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opencc-by-4.0May 2022View details →

Data for the journal article: 'Ecology of testate amoebae along an environmental gradient from bogs to calcareous fens in East-Central Europe: development of transfer functions for palaeoenvironmental reconstructions'

DATA DESCRIPTION: This repository provides training sets and R scripts for the development of three transfer function models that allow reconstructions of Holocene hydrochemical or hydrological (hydroclimatic) conditions from testate amoeba assemblages preserved in mires of East-Central Europe. Specifically, the repository contains (i) the full dataset and an R script for the development of the final MLRC model for inferring past water-mineral richness (expressed as pH) in various types of mires; (ii) the minerotrophic subset and an R script for the development of the final WAPLS com1 model for the reconstructions of past water-mineral richness (expressed as pH) in calcareous and rich fens; and (iii) the ombrotrophic subset and an R script for the development of the final PLS com2 model for inferring past depth to water table (DWT) in bogs and poor fens. Additionally, the repository includes the original versions of the full, minerotrophic and ombrotrophic training sets (i.e., the versions before removing outlier samples and rare taxa due to transfer function optimisation), and the compiled dataset, from which the three above-mentioned training sets were generated. For details, see <a href="https://doi.org/10.1016/j.palaeo.2022.111145">&Scaron;ímová et al. (2022)</a>. ARTICLE ABSTRACT: Testate amoebae play an important role in biomonitoring and the understanding of peatland (palaeo)ecology. However, their application has been mainly limited to Sphagnum-dominated peatlands, especially ombrotrophic bogs. To facilitate wider use of these microorganisms, we explored their ecology along a gradient from mineral-poor acidic bogs to mineral-rich calcareous fens with tufa formation using a new calibration dataset of over 250 samples from East-Central Europe. Specifically, we examined environmental controls on testate amoebae along the complete gradient and separately in the minerotrophic (pH >5.5) and ombrotrophic (pH <5) parts. Based on these findings, we developed and statistically evaluated transfer function models for the dominant factors controlling the community composition of these protists. Multivariate statistical analysis showed that groundwater pH was the main driver of species composition in the full and minerotrophic datasets. In contrast, testate amoeba communities in the ombrotrophic dataset were primarily structured by depth to water table (DWT). Under leave-one-out cross-validation (LOO), the best-performing model for DWT gave a prediction error (RMSEP) of 5.43 cm. The most robust models for groundwater mineral richness yielded RMSEPLOO of 0.45 and 0.27 pH units, for the full and the minerotrophic dataset respectively. This is the first study to present a complete set of testate amoeba-based transfer functions that allow reconstructions of Holocene hydrochemical and hydrological (hydroclimatic) variability in different mire types within one region. The new models open up the possibility for testate amoebae to become a valuable tool in palaeoecological research, although further work is needed to fully assess their performance and usefulness in practice.

opencc-zeroDec 2015View details →

Data from: How structured is the entangled bank? The surprisingly simple organization of multiplex ecological networks leads to increased persistence and resilience

Species are linked to each other by a myriad of positive and negative interactions. This complex spectrum of interactions constitutes a network of links that mediates ecological communities' response to perturbations, such as exploitation and climate change. In the last decades, there have been great advances in the study of intricate ecological networks. We have, nonetheless, lacked both the data and the tools to more rigorously understand the patterning of multiple interaction types between species (i.e., "multiplex networks"), as well as their consequences for community dynamics. Using network statistical modeling applied to a comprehensive ecological network, which includes trophic and diverse non-trophic links, we provide a first glimpse at what the full "entangled bank" of species looks like. The community exhibits clear multidimensional structure, which is taxonomically coherent and broadly predictable from species traits. Moreover, dynamic simulations suggest that this non-random patterning of how diverse non-trophic interactions map onto the food web could allow for higher species persistence and higher total biomass than expected by chance and tends to promote a higher robustness to extinctions.

opencc-zeroDec 2014View details →

Data from: Phylogenetic community ecology of soil biodiversity using mitochondrial metagenomics

High-throughput DNA methods hold great promise for the study of taxonomically intractable mesofauna of the soil. Here, we assess species diversity and community structure in a phylogenetic framework, by sequencing total DNA from bulk specimen samples and assembly of mitochondrial genomes. The combination of mitochondrial metagenomics and DNA barcode sequencing of 1494 specimens in 69 soil samples from three geographic regions in southern Iberia revealed >300 species of soil Coleoptera (beetles) from a broad spectrum of phylogenetic lineages. A set of 214 mitochondrial sequences longer than 3000 bp was generated and used to estimate a well-supported phylogenetic tree of the order Coleoptera. Shorter sequences, including cox1 barcodes, were placed on this mitogenomic tree. Raw Illumina reads were mapped against all available sequences to test for species present in local samples. This approach simultaneously established the species richness, phylogenetic composition and community turnover at species and phylogenetic levels. We find a strong signature of vertical structuring in soil fauna that shows high local community differentiation between deep soil and superficial horizons at phylogenetic levels. Within the two vertical layers, turnover among regions was primarily at the tip (species) level and was stronger in the deep soil than leaf litter communities, pointing to layer-mediated drivers determining species diversification, spatial structure and evolutionary assembly of soil communities. This integrated phylogenetic framework opens the application of phylogenetic community ecology to the mesofauna of the soil, among the most diverse and least well-understood ecosystems, and will propel both theoretical and applied soil science.

opencc-zeroDec 2015View details →

Data from: Human judgment vs. quantitative models for the management of ecological resources

Despite major advances in quantitative approaches to natural resource management, there has been resistance to using these tools in the actual practice of managing ecological populations. Given a managed system and a set of assumptions, translated into a model, optimization methods can be used to solve for the most cost-effective management actions. However, when the underlying assumptions are not met, such methods can potentially lead to decisions that harm the environment and economy. Managers who develop decisions based on past experience and judgment, without the aid of mathematical models, can potentially learn about the system and develop flexible management strategies. However, these strategies are often based on subjective criteria and equally invalid and often unstated assumptions. Given the drawbacks of both methods, it is unclear whether simple quantitative models improve environmental decision making over expert opinion. In this study, we explore how well students, using their experience and judgment, manage simulated fishery populations in an online computer game and compare their management outcomes to the performance of model-based decisions. We consider harvest decisions generated using four different quantitative models: (1) the model used to produce the simulated population dynamics observed in the game, with the values of all parameters known (as a control), (2) the same model, but with unknown parameter values that must be estimated during the game from observed data, (3) models that are structurally different from those used to simulate the population dynamics, and (4) a model that ignores age structure. Humans on average performed much worse than the models in cases 1–3, but in a small minority of scenarios, models produced worse outcomes than those resulting from students making decisions based on experience and judgment. When the models ignored age structure, they generated poorly performing management decisions, but still outperformed students using experience and judgment 66% of the time.

opencc-zeroJul 2022View details →

Data from: Links across ecological scales: Plant biomass responses to elevated CO2

Despite the wide agreement that increased plant biomass accumulation under elevated CO2 concentrations (e[CO2]) might play a key role in climate change, the effect of e[CO2] on plant biomass levels remains a major uncertainty in climate models. In the review associated with this dataset, we discuss the evidence for increased biomass levels under e[CO2] across multiple levels of ecological organization, scaling from physiological responses to changes in population-, community-, ecosystem-, and global-scale dynamics. We find that evidence for a sustained biomass response to e[CO2] varies across ecological scales, leading to diverging conclusions about the responses of individuals, populations, communities, and ecosystems. We identify key research gaps in our understanding of the effect of e[CO2] on plant biomass and highlight the need to integrate knowledge across scales of ecological organization so that large-scale modeling can represent the finer-scale mechanisms needed to constrain our understanding of future terrestrial C storage.

opencc-zeroAug 2022View details →

Supporting Data for Ocean acidification drives global reshuffling of ecological communities

The paradigm that climate change will alter global marine biodiversity is one of the most widely accepted. Yet, its predictions remain difficult to test because laboratory systems are inadequate at incorporating ecological complexity, and common biodiversity metrics have varying sensitivity to detect change. Here, we test for the prevalence of global responses in biodiversity and community-level change to future climate (acidification and warming) from studies at volcanic CO2 vents across four major global coastal ecosystems and studies in laboratory mesocosms. We detected globally replicable patterns of species replacements and community reshuffling under ocean acidification in major natural ecosystems, yet species diversity and other common biodiversity metrics were often insensitive to detect such community change, even under significant habitat loss. Where there was a lack of consistent patterns of biodiversity change, these were a function of similar numbers of studies observing negative vs positive species responses to climate stress. Laboratory studies showed weaker sensitivity to detect species replacements and community reshuffling in general. We conclude that common biodiversity metrics can be insensitive in revealing the anticipated effects of climate stress on biodiversity – even under significant biogenic habitat loss – and can mask widespread reshuffling of ecological communities in a future ocean. Whilst the influence of ocean acidification on community restructuring can be less evident than species loss, such changes can drive the dynamics of ecosystem stability or their functional change. Importantly, species identity matters, representing a substantial influence of future oceans.

opencc-zeroOct 2022View details →

Habitat heterogeneity affects the thermal ecology of the federally endangered blunt-nosed leopard lizard 2019 data

Global climate change is already contributing to the extirpation of numerous species worldwide, and sensitive species will continue to face challenges associated with rising temperatures throughout this century and beyond. It is especially important to evaluate the thermal ecology of endangered ectotherm species now so that mitigation measures can be taken as early as possible. A recent study of the thermal ecology of the federally endangered Blunt-Nosed Leopard Lizard (Gambelia sila) suggested that they face major activity restrictions due to thermal constraints in their desert habitat, but that large shade-providing shrubs act as thermal buffers to allow them to maintain surface activity without overheating. We replicated this study and also included a population of G. sila with no access to large shrubs to facilitate comparison of the thermal ecology of G. sila in shrubless and shrubbed populations. We found that G. sila without access to shrubs spent more time sheltering inside rodent burrows than lizards with access to shrubs, especially during the hot summer months. Lizards from a shrubbed population had higher midday body temperatures and therefore poorer thermoregulatory accuracy than G. sila from a shrubless population, suggesting that greater surface activity may represent a thermoregulatory tradeoff for G. sila. Lizards at both sites are currently constrained from using open, sunny microhabitats for much of the day during their short active seasons, and our projections suggest that climate change will exacerbate these restrictions and force G. sila to use rodent burrows for shelter even more than they do now, especially at sites without access to shrubs. The continued management of shrubs and of burrowing rodents at G. sila sites is therefore essential to the survival of this endangered species.

FIGURE 15. Francapseudes uniarticulatus. Female DBUA0002012.01a. A, cheliped. B, pereopod 1. C, pereopod 2. D, pereopod 3. E, pereopod 4. F, pereopod 5. G in The Apseudomorpha (Crustacea: Tanaidacea) of the Gulf of Cadiz and Horseshoe Continental Rise (NE Atlantic): A taxonomic review with new records, species, and ecological data

FIGURE 15. Francapseudes uniarticulatus. Female DBUA0002012.01a. A, cheliped. B, pereopod 1. C, pereopod 2. D, pereopod 3. E, pereopod 4. F, pereopod 5. G, pleopod.

FIGURE 14. Francapseudes uniarticulatus. Female DBUA0002012.01a. A, right mandible. B, left mandible. C, maxillule outer endite. D, maxillule inner endite. E, maxillule palp. F, maxilla. G, maxilliped palp. H in The Apseudomorpha (Crustacea: Tanaidacea) of the Gulf of Cadiz and Horseshoe Continental Rise (NE Atlantic): A taxonomic review with new records, species, and ecological data

FIGURE 14. Francapseudes uniarticulatus. Female DBUA0002012.01a. A, right mandible. B, left mandible. C, maxillule outer endite. D, maxillule inner endite. E, maxillule palp. F, maxilla. G, maxilliped palp. H, maxilliped endite.

FIGURE 13. Francapseudes uniarticulatus. Female DBUA0002012.01a. A in The Apseudomorpha (Crustacea: Tanaidacea) of the Gulf of Cadiz and Horseshoe Continental Rise (NE Atlantic): A taxonomic review with new records, species, and ecological data

FIGURE 13. Francapseudes uniarticulatus. Female DBUA0002012.01a. A, habitus (dorsal view). B, habitus (lateral view). C, antennule. D, antenna.

FIGURE 11. Leviapseudes segonzaci. Male DBUA0002010.06. A in The Apseudomorpha (Crustacea: Tanaidacea) of the Gulf of Cadiz and Horseshoe Continental Rise (NE Atlantic): A taxonomic review with new records, species, and ecological data

FIGURE 11. Leviapseudes segonzaci. Male DBUA0002010.06. A, habitus (lateral view). B, antennule. C, labrum. D, left mandible. E, right mandible. F, pereopod 4. G, pleopod.

FIGURE 9. Leviapseudes segonzaci. Female DBUA0002010.01a. A, cheliped. B, pereopod1. C, pereopod 2. D, pereopod 3. E, pereopod 4 in The Apseudomorpha (Crustacea: Tanaidacea) of the Gulf of Cadiz and Horseshoe Continental Rise (NE Atlantic): A taxonomic review with new records, species, and ecological data

FIGURE 9. Leviapseudes segonzaci. Female DBUA0002010.01a. A, cheliped. B, pereopod1. C, pereopod 2. D, pereopod 3. E, pereopod 4.

FIGURE 8. Leviapseudes segonzaci. Female DBUA0002010.01a. A, labrum. B, left mandible. C in The Apseudomorpha (Crustacea: Tanaidacea) of the Gulf of Cadiz and Horseshoe Continental Rise (NE Atlantic): A taxonomic review with new records, species, and ecological data

FIGURE 8. Leviapseudes segonzaci. Female DBUA0002010.01a. A, labrum. B, left mandible. C, incisor and setal row of right mandible. D, labium. E, maxillule inner endite. F; maxillule outer endite. G, maxillule palp. H, maxilla. I, maxilliped palp. J, maxilliped endite. K, epignath.

FIGURE 7. Leviapseudes segonzaci. Female DBUA0002010.01a. A in The Apseudomorpha (Crustacea: Tanaidacea) of the Gulf of Cadiz and Horseshoe Continental Rise (NE Atlantic): A taxonomic review with new records, species, and ecological data

FIGURE 7. Leviapseudes segonzaci. Female DBUA0002010.01a. A, habitus (dorsal view). B, habitus (lateral view). C, detail of pleonite 1 (lateral view). D, detail of pleotelson and uropod (lateral view). E, antennule. F, antenna (lateral view).

FIGURE 6 in The Apseudomorpha (Crustacea: Tanaidacea) of the Gulf of Cadiz and Horseshoe Continental Rise (NE Atlantic): A taxonomic review with new records, species, and ecological data

FIGURE 6. Atlantapseudes curvatus sp. nov. Male paratype DBUA0002004.01. A, cheliped. B, pereopod 1. C, pereopod 2. D, pereopod 3. E, Pereopod 4. F, pereopod 5. G, pereopod 6.

FIGURE 5 in The Apseudomorpha (Crustacea: Tanaidacea) of the Gulf of Cadiz and Horseshoe Continental Rise (NE Atlantic): A taxonomic review with new records, species, and ecological data

FIGURE 5. Atlantapseudes curvatus sp. nov. Female paratype DBUA0002002.01. A, pereopod 4. B, pereopod 5. C, pereopod 6.

FIGURE 4 in The Apseudomorpha (Crustacea: Tanaidacea) of the Gulf of Cadiz and Horseshoe Continental Rise (NE Atlantic): A taxonomic review with new records, species, and ecological data

FIGURE 4. Atlantapseudes curvatus sp. nov. Female paratype DBUA0002002.01. A, cheliped. B, pereopod 1. C, pereopod 2. D, pereopod 3.

FIGURE 3 in The Apseudomorpha (Crustacea: Tanaidacea) of the Gulf of Cadiz and Horseshoe Continental Rise (NE Atlantic): A taxonomic review with new records, species, and ecological data

FIGURE 3. Atlantapseudes curvatus sp. nov. Female paratype DBUA0002002.01. A, labrum. B, left mandible. C, detail of left mandible. D, detail of right mandible. E, right mandible palp. F, right mandible molar. G, labium. H, maxillule endites. I, maxillule palp. J, maxilla. K, maxilliped palp. L, maxilliped endite. M, epignath.

FIGURE 2 in The Apseudomorpha (Crustacea: Tanaidacea) of the Gulf of Cadiz and Horseshoe Continental Rise (NE Atlantic): A taxonomic review with new records, species, and ecological data

FIGURE 2. Atlantapseudes curvatus sp. nov. Female paratype DBUA0002002.01. A, habitus. B, antennule. C, antenna.

FIGURE 1 in The Apseudomorpha (Crustacea: Tanaidacea) of the Gulf of Cadiz and Horseshoe Continental Rise (NE Atlantic): A taxonomic review with new records, species, and ecological data

FIGURE 1. Map of the Gulf of Cadiz and Horseshoe abyssal plain showing the structures mentioned in this study. Triangles: Mud volcanoes. Circles: Carbonate mounds.