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opencc-zeroJan 2024View details →

Habitat simplification affects functional group structure along with taxonomic and phylogenetic diversity of temperate-zone ant assemblages over a ten-year period

Biodiversity is declining at various scales due to habitat simplification. Nevertheless, there is scarce information on how the biotic and abiotic changes linked to simplification affect several diversity dimensions, such as taxonomic, functional, and phylogenetic diversities. This study investigated whether transforming natural oak forests into induced grasslands affected species diversity, functional group structure, and phylogenetic diversity of ant assemblages inhabiting a temperate forest in central Mexico. We placed over 1,000 pitfall traps in five sampling events covering a ten-year period. We used Hill numbers to evaluate species diversity differences between vegetation types and patterns over time. Ant species were classified into stress-related functional groups, which were analyzed for their association with vegetation types and changes to their proportional abundance over time. We calculated the standardized effect size of the mean nearest taxon distance to quantify the evolutionary history and test for non-random patterns within vegetation types and sampling years. Species richness did not differ between vegetation types, yet grasslands showed greater diversity for the q=1 and q=2 orders. Besides, we found three ant species as bioindicators for each vegetation. Regarding functional structure, cold climate specialists were associated with oak forests. In contrast, generalist species were predominant in induced grasslands. Higher phylogenetic diversity with an overdispersed structure was associated with oak forest, whereas lower phylogenetic diversity and a clustered pattern were found in induced grassland. These results indicate that habitat simplification may not affect the number of ant species but rather increases their relative abundance and reorganizes the functional and phylogenetic structure in the ecosystem, particularly shift towards the dominance of evolutionary close-related species and broad-stress tolerant groups. These results highlight the importance of integrating further dimensions of diversity to properly evaluate the reassembly dynamics after habitat simplification and understand the mechanisms driving this biodiversity loss.

opencc-zeroDec 2023View details →

Predictive mapping of tree species assemblages in an African montane rainforest

Conservation of mountain ecosystems can benefit from knowledge of habitats and their distribution patterns. This benefit is particularly true for diverse ecosystems with high conservation values such as the "Afromontane" rainforests. We mapped the vegetation of one such forest: the rugged Bwindi Impenetrable Forest, Uganda—a World Heritage Site known for its many restricted-range plants and animal taxa including several iconic species. Given variation in elevation, terrain and human impacts across Bwindi, we hypothesised that these factors influence the composition and distribution of tree species. To test this, detailed surveys were carried out using stratified random sampling. We established 289 georeferenced sample sites (each with 15 trees ≥20 cm dbh) ranging from 1,320 to 2,467 m a.s.l. and measured 4,335 trees comprising 89 species that occurred in four or more sample sites. These data were analysed against twenty-one digitally mapped biophysical variables using various analytical techniques including non-metric multidimensional scaling (NMDS) and random forests. We identified six tree species assemblages with distinct compositions. Among the biophysical variables, elevation had the strongest correlation with the ordination (r2=0.5; p<0.001). The "out-of-bag" (OOB) estimate of the error rate for the best final model was 50.7% meaning that nearly half of the variation was accounted for using a limited set of variables. We demonstrate that it is possible to predict the spatial pattern of such a forest based on sampling across a highly complex landscape. Such methods offer accurate mapping of composition that can guide conservation.

opencc-zeroFeb 2024View details →

Effects of mowing on body size patterns in spider assemblages of mesic meadows

Habitat disturbance affects not only the abundance, species richness and species composition of the local fauna, but also the body size of specific individuals and body size patterns in animal assemblages. Particularly large disturbances occur in agroecosystems, where many agricultural treatments are carried out. One of them, which is most commonly applied to grasslands and which significantly damages the habitat structure, is mowing. We examined the effect of mowing on mean, skewness, and kurtosis of the body size in epigeic spider assemblages. The research was conducted on mesic meadows in eastern Poland, in an agricultural landscape typical for this region, consisting of a mosaic of meadows, fields and forests. Spiders were collected using pitfall traps in two sampling periods: the first before mowing and the second when part of the meadows had been mown. Mowing had no significant effect on mean body size, skewness and kurtosis of the body size in epigeic spider assemblages. However, after the cut, mown plots showed on average significantly smaller spider species than unmown plots. Both the value of skewness and kurtosis significantly increased after mowing, but to the same extent on both the control and mown plots. The decrease in mean body size and increase in skewness in spider assemblages were mainly due to an increase in the number of small species from the Linyphiidae family. It is likely that these species began to migrate (via ballooning) during the second sampling session, following the start of haying, and were thus caught in traps more frequently. Our study showed no clear, significant changes in the body size structure of epigeic spiders in mown meadows compared to unmown ones, which may suggest that the mowing, where extensive farming is practised, does not have a long-term significant negative impact on this group of invertebrates.

opencc-by-4.0Mar 2024View details →

Harmonized data and R code for "Coherent response of zoo- and phytoplankton assemblages to global warming since the Last Glacial Maximum"

Harmonized data and R code for "Coherent response of zoo- and phytoplankton assemblages to global warming since the Last Glacial Maximum" by Tonke Strack, Lukas Jonkers, Marina C. Rillo, Karl-Heinz Baumann, Helmut Hillebrand and Michal Kucera (submitted to Global Ecology and Biogeography, 2024). STRUCTURED ABSTRACT Aim: We use the fossil record of different marine plankton groups to determine how their biodiversity changed during past climate warming comparable to projected future warming. Location: North Atlantic Ocean and adjacent seas. Time series cover a latitudinal range of 75°N to 6°S. Time period: Past 24,000 years, i.e., from the Last Glacial Maximum (LGM) to the current warm period covering the last deglaciation. Major taxa studied: Planktonic foraminifera, dinoflagellates and coccolithophores. Methods: We analyse time series of fossil plankton communities using principal component analysis and generalised additive models to estimate the overall trend of temporal compositional change in each plankton group and identify periods of significant change. We further analyse local biodiversity change by analysing species richness, species gains and losses, and the effective number of species in each sample and compare alpha diversity to the LGM mean. Results: All plankton groups show remarkably similar trends in the rates and spatio-temporal dynamics of local biodiversity change and a pronounced non-linearity with climate change in the current warm period. Assemblages of planktonic foraminifera and dinoflagellates started to significantly change with the onset of global warming around 15,500 to 17,000 years ago and continued to change at the same pace during the current warm period until at least 5,000 years ago, while coccolithophores assemblages changed at a constant rate throughout the past 24,000 years seemingly irrespective of the prevailing temperature change. Main conclusions: The climate change during the transition from the LGM to the current warm period led to a long-lasting reshuffling of the zoo- and phytoplankton assemblages likely associated with the emergence of new ecological interactions and possibly a shift in the dominant drivers of plankton assemblage change from more abiotic-dominated causes during the last deglaciation to more biotic-dominated causes with the onset of the Holocene. CONTENT This dataset includes the harmonized assemblage data of the three investigated plankton groups (planktonic foraminifera, dinoflagellates and coccolithophores) as well as all the R code needed to re-produce the results of this study and it's main figures. Scripts written by Tonke Strack DATA SOURCES 1)  GMST: Osman, M. B. et al. Globally resolved surface temperatures since the Last Glacial Maximum.            Nature 599, 239-244, doi:10.1038/s41586-021-03984-4 (2021). 2) WOA18: Locarnini, R. A. et al. World Ocean Atlas 2018, Volume 1: Temperature. A. Mishonov, Technical Editor.            NOAA Atlas NESDIS 81, 52 (2019). 3) plankton assemblage data: individual data references provided in CoreList.csv DATA 1. Harmonized assemblage data*: FullDataTable_PF_harmonized.txt 2. Core list of additional information on time series: CoreList.csv 3. Reference lists for species names names: ReferenceList_PlanktonicForaminifera.csv, ReferenceList_Dino.csv, ReferenceList_Cocco.csv CODE 1. 01_LoadData.R: loads harmonized assemblage data from planktonic foraminifera, dinocyst and coccolithophores 2. 02_GMST_import.R: loads loads the globally resolved surface temperature since the LGM from Osman et al. (2011) 3. 03_DataAnalysis_PCA_GAM.R:  PCA/GAM analysis on the plankton assemblage data (results shown in Figure 2 and 3), sensititvity analysis (results shown in Figure 4), and some summary statistics 4. 04_DataAnalysis_MH_GAM_AlternativeApproach.R: alternative GAM approach using Morisita-Horn index (results shown in Figure S2, S3 and S4) 5. 05_DataAnalysis_BiodiversityChange.R: local biodiversity change analysis of individual time series  (results shown in Figure 5, 6 and S9) *Assemblage data of individual time series were manually downloaded, quality checked, taxonomically harmonized, and combined into one data file. Planktonic foraminifera data were harmonized following Siccha and Kuchera (2017). We merged Globigerinoides ruber ruber and Globigerinoides ruber  albus, because some studies only reported them together as Globigerinoides ruber. Also, P/D intergrades (an informal category of morphological intermediates between Neogloboquadrina incompta and Neogloboquadrina dutertrei) were merged with Neogloboquadrina incompta. Dinocyst taxonomy was harmonized following de Vernal et al. (2020) with slight additions following Zonneveld et al. (2013). Names that could not be resolved using synonym lists and assigned a harmonized name following de Vernal et al. (2020) and Zonneveld et al. (2013) were treated as unidentified specimens and were excluded from the assemblage analyses. These specimens were present in 4 time series and were rare taxa (relative abundances < 3%). The protoperidinoids were also excluded from further assemblage analyses as this category includes all unidentified brownish cysts (de Vernal et al., 2020). Coccolithophore taxonomy follows Young et al. (2003) and coccolith countings were conducted on a scanning-electron microscope (SEM) to ensure that all specimens are resolved to the species level. We merged Coccolithus pelagicus subspecies, because they were not distinguished in all studies.  Species not reported in the time series data were assumed to be absent (that is, zero abundance) which is in accordance with the completeness of the counts reported in the original studies. The original data were either given in absolute or relative abundances, and after excluding unnecessary columns (unidentified or rare taxa that could not be harmonised) the abundances were recalculated to 100 %. In total, 41 species of planktonic foraminifera, 30 species of coccolithophores and 53 species of organic-walled dinocysts were observed in our study. REFERENCES de Vernal, A., Radi, T., Zaragosi, S., Van Nieuwenhove, N., Rochon, A., Allan, E., . . . Richerol, T. (2020). Distribution of common modern dinoflagellate cyst taxa in surface sediments of the Northern Hemisphere in relation to environmental parameters: The new n=1968 database. Mar. Micropaleontol., 159. doi:10.1016/j.marmicro.2019.101796 Siccha, M. & Kucera, M. ForCenS, a curated database of planktonic foraminifera census counts in marine surface sediment samples. Sci. Data 4, 170109, doi:10.1038/sdata.2017.109 (2017). Young, J. R., Geisen, M., Cros, L., Kleijne, A., Sprengel, C., Probert, I., & Østergaard, J. B. (2003). A guide to extant coccolithophore taxonomy. Journal of Nannoplankton Research Special Issue, 1, 1-125. doi:10.58998/jnr2297 Zonneveld, K. A. F., Marret, F., Versteegh, G. J. M., Bogus, K., Bonnet, S., Bouimetarhan, I., . . . Young, M. (2013). Atlas of modern dinoflagellate cyst distribution based on 2405 data points. Rev. Palaeobot. Palynol., 191, 1-197. doi:10.1016/j.revpalbo.2012.08.003

opencc-zeroMar 2024View details →

Deer grazing drove an assemblage-level evolution of plant dwarfism in an insular system

Plant dwarfism, a syndrome characterised by a significant reduction in plant height and organ size, is a widely observed pattern of stress-tolerant life-form evolution that results from local adaptation to harsh environmental conditions. The drivers of assemblage-level dwarfism have primarily been attributed to abiotic factors, such as low temperature, aridity, poor soil fertility, or frequent fires. While biotic factors such as grazing pressure from herbivores can contribute to the establishment of plant dwarfism, these factors have rarely been tested at assemblage levels. Focusing on a dwarf plant assemblage comprising over 80 taxa on a small continental island in Japan with a high deer density, we hypothesised that historical deer grazing could also be a factor contributing to the large-scale convergent evolution of dwarfism. To test this hypothesis, we measured the size of 1,908 individual plants of 40 taxa-pairs, comprising both palatable and unpalatable pairs from the island and their counterpart taxa from neighbouring regions, and sought to assess which factors (i.e. low solar radiation, estimated divergence time, low nutrient conditions, and grazing pressure from deer) may have contributed to the formation of the dwarf plant assemblage on the island. We also performed genetic analysis to infer the timeframes for the establishment of dwarf taxa. Statistical analyses revealed that plant size was significantly reduced mainly among the palatable taxa growing on the island, with preferential grazing by deer being identified as the most significant factor influencing plant size. Furthermore, genetic analyses revealed that dwarf ecotypes may have evolved over tens of thousands of years. Synthesis: To the best of our knowledge, this study is the first to demonstrate that interactions with herbivores can shape the assemblage-level convergence of plant dwarfism. These findings enhance our current understanding of the formation of plant functional diversity.

opencc-by-4.0Dec 2013View details →

Fig. 1 in Predominance of Vibidia duodecimguttata (Poda, 1761) in the assemblages of ladybird beetles (Coleoptera: Coccinellidae) overwintering in floodplain forests

Fig. 1. Localization of the ladybird sampling sites (I-VI).

opencc-by-4.0Dec 2023View details →

Figure 3 in First Cretaceous teleostean otolith assemblage (Arkadelphia Formation, upper Maastrichtian) from Arkansas, USA, early Gadiformes, and the Western Interior Seaway

Figure 3. Location of the study area near Cabot, Lonoke County, Arkansas, USA.

Figure 20 in A late Eocene wood assemblage from the Crooked River Basin, Oregon, USA

Figure 20. Caption on pg. 45.

Figure 18 in A late Eocene wood assemblage from the Crooked River Basin, Oregon, USA

Figure 18. Caption on pg. 40.

Figure 15 in A late Eocene wood assemblage from the Crooked River Basin, Oregon, USA

Figure 15. Caption on pg. 32.

Figure 16 in A late Eocene wood assemblage from the Crooked River Basin, Oregon, USA

Figure 16. Caption on pg. 35.

Figure 17 in A late Eocene wood assemblage from the Crooked River Basin, Oregon, USA

Figure 17. Caption on pg. 37.

Figure 8 in A late Eocene wood assemblage from the Crooked River Basin, Oregon, USA

Figure 8. Caption on pg. 17.

Figure 13 in A late Eocene wood assemblage from the Crooked River Basin, Oregon, USA

Figure 13. Caption on pg. 28.

opencc-by-4.0Apr 2024View details →

Supporting dataset for manuscript "Role of metabolism, resistance, and/or antagonism as drivers of endomicrobiomes assemblage in Origanum heracleoticum L." by Giulia Semenzato et al. 2024

Raw data used for the analysis presented in the manuscript "Role of metabolism, resistance, and/or antagonism as drivers of endomicrobiomes assemblage in Origanum heracleoticum L." by authors Giulia Semenzato, Francesco Vitali, Arcangela Frascella, Ludovica Lollini, Stefano Mocali, Alessio Papini, Renato Fania, and Giovanni Emiliani  <ul> <li>phenome_combined_normalized_R.csv = activity values (AV) obtained after DuctApe elaboration of phenotype microarray data for carbon sources analysis. Control well signal was substracted.</li> <li>phenome_combined_nonNormalized_R.csv = activity values (AV) obtained after DuctApe elaboration of phenotype microarray data for resistance/sensibility sources analysis. Control well were signal not substracted.</li> <li>Rawdata_cross_streaking.csv = raw data obtained from cross-streaking experiment.</li> <li>Rawdata_MIC.csv = raw data obtained from MIC experiment.</li> <li>Raw_data_BIOLOG.zip = raw data from phenotype microarray readings.</li> </ul>

opencc-by-4.0Dec 2023View details →

Data and R code for Reddin et al. 'Marine species and assemblage change foreshadowed by their thermal bias over Early Jurassic warming''

This repository holds the raw and prepared datasets and R code to handle them for the manuscript Reddin et al. 'Marine species and assemblage change foreshadowed by their thermal bias over Early Jurassic warming'. Nature Communications

opencc-zeroSep 2021View details →

FIG. 6 in The lizard (Reptilia, Squamata) assemblage from the Paleocene of Montchenot (Paris Basin, MP6)

FIG. 6. —?Lacertidae, distal end of a left humerus, MNHN.F.MTC239, ventral view. Scale bar: 1 mm.

opencc-by-4.0Nov 2011View details →

Fig. 2 in Dynamics of fish assemblages on a continuous rocky reef and adjacent unconsolidated habitats at Fernando de Noronha Archipelago, tropical western Atlantic

Fig. 2. Mean values (±SE) of temporal fluctuation and temporal stability.

opencc-zeroDec 2021View details →

Chironomid assemblages and inferred summer temperature from the Last Glacial Period (ca. 98–46 ka), from Füramoos, Southern Germany

The data herein presents a new chironomid record and associated chironomid-based temperature reconstruction covering the time interval ca. 98–46 ka from the palaeolake Füramoos, Southern Germany. These data also include non-chironomid invertebrate remains, including Ceratopogonidae, Daphnia and Ephemeroptera as well as Characean oospores.