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  • 1
    In: Nature Communications, Springer Science and Business Media LLC, Vol. 13, No. 1 ( 2022-05-18)
    Abstract: There is still limited consensus on the evolutionary history of species-rich temperate alpine floras due to a lack of comparable and high-quality phylogenetic data covering multiple plant lineages. Here we reconstructed when and how European alpine plant lineages diversified, i.e., the tempo and drivers of speciation events. We performed full-plastome phylogenomics and used multi-clade comparative models applied to six representative angiosperm lineages that have diversified in European mountains (212 sampled species, 251 ingroup species total). Diversification rates remained surprisingly steady for most clades, even during the Pleistocene, with speciation events being mostly driven by geographic divergence and bedrock shifts. Interestingly, we inferred asymmetrical historical migration rates from siliceous to calcareous bedrocks, and from higher to lower elevations, likely due to repeated shrinkage and expansion of high elevation habitats during the Pleistocene. This may have buffered climate-related extinctions, but prevented speciation along elevation gradients as often documented for tropical alpine floras.
    Type of Medium: Online Resource
    ISSN: 2041-1723
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2022
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  • 2
    In: Biological Reviews, Wiley, Vol. 93, No. 2 ( 2018-05), p. 785-800
    Abstract: Knowledge of species composition and their interactions, in the form of interaction networks, is required to understand processes shaping their distribution over time and space. As such, comparing ecological networks along environmental gradients represents a promising new research avenue to understand the organization of life. Variation in the position and intensity of links within networks along environmental gradients may be driven by turnover in species composition, by variation in species abundances and by abiotic influences on species interactions. While investigating changes in species composition has a long tradition, so far only a limited number of studies have examined changes in species interactions between networks, often with differing approaches. Here, we review studies investigating variation in network structures along environmental gradients, highlighting how methodological decisions about standardization can influence their conclusions. Due to their complexity, variation among ecological networks is frequently studied using properties that summarize the distribution or topology of interactions such as number of links, connectance, or modularity. These properties can either be compared directly or using a procedure of standardization. While measures of network structure can be directly related to changes along environmental gradients, standardization is frequently used to facilitate interpretation of variation in network properties by controlling for some co‐variables, or via null models. Null models allow comparing the deviation of empirical networks from random expectations and are expected to provide a more mechanistic understanding of the factors shaping ecological networks when they are coupled with functional traits. As an illustration, we compare approaches to quantify the role of trait matching in driving the structure of plant–hummingbird mutualistic networks, i.e. a direct comparison, standardized by null models and hypothesis‐based metaweb. Overall, our analysis warns against a comparison of studies that rely on distinct forms of standardization, as they are likely to highlight different signals. Fostering a better understanding of the analytical tools available and the signal they detect will help produce deeper insights into how and why ecological networks vary along environmental gradients.
    Type of Medium: Online Resource
    ISSN: 1464-7931 , 1469-185X
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2018
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  • 3
    In: Plants, MDPI AG, Vol. 9, No. 4 ( 2020-04-01), p. 432-
    Abstract: Genome skimming has the potential for generating large data sets for DNA barcoding and wider biodiversity genomic studies, particularly via the assembly and annotation of full chloroplast (cpDNA) and nuclear ribosomal DNA (nrDNA) sequences. We compare the success of genome skims of 2051 herbarium specimens from Norway/Polar regions with 4604 freshly collected, silica gel dried specimens mainly from the European Alps and the Carpathians. Overall, we were able to assemble the full chloroplast genome for 67% of the samples and the full nrDNA cluster for 86%. Average insert length, cover and full cpDNA and rDNA assembly were considerably higher for silica gel dried than herbarium-preserved material. However, complete plastid genomes were still assembled for 54% of herbarium samples compared to 70% of silica dried samples. Moreover, there was comparable recovery of coding genes from both tissue sources (121 for silica gel dried and 118 for herbarium material) and only minor differences in assembly success of standard barcodes between silica dried (89% ITS2, 96% matK and rbcL) and herbarium material (87% ITS2, 98% matK and rbcL). The success rate was 〉 90% for all three markers in 1034 of 1036 genera in 160 families, and only Boraginaceae worked poorly, with 7 genera failing. Our study shows that large-scale genome skims are feasible and work well across most of the land plant families and genera we tested, independently of material type. It is therefore an efficient method for increasing the availability of plant biodiversity genomic data to support a multitude of downstream applications.
    Type of Medium: Online Resource
    ISSN: 2223-7747
    Language: English
    Publisher: MDPI AG
    Publication Date: 2020
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  • 4
    In: Global Ecology and Biogeography, Wiley, Vol. 23, No. 4 ( 2014-04), p. 414-424
    Abstract: The origins of ecological diversity in continental species assemblages have long intrigued biogeographers. We apply phylogenetic comparative analyses to disentangle the evolutionary patterns of ecological niches in an assemblage of E uropean birds. We compare phylogenetic patterns in trophic, habitat and climatic niche components. Location E urope. Methods From polygon range maps and handbook data we inferred the realized climatic, habitat and trophic niches of 405 species of breeding birds in E urope. We fitted P agel's lambda and kappa statistics, and conducted analyses of disparity through time to compare temporal patterns of ecological diversification on all niche axes together. All observed patterns were compared with expectations based on neutral ( B rownian) models of niche divergence. Results In this assemblage, patterns of phylogenetic signal (lambda) suggest that related species resemble each other less in regard to their climatic and habitat niches than they do in their trophic niche. Kappa estimates show that ecological divergence does not gradually increase with divergence time, and that this punctualism is stronger in climatic niches than in habitat and trophic niches. Observed niche disparity markedly exceeds levels expected from a Brownian model of ecological diversification, thus providing no evidence for past phylogenetic niche conservatism in these multivariate niches. Levels of multivariate disparity are greatest for the climatic niche, followed by disparity of the habitat and the trophic niches. Main conclusions Phylogenetic patterns in the three niche components differ within this avian assemblage. Variation in evolutionary rates (degree of gradualism, constancy through the tree) and/or non‐random macroecological sampling probably lead here to differences in the phylogenetic structure of niche components. Testing hypotheses on the origin of these patterns requires more complete phylogenetic trees of the birds, and extended ecological data on different niche components for all bird species.
    Type of Medium: Online Resource
    ISSN: 1466-822X , 1466-8238
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2014
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  • 5
    In: Global Ecology and Biogeography, Wiley, Vol. 23, No. 6 ( 2014-06), p. 620-632
    Abstract: Phylogenetic diversity patterns are increasingly being used to better understand the role of ecological and evolutionary processes in community assembly. Here, we quantify how these patterns are influenced by scale choices in terms of spatial and environmental extent and organismic scales. Location E uropean A lps. Methods We applied 42 sampling strategies differing in their combination of focal scales. For each resulting sub‐dataset, we estimated the phylogenetic diversity of the species pools, phylogenetic α‐diversities of local communities, and statistics commonly used together with null models in order to infer non‐random diversity patterns (i.e. phylogenetic clustering versus over‐dispersion). Finally, we studied the effects of scale choices on these measures using regression analyses. Results Scale choices were decisive for revealing signals in diversity patterns. Notably, changes in focal scales sometimes reversed a pattern of over‐dispersion into clustering. Organismic scale had a stronger effect than spatial and environmental extent. However, we did not find general rules for the direction of change from over‐dispersion to clustering with changing scales. Importantly, these scale issues had only a weak influence when focusing on regional diversity patterns that change along abiotic gradients. Main conclusions Our results call for caution when combining phylogenetic data with distributional data to study how and why communities differ from random expectations of phylogenetic relatedness. These analyses seem to be robust when the focus is on relating community diversity patterns to variation in habitat conditions, such as abiotic gradients. However, if the focus is on identifying relevant assembly rules for local communities, the uncertainty arising from a certain scale choice can be immense. In the latter case, it becomes necessary to test whether emerging patterns are robust to alternative scale choices.
    Type of Medium: Online Resource
    ISSN: 1466-822X , 1466-8238
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2014
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    detail.hit.zdb_id: 2021283-5
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  • 6
    In: Journal of Biogeography, Wiley, Vol. 47, No. 1 ( 2020-01), p. 44-58
    Abstract: The positive effect of primary productivity on animal species richness is one of the most conspicuous ecological features on Earth. However, less is known about the relationship between ecosystems primary productivity and the evolutionary history of biota. Here, we analyse how global primary productivity relates to the phylogenetic structure of vertebrate assemblages, and to the distribution of the most distinct lineages and recently diversified clades. Location Global. Taxon Amphibians, birds and mammals. Methods We calculated relative phylogenetic diversity (i.e. phylogenetic diversity corrected for species richness), standardized effect size of the richness of top 25% evolutionary distinct species and of top 25% species‐level lineage diversification rates. We related these three metrics to mean net primary productivity (NPP) at the global scale, and for each zoogeographic region. We also tested the influence of the spatial scaling of species pool on the overall analyses (global, hemispheric and zoogeographic regions‐based species pools). Results Phylogenetic diversity (corrected for species richness) of the three taxa decreases with NPP (in contrast with species richness) and varies considerably in space. High productivity sites harbour more closely related species than low productivity sites consistently across zoogeographic zones. However, the phylogenetically most distinct species are also found in high productivity sites, while the top most rapidly diversifying lineages are found in the least productive sites. Modifying the spatial extent of the species pool did not affect the results much. Conclusions Benign conditions in high productivity sites (a) result in denser niche packing and thus allow for the coexistence of many closely‐related species and (b) protect the persistence of evolutionary distinct species. Low productivity sites may harbour fewer, more distinct and temporarily more variable niches that allow maintenance of unique lineages for longer periods of time.
    Type of Medium: Online Resource
    ISSN: 0305-0270 , 1365-2699
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2020
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  • 7
    In: Journal of Biogeography, Wiley, Vol. 47, No. 1 ( 2020-01), p. 130-142
    Abstract: Statistical species distribution models (SDMs) are the most common tool to predict the impact of climate change on biodiversity. They can be tuned to fit relationships at various levels of complexity (defined here as parameterization complexity, number of predictors, and multicollinearity) that may co‐determine whether projections to novel climatic conditions are useful or misleading. Here, we assessed how model complexity affects the performance of model extrapolations and influences projections of species ranges under future climate change. Location Europe. Taxon 34 European tree species. Methods We sampled three replicates of predictor sets for all combinations of 10 levels ( n  = 3–12) of environmental variables (climate, terrain, soil) and 10 levels of multicollinearity. We used these sets for each species to fit four SDM algorithms at three levels of parameterization complexity. The 〉 100,000 resulting SDM fits were then evaluated under environmental block cross‐validation and projected to environmental conditions for 2061–2080 considering four climate models and two emission scenarios. Finally, we investigated the relationships of model design with model performance and projected distributional changes. Results Model complexity affected both model performance and projections of species distributional change. Fits of intermediate parameterization complexity performed best, and more complex parameterizations were associated with higher projected loss of current ranges. Model performance peaked at 10–11 variables but increasing number of variables had no consistent effect on distributional change projections. Multicollinearity had a low impact on model performance but distinctly increased projected loss of current ranges. Main conclusions SDM‐based climate change impact assessments should be based on ensembles of projections, varying SDM algorithms as well as parameterization complexity, besides emission scenarios and climate models. The number of predictor variables should be kept reasonably small and the classical threshold of maximum absolute Pearson correlation of 0.7 restricts collinearity‐driven effects in projections of species ranges.
    Type of Medium: Online Resource
    ISSN: 0305-0270 , 1365-2699
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2020
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    detail.hit.zdb_id: 188963-1
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  • 8
    In: Journal of Biogeography, Wiley, Vol. 47, No. 1 ( 2020-01), p. 1-12
    Abstract: Recent years have seen an exponential increase in the amount of data available in all sciences and application domains. Macroecology is part of this “Big Data” trend, with a strong rise in the volume of data that we are using for our research. Here, we summarize the most recent developments in macroecology in the age of Big Data that were presented at the 2018 annual meeting of the Specialist Group Macroecology of the Ecological Society of Germany, Austria and Switzerland (GfÖ). Supported by computational advances, macroecology has been a rapidly developing field over recent years. Our meeting highlighted important avenues for further progress in terms of standardized data collection, data integration, method development and process integration. In particular, we focus on (a) important data gaps and new initiatives to close them, for example through space‐ and airborne sensors, (b) how various data sources and types can be integrated, (c) how uncertainty can be assessed in data‐driven analyses and (d) how Big Data and machine learning approaches have opened new ways of investigating processes rather than simply describing patterns. We discuss how Big Data opens up new opportunities, but also poses new challenges to macroecological research. In the future, it will be essential to carefully assess data quality, the reproducibility of data compilation and analytical methods, and the communication of uncertainties. Major progress in the field will depend on the definition of data standards and workflows for macroecology, such that scientific quality and integrity are guaranteed, and collaboration in research projects is made easier.
    Type of Medium: Online Resource
    ISSN: 0305-0270 , 1365-2699
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2020
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    detail.hit.zdb_id: 188963-1
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  • 9
    In: Global Ecology and Biogeography, Wiley, Vol. 24, No. 12 ( 2015-12), p. 1401-1412
    Abstract: Previous research on how climatic niches vary across species ranges has focused on a limited number of species, mostly invasive, and has not, to date, been very conclusive. Here we assess the degree of niche conservatism between distant populations of native alpine plant species that have been separated for thousands of years. Location European A lps and F ennoscandia. Methods Of the studied pool of 888 terrestrial vascular plant species occurring in both the A lps and F ennoscandia, we used two complementary approaches to test and quantify climatic‐niche shifts for 31 species having strictly disjunct populations and 358 species having either a contiguous or a patchy distribution with distant populations. First, we used species distribution modelling to test for a region effect on each species' climatic niche. Second, we quantified niche overlap and shifts in niche width (i.e. ecological amplitude) and position (i.e. ecological optimum) within a bi‐dimensional climatic space. Results Only one species (3%) of the 31 species with strictly disjunct populations and 58 species (16%) of the 358 species with distant populations showed a region effect on their climatic niche. Niche overlap was higher for species with strictly disjunct populations than for species with distant populations and highest for arctic–alpine species. Climatic niches were, on average, wider and located towards warmer and wetter conditions in the Alps. Main conclusion Climatic niches seem to be generally conserved between populations that are separated between the A lps and F ennoscandia and have probably been so for 10,000–15,000 years. Therefore, the basic assumption of species distribution models that a species' climatic niche is constant in space and time – at least on time scales 10 4 years or less – seems to be largely valid for arctic–alpine plants.
    Type of Medium: Online Resource
    ISSN: 1466-822X , 1466-8238
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2015
    detail.hit.zdb_id: 1479787-2
    detail.hit.zdb_id: 2021283-5
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  • 10
    In: Global Ecology and Biogeography, Wiley, Vol. 30, No. 11 ( 2021-11), p. 2312-2325
    Abstract: While species distribution models (SDMs) are standard tools to predict species distributions, they can suffer from observation and sampling biases, particularly presence‐only SDMs, which often rely on species observations from non‐standardized sampling efforts. To address this issue, sampling background points with a target‐group strategy is commonly used, although more robust strategies and refinements could be implemented. Here, we exploited a dataset of plant species from the European Alps to propose and demonstrate efficient ways to correct for observer and sampling bias in presence‐only models. Innovation Recent methods correct for observer bias by including covariates related to accessibility in model calibrations (classic bias covariate correction, Classic‐BCC). However, depending on how species are sampled, accessibility covariates may not sufficiently capture observer bias. Here, we introduced BCCs more directly related to sampling effort, as well as a novel corrective method based on stratified resampling of the observational dataset before model calibration (environmental bias correction, EBC). We compared, individually and jointly, the effect of EBC and different BCC strategies, when modelling the distributions of 1,900 plant species. We evaluated model performance with spatial block split‐sampling and independent test data, and assessed the accuracy of plant diversity predictions across the European Alps. Main conclusions Implementing EBC with BCC showed best results for every evaluation method. Particularly, adding the observation density of a target group as a bias covariate (Target‐BCC) gave the most realistic modelled species distributions, with a clear positive correlation ( r  ≃ .5) found between predicted and expert‐based species richness. Although EBC must be carefully implemented in a species‐specific manner, such limitations may be addressed via automated diagnostics included in a provided R function. Implementing EBC and bias covariate correction together may allow future studies to address efficiently observer bias in presence‐only models, and overcome the standard need of an independent test dataset for model evaluation.
    Type of Medium: Online Resource
    ISSN: 1466-822X , 1466-8238
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2021
    detail.hit.zdb_id: 1479787-2
    detail.hit.zdb_id: 2021283-5
    SSG: 12
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