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List of works by Alexandre Antonelli

A Guide to Carrying Out a Phylogenomic Target Sequence Capture Project

scientific article published on 01 January 2019

A highly contiguous, scaffold-level nuclear genome assembly for the fever tree (Cinchona pubescens Vahl) as a novel resource for Rubiaceae research

scientific article published in 2022

A network approach for identifying and delimiting biogeographical regions ⬇️

scientific article published on 24 April 2015

A novel approach to study the morphology and chemistry of pollen in a phylogenetic context, applied to the halophytic taxon L.(Nitrariaceae)

scientific article published on 19 July 2018

A novel phylogenetic infrageneric classification of Baccharis (Asteraceae: Astereae), a highly diversified American genus

scientific article

A phylogenetic approach to detect selection on the target site of the antifouling compound irgarol in tolerant periphyton communities

scientific article published on 29 April 2009

A roadmap for global synthesis of the plant tree of life

scientific article published on 30 March 2018

A taxonomic, genetic and ecological data resource for the vascular plants of Britain and Ireland

scientific article published on 10 January 2022

Above‐ and below‐ground biodiversity responses to the prolonged flood pulse in central‐western Amazonia, Brazil

scientific article published on 03 December 2021

Absence of mammals and the evolution of New Zealand grasses

scientific article (publication date: 7 March 2011)

Addressing chemical pollution in biodiversity research

scientific article published in 2023

Advanced understanding of phylogenetic relationships, morphological evolution and biogeographic history of the mega-diverse plant genus Myrcia and its relatives (Myrtaceae: Myrteae)

scientific article published on 24 May 2019

Advancing biodiversity assessments with environmental DNA: Long-read technologies help reveal the drivers of Amazonian fungal diversity

scientific article published on 23 June 2020

Allele Phasing Greatly Improves the Phylogenetic Utility of Ultraconserved Elements

scientific article published on 01 January 2019

Allele phasing is critical to revealing a shared allopolyploid origin of Medicago arborea and M. strasseri (Fabaceae).

scientific article published on 27 January 2018

Amazonia is the primary source of Neotropical biodiversity.

scientific article

Amazonia through time: Andean uplift, climate change, landscape evolution, and biodiversity

scientific article (publication date: 12 November 2010)

An engine for global plant diversity: highest evolutionary turnover and emigration in the American tropics

scientific article

An horizon scan of biogeography

scientific article (publication date: 2013)

Ancient Polyploidy and Genome Evolution in Palms

scientific article published on 01 May 2019

Annotating public fungal ITS sequences from the built environment according to the MIxS-Built Environment standard – a report from a May 23-24, 2016 workshop (Gothenburg, Sweden)

scientific article (publication date: 26 September 2016)

Anthropogenic extinctions conceal widespread evolution of flightlessness in birds

scientific article published on 02 December 2020

Assessing Biotic and Abiotic Interactions of Microorganisms in Amazonia through Co-Occurrence Networks and DNA Metabarcoding

scientific article published on 19 February 2021

Assessing the impact of phylogenetic incongruence on taxonomy, floral evolution, biogeographical history, and phylogenetic diversity

scientific article

Available Climate Regimes Drive Niche Diversification during Range Expansion

scientific article

Bayesian estimation of speciation and extinction from incomplete fossil occurrence data

scientific article

Biodiversity assessments in the 21st century: the potential of insect traps to complement environmental samples for estimating eukaryotic and prokaryotic diversity using high-throughput DNA metabarcoding

scientific article published on 23 January 2019

Biodiversity from mountain building

Biodiversity seen through the perspective of insects: 10 simple rules on methodological choices and experimental design for genomic studies

scientific article published on 30 April 2019

Biodiversity: Multiple origins of mountain life

scientific article published on 12 August 2015

Biogeography: Drivers of bioregionalization

scientific article published on 06 March 2017

Biological evidence supports an early and complex emergence of the Isthmus of Panama

scientific article

Biosystematic studies in the Brazilian endemic genus Hoffmannseggella H. G. Jones (Orchidaceae: Laeliinae): a multiple approach applied to conservation ⬇️

scientific article published on 17 March 2007

Botanical Monography in the Anthropocene

Brain expansion in early hominins predicts carnivore extinctions in East Africa

scientific article published on 13 January 2020

Brazil Should Facilitate Research Permits

scientific article published on 01 October 2009

Building mountain biodiversity: Geological and evolutionary processes

scientific article published on 01 September 2019

Chilean Pitavia more closely related to Oceania and Old World Rutaceae than to Neotropical groups: evidence from two cpDNA non-coding regions, with a new subfamilial classification of the family

scientific article

Cinchona anderssonii (Rubiaceae), a new overlooked species from Bolivia

scientific article (publication date: 27 February 2017)

Cities: factor in their biological impact

scientific article published in Nature

Climate cooling promoted the expansion and radiation of a threatened group of South American orchids (Epidendroideae: Laeliinae)

Comment (1) on "Formation of the Isthmus of Panama" by O'Dea et al

scientific article

Conceptual and empirical advances in Neotropical biodiversity research

scientific article published on 04 October 2018

Connecting the multiple dimensions of global soil fungal diversity

scientific article published in December 2023

CoordinateCleaner : Standardized cleaning of occurrence records from biological collection databases

scientific article published in 2019

Decreased soil moisture due to warming drives phylogenetic diversity and community transitions in the tundra

scientific article

Disentangling the influence of climatic and geological changes on species radiations

article

Disproportionate extinction of South American mammals drove the asymmetry of the Great American Biotic Interchange

scientific article published on 05 October 2020

Drivers of bromeliad leaf and floral bract variation across a latitudinal gradient in the Atlantic Forest

scientific article published on 24 November 2019

Early Arrival and Climatically-Linked Geographic Expansion of New World Monkeys from Tiny African Ancestors

scientific article published on 01 January 2019

Ecology and evolution of the diaspore "burial syndrome".

scientific article published in December 2010

Embracing heterogeneity: Building the Tree of Life and the future of phylogenomics

Embracing heterogeneity: Building the Tree of Life and the future of phylogenomics

Embracing heterogeneity: Building the Tree of Life and the future of phylogenomics

Embracing heterogeneity: Building the Tree of Life and the future of phylogenomics

Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics

scientific article published on 14 February 2019

Endemic palm species shed light on habitat shifts and the assembly of the Cerrado and Restinga floras

scientific article

Endemism patterns are scale dependent

scientific article published on 30 April 2020

Environmental impact assessment in Brazilian Amazonia: Challenges and prospects to assess biodiversity

article

Environmentally driven extinction and opportunistic origination explain fern diversification patterns

scientific article

Estimating Age-dependent Extinction: Contrasting Evidence from Fossils and Phylogenies

scientific article published on 23 October 2017

Estimating Alpha, Beta, and Gamma Diversity Through Deep Learning

scientific article published on 19 April 2022

Estimating species diversity and distribution in the era of Big Data: to what extent can we trust public databases?

scientific article

Estimating the age of fire in the Cape flora of South Africa from an orchid phylogeny

scientific article (publication date: 22 January 2011)

Evidence for mtDNA capture in the jacamar Galbula leucogastra/chalcothorax species-complex and insights on the evolution of white-sand ecosystems in the Amazon basin

scientific article published on 17 July 2018

Evolution of cyanobacterial morphotypes: Taxa required for improved phylogenomic approaches

scientific article (publication date: July 2011)

Evolution of multicellularity coincided with increased diversification of cyanobacteria and the Great Oxidation Event

scientific article (publication date: 29 January 2013)

Evolutionary and ecological success is decoupled in mammals

scientific article published on 31 July 2018

Evolutionary history of New World monkeys revealed by molecular and fossil data

Evolutionary persistence in Gunnera and the contribution of southern plant groups to the tropical Andes biodiversity hotspot.

scientific article published on 16 March 2018

Expert‐based range maps cannot be replicated using data‐driven methods but macroecological conclusions arising from them can

scientific article published on 12 April 2024

Extinction risk and threats to plants and fungi

scientific article published on 29 September 2020

Finding needles in the haystack: where to look for rare species in the American tropics

article by Alexander Zizka et al published 1 March 2017 in Ecography

First record of Chomelia triflora (J.H. Kirkbr.) Delprete & Achille (Rubiaceae) from Brazil ⬇️

scientific article published on 28 July 2017

Fossil biogeography: a new model to infer dispersal, extinction and sampling from palaeontological data

scientific article

Fossil data support a pre-Cretaceous origin of flowering plants

scientific article published in 2021

Geological and climatic influences on mountain biodiversity

Global hotspots of plant phylogenetic diversity

scientific article published in 2023

Global variation in diversification rate and species richness are unlinked in plants

scientific article published on 29 June 2022

Guidelines for the effective and ethical sampling of herbaria ⬇️

scientific article published in 2024

Have giant lobelias evolved several times independently? Life form shifts and historical biogeography of the cosmopolitan and highly diverse subfamily Lobelioideae (Campanulaceae)

scientific article (publication date: 26 November 2009)

High-throughput metabarcoding reveals the effect of physicochemical soil properties on soil and litter biodiversity and community turnover across Amazonia

High-throughput metabarcoding reveals the effect of physicochemical soil properties on soil and litter biodiversity and community turnover across Amazonia

High-throughput metabarcoding reveals the effect of physicochemical soil properties on soil and litter biodiversity and community turnover across Amazonia

scientific article published in 2018

Higher level phylogeny and evolutionary trends in Campanulaceae subfam. Lobelioideae: molecular signal overshadows morphology

scientific article

Historical Biogeography of endemic seed plant genera in the Caribbean: Did GAARlandia play a role?

scientific article published on 24 October 2017

Historical chemical annotations of Cinchona bark collections are comparable to results from current day high-pressure liquid chromatography technologies

scientific article published on 04 November 2019

Human activity is altering the world's zoogeographical regions

scientific article published on 12 June 2019

Improved estimation of macroevolutionary rates from fossil data using a Bayesian framework

scientific article published on 12 September 2019

Improving ITS sequence data for identification of plant pathogenic fungi

article

Improving biodiversity protection through artificial intelligence

scientific article published on 24 March 2022

Increased resolution in the face of conflict: phylogenomics of the Neotropical bellflowers (Campanulaceae: Lobelioideae), a rapid plant radiation

scientific article published on 24 March 2022

Infomap Bioregions: Interactive Mapping of Biogeographical Regions from Species Distributions ⬇️

scientific article

International collaboration between collections‐based institutes for halting biodiversity loss and unlocking the useful properties of plants and fungi

scientific article published in 2020

Iriarteeae palms tracked the uplift of Andean Cordilleras

Lectotypification of Pentagonia macrophylla (Rubiaceae) revisited

article

Linking democracy and biodiversity conservation: Empirical evidence and research gaps

scientific article published on 24 June 2019

Locality or habitat? Exploring predictors of biodiversity in Amazonia

scientific article published in 2018

Loss of functional diversity through anthropogenic extinctions of island birds is not offset by biotic invasions ⬇️

scientific article published on 10 November 2021

Madagascar’s extraordinary biodiversity: Evolution, distribution, and use

Madagascar’s extraordinary biodiversity: Threats and opportunities

scientific article published on 2 December 2022

Mapping Africa's biodiversity: More of the same is just not good enough

scientific article published on 11 December 2020

Mass Extinction, Gradual Cooling, or Rapid Radiation? Reconstructing the Spatiotemporal Evolution of the Ancient Angiosperm Genus Hedyosmum (Chloranthaceae) Using Empirical and Simulated Approaches ⬇️

scientific article published on October 1, 2011

Mesoamerica is a cradle and the Atlantic Forest is a museum of Neotropical butterfly diversity: insights from the evolution and biogeography of Brassolini (Lepidoptera: Nymphalidae)

scientific article published on 24 February 2021

Mining threatens Colombian ecosystems

scientific article published on 29 March 2018

Model uncertainty in ancestral area reconstruction: A parsimonious solution?

scientific article published on June 2012

Molecular Clocks and Archeogenomics of a Late Period Egyptian Date Palm Leaf Reveal Introgression from Wild Relatives and Add Timestamps on the Domestication

scientific article published on 01 September 2021

Molecular Studies and Phylogeography of Amazonian Tetrapods and their Relation to Geological and Climatic Models

Mountains of diversity

scientific article published in Nature

Mountains of diversity

scientific article published on 01 March 2018

Multiple origins of mountain biodiversity in New Zealand's largest plant radiation ⬇️

scholarly article published in 2023

Museums and cradles of diversity are geographically coincident for narrowly distributed Neotropical snakes ⬇️

scientific article published on 5 November 2019

Neotropical Plant Evolution: Assembling the Big Picture

article by Colin E Hughes et al published 14 December 2012 in Botanical Journal of the Linnean Society

No one-size-fits-all solution to clean GBIF

scientific article published on 28 September 2020

On the Origin of Amazonian Landscapes and Biodiversity: A Synthesis

Origins of Biodiversity--Response

scientific article

Orthologous nuclear markers and new transcriptomes that broadly cover the phylogenetic diversity of Acanthaceae

scientific article published on 25 September 2019

PHYLACINE 1.2: The Phylogenetic Atlas of Mammal Macroecology

scientific article published on 01 October 2018

Past climate change and plant evolution in Western North America: a case study in Rosaceae

scientific article (publication date: 2012)

Patterns, biases and prospects in the distribution and diversity of Neotropical snakes

scientific article

Phylogenetic and functional clustering illustrate the roles of adaptive radiation and dispersal filtering in jointly shaping late‐Quaternary mammal assemblages on oceanic islands

scientific article

Phylogenomics and biogeography of the world's thrushes (Aves, Turdus): new evidence for a more parsimonious evolutionary history

scientific article published on 22 January 2020

Phylogenomics of the Palm Tribe Lepidocaryeae (Calamoideae: Arecaceae) and Description of a New Species of Mauritiella

scholarly article published in 2021

Phylogeny Predicts the Quantity of Antimalarial Alkaloids within the Iconic Yellow Cinchona Bark (Rubiaceae: Cinchona calisaya). ⬇️

scientific article

Phylogeny of the Tribe Cinchoneae (Rubiaceae), Its Position in Cinchonoideae, and Description of a New Genus, Ciliosemina

scientific article (publication date: February 2005)

Phylogeny, classification, and fruit evolution of the species-rich Neotropical bellflowers (Campanulaceae: Lobelioideae).

scientific article

Placement of Kuhlmanniodendron Fiaschi & Groppo in Lindackerieae (Achariaceae, Malpighiales) confirmed by analyses of rbcL sequences, with notes on pollen morphology and wood anatomy

scientific article published in 2010

Plant Power: Opportunities and challenges for meeting sustainable energy needs from the plant and fungal kingdoms

scientific article published on 29 September 2020

Plant and fungal collections: Current status, future perspectives

scientific article

Plastid phylogenomics resolves ambiguous relationships within the orchid family and provides a solid timeframe for biogeography and macroevolution

scientific article published on 25 March 2021

Pollination of the Lady's slipper orchid (Cypripedium calceolus) in Scandinavia - taxonomic and conservational aspects

article by Alexandre Antonelli et al published August 2009 in Nordic Journal of Botany

Pollinators drive floral evolution in an Atlantic Forest genus

scientific article published on 22 August 2020

Protecting and sustainably using the world’s plants and fungi

scientific article published in September 2020

Quaternary glaciation and the Great American Biotic Interchange

scholarly article

Rapid evolution of post-zygotic reproductive isolation is widespread in Arctic plant lineages

scientific article published on 01 January 2022

Reassessing the temporal evolution of orchids with new fossils and a Bayesian relaxed clock, with implications for the diversification of the rare South American genus Hoffmannseggella (Orchidaceae: Epidendroideae)

scientific article (publication date: 14 June 2010)

Recent and local diversification of Central American understorey palms

scientific article published in 2022

Recent origin and rapid speciation of Neotropical orchids in the world's richest plant biodiversity hotspot

scientific article published in July 2017

Recent origin of Neotropical orchids in the world's richest plant biodiversity hotspot

article

Reply to Lessios and Marko et al.: Early and progressive migration across the Isthmus of Panama is robust to missing data and biases

scientific article

Revised Species Delimitation in the Giant Water Lily Genus Victoria (Nymphaeaceae) Confirms a New Species and Has Implications for Its Conservation ⬇️

journal article from 'Frontiers in Plant Science' published in 2022

Revisiting taxonomy, morphological evolution, and fossil calibration strategies in Chloranthaceae

Revisiting the origin and diversification of vascular plants through a comprehensive Bayesian analysis of the fossil record

scientific article

SECAPR - A bioinformatics pipeline for the rapid and user-friendly processing of Illumina sequences, from raw reads to alignments

SECAPR—a bioinformatics pipeline for the rapid and user-friendly processing of targeted enriched Illumina sequences, from raw reads to alignments.

scientific article published on 13 July 2018

Seed banks needed to restore ecosystems

scientific article published on 13 January 2023

Selective extinction against redundant species buffers functional diversity

scientific article published on 22 July 2020

Settling a family feud: a high‐level phylogenomic framework for the Gentianales based on 353 nuclear genes and partial plastomes ⬇️

scientific article published in 2021

Small-world dynamics drove Phanerozoic divergence of burrowing behaviors

scientific article

Society for the Study of Systematic Biology symposium: Frontiers in Parametric Biogeography

scientific article

Soil fertility and flood regime are correlated with phylogenetic structure of Amazonian palm communities

scientific article published on 01 March 2019

Spatio‐temporal evolution of the catuaba clade in the Neotropics: Morphological shifts correlate with habitat transitions

scientific article published in 2022

Species limits in butterflies (Lepidoptera: Nymphalidae): Reconciling classical taxonomy with the multispecies coalescent

article published 29 October 2018

SpeciesGeoCoder: Fast Categorization of Species Occurrences for Analyses of Biodiversity, Biogeography, Ecology, and Evolution

scientific article

Spiny but photogenic: Amateur sightings complement herbarium specimens to reveal the bioregions of cacti

scientific article published in 2023

Target sequence capture of Barnadesioideae (Compositae) demonstrates the utility of low coverage loci in phylogenomic analyses

scholarly article published in 2022

Taxonomic revision of the genus Xenopholis Peters, 1869 (Serpentes: Dipsadidae): Integrating morphology with ecological niche

scientific article published on 11 December 2020

Tectonic blocks and molecular clocks

scientific article

Ten golden rules for reforestation to optimize carbon sequestration, biodiversity recovery and livelihood benefits

scientific article published on 25 January 2021

The 2030 Declaration on Scientific Plant and Fungal Collecting ⬇️

scientific article published on 30 September 2024

The Global Museum: natural history collections and the future of evolutionary science and public education

scientific article published on 28 January 2020

The Impact of Mutualisms on Species Richness

scientific article published on 17 April 2019

The Origin and Diversification of the Hyperdiverse Flora in the Chocó Biogeographic Region

scientific article published on 06 December 2019

The Peniophorella praetermissa species complex (Basidiomycota).

scientific article published on 7 October 2007

The abiotic and biotic drivers of rapid diversification in Andean bellflowers (Campanulaceae)

scientific article

The counteracting effects of anthropogenic speciation and extinction on mammal species richness and phylogenetic diversity

scientific article published in 2022

The discovery of the Amazonian tree flora with an updated checklist of all known tree taxa

scientific article

The ecological drivers of growth form evolution in flowering plants

scientific article published on 04 April 2022

The evolutionary history of the Central Asian steppe-desert taxon <i>Nitraria</i> (Nitrariaceae) as revealed by integration of fossil pollen morphology and molecular data

scientific article published in 2023

The global distribution of plants used by humans

scientific article published on 18 January 2024

The origin and evolution of open habitats in North America inferred by Bayesian deep learning models

scientific article published in 2022

The origin of multicellularity in cyanobacteria

scientific article (publication date: 14 February 2011)

The past and future human impact on mammalian diversity

scientific article published on 04 September 2020

The pitfalls of biodiversity proxies: Differences in richness patterns of birds, trees and understudied diversity across Amazonia

scientific article published on 16 December 2019

The pitfalls of taking science to the public

scientific article

The rise and fall of Neotropical biodiversity

scientific article published on 15 September 2021

The rise of angiosperms pushed conifers to decline during global cooling

scientific article published on 2 November 2020

The role of clade competition in the diversification of North American canids

scientific article

The roles of dispersal and mass extinction in shaping palm diversity across the Caribbean

The science and ethics of extinction

scientific article published on 01 April 2018

The use of chloroplast genome sequences to solve phylogenetic incongruences in Polystachya Hook (Orchidaceae Juss).

scientific article

Toward Unifying Global Hotspots of Wild and Domesticated Biodiversity

scientific article published on 31 August 2020

Toward a Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa.

scientific article

Towards a co‐crediting system for carbon and biodiversity

scientific article published in 2023

Towards a dynamic list of Amazonian tree species

scientific article published on 05 March 2019

Tracing the Evolution and Economic Potential of Konjac Glucomannan in Amorphophallus species (Araceae) using Molecular Phylogeny and RAPD Markers

scientific article (publication date: 27 October 2016)

Tracing the impact of the Andean uplift on Neotropical plant evolution

scientific article (publication date: 16 June 2009)

Trade-off between seed dispersal in space and time

scientific article published on 02 September 2020

Transitions between biomes are common and directional in Bombacoideae (Malvaceae)

scientific article published on 27 February 2020

Tree plantations: we must get them right

scientific article published on 01 August 2019

Two new species of Pavonia (Malvoideae, Malvaceae) from southern Bahia, Brazil

article

Undiscovered bird extinctions obscure the true magnitude of human-driven extinction waves

scientific article published in 2023

Unexpectedly High Beta-Diversity of Root-Associated Fungal Communities in the Bolivian Andes

scientific article

Unlocking the properties of plants and fungi for sustainable development

scientific article published on 01 November 2019

Unraveling the Phylogenomic Relationships of the Most Diverse African Palm Genus Raphia (Calamoideae, Arecaceae)

scientific article published on 23 April 2020

Untapped resources for medical research

scientific article

Uses and benefits of digital sequence information from plant genetic resources: Lessons learnt from botanical collections

scientific article

Vicariance or long-distance dispersal: historical biogeography of the pantropical subfamily Chrysophylloideae (Sapotaceae)

scholarly article by Igor V. Bartish et al published 1 September 2010 in Journal of Biogeography

What determines biogeographical ranges? Historical wanderings and ecological constraints in the danthonioid grasses

article

Why are there so many plant species in the Neotropics?

scientific article published on April 2011

Why are there so many plant species in the Neotropics?

scientific article published on 12 February 2019

Widespread homogenization of plant communities in the Anthropocene

scientific article published on 06 December 2021

outsider: Install and run programs, outside of R, inside of R

scientific article published on 23 January 2020

phylotaR: An Automated Pipeline for Retrieving Orthologous DNA Sequences from GenBank in R.

scientific article published on 5 June 2018

phylotaR: An automated pipeline for retrieving orthologous DNA sequences from GenBank in R

restez: Create and Query a Local Copy of GenBank in R

speciesgeocodeR: An R package for linking species occurrences, user-defined regions and phylogenetic trees for biogeography, ecology and evolution

article

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