Alexandre Antonelli

Alexandre Antonelli
Royal Botanic Gardens, Kew · Jodrell Laboratory

PhD

About

461
Publications
210,115
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
14,242
Citations
Citations since 2017
303 Research Items
11369 Citations
201720182019202020212022202305001,0001,5002,0002,500
201720182019202020212022202305001,0001,5002,0002,500
201720182019202020212022202305001,0001,5002,0002,500
201720182019202020212022202305001,0001,5002,0002,500
Introduction
I am interested in the evolution and distribution of biodiversity across various spatial and temporal scales. My lab has 4 major themes: 1) macro-evolution (estimating speciation, extinction and dispersal); 2) molecular phylogenetics (applying next-generation sequencing to infer species relationships); 3) biodiversity analyses (mapping and understanding patterns of taxonomic, phylogenetic and functional diversity); and 4) bioinformatics (development of open-source software).
Additional affiliations
July 2015 - present
University of Gothenburg
Position
  • Full Professor in Biodiversity and Systematics
Description
  • Principal Investigator for a relatively large research group.
January 2012 - June 2015
University of Gothenburg
Position
  • Associate professor, Senior lecturer
August 2010 - present
Gothenburg botanical garden
Position
  • Scientific curator
Education
January 2009 - July 2010
University of Zurich
Field of study
  • Evolutionary biology, botany
July 2003 - December 2008
University of Gothenburg
Field of study
  • Biology with focus on Evolution and Biodiversity
January 1996 - July 1996
University of Campinas
Field of study
  • Biology

Publications

Publications (461)
Preprint
Carbon crediting and land offsets for biodiversity protection are implemented to tackle the challenges of increasing greenhouse gas emissions and loss of global biodiversity, but these two mechanisms are not optimal when considered separately. Focusing solely on carbon capture – the primary goal of most carbon-focused offsetting commitments – often...
Article
Full-text available
Madagascar's biota is hyperdiverse and includes exceptional levels of endemicity. We review the current state of knowledge on Madagascar's past and current terrestrial and freshwater biodiversity by compiling and presenting comprehensive data on species diversity, endemism, and rates of species description and human uses, in addition to presenting...
Article
Full-text available
Madagascar's unique biota is heavily affected by human activity and is under intense threat. Here, we review the current state of knowledge on the conservation status of Madagascar's terrestrial and freshwater biodiversity by presenting data and analyses on documented and predicted species-level conservation statuses, the most prevalent and relevan...
Article
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 a...
Preprint
Full-text available
From traffic flows on road networks to electrical signals in brain networks, many real-world networks contain modular structures of different sizes and densities. In the networks where modular structures emerge due to coupling between nodes with similar dynamical functions, we can identify them using flow-based community detection methods. However,...
Article
Full-text available
The development and implementation of conservation actions that address urgent threats to biodiversity across the globe require large amounts of historic and current data. Machine learning approaches offer the tools to process, analyse and interpret large data sets, giving insights into trends and guiding evidence‐based allocation of limited resour...
Article
Full-text available
The origins and evolution of the outstanding Neotropical biodiversity are a matter of intense debate. A comprehensive understanding is hindered by the lack of deep-time comparative data across wide phylogenetic and ecological contexts. Here, we quantify the prevailing diversification trajectories and drivers of Neotropical diversification in a samp...
Article
Full-text available
The Andean fever tree (Cinchona L.; Rubiaceae) is a source of bioactive quinine alkaloids used to treat malaria. C. pubescens Vahl is a valuable cash crop within its native range in northwestern South America, however, genomic resources are lacking. Here we provide the first highly contiguous and annotated nuclear and plastid genome assemblies usin...
Article
Full-text available
Most of the unique and diverse vertebrate fauna that inhabits Madagascar derives from in situ diversification from colonisers that reached this continental island through overseas dispersal. The endemic Malagasy Scincinae lizards are amongst the most species-rich squamate groups on the island. They colonised all bioclimatic zones and display many e...
Preprint
Full-text available
The rapid decline of biodiversity as a consequence of increased environmental impact by human activities requires urgent action against the ongoing crisis. At the heart of conservation policy is the debate on quality versus quantity: should the post-2020 Global Biodiversity Framework focus on maximising total protected area, or pursue instead quali...
Article
Full-text available
Snakebites in sub-Saharan Africa account for 20,000 to 32,000 annual deaths. But since most data is retrieved from hospital or incomplete central databases, and many victims do not seek hospital treatment or prefer traditional remedies, the current numbers are likely underestimated. In order to reduce snakebite incidence by 50% by 2030 as targeted...
Article
Full-text available
Some of the most extensive terrestrial biomes today consist of open vegetation, including temperate grasslands and tropical savannas. These biomes originated relatively recently in Earth’s history, likely replacing forested habitats in the second half of the Cenozoic. However, the timing of their origination and expansion remains disputed. Here, we...
Preprint
Full-text available
We live in a time of highly accelerated extinction, which has the potential to mirror past mass extinction events. However, the rarity of these events and the restructuring of diversity that they cause complicate direct comparisons between the current extinction crisis and earlier mass extinctions. Among animals, turtles (Testudinata) are one of fe...
Article
Full-text available
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...
Article
Full-text available
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 Victoria (Nymphaeaceae). The systemat...
Article
Full-text available
Temperatures over the Arctic region are increasing at three times the rate of the global average. Consequently, Arctic vegetation is changing and trees are encroaching into the tundra. In this study, we examine the establishment and growth of mountain birch (Betula pubescens ssp. tortuosa), which forms the treeline in subarctic Europe, and its impa...
Preprint
Full-text available
Eight percent of all land surface has been designated as “Key Biodiversity Areas” (KBAs). Since these areas were established based on only 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 at a global scale by using data from 64,1...
Article
Full-text available
Human activities are causing massive increases in extinction rates but might also lead to drastic increases in speciation rates; for example, after human‐mediated spread of species to otherwise unreachable landmasses. The long‐term net anthropogenic effects on biodiversity therefore remain uncertain. Our aim was to assess the combined anthropogenic...
Article
Full-text available
Aim: Central America is largely covered by hyperdiverse, yet poorly understood, rain forests. Understorey palms are diverse components of these forests, but little is known about their historical assembly. It is not clear when palms in Central America reached present diversity levels and whether most species arrived from neighbouring regions or evo...
Article
Full-text available
Islands frequently harbour unique assemblages of species, yet their ecological roles and differences are largely ignored in island biogeography studies. Here, we examine eco‐evolutionary processes structuring mammal assemblages on oceanic islands worldwide, including all extant and extinct late‐Quaternary mammal species. We find island mammal assem...
Article
Full-text available
Over a million species face extinction, highlighting the urgent need for conservation policies that maximize the protection of biodiversity to sustain its manifold contributions to people’s lives. Here we present a novel framework for spatial conservation prioritization based on reinforcement learning that consistently outperforms available state-o...
Preprint
Full-text available
Over the last few centuries, millions of plant specimens have been collected and stored within herbaria and biocultural collections. They therefore represent a considerable resource for a broad range of scientific uses. However, collections degrade over time, and it is therefore increasingly difficult to characterise their genetic signatures. Here,...
Preprint
Full-text available
Background The Andean fever tree ( Cinchona L.; Rubiaceae) is the iconic source of bioactive quinine alkaloids which have been key to treating malaria for centuries. In particular, C. pubescens Vahl has been an important source of income for several countries in its native range in north-western South America. However, the genomic resources require...
Article
Full-text available
The reliable mapping of species richness is a crucial step for the identification of areas of high conservation priority, alongside other value and threat considerations. This is commonly done by overlapping range maps of individual species, which requires dense availability of occurrence data or relies on assumptions about the presence of species...
Article
Background and Aims The centropogonid clade (Lobelioideae: Campanulaceae) is an Andean-centered rapid radiation characterized by repeated convergent evolution of morphological traits, including fruit type and pollination syndromes. While previous studies have resolved relationships of lineages with fleshy fruits into subclades, relationships among...
Article
1. In flowering plants (angiosperms), the herbaceous habit has evolved repeatedly from the ancestral woody state and herbs evolved repeatedly back to woody plants. Yet, how common these transitions were and which ecological conditions promote the herbaceous habit is poorly known. Several hypotheses exist, postulating an advantage of the herbaceous...
Article
The biotic assembly of one of the most species‐rich savannas, the Brazilian Cerrado, has involved recruitment of lineages from several surrounding regions. However, we lack a clear understanding about the timing and pathways of biotic exchanges among these regions and about the role those interchanges had in the assembly of Neotropical biodiversity...
Preprint
Full-text available
Fungi play pivotal roles in ecosystem functioning, but little is known about their global patterns of diversity, endemicity, vulnerability to global change drivers and conservation priority areas. We applied the high-resolution PacBio sequencing technique to identify fungi based on a long DNA marker that revealed a high proportion of hitherto unkno...
Article
The study of diamond frogs (genus Rhombophryne, endemic to Madagascar) has been historically hampered by the paucity of available specimens, because of their low detectability in the field. Over the last 10 years, 13 new taxa have been described, and 20 named species are currently recognized. Nevertheless, undescribed diversity within the genus is...
Article
Full-text available
Target sequence capture has emerged as a powerful method to sequence hundreds or thousands of genomic regions in a cost- and time-efficient approach. In most cases, however, targeted regions lack full sequence information for certain samples, due to taxonomic, laboratory, or stochastic factors. Loci lacking molecular data for a large number of samp...
Preprint
Full-text available
The reliable mapping of species richness is a crucial step for the identification of areas of high conservation priority, alongside other value considerations. This is commonly done by overlapping range maps of individual species, which requires dense availability of occurrence data or relies on assumptions about the presence of species in unsample...
Article
Full-text available
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 easy online a...
Preprint
Full-text available
Background and Aims- The centropogonid clade (Lobelioideae: Campanulaceae) is an Andean-centered rapid radiation characterized by repeated convergent evolution of morphological traits, including fruit type and pollination syndromes. While previous studies have resolved relationships of lineages with fleshy fruits into subclades, relationships among...
Article
Full-text available
The Andes are the world's most biodiverse mountain chain, encompassing a complex array of ecosystems from tropical rainforests to alpine habitats. We provide a synthesis of Andean vascular plant diversity by estimating a list of all species with publicly available records, which we integrate with a phylogenetic dataset of 14 501 Neotropical plant s...
Article
Full-text available
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. H...
Article
Full-text available
Amazonia encompasses extensive forests in areas that are periodically inundated by overflowing rivers. The inundation depth and duration vary according to the slope of the terrain and distance to major water bodies. This creates a flooding gradient from the lowest lying seasonally flooded forest up into the unflooded forest, which directly affects...
Article
Full-text available
Background The great diversity in plant genome size and chromosome number is partly due to polyploidization (i.e. genome doubling events). The differences in genome size and chromosome number among diploid plant species can be a window into the intriguing phenomenon of past genome doubling that may be obscured through time by the process of diploid...
Article
Full-text available
Fungi are highly important biotic components of terrestrial ecosystems, but we still have a very limited understanding about their diversity and distribution. This data article releases a global soil fungal dataset of the Global Soil Mycobiome consortium (GSMc) to boost further research in fungal diversity, biogeography and macroecology. The datase...
Article
Full-text available
Human impacts reshape ecological communities through the extinction and introduction of species. The combined impact of these factors depends on whether non-native species fill the functional roles of extinct species, thus buffering the loss of functional diversity. This question has been difficult to address, because comprehensive information abou...
Article
Full-text available
en We use DNA sequence data to understand the evolutionary history of the genus Cavanillesia (Malvaceae), with particular emphasis on C. chicamochae, an emblematic succulent-trunked tree endemic to seasonally dry tropical forests (SDTFs) of the Chicamocha Canyon of Colombia, South America. Based on field sampling of multiple individuals from differ...
Preprint
Full-text available
Aim Leaves display a remarkable variety of shapes, each with potential ecological advantages in certain climates. Studies correlating leaf shape with either climate or height constraints have focused on intraspecific variation, while the macroecological drivers of shape remain poorly known. Here, we determine associations between climate and plant...
Article
The palm tribe Lepidocaryeae (Arecaceae) comprises seven genera and 51 currently accepted species that are distributed in lowland tropical forests and savannas across Africa and the Americas. Subtribal relationships within Lepidocaryeae have been a persistent challenge,limiting our understanding of its systematics, morphology, and biogeography. Sev...
Article
Full-text available
The increasing availability of short-read whole genome sequencing (WGS) provides unprecedented opportunities to study ecological and evolutionary processes. Although loci of interest can be extracted from WGS data and combined with target sequence data, this requires suitable bioinformatic workflows. Here, we test different assembly and locus extra...
Article
Full-text available
Background and aims: The Arctic tundra, with its extreme temperatures and short growing season, is evolutionarily young and harbors one of the most species-poor floras on Earth. Arctic species often show little phenotypic and genetic divergence across circumpolar ranges. However, strong intraspecific postzygotic reproductive isolation (RI) in term...
Preprint
Full-text available
Open vegetation today constitutes one of the most extensive biomes on earth, including temperate grasslands and tropical savannas. Yet these biomes originated relatively recently in earth history, likely replacing forested habitats as recently as the second half of the Cenozoic, although the timing of their origination and the dynamics of their exp...
Article
Full-text available
The subfamily Barnadesioideae (Compositae) is endemic to South America, comprising 10 genera and 80 species of mostly spiny herbs, subshrubs, shrubs, trees, or woody vines distributed from Venezuela to Argentina. Three genera, Dasyphyllum(27 species), Chuquiraga (22 spp.) and Barnadesia (19 spp.) contain 85% of the species, while the other seven ge...
Article
Full-text available
Aim Geo-referenced species occurrence records are a prime example of biodiversity data and a cornerstone of biodiversity research. Yet, their availability depends on non-biological factors, including the political framework in the region of collection. Here we present Bio-Dem (www.bio-dem.surge.sh), an open-source software to explore the relationsh...
Article
Full-text available
Digitized molecular data are vital to numerous aspects of scientific research and genetic resource use. The Convention on Biological Diversity currently refers to this as “Digital Sequence Information” (DSI), a term not widely adopted by science and lacking a clear definition. There are concerns over the access to genetic resources and absence of b...
Article
Full-text available
PREMISE: Comprising five families that vastly differ in species richness-ranging from Gelsemiaceae with 13 species to the Rubiaceae with 13,775 species-members of the Gentianales are often among the most species-rich and abundant plants in tropical forests. Despite considerable phylogenetic work within particular families and genera, several altern...
Article
Full-text available
The date palm, Phoenix dactylifera, has been a cornerstone of Middle Eastern and North African agriculture for millennia. It was first domesticated in the Persian Gulf, and its evolution appears to have been influenced by gene flow from two wild relatives, P. theophrasti, currently restricted to Crete and Turkey, and P. sylvestris, widespread from...
Article
Full-text available
Global warming leads to drastic changes in the diversity and structure of Arctic plant communities. Studies of functional diversity within the Arctic tundra biome have improved our understanding of plant responses to warming. However, these studies still show substantial unexplained variation in diversity responses. Complementary to functional dive...
Article
Full-text available
Environmental heterogeneity across the landscape can cause lineage divergence and speciation. The Geonoma macrostachys (Arecaceae) species complex has been proposed as a candidate case of ecological speciation in Amazonia due to evidence of habitat partitioning and pre-zygotic reproductive barriers between co-occurring morphotypes at a local scale....
Article
Full-text available
Aim Cross‐taxonomic congruence in biodiversity patterns is key to understanding the main drivers of community structure, for biogeographical regionalization and to guide conservation. We aim to map the patterns of phylogenetic turnover and disentangle the geographical and environmental factors that drive the phylogenetic composition of distinct fau...
Preprint
Full-text available
Amazonia encompasses forests that grow in areas that are periodically inundated by overflowing rivers. The inundation depth and duration vary according to the slope of the terrain, creating a flooding gradient. This gradient directly affects the biota, but the effect on soil organisms remains elusive. Here, we use DNA metabarcoding to estimate prok...
Article
Full-text available
Regional species diversity is explained ultimately by speciation, extinction and dispersal. Here, we estimate dispersal and speciation rates of Neotropical butterflies to propose an explanation for the distribution and diversity of extant species. We focused on the tribe Brassolini (owl butterflies and allies), a Neotropical group that comprises 17...
Preprint
Full-text available
In a recent paper we presented a new model, the Bayesian Brownian Bridge (BBB), to infer clade age based on fossil evidence and modern diversity. We benchmarked the method with extensive simulations, including a wide range of diversification histories and sampling heterogeneities that go well beyond the necessarily simplistic model assumptions. App...
Article
Full-text available
Flowering plants (angiosperms) are the most diverse of all land plants, becoming abundant in the Cretaceous and achieving dominance in the Cenozoic. However, the exact timing of their origin remains a controversial topic, with molecular clocks generally placing their origin much further back in time than the oldest unequivocal fossils. To resolve t...
Article
Full-text available
Recent phylogenomic analyses based on the maternally inherited plastid organelle have enlightened evolutionary relationships between the subfamilies of Orchidaceae and most of the tribes. However, uncertainty remains within several subtribes and genera for which phylogenetic relationships have not ever been tested in a phylogenomic context. To addr...
Preprint
Full-text available
The origin of the outstanding Neotropical biodiversity is still debated. A comprehensive understanding is hindered by the lack of deep-time comparative data across wide phylogenetic and ecological contexts. Here we define and evaluate four evolutionary scenarios assuming different diversity trajectories and drivers of Neotropical diversification. R...
Article
Full-text available
Species may co-occur due to responses to similar environmental conditions, biological associations, or simply because of coincident geographical distributions. Disentangling patterns of co-occurrence and potential biotic and abiotic interactions is crucial to understand ecosystem function. Here, we used DNA metabarcoding data from litter and minera...
Article
Unprecedented changes in the Earth’s biota are prompting urgent efforts to describe and conserve plant diversity. For centuries, botanical monographs — comprehensive systematic treatments of a family or genus — have been the gold standard for disseminating scientific information to accelerate research. The lack of a monograph compounds the risk tha...
Preprint
Full-text available
Species may co-occur due to responses to similar environmental conditions, biological associations, or simply because of coincident geographical distributions. Disentangling patterns of co-occurrence and potential biotic and abiotic interactions is crucial to understand ecosystem function. Here we used DNA metabarcoding data from litter and mineral...