indicating a turnover of species with similar traits. A compression of coral habitat occurred, with shallow (<5m) and deep (>8m) coral genera shifting towards the mid-depths (5-8m).</p> <p>We show that although reef species assemblages altered post disturbance, new communities retained similar ecosystem functions. This result could be linked to the stressors experienced by urban reefs, which reflect those that will occur at an increasing frequency globally in the near future. Yet, even after shifts to disturbed communities, these fully functioning reef systems may maintain high conservation value.</p>
Data from: Influence of abiotic and biotic factors on benthic marine community composition, structure and stability: a multidisciplinary approach to molluscan assemblages from the Miocene of northern Germany
<p><span>The Miocene mica-clay deposits of Groß Pampau (northern Germany) are well known for their diverse assemblages of marine mammals, particularly whales. Despite numerous systematic and biostratigraphic studies, an in-depth palaeoecological analysis of its diverse molluscan assemblages and a comprehensive palaeoenvironmental reconstruction are lacking. Here, we integrated new faunal, sedimentological, and geochemical data to reconstruct the marine palaeo-ecosystem of the late Miocene sedimentary succession of Groß Pampau, and to identify the drivers controlling the composition, ecological structure and temporal dynamics of its macrobenthic molluscan assemblages. Fossil evidence, coupled with analyses of clay mineral composition, grain size distribution, and geochemical data (total organic carbon, total nitrogen, δ<sup>13</sup>C, δ<sup>18</sup>O, δ<sup>15</sup>N of sediment and shells), suggest a warm-temperate, mesotrophic, low-energy, offshore marine setting mostly below storm wave base and a pronounced surface-to-bottom water temperature gradient. Low variability in sedimentological and geochemical signals indicates generally stable physico-chemical conditions, whereas occurrences of opportunistic species (<em>Varicorbula</em> <em>gibba</em>) point at </span><span>occasionally less favourable bottom conditions, possibly related to transient hypoxia</span><span>. Canonical correspondence analysis reveals that the distribution of molluscan assemblages correlates with total organic carbon and nitrogen content, suggesting organic matter availability at the seafloor as a controlling factor. A pattern of repetitive punctuated stasis of molluscan assemblages is defined by the temporal persistence in taxonomic and ecological composition, occasionally interrupted by shifts to a different faunal configuration. We suggest that both stable environmental conditions and biotic interactions, i.e. the top-down control exerted by carnivorous gastropods and environmental modification by ubiquitous burrowing deposit feeders, probably contributed to the observed temporal stability. Whereas comparison with Miocene molluscan assemblages of Gram, Denmark, revealed differences in the presence and relative abundance of genera, functional congruence indicates that offshore benthic ecosystems of the southern North Sea Basin functioned similarly.</span></p>
Data from: Influence of abiotic and biotic factors on benthic marine community composition, structure and stability: a multidisciplinary approach to molluscan assemblages from the Miocene of northern Germany
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Topography and logging structure liana community assemblages in an upland evergreen forest, Ghana
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Data from: Validating the power of mitochondrial metagenomics for community ecology and phylogenetics of complex assemblages
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Data from: Assemblage Accumulation Curves: A framework for resolving species accumulation in biological communities using chloroplast genome sequences
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