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  • 1
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    BioDeepTime: A database of biodiversity time series for modern and fossil assemblages
    Wiley ; 2023
    In:  Global Ecology and Biogeography Vol. 32, No. 10 ( 2023-10), p. 1680-1689
    Details
    In: Global Ecology and Biogeography, Wiley, Vol. 32, No. 10 ( 2023-10), p. 1680-1689
    Abstract: We have little understanding of how communities respond to varying magnitudes and rates of environmental perturbations across temporal scales. BioDeepTime harmonizes assemblage time series of presence and abundance data to help facilitate investigations of community dynamics across timescales and the response of communities to natural and anthropogenic stressors. BioDeepTime includes time series of terrestrial and aquatic assemblages of varying spatial and temporal grain and extent from the present‐day to millions of years ago. Main Types of Variables Included BioDeepTime currently contains 7,437,847 taxon records from 10,062 assemblage time series, each with a minimum of 10 time steps. Age constraints, sampling method, environment and taxonomic scope are provided for each time series. Spatial Location and Grain The database includes 8752 unique sampling locations from freshwater, marine and terrestrial ecosystems. Spatial grain represented by individual samples varies from quadrats on the order of several cm 2 to grid cells of ~100 km 2 . Time Period and Grain BioDeepTime in aggregate currently spans the last 451 million years, with the 10,062 modern and fossil assemblage time series ranging in extent from years to millions of years. The median extent of modern time series is 18.7 years and for fossil series is 54,872 years. Temporal grain, the time encompassed by individual samples, ranges from days to tens of thousands of years. Major Taxa and Level of Measurement The database contains information on 28,777 unique taxa with 4,769,789 records at the species level and another 271,218 records known to the genus level, including time series of benthic and planktonic foraminifera, coccolithophores, diatoms, ostracods, plants (pollen), radiolarians and other invertebrates and vertebrates. There are to date 7012 modern and 3050 fossil time series in BioDeepTime. Software Format SQLite, Comma‐separated values.
    Type of Medium: Online Resource
    ISSN: 1466-822X , 1466-8238
    URL: Issue
    URL: Article
    DOI: 10.1111/geb.v32.10
    DOI: 10.1111/geb.13735
    Language: English
    Publisher: Wiley
    Publication Date: 2023
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  • 2
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    fossilbrush : An R package for automated detection and resolution of anomalies in palaeontological occurrence data
    Wiley ; 2022
    In:  Methods in Ecology and Evolution Vol. 13, No. 11 ( 2022-11), p. 2404-2418
    Details
    In: Methods in Ecology and Evolution, Wiley, Vol. 13, No. 11 ( 2022-11), p. 2404-2418
    Abstract: Fossil occurrence databases are indispensable resources to the palaeontological community, yet present unique data cleaning challenges. Many studies devote significant attention to cleaning fossil occurrence data prior to analysis, but such efforts are typically bespoke and difficult to reproduce. There are also no standardised methods to detect and resolve errors despite the development of an ecosystem of cleaning tools fuelled by the concurrent growth of neontological occurrence databases. As fossil occurrence databases continue to increase in size, the demand for standardised, automated and reproducible methods to improve data quality will only grow. Here, we present semi‐automated cleaning solutions to address these issues with a new R package fossilbrush . We apply our cleaning protocols to the Paleobiology Database to assess the prevalence of anomalous entries and the efficacy and impact of our methods. We find that anomalies may be effectively resolved by comparison against a published compendium of stratigraphic ranges, improving the stratigraphic quality of the data, and through methods which detect outliers in taxon‐wise occurrence stratigraphic distributions. Despite this, anomalous entries remain prevalent throughout major clades, with often more than 30% of genera in major fossil groups (e.g. bivalves, echinoderms) displaying stratigraphically suspect occurrence records. Our methods provide a way to flag and resolve anomalous taxonomic data before downstream palaeobiological analysis and may also aid in the automation and targeting of future cleaning efforts. We stress, however, that our methods are semi‐automated and are primarily for the detection of potential anomalies for further scrutiny, as full automation should not be a substitute for expert vetting. We note that some of our methods do not rely on external databases for anomaly resolution and so are also applicable to occurrences in neontological databases, expanding the utility of the fossilbrush R package.
    Type of Medium: Online Resource
    ISSN: 2041-210X , 2041-210X
    URL: Issue
    URL: Article
    DOI: 10.1111/mee3.v13.11
    DOI: 10.1111/2041-210X.13966
    Language: English
    Publisher: Wiley
    Publication Date: 2022
    detail.hit.zdb_id: 2528492-7
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  • 3
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    Climate change disrupts core habitats of marine species
    Wiley ; 2023
    In:  Global Change Biology Vol. 29, No. 12 ( 2023-06), p. 3304-3317
    Details
    In: Global Change Biology, Wiley, Vol. 29, No. 12 ( 2023-06), p. 3304-3317
    Abstract: Driven by climate change, marine biodiversity is undergoing a phase of rapid change that has proven to be even faster than changes observed in terrestrial ecosystems. Understanding how these changes in species composition will affect future marine life is crucial for conservation management, especially due to increasing demands for marine natural resources. Here, we analyse predictions of a multiparameter habitat suitability model covering the global projected ranges of 〉 33,500 marine species from climate model projections under three CO 2 emission scenarios (RCP2.6, RCP4.5, RCP8.5) up to the year 2100. Our results show that the core habitat area will decline for many species, resulting in a net loss of 50% of the core habitat area for almost half of all marine species in 2100 under the high‐emission scenario RCP8.5. As an additional consequence of the continuing distributional reorganization of marine life, gaps around the equator will appear for 8% (RCP2.6), 24% (RCP4.5), and 88% (RCP8.5) of marine species with cross‐equatorial ranges. For many more species, continuous distributional ranges will be disrupted, thus reducing effective population size. In addition, high invasion rates in higher latitudes and polar regions will lead to substantial changes in the ecosystem and food web structure, particularly regarding the introduction of new predators. Overall, our study highlights that the degree of spatial and structural reorganization of marine life with ensued consequences for ecosystem functionality and conservation efforts will critically depend on the realized greenhouse gas emission pathway.
    Type of Medium: Online Resource
    ISSN: 1354-1013 , 1365-2486
    URL: Issue
    URL: Article
    DOI: 10.1111/gcb.v29.12
    DOI: 10.1111/gcb.16612
    Language: English
    Publisher: Wiley
    Publication Date: 2023
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    detail.hit.zdb_id: 2020313-5
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  • 4
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    Marine invertebrate migrations trace climate change over 450 million years
    Wiley ; 2020
    In:  Global Ecology and Biogeography Vol. 29, No. 7 ( 2020-07), p. 1280-1282
    Details
    In: Global Ecology and Biogeography, Wiley, Vol. 29, No. 7 ( 2020-07), p. 1280-1282
    Type of Medium: Online Resource
    ISSN: 1466-822X , 1466-8238
    URL: Issue
    URL: Article
    DOI: 10.1111/geb.v29.7
    DOI: 10.1111/geb.13114
    Language: English
    Publisher: Wiley
    Publication Date: 2020
    detail.hit.zdb_id: 1479787-2
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  • 5
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    The stability of coastal benthic biogeography over the last 10 million years
    Wiley ; 2018
    In:  Global Ecology and Biogeography Vol. 27, No. 9 ( 2018-09), p. 1106-1120
    Details
    In: Global Ecology and Biogeography, Wiley, Vol. 27, No. 9 ( 2018-09), p. 1106-1120
    Abstract: We demarcate marine benthic global bioregions based on fossil and recent occurrence data. Our main goal is to compare past and present biogeography and to extract major abiotic drivers of biogeographical patterns. We specifically test the hypothesis that global biogeography has changed markedly after the climatic fluctuations of the past 10 Myr. Location Worldwide. Time period Recent; late Miocene–Pleistocene interval. Major taxa studied Benthic taxa with a rich fossil record: Bivalvia, Brachiopoda, Bryozoa, Gastropoda, Echinodermata, Decapoda and reef corals. Methods We use occurrence data from the Ocean Biogeographic Information System (OBIS) and the Paleobiology Database to construct compositional networks and outline objective marine bioregions of benthic marine invertebrates using the “infomap” community detection algorithm. We assess the association of modern bioregions with a variety of environmental parameters by applying multivariate statistical analyses, such as principal components analysis, random forests and multiple logistic regressions. Results Recent first‐order bioregions for the coastal ocean are, in general, consistent across all taxa. Seawater temperature surpasses nutrients, primary production and salinity as a predictor of modern bioregion distributions. Despite substantial climatic variations, late Cenozoic biogeographical patterns recorded in fossils are very similar to modern ones. Main conclusions Biogeographical boundaries within oceans are strongly controlled by temperature gradients, but open oceanic and continental barriers determine the global biogeographical structure. The joint structure of a landmass distribution, deep ocean basins and the latitudinal temperature gradient defines bioregionalization of the benthic marine habitat, which did not change substantially over the past 10 Myr.
    Type of Medium: Online Resource
    ISSN: 1466-822X , 1466-8238
    URL: Issue
    URL: Article
    DOI: 10.1111/geb.v27.9
    DOI: 10.1111/geb.12771
    Language: English
    Publisher: Wiley
    Publication Date: 2018
    detail.hit.zdb_id: 1479787-2
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  • 6
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    The r package divDyn for quantifying diversity dynamics using fossil sampling data
    Wiley ; 2019
    In:  Methods in Ecology and Evolution Vol. 10, No. 5 ( 2019-05), p. 735-743
    Details
    In: Methods in Ecology and Evolution, Wiley, Vol. 10, No. 5 ( 2019-05), p. 735-743
    Abstract: Unbiased time series of diversity dynamics are vital for quantifying the grand history of life. Applications include identifying ancient mass extinctions and inferring both biotic and abiotic controls on diversification rates. We introduce divDyn, a new r package that facilitates the calculation of taxonomic richness, extinction and origination rates from time‐binned fossil data. State‐of‐the‐art counting protocols, and sampling standardization functions permit the reconstruction of biologically meaningful time series. Additional functions permit the partitioning of turnover rates by environmental affinity. Using divDyn, we display Phanerozoic‐scale diversity dynamics of marine invertebrates. With the help of the core function and standard subsampling options, we revisit the hypothesis of declining taxonomic rates over time, mass extinctions and equilibrial diversity dynamics and assess their methodological dependency. Our results suggest that rates declined only over the early Phanerozoic, only three mass extinctions stand out clearly, and evidence of equilibrial dynamics is dependent on the used methods. The modular and fast implementation of published methods ensures traceability, reproducibility and comparability of future studies.
    Type of Medium: Online Resource
    ISSN: 2041-210X , 2041-210X
    URL: Issue
    URL: Article
    DOI: 10.1111/mee3.2019.10.issue-5
    DOI: 10.1111/2041-210X.13161
    Language: English
    Publisher: Wiley
    Publication Date: 2019
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  • 7
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    Victims of ancient hyperthermal events herald the fates of marine clades and traits under global warming
    Wiley ; 2021
    In:  Global Change Biology Vol. 27, No. 4 ( 2021-02), p. 868-878
    Details
    In: Global Change Biology, Wiley, Vol. 27, No. 4 ( 2021-02), p. 868-878
    Abstract: Organismic groups vary non‐randomly in their vulnerability to extinction. However, it is unclear whether the same groups are consistently vulnerable, regardless of the dominant extinction drivers, or whether certain drivers have their own distinctive and predictable victims. Given the challenges presented by anthropogenic global warming, we focus on changes in extinction selectivity trends during ancient hyperthermal events: geologically rapid episodes of global warming. Focusing on the fossil record of the last 300 million years, we identify clades and traits of marine ectotherms that were more prone to extinction under the onset of six hyperthermal events than during other times. Hyperthermals enhanced the vulnerability of marine fauna that host photosymbionts, particularly zooxanthellate corals, the reef environments they provide, and genera with actively burrowing or swimming adult life‐stages. The extinction risk of larger sized fauna also increased relative to non‐hyperthermal times, while genera with a poorly buffered internal physiology did not become more vulnerable on average during hyperthermals. Hyperthermal‐vulnerable clades include rhynchonelliform brachiopods and bony fish, whereas resistant clades include cartilaginous fish, and ostreid and venerid bivalves. These extinction responses in the geological past mirror modern responses of these groups to warming, including range‐shift magnitudes, population losses, and experimental performance under climate‐related stressors. Accordingly, extinction mechanisms distinctive to rapid global warming may be indicated, including sensitivity to warming‐induced seawater deoxygenation. In anticipation of modern warming‐driven marine extinctions, the trends illustrated in the fossil record offer an expedient preview.
    Type of Medium: Online Resource
    ISSN: 1354-1013 , 1365-2486
    URL: Issue
    URL: Article
    DOI: 10.1111/gcb.v27.4
    DOI: 10.1111/gcb.15434
    Language: English
    Publisher: Wiley
    Publication Date: 2021
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  • 8
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    Marine invertebrate migrations trace climate change over 450 million years
    Wiley ; 2018
    In:  Global Ecology and Biogeography Vol. 27, No. 6 ( 2018-06), p. 704-713
    Details
    In: Global Ecology and Biogeography, Wiley, Vol. 27, No. 6 ( 2018-06), p. 704-713
    Abstract: Poleward migration is a clear response of marine organisms to current global warming but the generality and geographical uniformity of this response are unclear. Marine fossils are expected to record the range shift responses of taxa and ecosystems to past climate change. However, unequal sampling (natural and human) in time and space biases the fossil record, restricting previous studies of ancient migrations to individual taxa and events. We expect that temporal changes in the latitudinal distribution of surviving taxa will reveal range shifts to trace global climate change. Location Global. Time period Post‐Cambrian Phanerozoic aeon. Major taxa studied Well‐fossilized marine benthic invertebrates comprising stony corals, bivalves, gastropods, brachiopods, trilobites and calcifying sponges. Methods We track deviations in the latitudinal distribution of range centres of age boundary crossing taxa from the expected distribution, and compare responses across latitudes. We build deviation time series, spanning hundreds of million years, from fossil occurrences and test correlations with seawater temperature estimates derived from stable oxygen isotopes of fossils. Results Seawater temperature and latitudinal deviations from sampling are positively correlated over the post‐Cambrian Phanerozoic. Simulations suggest that sampling patterns are highly unlikely to drive this putative signal of range shifts. Systematically accounting for known sampling issues strengthens this correlation, so that climate is capable of explaining nearly a third of the variance in ancient latitudinal range shifts. The relationship is stronger in low latitude taxa than higher latitude taxa, and in warm ages than cool ages. Main conclusions Latitudinal range shifts occurred in concert with climate change throughout the post‐Cambrian Phanerozoic. Low latitude taxa show the clearest climate‐migration signal through time, corroborating predictions of their shift in a warming future.
    Type of Medium: Online Resource
    ISSN: 1466-822X , 1466-8238
    URL: Issue
    URL: Article
    DOI: 10.1111/geb.2018.27.issue-6
    DOI: 10.1111/geb.12732
    Language: English
    Publisher: Wiley
    Publication Date: 2018
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  • 9
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    Global warming generates predictable extinctions of warm‐ and cold‐water marine benthic invertebrates via thermal habitat loss
    Wiley ; 2022
    In:  Global Change Biology Vol. 28, No. 19 ( 2022-10), p. 5793-5807
    Details
    In: Global Change Biology, Wiley, Vol. 28, No. 19 ( 2022-10), p. 5793-5807
    Abstract: Anthropogenic global warming is redistributing marine life and may threaten tropical benthic invertebrates with several potential extinction mechanisms. The net impact of climate change on geographical extinction risk nevertheless remains uncertain. Evidence of widespread climate‐driven extinctions and of potentially unidentified mechanisms exists in the fossil record. We quantify organism extinction risk across thermal habitats, estimated by paleoclimate reconstructions, over the past 300 million years. Extinction patterns at seven known events of rapid global warming (hyperthermals) differ significantly from typical patterns, resembling those driven by global geometry under simulated global warming. As isotherms move poleward with warming, the interaction between the geometry of the globe and the temperature‐latitude relationship causes an uneven loss of thermal habitat and a bimodal latitudinal distribution of extinctions. Genera with thermal optima warmer than ~21°C show raised extinction odds, while extinction odds continually increase for genera with optima below ~11°C. Genera preferring intermediate temperatures generally have no additional extinction risk during hyperthermals, except under extreme conditions as the end‐Permian mass extinction. Widespread present‐day climate‐driven range shifts indicate that occupancy loss is already underway. Given the most‐likely projections of modern warming, our model, validated by seven past hyperthermal events, indicates that sustained warming has the potential to annihilate cold‐water habitat and its endemic species completely within centuries.
    Type of Medium: Online Resource
    ISSN: 1354-1013 , 1365-2486
    URL: Issue
    URL: Article
    DOI: 10.1111/gcb.v28.19
    DOI: 10.1111/gcb.16333
    Language: English
    Publisher: Wiley
    Publication Date: 2022
    detail.hit.zdb_id: 1281439-8
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  • 10
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    Reliable estimates of beta diversity with incomplete sampling
    Wiley ; 2018
    In:  Ecology Vol. 99, No. 5 ( 2018-05), p. 1051-1062
    Details
    In: Ecology, Wiley, Vol. 99, No. 5 ( 2018-05), p. 1051-1062
    Abstract: Beta diversity, the compositional variation among communities or assemblages, is crucial to understanding the principles of diversity assembly. The mean pairwise proportional dissimilarity expresses overall heterogeneity of samples in a data set and is among the most widely used and most robust measures of beta diversity. Obtaining a complete list of taxa and their abundances requires substantial taxonomic expertise and is time consuming. In addition, the information is generally incomplete due to sampling biases. Based on the concept of the ecological significance of dominant taxa, we explore whether determining proportional dissimilarity can be simplified based on dominant species. Using simulations and six case studies, we assess the correlation between complete community compositional data and reduced subsets of a varying number of dominant species. We find that gross beta diversity is usually depicted accurately when only the 80th percentile or five of the most abundant species of each site is considered. In data sets with very high evenness, at least the 10 most abundant species should be included. Focusing on dominant species also maintains the rank‐order of beta diversity among sites. Our new approach will allow ecologists and paleobiologists to produce a far greater amount of data on diversity patterns with less time and effort, supporting conservation studies and basic science.
    Type of Medium: Online Resource
    ISSN: 0012-9658 , 1939-9170
    URL: Issue
    URL: Article
    DOI: 10.1002/ecy.2018.99.issue-5
    DOI: 10.1002/ecy.2201
    RVK:
    WA 15000
    Language: English
    Publisher: Wiley
    Publication Date: 2018
    detail.hit.zdb_id: 1797-8
    detail.hit.zdb_id: 2010140-5
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