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Journal article
Brain expansion in early hominins predicts carnivore extinctions in East Africa
While the anthropogenic impact on ecosystems today is evident, it remains unclear if the detrimental effect of hominins on co‐occurring biodiversity is a recent phenomenon or has also been the pattern for earlier hominin species. We test this using the East African carnivore fossil record. We analyse the diversity of...Faurby, Søren ; Silvestro, Daniele ; Werdelin, Lars ; Antonelli, Alexandre
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Journal article
A roadmap for global synthesis of the plant tree of life
Providing science and society with an integrated, up‐to‐date, high quality, open, reproducible and sustainable plant tree of life would be a huge service that is now coming within reach. However, synthesizing the growing body of DNA sequence data in the public domain and disseminating the trees to a diverse audience... -
Journal article
Phylogenomics and biogeography of the world's thrushes (Aves, Turdus): new evidence for a more parsimonious evolutionary history
To elucidate the relationships and spatial range evolution across the world of the bird genus Turdus (Aves), we produced a large genomic dataset comprising ca 2 million nucleotides for ca 100 samples representing 53 species, including over 2000 loci. We estimated time-calibrated maximum-likelihood and multispecies coalescent phylogenies and carried out...Batista, Romina ; Olsson, Urban ; Andermann, Tobias ; Aleixo, Alexandre ; Ribas, Camila Cherem …
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Journal article
The Global Museum: natural history collections and the future of evolutionary science and public education
Natural history museums are unique spaces for interdisciplinary research and educational innovation. Through extensive exhibits and public programming and by hosting rich communities of amateurs, students, and researchers at all stages of their careers, they can provide a place-based window to focus on integration of science and discovery, as well... -
Journal article
A Guide to Carrying Out a Phylogenomic Target Sequence Capture Project
High-throughput DNA sequencing techniques enable time- and cost-effective sequencing of large portions of the genome. Instead of sequencing and annotating whole genomes, many phylogenetic studies focus sequencing effort on large sets of pre-selected loci, which further reduces costs and bioinformatic challenges while increasing coverage. One common approach that enriches loci...Andermann, Tobias ; Torres Jiménez, Maria Fernanda ; Matos-Maraví, Pável ; Batista, Romina ; Blanco-Pastor, José L. …
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Journal article
Endemism patterns are scale dependent
Areas of endemism are important in biogeography because they capture facets of biodiversity not represented elsewhere. However, the scales at which they are relevant to research and conservation are poorly analysed. Here, we calculate weighted endemism (WE) and phylogenetic endemism (PE) separately for all birds and amphibians across the globe....Daru, Barnabas H. ; Farooq, Harith ; Antonelli, Alexandre ; Faurby, Søren
biogeography, evolutionary ecology, and conservation biology
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Journal article
Unraveling the Phylogenomic Relationships of the Most Diverse African Palm Genus Raphia (Calamoideae, Arecaceae)
Palms are conspicuous floristic elements across the tropics. In continental Africa, even though there are less than 70 documented species, they are omnipresent across the tropical landscape. The genus Raphia has 20 accepted species in Africa and one species endemic to the Neotropics. It is the most economically important genus...Helmstetter, Andrew J. ; Kamga, Suzanne Mogue ; Bethune, Kevin ; Lautenschläger, Thea ; Zizka, Alexander …
Rain forests, Africa, Madagascar, Sequence capture, Exons, Phylogenomics, and Raphia
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Book chapter
Diversity, Endemism, and Evolutionary History of Montane Biotas Outside the Andean Region
Mountain ranges are important centers of biodiversity around the world. This high diversity is the result of the presence of different soil types and underlying bedrock, a variety of micro-climatic regimes, high topographic heterogeneity, a heterogeneous and complex vegetation cline, and a dynamic geo-climatic history. Neotropical research on mountains has... -
Book chapter
On the Young Savannas in the Land of Ancient Forests
Covering ancient geomorphological landscapes, and surrounded by some of the most diverse forests on Earth, the Neotropical savannas were once perceived by naturalists as ancient environments. However, current evidence suggests that tropical forests have existed in the Neotropics since the Paleocene, whereas most plant lineages present in South American savannas... -
Journal article
outsider: Install and run programs, outside of R, inside of R
In many areas of research, product development and software engineering, analytical pipelines – workflows connecting output from multiple software – are key for processing and running tests on data. They can provide results in a consistent, modular and transparent manner. Pipelines also make it easier to demonstrate the reproducibility of...Bennett, Dominic ; Hettling, Hannes ; Silvestro, Daniele ; Vos, Rutger ; Antonelli, Alexandre
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Research report
Exploring the Impact of Political Regimes on Biodiversity
National governments are the main actors responsible for mapping and protecting their biodiversity, but countries differ in their capacity, willingness, and effectiveness to do so. We quantify the global biodiversity managed by different regime types and developed a tool to explore the links between level of democracy and other key...Zizka, Alexander ; Rydén, Oskar ; Edler, Daniel ; Klein, Johannes ; Aronsson, Heléne …
Democracy, Regime type, Autocracy, Specimen collection, and Biodiversity
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Journal article
Trade‐off between seed dispersal in space and time.
Seed movement and delayed germination have long been thought to represent alternative risk‐spreading strategies, but current evidence covers limited scales and yields mixed results. Here we present the first global‐scale test of a negative correlation between dispersal and dormancy. The result demonstrates a strong and consistent pattern that species with...Chen, Si‐Chong ; Poschlod, Peter ; Antonelli, Alexandre ; Liu, Udayangani ; Dickie, John B.
Annual , Longevity, Lifespan, Seed dispersal, Seed bank, Dormancy, Germination, Perennial, and Iteroparity
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Journal article
Unlocking plant resources to support food security and promote sustainable agriculture.
Societal Impact Statement Biodiversity is essential to food security and nutrition locally and globally. By reviewing the global state of edible plants and highlighting key neglected and underutilized species (NUS), we attempt to unlock plant food resources and explore the role of fungi, which along with the wealth of traditional... -
Journal article
Plant and fungal collections: Current status, future perspectives.
Societal Impact Statement Plant and fungal specimens provide the auditable evidence that a particular organism occurred at a particular place, and at a particular point in time, verifying past occurrence and distribution. They also document the aspects of human exploration and culture. Collectively specimens form a global asset with significant... -
Journal article
Conservation Policy: Helping or hindering science to unlock properties of plants and fungi.
Societal Impact Statement Biodiversity loss is happening at an unprecedented rate. Understanding and protecting biodiversity has never been more urgent, and scientific research is key to this. Fair and transparent access and benefit sharing policies enable research to take place, whilst supporting sustainable livelihoods of communities and ensuring benefits are... -
Journal article
No one-size-fits-all solution to clean GBIF.
Species occurrence records provide the basis for many biodiversity studies. They derive from georeferenced specimens deposited in natural history collections and visual observations, such as those obtained through various mobile applications. Given the rapid increase in availability of such data, the control of quality and accuracy constitutes a particular concern.... -
Journal article
Disproportionate extinction of South American mammals drove the asymmetry of the Great American Biotic Interchange.
The interchange between the previously disconnected faunas of North and South America was a massive experiment in biological invasion. A major gap in our understanding of this invasion is why there was a drastic increase in the proportion of mammals of North American origin found in South America. Four nonmutually... -
Journal article
Taxonomic revision of the genus Xenopholis Peters, 1869 (Serpentes: Dipsadidae): Integrating morphology with ecological niche.
Gomes, Daniel Faustino ; Azevedo, Josué ; Murta-Fonseca, Roberta ; Faurby, Søren ; Antonelli, Alexandre …
Ecological niches, Spine , Skull , Dentition, Forests , Teeth , Taxonomy, and Brazil
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Journal article
Assessing Biotic and Abiotic Interactions of Microorganisms in Amazonia through Co-Occurrence Networks and DNA Metabarcoding.
Duarte Ritter, Camila ; Forster, Dominik ; Azevedo, Josué A. R. ; Antonelli, Alexandre ; Nilsson, R. Henrik …
Fungi, Bacterias, Biodiversity, Protists, Metabarcoding, and Tropics
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Journal article
Genomic and niche divergence in an Amazonian palm complex.
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Journal article
Contrasting patterns of phylogenetic turnover in amphibians and reptiles are driven by environment and geography in Neotropical savannahs.
Azevedo, Josué A. R. ; Nogueira, Cristiano de C. ; Antonelli, Alexandre ; Faurby, Søren
Beta diversity, Cerrado, Generalized dissimilarity modelling, Regionalization, Connectivity, and Herptofauna
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Journal article
Settling a family feud: A high-level phylogenomic framework for the gentianales based on 353 nuclear genes and partial plastomes.
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Journal article
Uses and benefits of digital sequence information from plant genetic resources: Lessons learnt from botanical collections.
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Journal article
The rise and fall of Neotropical biodiversity.
Antonelli, Alexandre
Conservation, Evolution, and Extinction
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Journal article
Bio-Dem, a tool to explore the relationship between biodiversity data availability and socio-political conditions in time and space.
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Journal article
Loss of functional diversity through anthropogenic extinctions of island birds is not offset by biotic invasions.
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Journal article
A bioinformatic platform to integrate target capture and whole genome sequences of various read depths for phylogenomics.
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Journal article
Touch me carefully: a step towards understanding morphological diversity in the South American spiny sunflowers Compositae, Barnadesioideae).
de Lima Ferreira, Paola ; Antonelli, Alexandre ; Groppo, Milton
Distribution, Neotropical flora, Eudicots, Morphology, Asteraceae, Taxonomy, and South America
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Journal article
Phylogenomics of the Palm Tribe Lepidocaryeae (Calamoideae: Arecaceae) and Description of a New Species of Mauritiella.
Torres Jiménez, Maria Fernanda ; Prata, Eduardo M. B. ; Zizka, Alexander ; Cohn-Haft, Mario ; de Oliveira, Ayslaner V. G. …
Amazonia, Phylogenomics, Palmae, Mauritiella, and Africa
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Journal article
The seasonally dry tropical forest species Cavanillesia chicamochae has a middle Quaternary origin.
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Journal article
Above‐ and below‐ground biodiversity responses to the prolonged flood pulse in central‐western Amazonia, Brazil.
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Journal article
Widespread homogenization of plant communities in the Anthropocene.
Native biodiversity decline and non-native species spread are major features of the Anthropocene. Both processes can drive biotic homogenization by reducing trait and phylogenetic differences in species assemblages between regions, thus diminishing the regional distinctiveness of biotas and likely have negative impacts on key ecosystem functions. However, a global assessment... -
Journal article
Above‐ and below‐ground biodiversity responses to the prolonged flood pulse in central‐western Amazonia, Brazil.
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Journal article
A taxonomic, genetic and ecological data resource for the vascular plants of Britain and Ireland.
The vascular flora of Britain and Ireland is among the most extensively studied in the world, but the current knowledge base is fragmentary, with taxonomic, ecological and genetic information scattered across different resources. Here we present the first comprehensive data repository of native and alien species optimized for fast and...Henniges, Marie C. ; Powell, Robyn F. ; Mian, Sahr ; Stace, Clive A. ; Walker, Kevin J. …
Taxonomy, Ireland, Great Britain, Plant ecology, Genetics, Biodiversity, Ecology, and Literature mining
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Journal article
Certification of açaí agroforestry increases the conservation potential of the Amazonian tree flora.
The harvesting of açaí berries (palm fruits from the genus ) in Amazonia has increased over the last 20 years due to a high local and global market demand and triggered by their widely acclaimed health benefits as a ‘superfood’. Although such increase represents a financial boom for local communities,...Damasco, Gabriel ; Anhalt, Mandy ; Perdiz, Ricardo O. ; Wittmann, Florian ; de Assis, Rafael L. …
Açaí management, Amazonia, Biodiversity conservation, Euterpe, and Flooded forests
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Journal article
Good news for habitat restoration projects: Eucalyptus does not inhibit the germination of Polylepis.
Meneses, Lidia ; Martinez, Yvonne Y. ; Antonelli, Alexandre ; Gareca, Edgar E.
Eucalyptus, Habitat restoration, Kewiña, Allelopathy, Reforestation, Polylepis, Exotic species, and Conservation
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Journal article
Target sequence capture of Barnadesioideae (Compositae) demonstrates the utility of low coverage loci in phylogenomic analyses.
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