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  • 1
    In: Global Ecology and Biogeography, Wiley, Vol. 27, No. 7 ( 2018-07), p. 760-786
    Abstract: The BioTIME database contains raw data on species identities and abundances in ecological assemblages through time. These data enable users to calculate temporal trends in biodiversity within and amongst assemblages using a broad range of metrics. BioTIME is being developed as a community‐led open‐source database of biodiversity time series. Our goal is to accelerate and facilitate quantitative analysis of temporal patterns of biodiversity in the Anthropocene. Main types of variables included The database contains 8,777,413 species abundance records, from assemblages consistently sampled for a minimum of 2 years, which need not necessarily be consecutive. In addition, the database contains metadata relating to sampling methodology and contextual information about each record. Spatial location and grain BioTIME is a global database of 547,161 unique sampling locations spanning the marine, freshwater and terrestrial realms. Grain size varies across datasets from 0.0000000158 km 2 (158 cm 2 ) to 100 km 2 (1,000,000,000,000 cm 2 ). Time period and grain BioTIME records span from 1874 to 2016. The minimal temporal grain across all datasets in BioTIME is a year. Major taxa and level of measurement BioTIME includes data from 44,440 species across the plant and animal kingdoms, ranging from plants, plankton and terrestrial invertebrates to small and large vertebrates. Software format .csv and .SQL.
    Type of Medium: Online Resource
    ISSN: 1466-822X , 1466-8238
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2018
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  • 2
    Online Resource
    Online Resource
    The Royal Society ; 1998
    In:  Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences Vol. 353, No. 1366 ( 1998-02-28), p. 275-286
    In: Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences, The Royal Society, Vol. 353, No. 1366 ( 1998-02-28), p. 275-286
    Abstract: Population differentiation is often viewed as an important step towards speciation, and part of the rationale for conserving variation at the intraspecific level is that the potential to generate more biological diversity should be retained. Yet, speciation is not an inevitable consequence of population divergence. This paper reviews recent work on the Trinidadian guppy, Poecilia reticulata , a species that is renowned for its capacity for population differentiation. Guppy populations evolve rapidly, within 10 to 10 2 generations, as a response to changes in selection exerted by predators. The rates of evolution involved can be up to seven orders of magnitude greater than those seen in the fossil record. Sexual selection, particuarly female choice, appears to reinforce the divergence that natural selection has generated. Perplexingly, however, there is no reproductive isolation (either prezygotic or postzygotic) between populations, even those that have been separated for at least 10 6 generations. Sexual conflict may be the key to explaining this absence of speciation. Male reproductive behaviour, particularly the high incidence of sneaky mating, may be instrumental in producing sufficient gene flow to prevent reproductive isolation. Sneaky mating has the potential to undermine female choice, and is known to be an important means of sperm transfer in wild populations. Sexual dimorphism, also a result of sexual conflict in guppies, may inhibit speciation in another way. Morphological differences between the sexes, that have arisen for reproductive reasons, mean that males and females are pre–adapted for different foraging niches. This, in turn, reduces the opportunity for the development of feeding polymorphisms, a mechanism that seems to have been important in the sympatric speciation of other fish species.
    Type of Medium: Online Resource
    ISSN: 0962-8436 , 1471-2970
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    Language: English
    Publisher: The Royal Society
    Publication Date: 1998
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  • 3
    In: Oikos, Wiley, Vol. 128, No. 8 ( 2019-08), p. 1079-1091
    Abstract: Humans have elevated global extinction rates and thus lowered global scale species richness. However, there is no a priori reason to expect that losses of global species richness should always, or even often, trickle down to losses of species richness at regional and local scales, even though this relationship is often assumed. Here, we show that scale can modulate our estimates of species richness change through time in the face of anthropogenic pressures, but not in a unidirectional way. Instead, the magnitude of species richness change through time can increase, decrease, reverse, or be unimodal across spatial scales. Using several case studies, we show different forms of scale‐dependent richness change through time in the face of anthropogenic pressures. For example, Central American corals show a homogenization pattern, where small scale richness is largely unchanged through time, while larger scale richness change is highly negative. Alternatively, birds in North America showed a differentiation effect, where species richness was again largely unchanged through time at small scales, but was more positive at larger scales. Finally, we collated data from a heterogeneous set of studies of different taxa measured through time from sites ranging from small plots to entire continents, and found highly variable patterns that nevertheless imply complex scale‐dependence in several taxa. In summary, understanding how biodiversity is changing in the Anthropocene requires an explicit recognition of the influence of spatial scale, and we conclude with some recommendations for how to better incorporate scale into our estimates of change.
    Type of Medium: Online Resource
    ISSN: 0030-1299 , 1600-0706
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2019
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  • 4
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 381, No. 6662 ( 2023-09-08), p. 1067-1071
    Abstract: Analysis of plant and animal communities spanning from 1960 to 2020 and across six taxon groups reveals prevailing decreases in body size.
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
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    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2023
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  • 5
    In: People and Nature, Wiley, Vol. 2, No. 2 ( 2020-06), p. 380-394
    Abstract: A free Plain Language Summary can be found within the Supporting Information of this article.
    Type of Medium: Online Resource
    ISSN: 2575-8314 , 2575-8314
    Language: English
    Publisher: Wiley
    Publication Date: 2020
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  • 6
    In: Ecological Monographs, Wiley
    Abstract: Based on sampling data, we propose a rigorous standardization method to measure and compare beta diversity across datasets. Here beta diversity, which quantifies the extent of among‐assemblage differentiation, relies on Whittaker's original multiplicative decomposition scheme, but we use Hill numbers for any diversity order q ≥  0. Richness‐based beta diversity ( q  = 0) quantifies the extent of species identity shift, whereas abundance‐based ( q   〉  0) beta diversity also quantifies the extent of difference among assemblages in species abundance. We adopt and define the assumptions of a statistical sampling model as the foundation for our approach, treating sampling data as a representative sample taken from an assemblage. The approach makes a clear distinction between the theoretical assemblage level (unknown properties/parameters of the assemblage) and the sampling data level (empirical/observed statistics computed from data). At the assemblage level, beta diversity for N assemblages reflects the interacting effect of the species abundance distribution and spatial/temporal aggregation of individuals in the assemblage. Under independent sampling, observed beta (= gamma/alpha) diversity depends not only on among‐assemblage differentiation but also on sampling effort/completeness, which in turn induces dependence of beta on alpha and gamma diversity. How to remove the dependence of richness‐based beta diversity on its gamma component (species pool) has been intensely debated. Our approach is to standardize gamma and alpha based on sample coverage (an objective measure of sample completeness). For a single assemblage, the iNEXT method was developed, through interpolation (rarefaction) and extrapolation with Hill numbers, to standardize samples by sampling effort/completeness. Here we adapt the iNEXT standardization to alpha and gamma diversity, that is, alpha and gamma diversity are both assessed at the same level of sample coverage, to formulate standardized, coverage‐based beta diversity. This extension of iNEXT to beta diversity required the development of novel concepts and theories, including a formal proof and simulation‐based demonstration that the resulting standardized beta diversity removes the dependence of beta diversity on both gamma and alpha values, and thus reflects the pure among‐assemblage differentiation. The proposed standardization is illustrated with spatial, temporal, and spatiotemporal datasets, while the freeware iNEXT.beta3D facilitates all computations and graphics.
    Type of Medium: Online Resource
    ISSN: 0012-9615 , 1557-7015
    Language: English
    Publisher: Wiley
    Publication Date: 2023
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  • 7
    In: Ecology Letters, Wiley, Vol. 12, No. 9 ( 2009-09), p. 873-886
    Abstract: Understanding the causes of spatial variation in species richness is a major research focus of biogeography and macroecology. Gridded environmental data and species richness maps have been used in increasingly sophisticated curve‐fitting analyses, but these methods have not brought us much closer to a mechanistic understanding of the patterns. During the past two decades, macroecologists have successfully addressed technical problems posed by spatial autocorrelation, intercorrelation of predictor variables and non‐linearity. However, curve‐fitting approaches are problematic because most theoretical models in macroecology do not make quantitative predictions, and they do not incorporate interactions among multiple forces. As an alternative, we propose a mechanistic modelling approach. We describe computer simulation models of the stochastic origin, spread, and extinction of species’ geographical ranges in an environmentally heterogeneous, gridded domain and describe progress to date regarding their implementation. The output from such a general simulation model (GSM) would, at a minimum, consist of the simulated distribution of species ranges on a map, yielding the predicted number of species in each grid cell of the domain. In contrast to curve‐fitting analysis, simulation modelling explicitly incorporates the processes believed to be affecting the geographical ranges of species and generates a number of quantitative predictions that can be compared to empirical patterns. We describe three of the ‘control knobs’ for a GSM that specify simple rules for dispersal, evolutionary origins and environmental gradients. Binary combinations of different knob settings correspond to eight distinct simulation models, five of which are already represented in the literature of macroecology. The output from such a GSM will include the predicted species richness per grid cell, the range size frequency distribution, the simulated phylogeny and simulated geographical ranges of the component species, all of which can be compared to empirical patterns. Challenges to the development of the GSM include the measurement of goodness of fit (GOF) between observed data and model predictions, as well as the estimation, optimization and interpretation of the model parameters. The simulation approach offers new insights into the origin and maintenance of species richness patterns, and may provide a common framework for investigating the effects of contemporary climate, evolutionary history and geometric constraints on global biodiversity gradients. With further development, the GSM has the potential to provide a conceptual bridge between macroecology and historical biogeography.
    Type of Medium: Online Resource
    ISSN: 1461-023X , 1461-0248
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2009
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  • 8
    Online Resource
    Online Resource
    American Association for the Advancement of Science (AAAS) ; 2020
    In:  Science Vol. 368, No. 6497 ( 2020-06-19), p. 1341-1347
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 368, No. 6497 ( 2020-06-19), p. 1341-1347
    Abstract: Global biodiversity assessments have highlighted land-use change as a key driver of biodiversity change. However, there is little empirical evidence of how habitat transformations such as forest loss and gain are reshaping biodiversity over time. We quantified how change in forest cover has influenced temporal shifts in populations and ecological assemblages from 6090 globally distributed time series across six taxonomic groups. We found that local-scale increases and decreases in abundance, species richness, and temporal species replacement (turnover) were intensified by as much as 48% after forest loss. Temporal lags in population- and assemblage-level shifts after forest loss extended up to 50 years and increased with species’ generation time. Our findings that forest loss catalyzes population and biodiversity change emphasize the complex biotic consequences of land-use change.
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
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    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2020
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  • 9
    In: Methods in Ecology and Evolution, Wiley, Vol. 12, No. 10 ( 2021-10), p. 1926-1940
    Abstract: Biodiversity is a multifaceted concept covering different levels of organization from genes to ecosystems. Biodiversity has at least three dimensions: (a) Taxonomic diversity (TD): a measure that is sensitive to the number and abundances of species. (b) Phylogenetic diversity (PD): a measure that incorporates not only species abundances but also species evolutionary histories. (c) Functional diversity (FD): a measure that considers not only species abundances but also species' traits. We integrate the three dimensions of diversity under a unified framework of Hill numbers and their generalizations. Our TD quantifies the effective number of equally abundant species, PD quantifies the effective total branch length, mean‐PD (PD divided by tree depth) quantifies the effective number of equally divergent lineages, and FD quantifies the effective number of equally distinct virtual functional groups (or functional ‘species’). Thus, TD, mean‐PD and FD are all in the same units of species/lineage equivalents and can be meaningfully compared. Like species richness, empirical TD, PD and FD based on sampling data depend on sampling effort and sample completeness. For TD (Hill numbers), the iNEXT (interpolation and extrapolation) standardization was developed for standardizing sample size or sample completeness (as measured by sample coverage, the fraction of individuals that belong to the observed species) to make objective comparisons across studies. This paper extends the iNEXT method to the iNEXT.3D standardization to encompass all three dimensions of diversity via sample size‐ and sample coverage‐based rarefaction and extrapolation under the unified framework. The asymptotic diversity estimates (i.e. sample size tends to infinity and sample coverage tends to unity) are also derived. In addition to individual‐based abundance data, the proposed iNEXT.3D standardization is adapted to deal with incidence‐based occurrence data. We apply the integrative framework and the proposed iNEXT.3D standardization to measure temporal alpha‐diversity changes for estuarine fish assemblage data spanning four decades. The influence of environmental drivers on diversity change are also assessed. Our analysis informs a mechanistic interpretation of biodiversity change in the three dimensions of diversity. The accompanying freeware, iNEXT.3D, developed during this project, facilitates all computation and graphics.
    Type of Medium: Online Resource
    ISSN: 2041-210X , 2041-210X
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2021
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  • 10
    In: Proceedings of the Royal Society B: Biological Sciences, The Royal Society, Vol. 280, No. 1750 ( 2013-01-07), p. 20121931-
    Abstract: Growing concern about biodiversity loss underscores the need to quantify and understand temporal change. Here, we review the opportunities presented by biodiversity time series, and address three related issues: (i) recognizing the characteristics of temporal data; (ii) selecting appropriate statistical procedures for analysing temporal data; and (iii) inferring and forecasting biodiversity change. With regard to the first issue, we draw attention to defining characteristics of biodiversity time series—lack of physical boundaries, uni-dimensionality, autocorrelation and directionality—that inform the choice of analytic methods. Second, we explore methods of quantifying change in biodiversity at different timescales, noting that autocorrelation can be viewed as a feature that sheds light on the underlying structure of temporal change. Finally, we address the transition from inferring to forecasting biodiversity change, highlighting potential pitfalls associated with phase-shifts and novel conditions.
    Type of Medium: Online Resource
    ISSN: 0962-8452 , 1471-2954
    Language: English
    Publisher: The Royal Society
    Publication Date: 2013
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