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Search Results
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Journal article
Phylogeny and re‐circumscription of Cheniella (Leguminosae: Cercidoideae) based on plastome data and morphology, with description of three new species.
Subfamily Cercidoideae is an early‐diverging lineage of Leguminosae, within which the number and classification of genera have been controversial. is a recently described genus in the Cercidoideae which requires revision and testing of its monophyly and circumscription. Here we infer the phylogenetic position and infrageneric relationships of as well as...Gu, Shi‐Ran ; Zeng, Qiu‐Biao ; Clark, Ruth ; Jiang, Kai‐Wen ; Pérez‐Escobar, Oscar Alejandro …
Bauhinia, Phylogeny, Re-circumscription, Southeast Asia, Phanera, Fabaceae, China, Cheniella, and Legume
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Journal article
Expert‐based range maps cannot be replicated using data‐driven methods but macroecological conclusions arising from them can.
Aronsson, Heléne ; Zizka, Alexander ; Antonelli, Alexandre ; Faurby, Søren
Range maps, Macroecology, IUCN ranges, Global biodiversity patterns, Biogeography, Bird distribution, and eBird global
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Journal article
A framework for tracing timber following the Ukraine invasion.
Scientific testing including stable isotope ratio analysis (SIRA) and trace element analysis (TEA) is critical for establishing plant origin, tackling deforestation and enforcing economic sanctions. Yet methods combining SIRA and TEA into robust models for origin verification and determination are lacking. Here we report a (1) large Eastern European timber... -
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Journal article
The origin of excavator nesting behavior and its impact on the evolution of Neotropical parrots.
How the origin of novel behaviors can shape the evolutionary trajectory of organisms in response to environmental change remains poorly understood. Birds, especially those with big brains like parrots, are benchmarks for their behavioral innovation capacity in novel environments. Here, we assess whether and how the emergence of open areas... -
Journal article
Undiscovered bird extinctions obscure the true magnitude of human-driven extinction waves.
Birds are among the best-studied animal groups, but their prehistoric diversity is poorly known due to low fossilization potential. Hence, while many human-driven bird extinctions (i.e., extinctions caused directly by human activities such as hunting, as well as indirectly through human-associated impacts such as land use change, fire, and the... -
Journal article
Connecting the multiple dimensions of global soil fungal diversity.
How the multiple facets of soil fungal diversity vary worldwide remains virtually unknown, hindering the management of this essential species-rich group. By sequencing high-resolution DNA markers in over 4000 topsoil samples from natural and human-altered ecosystems across all continents, we illustrate the distributions and drivers of different levels of taxonomic... -
Journal article
Pushing the Frontiers of Biodiversity Research: Unveiling the Global Diversity, Distribution, and Conservation of Fungi.
Fungi comprise approximately 20% of all eukaryotic species and are connected to virtually all life forms on Earth. Yet, their diversity remains contentious, their distribution elusive, and their conservation neglected. We aim to flip this situation by synthesizing current knowledge. We present a revised estimate of 2–3 million fungal species...Niskanen, Tuula ; Lücking, Robert ; Dahlberg, Anders ; Gaya, Ester ; Suz, Laura M. …
Fungi, Geographical distribution, Diversity, and Conservation
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Journal article
Online tree expansion could help solve the problem of scalability in Bayesian phylogenetics.
Bayesian phylogenetics is now facing a critical point. Over the last 20 years, Bayesian methods have reshaped phylogenetic inference and gained widespread popularity due to their high accuracy, the ability to quantify the uncertainty of inferences and the possibility of accommodating multiple aspects of evolutionary processes in the models that...Truszkowski, Jakub ; Perrigo, Allison ; Broman, David ; Ronquist, Fredrik ; Antonelli, Alexandre
Phylogeny, MCMC, Bayesian inference, and Sequential Monte Carlo
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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
Uses and benefits of digital sequence information from plant genetic resources: Lessons learnt from botanical collections.
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Journal article
Spiny but photogenic: Amateur sightings complement herbarium specimens to reveal the bioregions of cacti.
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Journal article
Towards a co-crediting system for carbon and biodiversity.
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Journal article
Rediscovery of the lost skink Proscelotes aenea and implications for conservation.
Biodiversity loss is recognized as a grand challenge of the twenty-first century but ascertaining when a species is “lost” can be incredibly difficult—since the absence of evidence is not evidence of absence. This may be a relatively easy task for large and conspicuous animals, but extremely difficult for those living...Puruleia, Ali ; Nanvonamuquitxo, Cristóvão ; Ernesto, Milagre ; Jamal, Abdurabe ; Amade, Iassine …
Skinks, Proscelotes aenea, Lumbo (Mozambique), Mozambique, and Threatened species
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Journal article
Repeated evolution of pollination syndromes in a highly diverse bromeliad lineage is correlated with shifts in life form and habitat.
Mutualistic plant-pollinator interactions play a critical role in the diversification of flowering plants. The spatiotemporal correlates of such interactions can be understood in a phylogenetic context. Here, we generate ddRAD-seq data for the highly diverse Vriesea-Stigmatodon lineage to test for correlated trait evolution among pollination syndromes and life form, habitat... -
Journal article
Machine learning enhances prediction of plants as potential sources of antimalarials.
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Book chapter
Foreword.
Antonelli, Alexandre
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Journal article
The origin of modern patterns of continental diversity in Mauritiinae palms: the Neotropical museum and the Afrotropical graveyard.
While the latitudinal diversity gradient has received much attention, biodiversity and species richness also vary between continents across similar latitudes. Fossil information can be used to understand the evolutionary mechanisms that generated such variation between continents of similar latitudes. We integrated fossil data into a phylogenetic analysis of the Mauritiinae... -
Journal article
A call for improving the Key Biodiversity Areas framework.
Eight percent of all land surface has been designated as “Key Biodiversity Areas” (KBAs). Since these areas were established based on two percent of all terrestrial species estimated to exist, we ask what would happen if we used all species on Earth to identify additional KBAs. We explore this question... -
Magazine article
Turn your garden into a biodiversity haven.
Antonelli, Alexandre
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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
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
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
Global patterns in endemicity and vulnerability of soil fungi.
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Journal article
Revised Species Delimitation in the Giant Water Lily Genus Victoria (Nymphaeaceae) Confirms a New Species and Has Implications for Its Conservation.
Reliably documenting plant diversity is necessary to protect and sustainably benefit from it. At the heart of this documentation lie species concepts and the practical methods used to delimit taxa. Here, we apply a total-evidence, iterative methodology to delimit and document species in the South American genus (Nymphaeaceae). The systematics... -
Journal article
Global variation in diversification rate and species richness are unlinked in plants.
Species richness varies immensely around the world. Variation in the rate of diversification (speciation minus extinction) is often hypothesized to explain this pattern, while alternative explanations invoke time or ecological carrying capacities as drivers. Focusing on seed plants, the world’s most important engineers of terrestrial ecosystems, we investigated the role...Tietje, Melanie ; Antonelli, Alexandre ; Baker, William J. ; Govaerts, Rafaël ; Smith, Stephen A. …
Diversification, Biogeography, Biodiversity, Macroecology, and Plant diversity drivers
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Journal article
The counteracting effects of anthropogenic speciation and extinction on mammal species richness and phylogenetic diversity.
Faurby, Søren ; Pedersen, Rasmus Østergaard ; Svenning, Jens‐Christian ; Antonelli, Alexandre
Extinction, Speciation, Mammals, Phylogenetic diversity, Anthropogenic, and Species diversity
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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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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
The rise and fall of Neotropical biodiversity.
Antonelli, Alexandre
Conservation, Evolution, and Extinction
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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
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
A bioinformatic platform to integrate target capture and whole genome sequences of various read depths for phylogenomics.
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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
International collaboration between collections‐based institutes for halting biodiversity loss and unlocking the useful properties of plants and fungi
Societal Impact Statement The United Nations' Sustainable Development Goal (SDG) 17 calls for “strong global partnerships and cooperation” to support the other SDGs. The collections‐based science community offers many examples of conservation of plant and fungal biodiversity, sharing, repatriation and aggregation of data, access to new technologies, supply of plant... -
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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Journal article
Above‐ and below‐ground biodiversity responses to the prolonged flood pulse in central‐western Amazonia, Brazil.
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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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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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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... -
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... -
Journal article
Botanical Monography in the Anthropocene
Botanical monographs have been the gold standard for communicating comprehensive systematic information about plants for over 300 years. Monographs catalyse species discovery, biodiversity documentation and conservation, and facilitate downstream research on wild and cultivated plant species. Increased availability of DNA sequence data and digitised resources now provide powerful resources for...Grace, Olwen M. ; Pérez-Escobar, Oscar A. ; Lucas, Eve J. ; Vorontsova, Maria S. ; Lewis, Gwilym P. …
conservation, Tree of Life, taxonomy , plants systematics , and biodiversity
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Journal article
Ten golden rules for reforestation to optimize carbon sequestration, biodiversity recovery and livelihood benefits
Urgent solutions to global climate change are needed. Ambitious tree‐planting initiatives, many already underway, aim to sequester enormous quantities of carbon to partly compensate for anthropogenic CO2 emissions, which are a major cause of rising global temperatures. However, tree planting that is poorly planned and executed could actually increase CO2... -
Journal article
sampbias, a method for quantifying geographic sampling biases in species distribution data
Geo‐referenced species occurrences from public databases have become essential to biodiversity research and conservation. However, geographical biases are widely recognized as a factor limiting the usefulness of such data for understanding species diversity and distribution. In particular, differences in sampling intensity across a landscape due to differences in human accessibility...Zizka, Alexander ; Antonelli, Alexandre ; Silvestro, Daniele
collection effort, Global Biodiversity Information Facility (GBIF), roadside bias, presence only data, and sampling intensity
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Journal article
iucn_sim: a new program to simulate future extinctions based on IUCN threat status
The ongoing environmental crisis poses an urgent need to forecast the who, where and when of future species extinctions, as such information is crucial for targeting conservation efforts. Commonly, such forecasts are made based on conservation status assessments produced by the International Union for Conservation of Nature (IUCN). However, when...Andermann, Tobias ; Faurby, Søren ; Cooke, Robert ; Silvestro, Daniele ; Antonelli, Alexandre
generation length, extinction, MCMC, Bayesian , Aves , and IUCN
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Journal article
raxmlGUI 2.0: A graphical interface and toolkit for phylogenetic analyses using RAxML
raxmlGUI is a graphical user interface to RAxML, one of the most popular and widely used softwares for phylogenetic inference using maximum likelihood. Here we present raxmlGUI 2.0, a complete rewrite of the GUI which seamlessly integrates RAxML binaries for all major operating systems with an intuitive graphical front‐end to...Edler, Daniel ; Klein, Johannes ; Antonelli, Alexandre ; Silvestro, Daniele
phylogenetics, evolutionary biology, software, bioinformatics, and molecular biology
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Journal article
Extinction risk and threats to plants and fungi
Societal Impact Statement There is increasing awareness that plants and fungi, as natural solutions, can play an important role in tackling ongoing global environmental challenges. We illustrate how understanding current and projected threats to plants and fungi is necessary to manage and mitigate risks, while building awareness of gaps and... -
Editorial
Protecting and sustainably using the world’s plants and fungi
This special issue – Protecting and sustainably using the world’s plants and fungi – features the research that underpins Kew’s State of the World’s Plants and Fungi 2020 report. This special issue, and the associated report, are global efforts representing work from 210 authors, in 97 institutions, across 42 countries...Antonelli, Alexandre ; Hiscock, Simon ; Lennon, Sarah ; Simmonds, Monique ; Smith, Rhian J. …
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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
WEGE: A new metric for ranking locations for biodiversity conservation
Aim Effective policymaking for biological conservation requires the identification and ranking of the most important areas for protection or management. One of the most frequently used systems for selecting priority areas is the Key Biodiversity Areas (hereafter KBAs), developed by the International Union for Conservation of Nature (IUCN). However, KBAs...Farooq, Harith ; Azevedo, Josué ; Belluardo, Francesco ; Nanvonamuquitxo, Cristóvão ; Bennett, Dominic …
conservation, policymaking, WEGE, Key Biodiversity Area, prioritization, KBAs, and EDGE
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Journal article
Pollinators drive floral evolution in an Atlantic Forest genus
Pollinators are important drivers of angiosperm diversification at both micro and macroevolutionary scales. Both hummingbirds and bats pollinate the species-rich and morphologically diverse genus Vriesea across its distribution in the Brazilian Atlantic Forest. Here, we (1) determine if floral traits predict functional groups of pollinators as documented, confirming the pollination... -
Journal article
Toward Unifying Global Hotspots of Wild and Domesticated Biodiversity
Global biodiversity hotspots are areas containing high levels of species richness, endemism and threat. Similarly, regions of agriculturally relevant diversity have been identified where many domesticated plants and animals originated, and co-occurred with their wild ancestors and relatives. The agro-biodiversity in these regions has, likewise, often been considered threatened. Biodiversity... -
Journal article
Advancing biodiversity assessments with environmental DNA: Long‐read technologies help reveal the drivers of Amazonian fungal diversity
Fungi are a key component of tropical biodiversity. However, due to their inconspicuous and largely subterranean nature, they are usually neglected in biodiversity inventories. The goal of this study was to identify the key determinants of fungal richness, community composition, and turnover in tropical rainforests. We tested specifically for the... -
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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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
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
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
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
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
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